CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Pseudoknotted RNAs
extended base pair definition

	Only pseudoknotted RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. The "extended" secondary structure definition includes all interacting bases using Watson-Crick, Hoogsteen or sugar edges, in both cis and trans orientations, including also base pairs conforming to the "standard" definition (the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry). Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: June 16, 2013
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 30000
Number of RNA sequences: 88
Robustness test: no

Important! This ranking will be updated in future, when predictions for new RNAs are generated by the methods being tested. This ranking shows the performance of methods as of June 16, 2013.

In the summary below ranks have been assigned only to methods, for which at least 40% of comparisons with other methods is valid (i.e. at least 40% (in case of this ranking: 23) of the comparisons were based on at least 10 predictions for common targets).

The ratio 40% / 60% was chosen in order not to bias methods for which not enough predictions have been collected.

Summary of pairwise comparisons

58 methods predicting RNA secondary structure were compared with each other (thus each method has 57 comparisons with other methods (sum of values from columns "Wins", "Losses", "=" and "?" in each row)).

Legend:

=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)
N/A	a method for which more than 34 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Tested since	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	CentroidAlifold(20)	yes	2009-07-01	48	1	0	8	37	36
2	PETfold_pre2.0(seed)	no	2011-11-03	46	0	0	11	27	27
3	RNAalifold(20)	no	2009-02-18	45	5	0	7	39	38
4	MXScarna(seed)	no	2009-06-15	44	6	1	6	53	51
5	PPfold(20)	yes	2011-04-18	42	3	1	11	22	20
6	ContextFold	yes	2011-11-15	40	7	2	8	44	43
7	RNASampler(20)	no	2009-02-18	39	10	1	7	39	38
8	PETfold_pre2.0(20)	no	2011-11-03	38	2	1	16	19	19
9	TurboFold(20)	no	2011-04-20	38	7	1	11	22	20
10	MXScarna(20)	no	2009-02-18	38	11	1	7	39	38
11	RNAalifold(seed)	no	2009-02-18	37	6	3	11	54	28
12	Murlet(20)	yes	2009-02-18	36	12	2	7	39	38
13	CentroidAlifold(seed)	yes	2009-07-01	35	13	3	6	52	51
14	Carnac(20)	no	2009-02-18	34	12	4	7	39	38
15	IPknot	yes	2011-07-01	34	15	1	7	47	46
16	CentroidHomfold‑LAST	yes	2011-05-11	31	17	2	7	48	39
17	Contrafold	yes	2009-02-18	31	20	1	5	88	87
18	Sfold	no	2009-02-18	30	19	3	5	88	87
19	HotKnots	no	2009-02-18	30	21	1	5	88	82
20	CentroidFold	yes	2009-08-01	28	21	3	5	82	81
21	TurboFold(seed)	no	2011-04-20	27	11	3	16	30	14
22	MaxExpect	yes	2009-10-15	27	21	4	5	79	77
23	RSpredict(20)	no	2009-06-03	25	24	1	7	38	37
24	PknotsRG	no	2009-02-18	25	23	4	5	88	86
25	CMfinder(20)	yes	2012-09-01	24	14	2	17	14	11
26	UNAFold	no	2009-02-18	23	27	2	5	88	87
27	ProbKnot	yes	2010-08-10	22	27	3	5	62	61
28	Cylofold	no	2010-06-08	21	22	4	10	63	41
29	RNAfold	no	2009-02-18	21	28	3	5	88	87
30	RNASampler(seed)	no	2009-02-18	20	6	6	25	54	14
31	RNAsubopt	no	2009-02-18	20	30	2	5	88	82
32	Multilign(20)	no	2011-03-01	19	22	2	14	22	19
33	Afold	no	2009-02-18	18	20	4	15	88	54
34	RNAshapes	no	2009-02-18	17	33	2	5	88	82
35	Fold	no	2010-03-15	16	33	3	5	64	63
36	McQFold	yes	2009-02-18	15	35	2	5	88	87
37	RNASLOpt	no	2011-11-01	14	32	3	8	44	41
38	Mastr(20)	yes	2009-02-18	13	34	3	7	39	38
39	Multilign(seed)	no	2011-03-01	12	3	9	33	30	10
40	Pknots	no	2009-02-18	12	37	3	5	88	77
41	Vsfold4	no	2009-02-18	11	40	0	6	88	75
42	CRWrnafold	yes	2011-08-23	10	13	1	33	46	15
43	Murlet(seed)	yes	2009-02-18	8	36	2	11	54	24
44	Vsfold5	no	2009-02-18	7	42	2	6	88	75
45	MCFold	yes	2009-02-18	6	45	0	6	88	66
46	Alterna	no	2009-02-18	5	27	1	24	88	35
47	RDfolder	no	2009-02-18	5	36	1	15	88	42
48	RNAwolf	yes	2011-07-01	5	44	1	7	47	46
49	NanoFolder	yes	2011-11-17	3	39	0	15	40	26
50	Carnac(seed)	no	2009-02-18	2	44	1	10	54	29
51	RSpredict(seed)	no	2009-06-03	2	48	1	6	53	52
52	PPfold(seed)	yes	2011-04-18	1	45	2	9	30	27
53	Mastr(seed)	yes	2009-02-18	0	51	0	6	54	52
N/A	CMfinder(seed)	yes	2012-09-01	0	0	0	57	19	0
N/A	DAFS(seed)	yes	2012-11-20	0	0	0	57	17	0
N/A	DAFS(20)	yes	2012-11-20	0	0	0	57	13	0
N/A	PETfold_2.0(seed)	no	2013-05-20	0	0	0	57	2	2
N/A	PETfold_2.0(20)	no	2013-05-20	0	0	0	57	1	1

Detailed results of pairwise comparisons between methods

Legend:

+	method on the left scored higher in this pairwise comparison
-	method on the left scored lower in this pairwise comparison
=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)

P-values were obtained using Wilcoxon signed-rank test taking 2 sets of 40 MCC values obtained for 40 random subsets of 90% of the dataset for each pair of methods. If the P-value is lower than 0.001 and there are at least 10 sequences on which benchmark was performed, the difference between the performance of two methods is assumed to be statistically sound.


CentroidAlifold(20)		- PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 CentroidAlifold(20): 0.656 Sensitivity PETfold_pre2.0(seed): 0.597 CentroidAlifold(20): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.870 CentroidAlifold(20): 0.864 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAalifold(20): 0.656 Sensitivity CentroidAlifold(20): 0.529 RNAalifold(20): 0.513 Positive Predictive Value CentroidAlifold(20): 0.882 RNAalifold(20): 0.841 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.679 MXScarna(seed): 0.643 Sensitivity CentroidAlifold(20): 0.526 MXScarna(seed): 0.526 Positive Predictive Value CentroidAlifold(20): 0.880 MXScarna(seed): 0.789 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 PPfold(20): 0.663 Sensitivity CentroidAlifold(20): 0.514 PPfold(20): 0.528 Positive Predictive Value CentroidAlifold(20): 0.877 PPfold(20): 0.836 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.656 ContextFold: 0.617 Sensitivity CentroidAlifold(20): 0.501 ContextFold: 0.499 Positive Predictive Value CentroidAlifold(20): 0.864 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNASampler(20): 0.613 Sensitivity CentroidAlifold(20): 0.529 RNASampler(20): 0.475 Positive Predictive Value CentroidAlifold(20): 0.882 RNASampler(20): 0.795 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.656 PETfold_pre2.0(20): 0.649 Sensitivity CentroidAlifold(20): 0.501 PETfold_pre2.0(20): 0.530 Positive Predictive Value CentroidAlifold(20): 0.864 PETfold_pre2.0(20): 0.798 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.43703343543e-08	+ CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 TurboFold(20): 0.616 Sensitivity CentroidAlifold(20): 0.514 TurboFold(20): 0.508 Positive Predictive Value CentroidAlifold(20): 0.877 TurboFold(20): 0.752 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 MXScarna(20): 0.611 Sensitivity CentroidAlifold(20): 0.529 MXScarna(20): 0.510 Positive Predictive Value CentroidAlifold(20): 0.882 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.612 RNAalifold(seed): 0.560 Sensitivity CentroidAlifold(20): 0.429 RNAalifold(seed): 0.339 Positive Predictive Value CentroidAlifold(20): 0.877 RNAalifold(seed): 0.928 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.16131455263e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Murlet(20): 0.589 Sensitivity CentroidAlifold(20): 0.529 Murlet(20): 0.439 Positive Predictive Value CentroidAlifold(20): 0.882 Murlet(20): 0.795 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 CentroidAlifold(seed): 0.587 Sensitivity CentroidAlifold(20): 0.529 CentroidAlifold(seed): 0.368 Positive Predictive Value CentroidAlifold(20): 0.882 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Carnac(20): 0.592 Sensitivity CentroidAlifold(20): 0.529 Carnac(20): 0.392 Positive Predictive Value CentroidAlifold(20): 0.882 Carnac(20): 0.898 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.669 IPknot: 0.526 Sensitivity CentroidAlifold(20): 0.511 IPknot: 0.433 Positive Predictive Value CentroidAlifold(20): 0.880 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.686 CentroidHomfold‑LAST: 0.584 Sensitivity CentroidAlifold(20): 0.533 CentroidHomfold‑LAST: 0.491 Positive Predictive Value CentroidAlifold(20): 0.887 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Contrafold: 0.541 Sensitivity CentroidAlifold(20): 0.529 Contrafold: 0.478 Positive Predictive Value CentroidAlifold(20): 0.882 Contrafold: 0.617 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Sfold: 0.558 Sensitivity CentroidAlifold(20): 0.529 Sfold: 0.466 Positive Predictive Value CentroidAlifold(20): 0.882 Sfold: 0.673 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.682 HotKnots: 0.531 Sensitivity CentroidAlifold(20): 0.529 HotKnots: 0.475 Positive Predictive Value CentroidAlifold(20): 0.882 HotKnots: 0.599 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 CentroidFold: 0.542 Sensitivity CentroidAlifold(20): 0.529 CentroidFold: 0.459 Positive Predictive Value CentroidAlifold(20): 0.882 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.567 TurboFold(seed): 0.484 Sensitivity CentroidAlifold(20): 0.382 TurboFold(seed): 0.393 Positive Predictive Value CentroidAlifold(20): 0.848 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.682 MaxExpect: 0.557 Sensitivity CentroidAlifold(20): 0.529 MaxExpect: 0.481 Positive Predictive Value CentroidAlifold(20): 0.882 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.683 RSpredict(20): 0.549 Sensitivity CentroidAlifold(20): 0.532 RSpredict(20): 0.434 Positive Predictive Value CentroidAlifold(20): 0.880 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.682 PknotsRG: 0.555 Sensitivity CentroidAlifold(20): 0.529 PknotsRG: 0.494 Positive Predictive Value CentroidAlifold(20): 0.882 PknotsRG: 0.628 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.667 CMfinder(20): 0.521 Sensitivity CentroidAlifold(20): 0.524 CMfinder(20): 0.366 Positive Predictive Value CentroidAlifold(20): 0.853 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.38194587311e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 UNAFold: 0.542 Sensitivity CentroidAlifold(20): 0.529 UNAFold: 0.476 Positive Predictive Value CentroidAlifold(20): 0.882 UNAFold: 0.621 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.677 ProbKnot: 0.548 Sensitivity CentroidAlifold(20): 0.518 ProbKnot: 0.484 Positive Predictive Value CentroidAlifold(20): 0.887 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.746 Cylofold: 0.642 Sensitivity CentroidAlifold(20): 0.603 Cylofold: 0.543 Positive Predictive Value CentroidAlifold(20): 0.928 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAfold: 0.538 Sensitivity CentroidAlifold(20): 0.529 RNAfold: 0.478 Positive Predictive Value CentroidAlifold(20): 0.882 RNAfold: 0.610 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.495 RNASampler(seed): 0.458 Sensitivity CentroidAlifold(20): 0.319 RNASampler(seed): 0.334 Positive Predictive Value CentroidAlifold(20): 0.772 RNASampler(seed): 0.632 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAsubopt: 0.540 Sensitivity CentroidAlifold(20): 0.529 RNAsubopt: 0.483 Positive Predictive Value CentroidAlifold(20): 0.882 RNAsubopt: 0.609 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.688 Multilign(20): 0.534 Sensitivity CentroidAlifold(20): 0.537 Multilign(20): 0.449 Positive Predictive Value CentroidAlifold(20): 0.884 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.647 Afold: 0.507 Sensitivity CentroidAlifold(20): 0.492 Afold: 0.462 Positive Predictive Value CentroidAlifold(20): 0.853 Afold: 0.559 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAshapes: 0.517 Sensitivity CentroidAlifold(20): 0.529 RNAshapes: 0.455 Positive Predictive Value CentroidAlifold(20): 0.882 RNAshapes: 0.594 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.677 Fold: 0.531 Sensitivity CentroidAlifold(20): 0.518 Fold: 0.471 Positive Predictive Value CentroidAlifold(20): 0.887 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 McQFold: 0.511 Sensitivity CentroidAlifold(20): 0.529 McQFold: 0.438 Positive Predictive Value CentroidAlifold(20): 0.882 McQFold: 0.601 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.656 RNASLOpt: 0.463 Sensitivity CentroidAlifold(20): 0.501 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.864 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Mastr(20): 0.496 Sensitivity CentroidAlifold(20): 0.529 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(20): 0.882 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.569 Multilign(seed): 0.497 Sensitivity CentroidAlifold(20): 0.369 Multilign(seed): 0.369 Positive Predictive Value CentroidAlifold(20): 0.882 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Pknots: 0.486 Sensitivity CentroidAlifold(20): 0.544 Pknots: 0.439 Positive Predictive Value CentroidAlifold(20): 0.882 Pknots: 0.546 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Vsfold4: 0.460 Sensitivity CentroidAlifold(20): 0.541 Vsfold4: 0.383 Positive Predictive Value CentroidAlifold(20): 0.885 Vsfold4: 0.559 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.687 CRWrnafold: 0.546 Sensitivity CentroidAlifold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value CentroidAlifold(20): 0.924 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.618 Murlet(seed): 0.453 Sensitivity CentroidAlifold(20): 0.438 Murlet(seed): 0.240 Positive Predictive Value CentroidAlifold(20): 0.877 Murlet(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Vsfold5: 0.418 Sensitivity CentroidAlifold(20): 0.541 Vsfold5: 0.353 Positive Predictive Value CentroidAlifold(20): 0.885 Vsfold5: 0.501 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.684 MCFold: 0.397 Sensitivity CentroidAlifold(20): 0.539 MCFold: 0.414 Positive Predictive Value CentroidAlifold(20): 0.872 MCFold: 0.388 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.775 Alterna: 0.537 Sensitivity CentroidAlifold(20): 0.635 Alterna: 0.465 Positive Predictive Value CentroidAlifold(20): 0.952 Alterna: 0.630 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.771 RDfolder: 0.552 Sensitivity CentroidAlifold(20): 0.620 RDfolder: 0.436 Positive Predictive Value CentroidAlifold(20): 0.962 RDfolder: 0.708 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.669 RNAwolf: 0.348 Sensitivity CentroidAlifold(20): 0.511 RNAwolf: 0.328 Positive Predictive Value CentroidAlifold(20): 0.880 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.664 NanoFolder: 0.269 Sensitivity CentroidAlifold(20): 0.516 NanoFolder: 0.280 Positive Predictive Value CentroidAlifold(20): 0.859 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.645 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.481 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.868 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.683 RSpredict(seed): 0.163 Sensitivity CentroidAlifold(20): 0.532 RSpredict(seed): 0.063 Positive Predictive Value CentroidAlifold(20): 0.880 RSpredict(seed): 0.429 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 PPfold(seed): 0.072 Sensitivity CentroidAlifold(20): 0.514 PPfold(seed): 0.012 Positive Predictive Value CentroidAlifold(20): 0.877 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	? CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidAlifold(20): 0.662 Sensitivity PETfold_2.0(seed): 0.614 CentroidAlifold(20): 0.474 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidAlifold(20): 0.931 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A DAFS(20): N/A Sensitivity CentroidAlifold(20): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.662 PETfold_2.0(20): 0.647 Sensitivity CentroidAlifold(20): 0.474 PETfold_2.0(20): 0.509 Positive Predictive Value CentroidAlifold(20): 0.931 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient DAFS(seed): N/A CentroidAlifold(20): N/A Sensitivity DAFS(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value DAFS(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.529 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.882 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(seed)	18 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 CentroidAlifold(20): 0.656 Sensitivity PETfold_pre2.0(seed): 0.597 CentroidAlifold(20): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.870 CentroidAlifold(20): 0.864 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.74172190343e-08		+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(seed): 0.597 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.713 MXScarna(seed): 0.632 Sensitivity PETfold_pre2.0(seed): 0.600 MXScarna(seed): 0.525 Positive Predictive Value PETfold_pre2.0(seed): 0.848 MXScarna(seed): 0.763 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 PPfold(20): 0.649 Sensitivity PETfold_pre2.0(seed): 0.595 PPfold(20): 0.517 Positive Predictive Value PETfold_pre2.0(seed): 0.864 PPfold(20): 0.819 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ContextFold: 0.670 Sensitivity PETfold_pre2.0(seed): 0.602 ContextFold: 0.552 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ContextFold: 0.815 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(seed): 0.597 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.674 PETfold_pre2.0(20): 0.632 Sensitivity PETfold_pre2.0(seed): 0.538 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.846 PETfold_pre2.0(20): 0.806 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(seed): 0.595 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(seed): 0.864 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(seed): 0.597 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.870 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAalifold(seed): 0.637 Sensitivity PETfold_pre2.0(seed): 0.570 RNAalifold(seed): 0.477 Positive Predictive Value PETfold_pre2.0(seed): 0.811 RNAalifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(seed): 0.597 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidAlifold(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidAlifold(seed): 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(seed): 0.597 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.99051034341e-09	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 IPknot: 0.587 Sensitivity PETfold_pre2.0(seed): 0.602 IPknot: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.850 IPknot: 0.703 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidHomfold‑LAST: 0.574 Sensitivity PETfold_pre2.0(seed): 0.606 CentroidHomfold‑LAST: 0.489 Positive Predictive Value PETfold_pre2.0(seed): 0.882 CentroidHomfold‑LAST: 0.680 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Contrafold: 0.565 Sensitivity PETfold_pre2.0(seed): 0.602 Contrafold: 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Contrafold: 0.650 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Sfold: 0.505 Sensitivity PETfold_pre2.0(seed): 0.602 Sfold: 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Sfold: 0.601 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 HotKnots: 0.504 Sensitivity PETfold_pre2.0(seed): 0.595 HotKnots: 0.450 Positive Predictive Value PETfold_pre2.0(seed): 0.879 HotKnots: 0.570 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidFold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidFold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidFold: 0.625 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.645 TurboFold(seed): 0.504 Sensitivity PETfold_pre2.0(seed): 0.511 TurboFold(seed): 0.416 Positive Predictive Value PETfold_pre2.0(seed): 0.818 TurboFold(seed): 0.616 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 MaxExpect: 0.509 Sensitivity PETfold_pre2.0(seed): 0.602 MaxExpect: 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.850 MaxExpect: 0.592 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.669 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.534 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(seed): 0.841 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(seed): 0.595 PknotsRG: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.879 PknotsRG: 0.636 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(seed): 0.622 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(seed): 0.885 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 UNAFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.602 UNAFold: 0.414 Positive Predictive Value PETfold_pre2.0(seed): 0.850 UNAFold: 0.544 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ProbKnot: 0.513 Sensitivity PETfold_pre2.0(seed): 0.602 ProbKnot: 0.447 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ProbKnot: 0.590 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.726 Cylofold: 0.563 Sensitivity PETfold_pre2.0(seed): 0.609 Cylofold: 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.871 Cylofold: 0.681 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAfold: 0.500 Sensitivity PETfold_pre2.0(seed): 0.602 RNAfold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAfold: 0.573 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	? PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.594 RNASampler(seed): 0.333 Sensitivity PETfold_pre2.0(seed): 0.453 RNASampler(seed): 0.224 Positive Predictive Value PETfold_pre2.0(seed): 0.782 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAsubopt: 0.525 Sensitivity PETfold_pre2.0(seed): 0.595 RNAsubopt: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAsubopt: 0.599 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(seed): 0.616 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.86595104665e-08	? PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.639 Afold: 0.453 Sensitivity PETfold_pre2.0(seed): 0.521 Afold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Afold: 0.503 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAshapes: 0.491 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAshapes: 0.567 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Fold: 0.486 Sensitivity PETfold_pre2.0(seed): 0.602 Fold: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Fold: 0.551 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 McQFold: 0.484 Sensitivity PETfold_pre2.0(seed): 0.602 McQFold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.850 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNASLOpt: 0.499 Sensitivity PETfold_pre2.0(seed): 0.595 RNASLOpt: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(seed): 0.597 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.658 Multilign(seed): 0.533 Sensitivity PETfold_pre2.0(seed): 0.510 Multilign(seed): 0.411 Positive Predictive Value PETfold_pre2.0(seed): 0.851 Multilign(seed): 0.698 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Pknots: 0.457 Sensitivity PETfold_pre2.0(seed): 0.595 Pknots: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Pknots: 0.519 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold4: 0.452 Sensitivity PETfold_pre2.0(seed): 0.605 Vsfold4: 0.371 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold4: 0.559 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	? PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.675 CRWrnafold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.553 CRWrnafold: 0.461 Positive Predictive Value PETfold_pre2.0(seed): 0.828 CRWrnafold: 0.599 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.640 Murlet(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.508 Murlet(seed): 0.213 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold5: 0.403 Sensitivity PETfold_pre2.0(seed): 0.606 Vsfold5: 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 MCFold: 0.384 Sensitivity PETfold_pre2.0(seed): 0.579 MCFold: 0.397 Positive Predictive Value PETfold_pre2.0(seed): 0.857 MCFold: 0.379 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.69265863073e-08	? PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Alterna: 0.545 Sensitivity PETfold_pre2.0(seed): 0.540 Alterna: 0.460 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RDfolder: 0.395 Sensitivity PETfold_pre2.0(seed): 0.588 RDfolder: 0.311 Positive Predictive Value PETfold_pre2.0(seed): 0.865 RDfolder: 0.514 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAwolf: 0.404 Sensitivity PETfold_pre2.0(seed): 0.602 RNAwolf: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 NanoFolder: 0.290 Sensitivity PETfold_pre2.0(seed): 0.605 NanoFolder: 0.301 Positive Predictive Value PETfold_pre2.0(seed): 0.885 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.687 Carnac(seed): 0.467 Sensitivity PETfold_pre2.0(seed): 0.577 Carnac(seed): 0.245 Positive Predictive Value PETfold_pre2.0(seed): 0.820 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.688 RSpredict(seed): 0.416 Sensitivity PETfold_pre2.0(seed): 0.566 RSpredict(seed): 0.264 Positive Predictive Value PETfold_pre2.0(seed): 0.838 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 PPfold(seed): 0.156 Sensitivity PETfold_pre2.0(seed): 0.594 PPfold(seed): 0.036 Positive Predictive Value PETfold_pre2.0(seed): 0.875 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.775 PETfold_2.0(seed): 0.769 Sensitivity PETfold_pre2.0(seed): 0.642 PETfold_2.0(seed): 0.642 Positive Predictive Value PETfold_pre2.0(seed): 0.938 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Mastr(seed): 0.034 Sensitivity PETfold_pre2.0(seed): 0.595 Mastr(seed): 0.003 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08
RNAalifold(20)	36 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAalifold(20): 0.656 Sensitivity CentroidAlifold(20): 0.529 RNAalifold(20): 0.513 Positive Predictive Value CentroidAlifold(20): 0.882 RNAalifold(20): 0.841 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(seed): 0.597 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08		+ RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.652 MXScarna(seed): 0.646 Sensitivity RNAalifold(20): 0.509 MXScarna(seed): 0.529 Positive Predictive Value RNAalifold(20): 0.840 MXScarna(seed): 0.791 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNAalifold(20): 0.643 Sensitivity PPfold(20): 0.528 RNAalifold(20): 0.503 Positive Predictive Value PPfold(20): 0.836 RNAalifold(20): 0.826 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ RNAalifold(20) vs ContextFold Matthews Correlation Coefficient RNAalifold(20): 0.629 ContextFold: 0.617 Sensitivity RNAalifold(20): 0.488 ContextFold: 0.499 Positive Predictive Value RNAalifold(20): 0.815 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.0280318107e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 RNASampler(20): 0.612 Sensitivity RNAalifold(20): 0.511 RNASampler(20): 0.471 Positive Predictive Value RNAalifold(20): 0.846 RNASampler(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(20): 0.530 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.643 TurboFold(20): 0.616 Sensitivity RNAalifold(20): 0.503 TurboFold(20): 0.508 Positive Predictive Value RNAalifold(20): 0.826 TurboFold(20): 0.752 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 MXScarna(20): 0.611 Sensitivity RNAalifold(20): 0.511 MXScarna(20): 0.509 Positive Predictive Value RNAalifold(20): 0.846 MXScarna(20): 0.737 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.572 RNAalifold(seed): 0.559 Sensitivity RNAalifold(20): 0.419 RNAalifold(seed): 0.338 Positive Predictive Value RNAalifold(20): 0.785 RNAalifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.53460261044e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Murlet(20): 0.590 Sensitivity RNAalifold(20): 0.511 Murlet(20): 0.438 Positive Predictive Value RNAalifold(20): 0.846 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.656 CentroidAlifold(seed): 0.587 Sensitivity RNAalifold(20): 0.513 CentroidAlifold(seed): 0.368 Positive Predictive Value RNAalifold(20): 0.841 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Carnac(20): 0.590 Sensitivity RNAalifold(20): 0.511 Carnac(20): 0.389 Positive Predictive Value RNAalifold(20): 0.846 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.644 IPknot: 0.526 Sensitivity RNAalifold(20): 0.503 IPknot: 0.433 Positive Predictive Value RNAalifold(20): 0.829 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(20): 0.660 CentroidHomfold‑LAST: 0.584 Sensitivity RNAalifold(20): 0.519 CentroidHomfold‑LAST: 0.491 Positive Predictive Value RNAalifold(20): 0.844 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.656 Contrafold: 0.536 Sensitivity RNAalifold(20): 0.511 Contrafold: 0.472 Positive Predictive Value RNAalifold(20): 0.846 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.656 Sfold: 0.560 Sensitivity RNAalifold(20): 0.511 Sfold: 0.466 Positive Predictive Value RNAalifold(20): 0.846 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.656 HotKnots: 0.533 Sensitivity RNAalifold(20): 0.511 HotKnots: 0.475 Positive Predictive Value RNAalifold(20): 0.846 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.656 CentroidFold: 0.542 Sensitivity RNAalifold(20): 0.513 CentroidFold: 0.459 Positive Predictive Value RNAalifold(20): 0.841 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.527 TurboFold(seed): 0.484 Sensitivity RNAalifold(20): 0.393 TurboFold(seed): 0.393 Positive Predictive Value RNAalifold(20): 0.711 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.22791024781e-09	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.656 MaxExpect: 0.557 Sensitivity RNAalifold(20): 0.513 MaxExpect: 0.481 Positive Predictive Value RNAalifold(20): 0.841 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.655 RSpredict(20): 0.552 Sensitivity RNAalifold(20): 0.513 RSpredict(20): 0.436 Positive Predictive Value RNAalifold(20): 0.841 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.656 PknotsRG: 0.557 Sensitivity RNAalifold(20): 0.511 PknotsRG: 0.494 Positive Predictive Value RNAalifold(20): 0.846 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.662 CMfinder(20): 0.521 Sensitivity RNAalifold(20): 0.521 CMfinder(20): 0.366 Positive Predictive Value RNAalifold(20): 0.844 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.656 UNAFold: 0.543 Sensitivity RNAalifold(20): 0.511 UNAFold: 0.475 Positive Predictive Value RNAalifold(20): 0.846 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.649 ProbKnot: 0.548 Sensitivity RNAalifold(20): 0.503 ProbKnot: 0.484 Positive Predictive Value RNAalifold(20): 0.840 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.720 Cylofold: 0.642 Sensitivity RNAalifold(20): 0.577 Cylofold: 0.543 Positive Predictive Value RNAalifold(20): 0.902 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAfold: 0.540 Sensitivity RNAalifold(20): 0.511 RNAfold: 0.477 Positive Predictive Value RNAalifold(20): 0.846 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 RNAalifold(20): 0.466 Sensitivity RNASampler(seed): 0.353 RNAalifold(20): 0.356 Positive Predictive Value RNASampler(seed): 0.652 RNAalifold(20): 0.614 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71178597147e-06	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAsubopt: 0.534 Sensitivity RNAalifold(20): 0.511 RNAsubopt: 0.477 Positive Predictive Value RNAalifold(20): 0.846 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Multilign(20): 0.534 Sensitivity RNAalifold(20): 0.521 Multilign(20): 0.449 Positive Predictive Value RNAalifold(20): 0.841 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.609 Afold: 0.511 Sensitivity RNAalifold(20): 0.468 Afold: 0.460 Positive Predictive Value RNAalifold(20): 0.795 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAshapes: 0.517 Sensitivity RNAalifold(20): 0.511 RNAshapes: 0.453 Positive Predictive Value RNAalifold(20): 0.846 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.649 Fold: 0.531 Sensitivity RNAalifold(20): 0.503 Fold: 0.471 Positive Predictive Value RNAalifold(20): 0.840 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.656 McQFold: 0.506 Sensitivity RNAalifold(20): 0.511 McQFold: 0.433 Positive Predictive Value RNAalifold(20): 0.846 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.629 RNASLOpt: 0.463 Sensitivity RNAalifold(20): 0.488 RNASLOpt: 0.383 Positive Predictive Value RNAalifold(20): 0.815 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(20): 0.500 Sensitivity RNAalifold(20): 0.511 Mastr(20): 0.336 Positive Predictive Value RNAalifold(20): 0.846 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.556 Multilign(seed): 0.497 Sensitivity RNAalifold(20): 0.409 Multilign(seed): 0.369 Positive Predictive Value RNAalifold(20): 0.761 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.667 Pknots: 0.481 Sensitivity RNAalifold(20): 0.527 Pknots: 0.433 Positive Predictive Value RNAalifold(20): 0.848 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.665 Vsfold4: 0.459 Sensitivity RNAalifold(20): 0.520 Vsfold4: 0.381 Positive Predictive Value RNAalifold(20): 0.854 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.620 CRWrnafold: 0.546 Sensitivity RNAalifold(20): 0.479 CRWrnafold: 0.483 Positive Predictive Value RNAalifold(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.579 Murlet(seed): 0.454 Sensitivity RNAalifold(20): 0.433 Murlet(seed): 0.241 Positive Predictive Value RNAalifold(20): 0.779 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.665 Vsfold5: 0.409 Sensitivity RNAalifold(20): 0.520 Vsfold5: 0.345 Positive Predictive Value RNAalifold(20): 0.854 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.658 MCFold: 0.402 Sensitivity RNAalifold(20): 0.525 MCFold: 0.418 Positive Predictive Value RNAalifold(20): 0.829 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.757 Alterna: 0.553 Sensitivity RNAalifold(20): 0.619 Alterna: 0.480 Positive Predictive Value RNAalifold(20): 0.930 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.744 RDfolder: 0.563 Sensitivity RNAalifold(20): 0.590 RDfolder: 0.447 Positive Predictive Value RNAalifold(20): 0.944 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAwolf: 0.348 Sensitivity RNAalifold(20): 0.503 RNAwolf: 0.328 Positive Predictive Value RNAalifold(20): 0.829 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.637 NanoFolder: 0.269 Sensitivity RNAalifold(20): 0.504 NanoFolder: 0.280 Positive Predictive Value RNAalifold(20): 0.811 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.612 Carnac(seed): 0.110 Sensitivity RNAalifold(20): 0.471 Carnac(seed): 0.012 Positive Predictive Value RNAalifold(20): 0.799 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.655 RSpredict(seed): 0.174 Sensitivity RNAalifold(20): 0.513 RSpredict(seed): 0.068 Positive Predictive Value RNAalifold(20): 0.841 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.643 PPfold(seed): 0.072 Sensitivity RNAalifold(20): 0.503 PPfold(seed): 0.012 Positive Predictive Value RNAalifold(20): 0.826 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	? RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNAalifold(20): 0.654 Sensitivity PETfold_2.0(seed): 0.614 RNAalifold(20): 0.491 Positive Predictive Value PETfold_2.0(seed): 0.946 RNAalifold(20): 0.875 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(20): N/A Sensitivity RNAalifold(20): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(20): 0.654 PETfold_2.0(20): 0.647 Sensitivity RNAalifold(20): 0.491 PETfold_2.0(20): 0.509 Positive Predictive Value RNAalifold(20): 0.875 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(seed): N/A Sensitivity RNAalifold(20): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.511 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.846 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(seed)	35 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.679 MXScarna(seed): 0.643 Sensitivity CentroidAlifold(20): 0.526 MXScarna(seed): 0.526 Positive Predictive Value CentroidAlifold(20): 0.880 MXScarna(seed): 0.789 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.713 MXScarna(seed): 0.632 Sensitivity PETfold_pre2.0(seed): 0.600 MXScarna(seed): 0.525 Positive Predictive Value PETfold_pre2.0(seed): 0.848 MXScarna(seed): 0.763 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	36 RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.652 MXScarna(seed): 0.646 Sensitivity RNAalifold(20): 0.509 MXScarna(seed): 0.529 Positive Predictive Value RNAalifold(20): 0.840 MXScarna(seed): 0.791 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08		- PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.657 MXScarna(seed): 0.615 Sensitivity PPfold(20): 0.522 MXScarna(seed): 0.494 Positive Predictive Value PPfold(20): 0.831 MXScarna(seed): 0.772 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	- ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.669 MXScarna(seed): 0.632 Sensitivity ContextFold: 0.551 MXScarna(seed): 0.525 Positive Predictive Value ContextFold: 0.814 MXScarna(seed): 0.763 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 RNASampler(20): 0.612 Sensitivity MXScarna(seed): 0.529 RNASampler(20): 0.474 Positive Predictive Value MXScarna(seed): 0.791 RNASampler(20): 0.793 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.642 MXScarna(seed): 0.595 Sensitivity PETfold_pre2.0(20): 0.524 MXScarna(seed): 0.476 Positive Predictive Value PETfold_pre2.0(20): 0.791 MXScarna(seed): 0.748 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.615 TurboFold(20): 0.607 Sensitivity MXScarna(seed): 0.494 TurboFold(20): 0.499 Positive Predictive Value MXScarna(seed): 0.772 TurboFold(20): 0.743 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.67241913479e-07	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 MXScarna(20): 0.610 Sensitivity MXScarna(seed): 0.529 MXScarna(20): 0.510 Positive Predictive Value MXScarna(seed): 0.791 MXScarna(20): 0.734 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.612 RNAalifold(seed): 0.606 Sensitivity MXScarna(seed): 0.499 RNAalifold(seed): 0.427 Positive Predictive Value MXScarna(seed): 0.751 RNAalifold(seed): 0.861 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.7429475951e-07	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 Murlet(20): 0.586 Sensitivity MXScarna(seed): 0.529 Murlet(20): 0.436 Positive Predictive Value MXScarna(seed): 0.791 Murlet(20): 0.792 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.644 CentroidAlifold(seed): 0.619 Sensitivity MXScarna(seed): 0.534 CentroidAlifold(seed): 0.427 Positive Predictive Value MXScarna(seed): 0.778 CentroidAlifold(seed): 0.899 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 Carnac(20): 0.588 Sensitivity MXScarna(seed): 0.529 Carnac(20): 0.387 Positive Predictive Value MXScarna(seed): 0.791 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.638 IPknot: 0.594 Sensitivity MXScarna(seed): 0.529 IPknot: 0.495 Positive Predictive Value MXScarna(seed): 0.770 IPknot: 0.714 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.620 CentroidHomfold‑LAST: 0.584 Sensitivity MXScarna(seed): 0.503 CentroidHomfold‑LAST: 0.491 Positive Predictive Value MXScarna(seed): 0.770 CentroidHomfold‑LAST: 0.701 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.646 Contrafold: 0.568 Sensitivity MXScarna(seed): 0.536 Contrafold: 0.504 Positive Predictive Value MXScarna(seed): 0.779 Contrafold: 0.642 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.646 Sfold: 0.542 Sensitivity MXScarna(seed): 0.536 Sfold: 0.461 Positive Predictive Value MXScarna(seed): 0.779 Sfold: 0.638 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.638 HotKnots: 0.543 Sensitivity MXScarna(seed): 0.522 HotKnots: 0.491 Positive Predictive Value MXScarna(seed): 0.783 HotKnots: 0.606 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.644 CentroidFold: 0.556 Sensitivity MXScarna(seed): 0.534 CentroidFold: 0.474 Positive Predictive Value MXScarna(seed): 0.778 CentroidFold: 0.654 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.539 TurboFold(seed): 0.529 Sensitivity MXScarna(seed): 0.413 TurboFold(seed): 0.434 Positive Predictive Value MXScarna(seed): 0.709 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.10997767043e-07	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.641 MaxExpect: 0.544 Sensitivity MXScarna(seed): 0.531 MaxExpect: 0.476 Positive Predictive Value MXScarna(seed): 0.773 MaxExpect: 0.624 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.649 RSpredict(20): 0.547 Sensitivity MXScarna(seed): 0.532 RSpredict(20): 0.432 Positive Predictive Value MXScarna(seed): 0.795 RSpredict(20): 0.698 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.638 PknotsRG: 0.562 Sensitivity MXScarna(seed): 0.522 PknotsRG: 0.505 Positive Predictive Value MXScarna(seed): 0.783 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.603 CMfinder(20): 0.504 Sensitivity MXScarna(seed): 0.494 CMfinder(20): 0.350 Positive Predictive Value MXScarna(seed): 0.741 CMfinder(20): 0.730 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.646 UNAFold: 0.524 Sensitivity MXScarna(seed): 0.536 UNAFold: 0.464 Positive Predictive Value MXScarna(seed): 0.779 UNAFold: 0.595 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.640 ProbKnot: 0.536 Sensitivity MXScarna(seed): 0.531 ProbKnot: 0.476 Positive Predictive Value MXScarna(seed): 0.773 ProbKnot: 0.605 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.658 Cylofold: 0.618 Sensitivity MXScarna(seed): 0.545 Cylofold: 0.519 Positive Predictive Value MXScarna(seed): 0.800 Cylofold: 0.741 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.646 RNAfold: 0.533 Sensitivity MXScarna(seed): 0.536 RNAfold: 0.474 Positive Predictive Value MXScarna(seed): 0.779 RNAfold: 0.600 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.506 RNASampler(seed): 0.482 Sensitivity MXScarna(seed): 0.380 RNASampler(seed): 0.342 Positive Predictive Value MXScarna(seed): 0.677 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAsubopt: 0.538 Sensitivity MXScarna(seed): 0.522 RNAsubopt: 0.486 Positive Predictive Value MXScarna(seed): 0.783 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.634 Multilign(20): 0.521 Sensitivity MXScarna(seed): 0.518 Multilign(20): 0.438 Positive Predictive Value MXScarna(seed): 0.782 Multilign(20): 0.627 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.623 Afold: 0.500 Sensitivity MXScarna(seed): 0.507 Afold: 0.463 Positive Predictive Value MXScarna(seed): 0.767 Afold: 0.544 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAshapes: 0.523 Sensitivity MXScarna(seed): 0.522 RNAshapes: 0.464 Positive Predictive Value MXScarna(seed): 0.783 RNAshapes: 0.594 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.639 Fold: 0.520 Sensitivity MXScarna(seed): 0.530 Fold: 0.464 Positive Predictive Value MXScarna(seed): 0.772 Fold: 0.584 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.646 McQFold: 0.506 Sensitivity MXScarna(seed): 0.536 McQFold: 0.436 Positive Predictive Value MXScarna(seed): 0.779 McQFold: 0.589 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.605 RNASLOpt: 0.488 Sensitivity MXScarna(seed): 0.487 RNASLOpt: 0.398 Positive Predictive Value MXScarna(seed): 0.757 RNASLOpt: 0.604 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 Mastr(20): 0.493 Sensitivity MXScarna(seed): 0.529 Mastr(20): 0.330 Positive Predictive Value MXScarna(seed): 0.791 Mastr(20): 0.742 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 MXScarna(seed): 0.555 Sensitivity Multilign(seed): 0.432 MXScarna(seed): 0.432 Positive Predictive Value Multilign(seed): 0.723 MXScarna(seed): 0.719 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00343916605433	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.644 Pknots: 0.533 Sensitivity MXScarna(seed): 0.528 Pknots: 0.478 Positive Predictive Value MXScarna(seed): 0.791 Pknots: 0.600 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.641 Vsfold4: 0.485 Sensitivity MXScarna(seed): 0.526 Vsfold4: 0.408 Positive Predictive Value MXScarna(seed): 0.784 Vsfold4: 0.581 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.610 CRWrnafold: 0.536 Sensitivity MXScarna(seed): 0.490 CRWrnafold: 0.472 Positive Predictive Value MXScarna(seed): 0.765 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.581 Murlet(seed): 0.448 Sensitivity MXScarna(seed): 0.456 Murlet(seed): 0.245 Positive Predictive Value MXScarna(seed): 0.745 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.640 Vsfold5: 0.446 Sensitivity MXScarna(seed): 0.526 Vsfold5: 0.381 Positive Predictive Value MXScarna(seed): 0.783 Vsfold5: 0.529 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.634 MCFold: 0.418 Sensitivity MXScarna(seed): 0.517 MCFold: 0.436 Positive Predictive Value MXScarna(seed): 0.782 MCFold: 0.408 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.693 Alterna: 0.572 Sensitivity MXScarna(seed): 0.560 Alterna: 0.500 Positive Predictive Value MXScarna(seed): 0.864 Alterna: 0.664 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.685 RDfolder: 0.504 Sensitivity MXScarna(seed): 0.556 RDfolder: 0.407 Positive Predictive Value MXScarna(seed): 0.852 RDfolder: 0.634 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAwolf: 0.409 Sensitivity MXScarna(seed): 0.529 RNAwolf: 0.379 Positive Predictive Value MXScarna(seed): 0.770 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.611 NanoFolder: 0.273 Sensitivity MXScarna(seed): 0.499 NanoFolder: 0.284 Positive Predictive Value MXScarna(seed): 0.754 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.630 Carnac(seed): 0.392 Sensitivity MXScarna(seed): 0.522 Carnac(seed): 0.172 Positive Predictive Value MXScarna(seed): 0.760 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.647 RSpredict(seed): 0.340 Sensitivity MXScarna(seed): 0.538 RSpredict(seed): 0.191 Positive Predictive Value MXScarna(seed): 0.781 RSpredict(seed): 0.606 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.620 PPfold(seed): 0.150 Sensitivity MXScarna(seed): 0.499 PPfold(seed): 0.033 Positive Predictive Value MXScarna(seed): 0.775 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MXScarna(seed): 0.682 Sensitivity PETfold_2.0(seed): 0.642 MXScarna(seed): 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 MXScarna(seed): 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs DAFS(20) Matthews Correlation Coefficient MXScarna(seed): N/A DAFS(20): N/A Sensitivity MXScarna(seed): N/A DAFS(20): N/A Positive Predictive Value MXScarna(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MXScarna(seed): 0.563 Sensitivity PETfold_2.0(20): 0.509 MXScarna(seed): 0.456 Positive Predictive Value PETfold_2.0(20): 0.829 MXScarna(seed): 0.703 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs MXScarna(seed) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(seed): N/A Sensitivity DAFS(seed): N/A MXScarna(seed): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.638 Mastr(seed): 0.024 Sensitivity MXScarna(seed): 0.522 Mastr(seed): 0.002 Positive Predictive Value MXScarna(seed): 0.783 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(20)	20 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 PPfold(20): 0.663 Sensitivity CentroidAlifold(20): 0.514 PPfold(20): 0.528 Positive Predictive Value CentroidAlifold(20): 0.877 PPfold(20): 0.836 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	17 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 PPfold(20): 0.649 Sensitivity PETfold_pre2.0(seed): 0.595 PPfold(20): 0.517 Positive Predictive Value PETfold_pre2.0(seed): 0.864 PPfold(20): 0.819 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	20 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNAalifold(20): 0.643 Sensitivity PPfold(20): 0.528 RNAalifold(20): 0.503 Positive Predictive Value PPfold(20): 0.836 RNAalifold(20): 0.826 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	19 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.657 MXScarna(seed): 0.615 Sensitivity PPfold(20): 0.522 MXScarna(seed): 0.494 Positive Predictive Value PPfold(20): 0.831 MXScarna(seed): 0.772 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08		+ PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.649 ContextFold: 0.605 Sensitivity PPfold(20): 0.517 ContextFold: 0.492 Positive Predictive Value PPfold(20): 0.819 ContextFold: 0.749 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.42071836373e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNASampler(20): 0.582 Sensitivity PPfold(20): 0.528 RNASampler(20): 0.450 Positive Predictive Value PPfold(20): 0.836 RNASampler(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	= PPfold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(20): 0.649 PETfold_pre2.0(20): 0.649 Sensitivity PPfold(20): 0.517 PETfold_pre2.0(20): 0.532 Positive Predictive Value PPfold(20): 0.819 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00876167151132	+ PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.663 TurboFold(20): 0.616 Sensitivity PPfold(20): 0.528 TurboFold(20): 0.508 Positive Predictive Value PPfold(20): 0.836 TurboFold(20): 0.752 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.663 MXScarna(20): 0.578 Sensitivity PPfold(20): 0.528 MXScarna(20): 0.476 Positive Predictive Value PPfold(20): 0.836 MXScarna(20): 0.706 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	- RNAalifold(seed) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.543 PPfold(20): 0.509 Sensitivity RNAalifold(seed): 0.313 PPfold(20): 0.371 Positive Predictive Value RNAalifold(seed): 0.947 PPfold(20): 0.702 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.00475527001e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.663 Murlet(20): 0.580 Sensitivity PPfold(20): 0.528 Murlet(20): 0.439 Positive Predictive Value PPfold(20): 0.836 Murlet(20): 0.772 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.663 CentroidAlifold(seed): 0.558 Sensitivity PPfold(20): 0.528 CentroidAlifold(seed): 0.330 Positive Predictive Value PPfold(20): 0.836 CentroidAlifold(seed): 0.949 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.663 Carnac(20): 0.565 Sensitivity PPfold(20): 0.528 Carnac(20): 0.372 Positive Predictive Value PPfold(20): 0.836 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.663 IPknot: 0.535 Sensitivity PPfold(20): 0.528 IPknot: 0.443 Positive Predictive Value PPfold(20): 0.836 IPknot: 0.651 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.684 CentroidHomfold‑LAST: 0.589 Sensitivity PPfold(20): 0.552 CentroidHomfold‑LAST: 0.501 Positive Predictive Value PPfold(20): 0.851 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.663 Contrafold: 0.523 Sensitivity PPfold(20): 0.528 Contrafold: 0.460 Positive Predictive Value PPfold(20): 0.836 Contrafold: 0.602 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.663 Sfold: 0.526 Sensitivity PPfold(20): 0.528 Sfold: 0.439 Positive Predictive Value PPfold(20): 0.836 Sfold: 0.635 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.663 HotKnots: 0.497 Sensitivity PPfold(20): 0.528 HotKnots: 0.443 Positive Predictive Value PPfold(20): 0.836 HotKnots: 0.564 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.663 CentroidFold: 0.474 Sensitivity PPfold(20): 0.528 CentroidFold: 0.400 Positive Predictive Value PPfold(20): 0.836 CentroidFold: 0.568 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.531 TurboFold(seed): 0.484 Sensitivity PPfold(20): 0.393 TurboFold(seed): 0.393 Positive Predictive Value PPfold(20): 0.722 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.663 MaxExpect: 0.503 Sensitivity PPfold(20): 0.528 MaxExpect: 0.431 Positive Predictive Value PPfold(20): 0.836 MaxExpect: 0.594 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(20): 0.520 Sensitivity PPfold(20): 0.528 RSpredict(20): 0.398 Positive Predictive Value PPfold(20): 0.836 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.663 PknotsRG: 0.541 Sensitivity PPfold(20): 0.528 PknotsRG: 0.479 Positive Predictive Value PPfold(20): 0.836 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.678 CMfinder(20): 0.539 Sensitivity PPfold(20): 0.554 CMfinder(20): 0.389 Positive Predictive Value PPfold(20): 0.833 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.663 UNAFold: 0.487 Sensitivity PPfold(20): 0.528 UNAFold: 0.427 Positive Predictive Value PPfold(20): 0.836 UNAFold: 0.561 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.663 ProbKnot: 0.502 Sensitivity PPfold(20): 0.528 ProbKnot: 0.441 Positive Predictive Value PPfold(20): 0.836 ProbKnot: 0.578 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.743 Cylofold: 0.628 Sensitivity PPfold(20): 0.608 Cylofold: 0.529 Positive Predictive Value PPfold(20): 0.912 Cylofold: 0.751 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.663 RNAfold: 0.506 Sensitivity PPfold(20): 0.528 RNAfold: 0.446 Positive Predictive Value PPfold(20): 0.836 RNAfold: 0.581 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.423 PPfold(20): 0.419 Sensitivity RNASampler(seed): 0.300 PPfold(20): 0.300 Positive Predictive Value RNASampler(seed): 0.600 PPfold(20): 0.590 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.663 RNAsubopt: 0.526 Sensitivity PPfold(20): 0.528 RNAsubopt: 0.468 Positive Predictive Value PPfold(20): 0.836 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.81788725234e-08	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.684 Multilign(20): 0.534 Sensitivity PPfold(20): 0.552 Multilign(20): 0.449 Positive Predictive Value PPfold(20): 0.851 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	? PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.541 Afold: 0.476 Sensitivity PPfold(20): 0.411 Afold: 0.423 Positive Predictive Value PPfold(20): 0.719 Afold: 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.663 RNAshapes: 0.503 Sensitivity PPfold(20): 0.528 RNAshapes: 0.443 Positive Predictive Value PPfold(20): 0.836 RNAshapes: 0.576 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.663 Fold: 0.479 Sensitivity PPfold(20): 0.528 Fold: 0.426 Positive Predictive Value PPfold(20): 0.836 Fold: 0.546 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.663 McQFold: 0.485 Sensitivity PPfold(20): 0.528 McQFold: 0.416 Positive Predictive Value PPfold(20): 0.836 McQFold: 0.572 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.649 RNASLOpt: 0.464 Sensitivity PPfold(20): 0.517 RNASLOpt: 0.387 Positive Predictive Value PPfold(20): 0.819 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(20): 0.518 Sensitivity PPfold(20): 0.528 Mastr(20): 0.357 Positive Predictive Value PPfold(20): 0.836 Mastr(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.543 Multilign(seed): 0.497 Sensitivity PPfold(20): 0.394 Multilign(seed): 0.369 Positive Predictive Value PPfold(20): 0.755 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.663 Pknots: 0.426 Sensitivity PPfold(20): 0.528 Pknots: 0.381 Positive Predictive Value PPfold(20): 0.836 Pknots: 0.484 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.684 Vsfold4: 0.451 Sensitivity PPfold(20): 0.552 Vsfold4: 0.374 Positive Predictive Value PPfold(20): 0.851 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.7968284078e-08	? PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.657 CRWrnafold: 0.546 Sensitivity PPfold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value PPfold(20): 0.846 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.509 Murlet(seed): 0.429 Sensitivity PPfold(20): 0.371 Murlet(seed): 0.219 Positive Predictive Value PPfold(20): 0.702 Murlet(seed): 0.843 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.31583660336e-08	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.684 Vsfold5: 0.410 Sensitivity PPfold(20): 0.552 Vsfold5: 0.352 Positive Predictive Value PPfold(20): 0.851 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.646 MCFold: 0.396 Sensitivity PPfold(20): 0.510 MCFold: 0.406 Positive Predictive Value PPfold(20): 0.822 MCFold: 0.394 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.743 Alterna: 0.584 Sensitivity PPfold(20): 0.592 Alterna: 0.495 Positive Predictive Value PPfold(20): 0.938 Alterna: 0.699 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.737 RDfolder: 0.489 Sensitivity PPfold(20): 0.585 RDfolder: 0.365 Positive Predictive Value PPfold(20): 0.934 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.663 RNAwolf: 0.343 Sensitivity PPfold(20): 0.528 RNAwolf: 0.325 Positive Predictive Value PPfold(20): 0.836 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.664 NanoFolder: 0.271 Sensitivity PPfold(20): 0.541 NanoFolder: 0.286 Positive Predictive Value PPfold(20): 0.818 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.547 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.407 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.742 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.28433927253e-09	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(seed): 0.129 Sensitivity PPfold(20): 0.528 RSpredict(seed): 0.048 Positive Predictive Value PPfold(20): 0.836 RSpredict(seed): 0.361 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.663 PPfold(seed): 0.072 Sensitivity PPfold(20): 0.528 PPfold(seed): 0.012 Positive Predictive Value PPfold(20): 0.836 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	? PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(seed): N/A Sensitivity PPfold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs DAFS(20) Matthews Correlation Coefficient PPfold(20): N/A DAFS(20): N/A Sensitivity PPfold(20): N/A DAFS(20): N/A Positive Predictive Value PPfold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(20): N/A Sensitivity PPfold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs DAFS(seed) Matthews Correlation Coefficient PPfold(20): N/A DAFS(seed): N/A Sensitivity PPfold(20): N/A DAFS(seed): N/A Positive Predictive Value PPfold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.528 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.836 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08
ContextFold	18 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.656 ContextFold: 0.617 Sensitivity CentroidAlifold(20): 0.501 ContextFold: 0.499 Positive Predictive Value CentroidAlifold(20): 0.864 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	26 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ContextFold: 0.670 Sensitivity PETfold_pre2.0(seed): 0.602 ContextFold: 0.552 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ContextFold: 0.815 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 RNAalifold(20) vs ContextFold Matthews Correlation Coefficient RNAalifold(20): 0.629 ContextFold: 0.617 Sensitivity RNAalifold(20): 0.488 ContextFold: 0.499 Positive Predictive Value RNAalifold(20): 0.815 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.0280318107e-08	25 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.669 MXScarna(seed): 0.632 Sensitivity ContextFold: 0.551 MXScarna(seed): 0.525 Positive Predictive Value ContextFold: 0.814 MXScarna(seed): 0.763 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.649 ContextFold: 0.605 Sensitivity PPfold(20): 0.517 ContextFold: 0.492 Positive Predictive Value PPfold(20): 0.819 ContextFold: 0.749 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.42071836373e-08		+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.617 RNASampler(20): 0.561 Sensitivity ContextFold: 0.499 RNASampler(20): 0.429 Positive Predictive Value ContextFold: 0.767 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.5677163434e-08	- PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ContextFold: 0.617 Sensitivity PETfold_pre2.0(20): 0.530 ContextFold: 0.499 Positive Predictive Value PETfold_pre2.0(20): 0.798 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.26346675981e-08	= TurboFold(20) vs ContextFold Matthews Correlation Coefficient TurboFold(20): 0.606 ContextFold: 0.605 Sensitivity TurboFold(20): 0.502 ContextFold: 0.492 Positive Predictive Value TurboFold(20): 0.737 ContextFold: 0.749 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0184072909178	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.617 MXScarna(20): 0.570 Sensitivity ContextFold: 0.499 MXScarna(20): 0.470 Positive Predictive Value ContextFold: 0.767 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	= RNAalifold(seed) vs ContextFold Matthews Correlation Coefficient RNAalifold(seed): 0.637 ContextFold: 0.635 Sensitivity RNAalifold(seed): 0.477 ContextFold: 0.524 Positive Predictive Value RNAalifold(seed): 0.849 ContextFold: 0.769 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0626385029064	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.617 Murlet(20): 0.564 Sensitivity ContextFold: 0.499 Murlet(20): 0.418 Positive Predictive Value ContextFold: 0.767 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.670 CentroidAlifold(seed): 0.628 Sensitivity ContextFold: 0.552 CentroidAlifold(seed): 0.443 Positive Predictive Value ContextFold: 0.815 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.617 Carnac(20): 0.547 Sensitivity ContextFold: 0.499 Carnac(20): 0.351 Positive Predictive Value ContextFold: 0.767 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.536 IPknot: 0.506 Sensitivity ContextFold: 0.440 IPknot: 0.406 Positive Predictive Value ContextFold: 0.654 IPknot: 0.633 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.597 CentroidHomfold‑LAST: 0.498 Sensitivity ContextFold: 0.485 CentroidHomfold‑LAST: 0.368 Positive Predictive Value ContextFold: 0.738 CentroidHomfold‑LAST: 0.679 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.536 Contrafold: 0.453 Sensitivity ContextFold: 0.440 Contrafold: 0.389 Positive Predictive Value ContextFold: 0.654 Contrafold: 0.528 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.536 Sfold: 0.460 Sensitivity ContextFold: 0.440 Sfold: 0.387 Positive Predictive Value ContextFold: 0.654 Sfold: 0.548 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.578 HotKnots: 0.489 Sensitivity ContextFold: 0.471 HotKnots: 0.432 Positive Predictive Value ContextFold: 0.713 HotKnots: 0.559 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.536 CentroidFold: 0.437 Sensitivity ContextFold: 0.440 CentroidFold: 0.349 Positive Predictive Value ContextFold: 0.654 CentroidFold: 0.550 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.504 ContextFold: 0.480 Sensitivity TurboFold(seed): 0.416 ContextFold: 0.385 Positive Predictive Value TurboFold(seed): 0.616 ContextFold: 0.605 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.58782420473e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.536 MaxExpect: 0.439 Sensitivity ContextFold: 0.440 MaxExpect: 0.378 Positive Predictive Value ContextFold: 0.654 MaxExpect: 0.511 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.605 RSpredict(20): 0.491 Sensitivity ContextFold: 0.492 RSpredict(20): 0.373 Positive Predictive Value ContextFold: 0.749 RSpredict(20): 0.653 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.478 PknotsRG: 0.446 Sensitivity ContextFold: 0.389 PknotsRG: 0.394 Positive Predictive Value ContextFold: 0.588 PknotsRG: 0.508 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.641 CMfinder(20): 0.521 Sensitivity ContextFold: 0.528 CMfinder(20): 0.366 Positive Predictive Value ContextFold: 0.783 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.536 UNAFold: 0.438 Sensitivity ContextFold: 0.440 UNAFold: 0.383 Positive Predictive Value ContextFold: 0.654 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.536 ProbKnot: 0.438 Sensitivity ContextFold: 0.440 ProbKnot: 0.382 Positive Predictive Value ContextFold: 0.654 ProbKnot: 0.502 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.595 Cylofold: 0.466 Sensitivity ContextFold: 0.491 Cylofold: 0.390 Positive Predictive Value ContextFold: 0.726 Cylofold: 0.565 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.536 RNAfold: 0.440 Sensitivity ContextFold: 0.440 RNAfold: 0.386 Positive Predictive Value ContextFold: 0.654 RNAfold: 0.503 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.394 RNASampler(seed): 0.333 Sensitivity ContextFold: 0.322 RNASampler(seed): 0.224 Positive Predictive Value ContextFold: 0.488 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.578 RNAsubopt: 0.462 Sensitivity ContextFold: 0.471 RNAsubopt: 0.408 Positive Predictive Value ContextFold: 0.713 RNAsubopt: 0.529 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.628 Multilign(20): 0.514 Sensitivity ContextFold: 0.514 Multilign(20): 0.433 Positive Predictive Value ContextFold: 0.771 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.7402423548e-08	- Afold vs ContextFold Matthews Correlation Coefficient Afold: 0.337 ContextFold: 0.326 Sensitivity Afold: 0.303 ContextFold: 0.268 Positive Predictive Value Afold: 0.376 ContextFold: 0.398 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.0017973759e-06	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.578 RNAshapes: 0.445 Sensitivity ContextFold: 0.471 RNAshapes: 0.386 Positive Predictive Value ContextFold: 0.713 RNAshapes: 0.519 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.536 Fold: 0.403 Sensitivity ContextFold: 0.440 Fold: 0.357 Positive Predictive Value ContextFold: 0.654 Fold: 0.457 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.536 McQFold: 0.368 Sensitivity ContextFold: 0.440 McQFold: 0.312 Positive Predictive Value ContextFold: 0.654 McQFold: 0.434 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.578 RNASLOpt: 0.427 Sensitivity ContextFold: 0.471 RNASLOpt: 0.341 Positive Predictive Value ContextFold: 0.713 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.617 Mastr(20): 0.465 Sensitivity ContextFold: 0.499 Mastr(20): 0.313 Positive Predictive Value ContextFold: 0.767 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	? Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.533 ContextFold: 0.500 Sensitivity Multilign(seed): 0.411 ContextFold: 0.408 Positive Predictive Value Multilign(seed): 0.698 ContextFold: 0.620 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.571 Pknots: 0.424 Sensitivity ContextFold: 0.469 Pknots: 0.382 Positive Predictive Value ContextFold: 0.702 Pknots: 0.477 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.578 Vsfold4: 0.393 Sensitivity ContextFold: 0.471 Vsfold4: 0.321 Positive Predictive Value ContextFold: 0.714 Vsfold4: 0.488 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.590 CRWrnafold: 0.445 Sensitivity ContextFold: 0.477 CRWrnafold: 0.391 Positive Predictive Value ContextFold: 0.736 CRWrnafold: 0.514 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.01312059156e-09	+ ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.491 Murlet(seed): 0.403 Sensitivity ContextFold: 0.397 Murlet(seed): 0.213 Positive Predictive Value ContextFold: 0.613 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.27752322258e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.592 Vsfold5: 0.358 Sensitivity ContextFold: 0.484 Vsfold5: 0.307 Positive Predictive Value ContextFold: 0.730 Vsfold5: 0.426 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.530 MCFold: 0.358 Sensitivity ContextFold: 0.434 MCFold: 0.366 Positive Predictive Value ContextFold: 0.652 MCFold: 0.357 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.558 Alterna: 0.432 Sensitivity ContextFold: 0.452 Alterna: 0.379 Positive Predictive Value ContextFold: 0.700 Alterna: 0.505 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.631 RDfolder: 0.396 Sensitivity ContextFold: 0.507 RDfolder: 0.302 Positive Predictive Value ContextFold: 0.795 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.69265863073e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.536 RNAwolf: 0.307 Sensitivity ContextFold: 0.440 RNAwolf: 0.284 Positive Predictive Value ContextFold: 0.654 RNAwolf: 0.333 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.556 NanoFolder: 0.272 Sensitivity ContextFold: 0.451 NanoFolder: 0.284 Positive Predictive Value ContextFold: 0.691 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.642 Carnac(seed): 0.467 Sensitivity ContextFold: 0.530 Carnac(seed): 0.245 Positive Predictive Value ContextFold: 0.778 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.667 RSpredict(seed): 0.397 Sensitivity ContextFold: 0.551 RSpredict(seed): 0.251 Positive Predictive Value ContextFold: 0.809 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.85839946686e-08	+ ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.620 PPfold(seed): 0.156 Sensitivity ContextFold: 0.506 PPfold(seed): 0.036 Positive Predictive Value ContextFold: 0.765 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	? ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs PETfold_2.0(seed) Matthews Correlation Coefficient ContextFold: 0.780 PETfold_2.0(seed): 0.769 Sensitivity ContextFold: 0.632 PETfold_2.0(seed): 0.642 Positive Predictive Value ContextFold: 0.968 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs DAFS(20) Matthews Correlation Coefficient ContextFold: N/A DAFS(20): N/A Sensitivity ContextFold: N/A DAFS(20): N/A Positive Predictive Value ContextFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs PETfold_2.0(20) Matthews Correlation Coefficient ContextFold: 0.760 PETfold_2.0(20): 0.647 Sensitivity ContextFold: 0.579 PETfold_2.0(20): 0.509 Positive Predictive Value ContextFold: 1.000 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs DAFS(seed) Matthews Correlation Coefficient ContextFold: N/A DAFS(seed): N/A Sensitivity ContextFold: N/A DAFS(seed): N/A Positive Predictive Value ContextFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.628 Mastr(seed): 0.034 Sensitivity ContextFold: 0.510 Mastr(seed): 0.003 Positive Predictive Value ContextFold: 0.778 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08
RNASampler(20)	36 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNASampler(20): 0.613 Sensitivity CentroidAlifold(20): 0.529 RNASampler(20): 0.475 Positive Predictive Value CentroidAlifold(20): 0.882 RNASampler(20): 0.795 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(seed): 0.597 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(seed): 0.870 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	38 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 RNASampler(20): 0.612 Sensitivity RNAalifold(20): 0.511 RNASampler(20): 0.471 Positive Predictive Value RNAalifold(20): 0.846 RNASampler(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 RNASampler(20): 0.612 Sensitivity MXScarna(seed): 0.529 RNASampler(20): 0.474 Positive Predictive Value MXScarna(seed): 0.791 RNASampler(20): 0.793 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.663 RNASampler(20): 0.582 Sensitivity PPfold(20): 0.528 RNASampler(20): 0.450 Positive Predictive Value PPfold(20): 0.836 RNASampler(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	18 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.617 RNASampler(20): 0.561 Sensitivity ContextFold: 0.499 RNASampler(20): 0.429 Positive Predictive Value ContextFold: 0.767 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.5677163434e-08		- PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(20): 0.530 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	- TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.616 RNASampler(20): 0.582 Sensitivity TurboFold(20): 0.508 RNASampler(20): 0.450 Positive Predictive Value TurboFold(20): 0.752 RNASampler(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	= RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.612 MXScarna(20): 0.611 Sensitivity RNASampler(20): 0.471 MXScarna(20): 0.509 Positive Predictive Value RNASampler(20): 0.799 MXScarna(20): 0.737 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.0393070676946	- RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 RNASampler(20): 0.538 Sensitivity RNAalifold(seed): 0.338 RNASampler(20): 0.403 Positive Predictive Value RNAalifold(seed): 0.929 RNASampler(20): 0.721 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.612 Murlet(20): 0.590 Sensitivity RNASampler(20): 0.471 Murlet(20): 0.438 Positive Predictive Value RNASampler(20): 0.799 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.613 CentroidAlifold(seed): 0.587 Sensitivity RNASampler(20): 0.475 CentroidAlifold(seed): 0.368 Positive Predictive Value RNASampler(20): 0.795 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.612 Carnac(20): 0.590 Sensitivity RNASampler(20): 0.471 Carnac(20): 0.389 Positive Predictive Value RNASampler(20): 0.799 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.585 IPknot: 0.526 Sensitivity RNASampler(20): 0.448 IPknot: 0.433 Positive Predictive Value RNASampler(20): 0.768 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.605 CentroidHomfold‑LAST: 0.584 Sensitivity RNASampler(20): 0.466 CentroidHomfold‑LAST: 0.491 Positive Predictive Value RNASampler(20): 0.791 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.14303126762e-07	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.612 Contrafold: 0.536 Sensitivity RNASampler(20): 0.471 Contrafold: 0.472 Positive Predictive Value RNASampler(20): 0.799 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.612 Sfold: 0.560 Sensitivity RNASampler(20): 0.471 Sfold: 0.466 Positive Predictive Value RNASampler(20): 0.799 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.612 HotKnots: 0.533 Sensitivity RNASampler(20): 0.471 HotKnots: 0.475 Positive Predictive Value RNASampler(20): 0.799 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.613 CentroidFold: 0.542 Sensitivity RNASampler(20): 0.475 CentroidFold: 0.459 Positive Predictive Value RNASampler(20): 0.795 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.498 TurboFold(seed): 0.484 Sensitivity RNASampler(20): 0.371 TurboFold(seed): 0.393 Positive Predictive Value RNASampler(20): 0.675 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.29209047668e-09	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.613 MaxExpect: 0.557 Sensitivity RNASampler(20): 0.475 MaxExpect: 0.481 Positive Predictive Value RNASampler(20): 0.795 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.616 RSpredict(20): 0.552 Sensitivity RNASampler(20): 0.481 RSpredict(20): 0.436 Positive Predictive Value RNASampler(20): 0.792 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.612 PknotsRG: 0.557 Sensitivity RNASampler(20): 0.471 PknotsRG: 0.494 Positive Predictive Value RNASampler(20): 0.799 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.565 CMfinder(20): 0.521 Sensitivity RNASampler(20): 0.436 CMfinder(20): 0.366 Positive Predictive Value RNASampler(20): 0.738 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.5281770229e-09	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.612 UNAFold: 0.543 Sensitivity RNASampler(20): 0.471 UNAFold: 0.475 Positive Predictive Value RNASampler(20): 0.799 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.600 ProbKnot: 0.548 Sensitivity RNASampler(20): 0.458 ProbKnot: 0.484 Positive Predictive Value RNASampler(20): 0.790 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.674 Cylofold: 0.642 Sensitivity RNASampler(20): 0.528 Cylofold: 0.543 Positive Predictive Value RNASampler(20): 0.865 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.612 RNAfold: 0.540 Sensitivity RNASampler(20): 0.471 RNAfold: 0.477 Positive Predictive Value RNASampler(20): 0.799 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 RNASampler(20): 0.449 Sensitivity RNASampler(seed): 0.353 RNASampler(20): 0.356 Positive Predictive Value RNASampler(seed): 0.652 RNASampler(20): 0.571 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.612 RNAsubopt: 0.534 Sensitivity RNASampler(20): 0.471 RNAsubopt: 0.477 Positive Predictive Value RNASampler(20): 0.799 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.604 Multilign(20): 0.534 Sensitivity RNASampler(20): 0.470 Multilign(20): 0.449 Positive Predictive Value RNASampler(20): 0.780 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.585 Afold: 0.511 Sensitivity RNASampler(20): 0.447 Afold: 0.460 Positive Predictive Value RNASampler(20): 0.769 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.612 RNAshapes: 0.517 Sensitivity RNASampler(20): 0.471 RNAshapes: 0.453 Positive Predictive Value RNASampler(20): 0.799 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.600 Fold: 0.531 Sensitivity RNASampler(20): 0.458 Fold: 0.471 Positive Predictive Value RNASampler(20): 0.790 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.612 McQFold: 0.506 Sensitivity RNASampler(20): 0.471 McQFold: 0.433 Positive Predictive Value RNASampler(20): 0.799 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.561 RNASLOpt: 0.463 Sensitivity RNASampler(20): 0.429 RNASLOpt: 0.383 Positive Predictive Value RNASampler(20): 0.738 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.612 Mastr(20): 0.500 Sensitivity RNASampler(20): 0.471 Mastr(20): 0.336 Positive Predictive Value RNASampler(20): 0.799 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RNASampler(20) Matthews Correlation Coefficient Multilign(seed): 0.497 RNASampler(20): 0.480 Sensitivity Multilign(seed): 0.369 RNASampler(20): 0.345 Positive Predictive Value Multilign(seed): 0.676 RNASampler(20): 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.624 Pknots: 0.481 Sensitivity RNASampler(20): 0.485 Pknots: 0.433 Positive Predictive Value RNASampler(20): 0.807 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.623 Vsfold4: 0.459 Sensitivity RNASampler(20): 0.481 Vsfold4: 0.381 Positive Predictive Value RNASampler(20): 0.812 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.618 CRWrnafold: 0.546 Sensitivity RNASampler(20): 0.462 CRWrnafold: 0.483 Positive Predictive Value RNASampler(20): 0.832 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.551 Murlet(seed): 0.454 Sensitivity RNASampler(20): 0.421 Murlet(seed): 0.241 Positive Predictive Value RNASampler(20): 0.727 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.54229534325e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.623 Vsfold5: 0.409 Sensitivity RNASampler(20): 0.481 Vsfold5: 0.345 Positive Predictive Value RNASampler(20): 0.812 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.622 MCFold: 0.402 Sensitivity RNASampler(20): 0.493 MCFold: 0.418 Positive Predictive Value RNASampler(20): 0.788 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.772 Alterna: 0.553 Sensitivity RNASampler(20): 0.628 Alterna: 0.480 Positive Predictive Value RNASampler(20): 0.953 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.66062906821e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.754 RDfolder: 0.563 Sensitivity RNASampler(20): 0.603 RDfolder: 0.447 Positive Predictive Value RNASampler(20): 0.949 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.585 RNAwolf: 0.348 Sensitivity RNASampler(20): 0.448 RNAwolf: 0.328 Positive Predictive Value RNASampler(20): 0.768 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.572 NanoFolder: 0.269 Sensitivity RNASampler(20): 0.442 NanoFolder: 0.280 Positive Predictive Value RNASampler(20): 0.745 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.590 Carnac(seed): 0.110 Sensitivity RNASampler(20): 0.454 Carnac(seed): 0.012 Positive Predictive Value RNASampler(20): 0.770 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.616 RSpredict(seed): 0.174 Sensitivity RNASampler(20): 0.481 RSpredict(seed): 0.068 Positive Predictive Value RNASampler(20): 0.792 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.582 PPfold(seed): 0.072 Sensitivity RNASampler(20): 0.450 PPfold(seed): 0.012 Positive Predictive Value RNASampler(20): 0.757 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	? RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNASampler(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(seed): 0.946 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs DAFS(20) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(20): N/A Sensitivity RNASampler(20): N/A DAFS(20): N/A Positive Predictive Value RNASampler(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASampler(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(seed): N/A Sensitivity RNASampler(20): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.612 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.471 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.799 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(20)	18 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.656 PETfold_pre2.0(20): 0.649 Sensitivity CentroidAlifold(20): 0.501 PETfold_pre2.0(20): 0.530 Positive Predictive Value CentroidAlifold(20): 0.864 PETfold_pre2.0(20): 0.798 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.43703343543e-08	19 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.674 PETfold_pre2.0(20): 0.632 Sensitivity PETfold_pre2.0(seed): 0.538 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.846 PETfold_pre2.0(20): 0.806 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	18 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAalifold(20): 0.629 Sensitivity PETfold_pre2.0(20): 0.530 RNAalifold(20): 0.488 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAalifold(20): 0.815 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	17 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.642 MXScarna(seed): 0.595 Sensitivity PETfold_pre2.0(20): 0.524 MXScarna(seed): 0.476 Positive Predictive Value PETfold_pre2.0(20): 0.791 MXScarna(seed): 0.748 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-08	17 PPfold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(20): 0.649 PETfold_pre2.0(20): 0.649 Sensitivity PPfold(20): 0.517 PETfold_pre2.0(20): 0.532 Positive Predictive Value PPfold(20): 0.819 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00876167151132	18 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ContextFold: 0.617 Sensitivity PETfold_pre2.0(20): 0.530 ContextFold: 0.499 Positive Predictive Value PETfold_pre2.0(20): 0.798 ContextFold: 0.767 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.26346675981e-08	18 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASampler(20): 0.561 Sensitivity PETfold_pre2.0(20): 0.530 RNASampler(20): 0.429 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASampler(20): 0.738 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08		+ PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(20): 0.532 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(20): 0.530 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(20): 0.798 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	? RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.527 PETfold_pre2.0(20): 0.449 Sensitivity RNAalifold(seed): 0.278 PETfold_pre2.0(20): 0.342 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(20): 0.530 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(20): 0.798 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidAlifold(seed): 0.533 Sensitivity PETfold_pre2.0(20): 0.530 CentroidAlifold(seed): 0.306 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.42071836373e-08	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(20): 0.530 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(20): 0.798 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 IPknot: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 IPknot: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 IPknot: 0.614 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 CentroidHomfold‑LAST: 0.565 Sensitivity PETfold_pre2.0(20): 0.559 CentroidHomfold‑LAST: 0.482 Positive Predictive Value PETfold_pre2.0(20): 0.826 CentroidHomfold‑LAST: 0.668 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Contrafold: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.798 Contrafold: 0.579 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Sfold: 0.500 Sensitivity PETfold_pre2.0(20): 0.530 Sfold: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 HotKnots: 0.474 Sensitivity PETfold_pre2.0(20): 0.530 HotKnots: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.798 HotKnots: 0.535 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidFold: 0.445 Sensitivity PETfold_pre2.0(20): 0.530 CentroidFold: 0.376 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.91763127434e-08	? PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.488 TurboFold(seed): 0.437 Sensitivity PETfold_pre2.0(20): 0.375 TurboFold(seed): 0.358 Positive Predictive Value PETfold_pre2.0(20): 0.639 TurboFold(seed): 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MaxExpect: 0.481 Sensitivity PETfold_pre2.0(20): 0.530 MaxExpect: 0.412 Positive Predictive Value PETfold_pre2.0(20): 0.798 MaxExpect: 0.568 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PknotsRG: 0.522 Sensitivity PETfold_pre2.0(20): 0.530 PknotsRG: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.798 PknotsRG: 0.593 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(20): 0.564 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(20): 0.826 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 UNAFold: 0.462 Sensitivity PETfold_pre2.0(20): 0.530 UNAFold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 UNAFold: 0.531 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ProbKnot: 0.484 Sensitivity PETfold_pre2.0(20): 0.530 ProbKnot: 0.424 Positive Predictive Value PETfold_pre2.0(20): 0.798 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 Cylofold: 0.611 Sensitivity PETfold_pre2.0(20): 0.624 Cylofold: 0.521 Positive Predictive Value PETfold_pre2.0(20): 0.896 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAfold: 0.483 Sensitivity PETfold_pre2.0(20): 0.530 RNAfold: 0.428 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAfold: 0.552 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.299 PETfold_pre2.0(20): 0.262 Sensitivity RNASampler(seed): 0.214 PETfold_pre2.0(20): 0.195 Positive Predictive Value RNASampler(seed): 0.423 PETfold_pre2.0(20): 0.357 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAsubopt: 0.505 Sensitivity PETfold_pre2.0(20): 0.530 RNAsubopt: 0.451 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAsubopt: 0.572 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(20): 0.564 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(20): 0.825 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.87872347734e-08	? PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.526 Afold: 0.416 Sensitivity PETfold_pre2.0(20): 0.410 Afold: 0.381 Positive Predictive Value PETfold_pre2.0(20): 0.679 Afold: 0.459 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAshapes: 0.454 Sensitivity PETfold_pre2.0(20): 0.530 RNAshapes: 0.402 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Fold: 0.458 Sensitivity PETfold_pre2.0(20): 0.530 Fold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 Fold: 0.521 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 McQFold: 0.449 Sensitivity PETfold_pre2.0(20): 0.530 McQFold: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 McQFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASLOpt: 0.463 Sensitivity PETfold_pre2.0(20): 0.530 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.443 Multilign(seed): 0.401 Sensitivity PETfold_pre2.0(20): 0.323 Multilign(seed): 0.283 Positive Predictive Value PETfold_pre2.0(20): 0.612 Multilign(seed): 0.571 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Pknots: 0.381 Sensitivity PETfold_pre2.0(20): 0.530 Pknots: 0.342 Positive Predictive Value PETfold_pre2.0(20): 0.798 Pknots: 0.431 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold4: 0.421 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold4: 0.346 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold4: 0.519 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	? PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CRWrnafold: 0.531 Sensitivity PETfold_pre2.0(20): 0.497 CRWrnafold: 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 CRWrnafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.449 Murlet(seed): 0.407 Sensitivity PETfold_pre2.0(20): 0.342 Murlet(seed): 0.195 Positive Predictive Value PETfold_pre2.0(20): 0.595 Murlet(seed): 0.852 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold5: 0.378 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold5: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold5: 0.450 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.628 MCFold: 0.382 Sensitivity PETfold_pre2.0(20): 0.512 MCFold: 0.393 Positive Predictive Value PETfold_pre2.0(20): 0.775 MCFold: 0.378 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.733 RDfolder: 0.535 Sensitivity PETfold_pre2.0(20): 0.587 RDfolder: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.920 RDfolder: 0.704 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAwolf: 0.312 Sensitivity PETfold_pre2.0(20): 0.530 RNAwolf: 0.295 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAwolf: 0.338 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.667 NanoFolder: 0.269 Sensitivity PETfold_pre2.0(20): 0.552 NanoFolder: 0.280 Positive Predictive Value PETfold_pre2.0(20): 0.810 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	? PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.516 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.400 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.670 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(seed): 0.294 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(seed): 0.144 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PPfold(seed): 0.077 Sensitivity PETfold_pre2.0(20): 0.532 PPfold(seed): 0.014 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.02510705504e-08	? PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_pre2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_pre2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.647 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(20): 0.509 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(20): 0.829 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs DAFS(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(seed): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08
TurboFold(20)	20 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 TurboFold(20): 0.616 Sensitivity CentroidAlifold(20): 0.514 TurboFold(20): 0.508 Positive Predictive Value CentroidAlifold(20): 0.877 TurboFold(20): 0.752 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(seed): 0.595 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(seed): 0.864 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.27388928538e-08	20 RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.643 TurboFold(20): 0.616 Sensitivity RNAalifold(20): 0.503 TurboFold(20): 0.508 Positive Predictive Value RNAalifold(20): 0.826 TurboFold(20): 0.752 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	19 MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.615 TurboFold(20): 0.607 Sensitivity MXScarna(seed): 0.494 TurboFold(20): 0.499 Positive Predictive Value MXScarna(seed): 0.772 TurboFold(20): 0.743 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.67241913479e-07	20 PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.663 TurboFold(20): 0.616 Sensitivity PPfold(20): 0.528 TurboFold(20): 0.508 Positive Predictive Value PPfold(20): 0.836 TurboFold(20): 0.752 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 TurboFold(20) vs ContextFold Matthews Correlation Coefficient TurboFold(20): 0.606 ContextFold: 0.605 Sensitivity TurboFold(20): 0.502 ContextFold: 0.492 Positive Predictive Value TurboFold(20): 0.737 ContextFold: 0.749 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0184072909178	20 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.616 RNASampler(20): 0.582 Sensitivity TurboFold(20): 0.508 RNASampler(20): 0.450 Positive Predictive Value TurboFold(20): 0.752 RNASampler(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	17 PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 TurboFold(20): 0.606 Sensitivity PETfold_pre2.0(20): 0.532 TurboFold(20): 0.502 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(20): 0.737 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08		+ TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.616 MXScarna(20): 0.578 Sensitivity TurboFold(20): 0.508 MXScarna(20): 0.476 Positive Predictive Value TurboFold(20): 0.752 MXScarna(20): 0.706 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	- RNAalifold(seed) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.543 TurboFold(20): 0.488 Sensitivity RNAalifold(seed): 0.313 TurboFold(20): 0.389 Positive Predictive Value RNAalifold(seed): 0.947 TurboFold(20): 0.619 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.78774507289e-09	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.616 Murlet(20): 0.580 Sensitivity TurboFold(20): 0.508 Murlet(20): 0.439 Positive Predictive Value TurboFold(20): 0.752 Murlet(20): 0.772 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 CentroidAlifold(seed): 0.558 Sensitivity TurboFold(20): 0.508 CentroidAlifold(seed): 0.330 Positive Predictive Value TurboFold(20): 0.752 CentroidAlifold(seed): 0.949 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.616 Carnac(20): 0.565 Sensitivity TurboFold(20): 0.508 Carnac(20): 0.372 Positive Predictive Value TurboFold(20): 0.752 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.616 IPknot: 0.535 Sensitivity TurboFold(20): 0.508 IPknot: 0.443 Positive Predictive Value TurboFold(20): 0.752 IPknot: 0.651 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.631 CentroidHomfold‑LAST: 0.589 Sensitivity TurboFold(20): 0.526 CentroidHomfold‑LAST: 0.501 Positive Predictive Value TurboFold(20): 0.762 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.616 Contrafold: 0.523 Sensitivity TurboFold(20): 0.508 Contrafold: 0.460 Positive Predictive Value TurboFold(20): 0.752 Contrafold: 0.602 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.616 Sfold: 0.526 Sensitivity TurboFold(20): 0.508 Sfold: 0.439 Positive Predictive Value TurboFold(20): 0.752 Sfold: 0.635 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.616 HotKnots: 0.497 Sensitivity TurboFold(20): 0.508 HotKnots: 0.443 Positive Predictive Value TurboFold(20): 0.752 HotKnots: 0.564 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.616 CentroidFold: 0.474 Sensitivity TurboFold(20): 0.508 CentroidFold: 0.400 Positive Predictive Value TurboFold(20): 0.752 CentroidFold: 0.568 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.491 TurboFold(seed): 0.484 Sensitivity TurboFold(20): 0.393 TurboFold(seed): 0.393 Positive Predictive Value TurboFold(20): 0.619 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.10218298521e-08	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.616 MaxExpect: 0.503 Sensitivity TurboFold(20): 0.508 MaxExpect: 0.431 Positive Predictive Value TurboFold(20): 0.752 MaxExpect: 0.594 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.616 RSpredict(20): 0.520 Sensitivity TurboFold(20): 0.508 RSpredict(20): 0.398 Positive Predictive Value TurboFold(20): 0.752 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.616 PknotsRG: 0.541 Sensitivity TurboFold(20): 0.508 PknotsRG: 0.479 Positive Predictive Value TurboFold(20): 0.752 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.634 CMfinder(20): 0.539 Sensitivity TurboFold(20): 0.541 CMfinder(20): 0.389 Positive Predictive Value TurboFold(20): 0.747 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.616 UNAFold: 0.487 Sensitivity TurboFold(20): 0.508 UNAFold: 0.427 Positive Predictive Value TurboFold(20): 0.752 UNAFold: 0.561 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.616 ProbKnot: 0.502 Sensitivity TurboFold(20): 0.508 ProbKnot: 0.441 Positive Predictive Value TurboFold(20): 0.752 ProbKnot: 0.578 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.693 Cylofold: 0.628 Sensitivity TurboFold(20): 0.562 Cylofold: 0.529 Positive Predictive Value TurboFold(20): 0.860 Cylofold: 0.751 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.616 RNAfold: 0.506 Sensitivity TurboFold(20): 0.508 RNAfold: 0.446 Positive Predictive Value TurboFold(20): 0.752 RNAfold: 0.581 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	? RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): 0.423 TurboFold(20): 0.408 Sensitivity RNASampler(seed): 0.300 TurboFold(20): 0.335 Positive Predictive Value RNASampler(seed): 0.600 TurboFold(20): 0.503 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.616 RNAsubopt: 0.526 Sensitivity TurboFold(20): 0.508 RNAsubopt: 0.468 Positive Predictive Value TurboFold(20): 0.752 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.631 Multilign(20): 0.534 Sensitivity TurboFold(20): 0.526 Multilign(20): 0.449 Positive Predictive Value TurboFold(20): 0.762 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	? TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.510 Afold: 0.476 Sensitivity TurboFold(20): 0.417 Afold: 0.423 Positive Predictive Value TurboFold(20): 0.631 Afold: 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.616 RNAshapes: 0.503 Sensitivity TurboFold(20): 0.508 RNAshapes: 0.443 Positive Predictive Value TurboFold(20): 0.752 RNAshapes: 0.576 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.616 Fold: 0.479 Sensitivity TurboFold(20): 0.508 Fold: 0.426 Positive Predictive Value TurboFold(20): 0.752 Fold: 0.546 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.616 McQFold: 0.485 Sensitivity TurboFold(20): 0.508 McQFold: 0.416 Positive Predictive Value TurboFold(20): 0.752 McQFold: 0.572 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.606 RNASLOpt: 0.464 Sensitivity TurboFold(20): 0.502 RNASLOpt: 0.387 Positive Predictive Value TurboFold(20): 0.737 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.616 Mastr(20): 0.518 Sensitivity TurboFold(20): 0.508 Mastr(20): 0.357 Positive Predictive Value TurboFold(20): 0.752 Mastr(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.497 TurboFold(20): 0.489 Sensitivity Multilign(seed): 0.369 TurboFold(20): 0.374 Positive Predictive Value Multilign(seed): 0.676 TurboFold(20): 0.644 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.616 Pknots: 0.426 Sensitivity TurboFold(20): 0.508 Pknots: 0.381 Positive Predictive Value TurboFold(20): 0.752 Pknots: 0.484 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.631 Vsfold4: 0.451 Sensitivity TurboFold(20): 0.526 Vsfold4: 0.374 Positive Predictive Value TurboFold(20): 0.762 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30280588002e-08	? TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.570 CRWrnafold: 0.546 Sensitivity TurboFold(20): 0.453 CRWrnafold: 0.483 Positive Predictive Value TurboFold(20): 0.723 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.488 Murlet(seed): 0.429 Sensitivity TurboFold(20): 0.389 Murlet(seed): 0.219 Positive Predictive Value TurboFold(20): 0.619 Murlet(seed): 0.843 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12659692944e-08	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.631 Vsfold5: 0.410 Sensitivity TurboFold(20): 0.526 Vsfold5: 0.352 Positive Predictive Value TurboFold(20): 0.762 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.606 MCFold: 0.396 Sensitivity TurboFold(20): 0.500 MCFold: 0.406 Positive Predictive Value TurboFold(20): 0.739 MCFold: 0.394 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.676 Alterna: 0.584 Sensitivity TurboFold(20): 0.544 Alterna: 0.495 Positive Predictive Value TurboFold(20): 0.848 Alterna: 0.699 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.671 RDfolder: 0.489 Sensitivity TurboFold(20): 0.531 RDfolder: 0.365 Positive Predictive Value TurboFold(20): 0.853 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.616 RNAwolf: 0.343 Sensitivity TurboFold(20): 0.508 RNAwolf: 0.325 Positive Predictive Value TurboFold(20): 0.752 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.608 NanoFolder: 0.271 Sensitivity TurboFold(20): 0.513 NanoFolder: 0.286 Positive Predictive Value TurboFold(20): 0.724 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.517 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.414 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.651 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08	+ TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 RSpredict(seed): 0.129 Sensitivity TurboFold(20): 0.508 RSpredict(seed): 0.048 Positive Predictive Value TurboFold(20): 0.752 RSpredict(seed): 0.361 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 PPfold(seed): 0.072 Sensitivity TurboFold(20): 0.508 PPfold(seed): 0.012 Positive Predictive Value TurboFold(20): 0.752 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	? TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(seed): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs DAFS(20) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(20): N/A Sensitivity TurboFold(20): N/A DAFS(20): N/A Positive Predictive Value TurboFold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(seed): N/A Sensitivity TurboFold(20): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.508 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.752 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08
MXScarna(20)	36 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 MXScarna(20): 0.611 Sensitivity CentroidAlifold(20): 0.529 MXScarna(20): 0.510 Positive Predictive Value CentroidAlifold(20): 0.882 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(seed): 0.597 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.870 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.26346675981e-08	38 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 MXScarna(20): 0.611 Sensitivity RNAalifold(20): 0.511 MXScarna(20): 0.509 Positive Predictive Value RNAalifold(20): 0.846 MXScarna(20): 0.737 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	36 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 MXScarna(20): 0.610 Sensitivity MXScarna(seed): 0.529 MXScarna(20): 0.510 Positive Predictive Value MXScarna(seed): 0.791 MXScarna(20): 0.734 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.663 MXScarna(20): 0.578 Sensitivity PPfold(20): 0.528 MXScarna(20): 0.476 Positive Predictive Value PPfold(20): 0.836 MXScarna(20): 0.706 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	18 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.617 MXScarna(20): 0.570 Sensitivity ContextFold: 0.499 MXScarna(20): 0.470 Positive Predictive Value ContextFold: 0.767 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	38 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.612 MXScarna(20): 0.611 Sensitivity RNASampler(20): 0.471 MXScarna(20): 0.509 Positive Predictive Value RNASampler(20): 0.799 MXScarna(20): 0.737 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.0393070676946	18 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MXScarna(20): 0.570 Sensitivity PETfold_pre2.0(20): 0.530 MXScarna(20): 0.470 Positive Predictive Value PETfold_pre2.0(20): 0.798 MXScarna(20): 0.696 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	20 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.616 MXScarna(20): 0.578 Sensitivity TurboFold(20): 0.508 MXScarna(20): 0.476 Positive Predictive Value TurboFold(20): 0.752 MXScarna(20): 0.706 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08		- RNAalifold(seed) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 MXScarna(20): 0.547 Sensitivity RNAalifold(seed): 0.338 MXScarna(20): 0.434 Positive Predictive Value RNAalifold(seed): 0.929 MXScarna(20): 0.693 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.611 Murlet(20): 0.590 Sensitivity MXScarna(20): 0.509 Murlet(20): 0.438 Positive Predictive Value MXScarna(20): 0.737 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.611 CentroidAlifold(seed): 0.587 Sensitivity MXScarna(20): 0.510 CentroidAlifold(seed): 0.368 Positive Predictive Value MXScarna(20): 0.736 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.611 Carnac(20): 0.590 Sensitivity MXScarna(20): 0.509 Carnac(20): 0.389 Positive Predictive Value MXScarna(20): 0.737 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.590 IPknot: 0.526 Sensitivity MXScarna(20): 0.486 IPknot: 0.433 Positive Predictive Value MXScarna(20): 0.720 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(20): 0.606 CentroidHomfold‑LAST: 0.584 Sensitivity MXScarna(20): 0.505 CentroidHomfold‑LAST: 0.491 Positive Predictive Value MXScarna(20): 0.733 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.611 Contrafold: 0.536 Sensitivity MXScarna(20): 0.509 Contrafold: 0.472 Positive Predictive Value MXScarna(20): 0.737 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.611 Sfold: 0.560 Sensitivity MXScarna(20): 0.509 Sfold: 0.466 Positive Predictive Value MXScarna(20): 0.737 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.611 HotKnots: 0.533 Sensitivity MXScarna(20): 0.509 HotKnots: 0.475 Positive Predictive Value MXScarna(20): 0.737 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.611 CentroidFold: 0.542 Sensitivity MXScarna(20): 0.510 CentroidFold: 0.459 Positive Predictive Value MXScarna(20): 0.736 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.484 MXScarna(20): 0.478 Sensitivity TurboFold(seed): 0.393 MXScarna(20): 0.371 Positive Predictive Value TurboFold(seed): 0.601 MXScarna(20): 0.622 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.34181747534e-06	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.611 MaxExpect: 0.557 Sensitivity MXScarna(20): 0.510 MaxExpect: 0.481 Positive Predictive Value MXScarna(20): 0.736 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.609 RSpredict(20): 0.552 Sensitivity MXScarna(20): 0.509 RSpredict(20): 0.436 Positive Predictive Value MXScarna(20): 0.732 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.611 PknotsRG: 0.557 Sensitivity MXScarna(20): 0.509 PknotsRG: 0.494 Positive Predictive Value MXScarna(20): 0.737 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.600 CMfinder(20): 0.521 Sensitivity MXScarna(20): 0.506 CMfinder(20): 0.366 Positive Predictive Value MXScarna(20): 0.717 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.611 UNAFold: 0.543 Sensitivity MXScarna(20): 0.509 UNAFold: 0.475 Positive Predictive Value MXScarna(20): 0.737 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.606 ProbKnot: 0.548 Sensitivity MXScarna(20): 0.503 ProbKnot: 0.484 Positive Predictive Value MXScarna(20): 0.734 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.663 Cylofold: 0.642 Sensitivity MXScarna(20): 0.556 Cylofold: 0.543 Positive Predictive Value MXScarna(20): 0.796 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.611 RNAfold: 0.540 Sensitivity MXScarna(20): 0.509 RNAfold: 0.477 Positive Predictive Value MXScarna(20): 0.737 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 MXScarna(20): 0.464 Sensitivity RNASampler(seed): 0.353 MXScarna(20): 0.368 Positive Predictive Value RNASampler(seed): 0.652 MXScarna(20): 0.590 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.43284180886e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.611 RNAsubopt: 0.534 Sensitivity MXScarna(20): 0.509 RNAsubopt: 0.477 Positive Predictive Value MXScarna(20): 0.737 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.595 Multilign(20): 0.534 Sensitivity MXScarna(20): 0.496 Multilign(20): 0.449 Positive Predictive Value MXScarna(20): 0.719 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.575 Afold: 0.511 Sensitivity MXScarna(20): 0.479 Afold: 0.460 Positive Predictive Value MXScarna(20): 0.694 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.611 RNAshapes: 0.517 Sensitivity MXScarna(20): 0.509 RNAshapes: 0.453 Positive Predictive Value MXScarna(20): 0.737 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.606 Fold: 0.531 Sensitivity MXScarna(20): 0.503 Fold: 0.471 Positive Predictive Value MXScarna(20): 0.734 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.611 McQFold: 0.506 Sensitivity MXScarna(20): 0.509 McQFold: 0.433 Positive Predictive Value MXScarna(20): 0.737 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.570 RNASLOpt: 0.463 Sensitivity MXScarna(20): 0.470 RNASLOpt: 0.383 Positive Predictive Value MXScarna(20): 0.696 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.611 Mastr(20): 0.500 Sensitivity MXScarna(20): 0.509 Mastr(20): 0.336 Positive Predictive Value MXScarna(20): 0.737 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.502 Multilign(seed): 0.497 Sensitivity MXScarna(20): 0.384 Multilign(seed): 0.369 Positive Predictive Value MXScarna(20): 0.661 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.620 Pknots: 0.481 Sensitivity MXScarna(20): 0.519 Pknots: 0.433 Positive Predictive Value MXScarna(20): 0.746 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.620 Vsfold4: 0.459 Sensitivity MXScarna(20): 0.520 Vsfold4: 0.381 Positive Predictive Value MXScarna(20): 0.743 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.569 CRWrnafold: 0.546 Sensitivity MXScarna(20): 0.466 CRWrnafold: 0.483 Positive Predictive Value MXScarna(20): 0.701 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.555 Murlet(seed): 0.454 Sensitivity MXScarna(20): 0.439 Murlet(seed): 0.241 Positive Predictive Value MXScarna(20): 0.706 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.620 Vsfold5: 0.409 Sensitivity MXScarna(20): 0.520 Vsfold5: 0.345 Positive Predictive Value MXScarna(20): 0.743 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.609 MCFold: 0.402 Sensitivity MXScarna(20): 0.509 MCFold: 0.418 Positive Predictive Value MXScarna(20): 0.733 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.738 Alterna: 0.553 Sensitivity MXScarna(20): 0.619 Alterna: 0.480 Positive Predictive Value MXScarna(20): 0.885 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.718 RDfolder: 0.563 Sensitivity MXScarna(20): 0.590 RDfolder: 0.447 Positive Predictive Value MXScarna(20): 0.880 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.590 RNAwolf: 0.348 Sensitivity MXScarna(20): 0.486 RNAwolf: 0.328 Positive Predictive Value MXScarna(20): 0.720 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.586 NanoFolder: 0.269 Sensitivity MXScarna(20): 0.498 NanoFolder: 0.280 Positive Predictive Value MXScarna(20): 0.695 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.578 Carnac(seed): 0.110 Sensitivity MXScarna(20): 0.474 Carnac(seed): 0.012 Positive Predictive Value MXScarna(20): 0.710 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.609 RSpredict(seed): 0.174 Sensitivity MXScarna(20): 0.509 RSpredict(seed): 0.068 Positive Predictive Value MXScarna(20): 0.732 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.578 PPfold(seed): 0.072 Sensitivity MXScarna(20): 0.476 PPfold(seed): 0.012 Positive Predictive Value MXScarna(20): 0.706 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 MXScarna(20): 0.741 Sensitivity PETfold_2.0(seed): 0.614 MXScarna(20): 0.614 Positive Predictive Value PETfold_2.0(seed): 0.946 MXScarna(20): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs DAFS(20) Matthews Correlation Coefficient MXScarna(20): N/A DAFS(20): N/A Sensitivity MXScarna(20): N/A DAFS(20): N/A Positive Predictive Value MXScarna(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(20) vs PETfold_2.0(20) Matthews Correlation Coefficient MXScarna(20): 0.741 PETfold_2.0(20): 0.647 Sensitivity MXScarna(20): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value MXScarna(20): 0.897 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs MXScarna(20) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(20): N/A Sensitivity DAFS(seed): N/A MXScarna(20): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.611 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.509 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.737 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(seed)	18 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.612 RNAalifold(seed): 0.560 Sensitivity CentroidAlifold(20): 0.429 RNAalifold(seed): 0.339 Positive Predictive Value CentroidAlifold(20): 0.877 RNAalifold(seed): 0.928 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.16131455263e-08	14 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAalifold(seed): 0.637 Sensitivity PETfold_pre2.0(seed): 0.570 RNAalifold(seed): 0.477 Positive Predictive Value PETfold_pre2.0(seed): 0.811 RNAalifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	19 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.572 RNAalifold(seed): 0.559 Sensitivity RNAalifold(20): 0.419 RNAalifold(seed): 0.338 Positive Predictive Value RNAalifold(20): 0.785 RNAalifold(seed): 0.929 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.53460261044e-08	28 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.612 RNAalifold(seed): 0.606 Sensitivity MXScarna(seed): 0.499 RNAalifold(seed): 0.427 Positive Predictive Value MXScarna(seed): 0.751 RNAalifold(seed): 0.861 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.7429475951e-07	10 RNAalifold(seed) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.543 PPfold(20): 0.509 Sensitivity RNAalifold(seed): 0.313 PPfold(20): 0.371 Positive Predictive Value RNAalifold(seed): 0.947 PPfold(20): 0.702 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.00475527001e-08	14 RNAalifold(seed) vs ContextFold Matthews Correlation Coefficient RNAalifold(seed): 0.637 ContextFold: 0.635 Sensitivity RNAalifold(seed): 0.477 ContextFold: 0.524 Positive Predictive Value RNAalifold(seed): 0.849 ContextFold: 0.769 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0626385029064	19 RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 RNASampler(20): 0.538 Sensitivity RNAalifold(seed): 0.338 RNASampler(20): 0.403 Positive Predictive Value RNAalifold(seed): 0.929 RNASampler(20): 0.721 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.32677072069e-08	8 RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.527 PETfold_pre2.0(20): 0.449 Sensitivity RNAalifold(seed): 0.278 PETfold_pre2.0(20): 0.342 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 RNAalifold(seed) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.543 TurboFold(20): 0.488 Sensitivity RNAalifold(seed): 0.313 TurboFold(20): 0.389 Positive Predictive Value RNAalifold(seed): 0.947 TurboFold(20): 0.619 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.78774507289e-09	19 RNAalifold(seed) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 MXScarna(20): 0.547 Sensitivity RNAalifold(seed): 0.338 MXScarna(20): 0.434 Positive Predictive Value RNAalifold(seed): 0.929 MXScarna(20): 0.693 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08		+ RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 Murlet(20): 0.493 Sensitivity RNAalifold(seed): 0.338 Murlet(20): 0.341 Positive Predictive Value RNAalifold(seed): 0.929 Murlet(20): 0.714 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	- CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.674 RNAalifold(seed): 0.606 Sensitivity CentroidAlifold(seed): 0.509 RNAalifold(seed): 0.428 Positive Predictive Value CentroidAlifold(seed): 0.892 RNAalifold(seed): 0.860 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 Carnac(20): 0.517 Sensitivity RNAalifold(seed): 0.338 Carnac(20): 0.285 Positive Predictive Value RNAalifold(seed): 0.929 Carnac(20): 0.940 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.635 IPknot: 0.587 Sensitivity RNAalifold(seed): 0.475 IPknot: 0.489 Positive Predictive Value RNAalifold(seed): 0.849 IPknot: 0.706 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 4.61330405444e-08	+ RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.553 CentroidHomfold‑LAST: 0.496 Sensitivity RNAalifold(seed): 0.350 CentroidHomfold‑LAST: 0.415 Positive Predictive Value RNAalifold(seed): 0.880 CentroidHomfold‑LAST: 0.599 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.606 Contrafold: 0.565 Sensitivity RNAalifold(seed): 0.427 Contrafold: 0.499 Positive Predictive Value RNAalifold(seed): 0.861 Contrafold: 0.642 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.10039559051e-07	+ RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.606 Sfold: 0.526 Sensitivity RNAalifold(seed): 0.427 Sfold: 0.446 Positive Predictive Value RNAalifold(seed): 0.861 Sfold: 0.622 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 7.51223576774e-08	+ RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.549 HotKnots: 0.518 Sensitivity RNAalifold(seed): 0.338 HotKnots: 0.474 Positive Predictive Value RNAalifold(seed): 0.895 HotKnots: 0.571 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.6410608252e-08	+ RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.606 CentroidFold: 0.554 Sensitivity RNAalifold(seed): 0.428 CentroidFold: 0.466 Positive Predictive Value RNAalifold(seed): 0.860 CentroidFold: 0.658 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.527 TurboFold(seed): 0.508 Sensitivity RNAalifold(seed): 0.320 TurboFold(seed): 0.416 Positive Predictive Value RNAalifold(seed): 0.874 TurboFold(seed): 0.626 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.45609004183e-07	+ RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.604 MaxExpect: 0.510 Sensitivity RNAalifold(seed): 0.426 MaxExpect: 0.446 Positive Predictive Value RNAalifold(seed): 0.857 MaxExpect: 0.585 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 RSpredict(20): 0.440 Sensitivity RNAalifold(seed): 0.338 RSpredict(20): 0.338 Positive Predictive Value RNAalifold(seed): 0.929 RSpredict(20): 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	+ RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.549 PknotsRG: 0.544 Sensitivity RNAalifold(seed): 0.338 PknotsRG: 0.494 Positive Predictive Value RNAalifold(seed): 0.895 PknotsRG: 0.603 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000552293176012	? RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): 0.507 CMfinder(20): 0.333 Sensitivity RNAalifold(seed): 0.257 CMfinder(20): 0.208 Positive Predictive Value RNAalifold(seed): 1.000 CMfinder(20): 0.538 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.606 UNAFold: 0.499 Sensitivity RNAalifold(seed): 0.427 UNAFold: 0.442 Positive Predictive Value RNAalifold(seed): 0.861 UNAFold: 0.564 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.602 ProbKnot: 0.495 Sensitivity RNAalifold(seed): 0.425 ProbKnot: 0.442 Positive Predictive Value RNAalifold(seed): 0.854 ProbKnot: 0.556 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	= Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.600 RNAalifold(seed): 0.594 Sensitivity Cylofold: 0.491 RNAalifold(seed): 0.399 Positive Predictive Value Cylofold: 0.739 RNAalifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.311982599612	+ RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.606 RNAfold: 0.508 Sensitivity RNAalifold(seed): 0.427 RNAfold: 0.453 Positive Predictive Value RNAalifold(seed): 0.861 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.503 RNASampler(seed): 0.482 Sensitivity RNAalifold(seed): 0.295 RNASampler(seed): 0.342 Positive Predictive Value RNAalifold(seed): 0.863 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.549 RNAsubopt: 0.510 Sensitivity RNAalifold(seed): 0.338 RNAsubopt: 0.465 Positive Predictive Value RNAalifold(seed): 0.895 RNAsubopt: 0.564 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.563 Multilign(20): 0.380 Sensitivity RNAalifold(seed): 0.338 Multilign(20): 0.317 Positive Predictive Value RNAalifold(seed): 0.942 Multilign(20): 0.462 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	- Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.501 RNAalifold(seed): 0.484 Sensitivity Afold: 0.466 RNAalifold(seed): 0.283 Positive Predictive Value Afold: 0.541 RNAalifold(seed): 0.829 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.81039766894e-08	+ RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.549 RNAshapes: 0.515 Sensitivity RNAalifold(seed): 0.338 RNAshapes: 0.460 Positive Predictive Value RNAalifold(seed): 0.895 RNAshapes: 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.602 Fold: 0.461 Sensitivity RNAalifold(seed): 0.425 Fold: 0.416 Positive Predictive Value RNAalifold(seed): 0.854 Fold: 0.513 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.606 McQFold: 0.500 Sensitivity RNAalifold(seed): 0.427 McQFold: 0.437 Positive Predictive Value RNAalifold(seed): 0.861 McQFold: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.544 RNASLOpt: 0.449 Sensitivity RNAalifold(seed): 0.327 RNASLOpt: 0.376 Positive Predictive Value RNAalifold(seed): 0.910 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 Mastr(20): 0.353 Sensitivity RNAalifold(seed): 0.338 Mastr(20): 0.166 Positive Predictive Value RNAalifold(seed): 0.929 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.02510705504e-08	= Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 RNAalifold(seed): 0.554 Sensitivity Multilign(seed): 0.432 RNAalifold(seed): 0.356 Positive Predictive Value Multilign(seed): 0.723 RNAalifold(seed): 0.868 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.304583021065	+ RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.581 Pknots: 0.535 Sensitivity RNAalifold(seed): 0.370 Pknots: 0.486 Positive Predictive Value RNAalifold(seed): 0.917 Pknots: 0.594 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.542 Vsfold4: 0.457 Sensitivity RNAalifold(seed): 0.333 Vsfold4: 0.388 Positive Predictive Value RNAalifold(seed): 0.887 Vsfold4: 0.542 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	? RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.500 CRWrnafold: 0.419 Sensitivity RNAalifold(seed): 0.320 CRWrnafold: 0.377 Positive Predictive Value RNAalifold(seed): 0.789 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.588 Murlet(seed): 0.448 Sensitivity RNAalifold(seed): 0.378 Murlet(seed): 0.245 Positive Predictive Value RNAalifold(seed): 0.917 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.548 Vsfold5: 0.437 Sensitivity RNAalifold(seed): 0.340 Vsfold5: 0.377 Positive Predictive Value RNAalifold(seed): 0.888 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.553 MCFold: 0.397 Sensitivity RNAalifold(seed): 0.342 MCFold: 0.411 Positive Predictive Value RNAalifold(seed): 0.898 MCFold: 0.389 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.668 RNAalifold(seed): 0.570 Sensitivity Alterna: 0.562 RNAalifold(seed): 0.404 Positive Predictive Value Alterna: 0.802 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.595 RDfolder: 0.515 Sensitivity RNAalifold(seed): 0.413 RDfolder: 0.398 Positive Predictive Value RNAalifold(seed): 0.865 RDfolder: 0.678 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.635 RNAwolf: 0.408 Sensitivity RNAalifold(seed): 0.475 RNAwolf: 0.381 Positive Predictive Value RNAalifold(seed): 0.849 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.36983135185e-08	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.488 NanoFolder: 0.253 Sensitivity RNAalifold(seed): 0.280 NanoFolder: 0.276 Positive Predictive Value RNAalifold(seed): 0.855 NanoFolder: 0.241 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.634 Carnac(seed): 0.414 Sensitivity RNAalifold(seed): 0.465 Carnac(seed): 0.192 Positive Predictive Value RNAalifold(seed): 0.867 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.606 RSpredict(seed): 0.428 Sensitivity RNAalifold(seed): 0.427 RSpredict(seed): 0.273 Positive Predictive Value RNAalifold(seed): 0.861 RSpredict(seed): 0.673 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.553 PPfold(seed): 0.204 Sensitivity RNAalifold(seed): 0.343 PPfold(seed): 0.061 Positive Predictive Value RNAalifold(seed): 0.897 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	? RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RNAalifold(seed): 0.706 Sensitivity PETfold_2.0(seed): 0.684 RNAalifold(seed): 0.500 Positive Predictive Value PETfold_2.0(seed): 0.897 RNAalifold(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(20): N/A Sensitivity RNAalifold(seed): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(seed): N/A PETfold_2.0(20): N/A Sensitivity RNAalifold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNAalifold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(seed): N/A Sensitivity RNAalifold(seed): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.549 Mastr(seed): 0.032 Sensitivity RNAalifold(seed): 0.338 Mastr(seed): 0.003 Positive Predictive Value RNAalifold(seed): 0.895 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08
Murlet(20)	36 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Murlet(20): 0.589 Sensitivity CentroidAlifold(20): 0.529 Murlet(20): 0.439 Positive Predictive Value CentroidAlifold(20): 0.882 Murlet(20): 0.795 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(seed): 0.597 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	38 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Murlet(20): 0.590 Sensitivity RNAalifold(20): 0.511 Murlet(20): 0.438 Positive Predictive Value RNAalifold(20): 0.846 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 Murlet(20): 0.586 Sensitivity MXScarna(seed): 0.529 Murlet(20): 0.436 Positive Predictive Value MXScarna(seed): 0.791 Murlet(20): 0.792 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.663 Murlet(20): 0.580 Sensitivity PPfold(20): 0.528 Murlet(20): 0.439 Positive Predictive Value PPfold(20): 0.836 Murlet(20): 0.772 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	18 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.617 Murlet(20): 0.564 Sensitivity ContextFold: 0.499 Murlet(20): 0.418 Positive Predictive Value ContextFold: 0.767 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	38 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.612 Murlet(20): 0.590 Sensitivity RNASampler(20): 0.471 Murlet(20): 0.438 Positive Predictive Value RNASampler(20): 0.799 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Murlet(20): 0.564 Sensitivity PETfold_pre2.0(20): 0.530 Murlet(20): 0.418 Positive Predictive Value PETfold_pre2.0(20): 0.798 Murlet(20): 0.765 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	20 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.616 Murlet(20): 0.580 Sensitivity TurboFold(20): 0.508 Murlet(20): 0.439 Positive Predictive Value TurboFold(20): 0.752 Murlet(20): 0.772 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	38 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.611 Murlet(20): 0.590 Sensitivity MXScarna(20): 0.509 Murlet(20): 0.438 Positive Predictive Value MXScarna(20): 0.737 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 Murlet(20): 0.493 Sensitivity RNAalifold(seed): 0.338 Murlet(20): 0.341 Positive Predictive Value RNAalifold(seed): 0.929 Murlet(20): 0.714 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08		= Murlet(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Murlet(20): 0.589 CentroidAlifold(seed): 0.587 Sensitivity Murlet(20): 0.439 CentroidAlifold(seed): 0.368 Positive Predictive Value Murlet(20): 0.795 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.382290189588	= Carnac(20) vs Murlet(20) Matthews Correlation Coefficient Carnac(20): 0.590 Murlet(20): 0.590 Sensitivity Carnac(20): 0.389 Murlet(20): 0.438 Positive Predictive Value Carnac(20): 0.899 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.339915559821	+ Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.583 IPknot: 0.526 Sensitivity Murlet(20): 0.437 IPknot: 0.433 Positive Predictive Value Murlet(20): 0.784 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Murlet(20): 0.599 CentroidHomfold‑LAST: 0.584 Sensitivity Murlet(20): 0.451 CentroidHomfold‑LAST: 0.491 Positive Predictive Value Murlet(20): 0.800 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.40326410557e-07	+ Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.590 Contrafold: 0.536 Sensitivity Murlet(20): 0.438 Contrafold: 0.472 Positive Predictive Value Murlet(20): 0.799 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.590 Sfold: 0.560 Sensitivity Murlet(20): 0.438 Sfold: 0.466 Positive Predictive Value Murlet(20): 0.799 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.590 HotKnots: 0.533 Sensitivity Murlet(20): 0.438 HotKnots: 0.475 Positive Predictive Value Murlet(20): 0.799 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.589 CentroidFold: 0.542 Sensitivity Murlet(20): 0.439 CentroidFold: 0.459 Positive Predictive Value Murlet(20): 0.795 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs TurboFold(seed) Matthews Correlation Coefficient Murlet(20): 0.494 TurboFold(seed): 0.484 Sensitivity Murlet(20): 0.354 TurboFold(seed): 0.393 Positive Predictive Value Murlet(20): 0.694 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.2838375299e-05	+ Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.589 MaxExpect: 0.557 Sensitivity Murlet(20): 0.439 MaxExpect: 0.481 Positive Predictive Value Murlet(20): 0.795 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.589 RSpredict(20): 0.552 Sensitivity Murlet(20): 0.441 RSpredict(20): 0.436 Positive Predictive Value Murlet(20): 0.790 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.590 PknotsRG: 0.557 Sensitivity Murlet(20): 0.438 PknotsRG: 0.494 Positive Predictive Value Murlet(20): 0.799 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.606 CMfinder(20): 0.521 Sensitivity Murlet(20): 0.456 CMfinder(20): 0.366 Positive Predictive Value Murlet(20): 0.809 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.68522644707e-09	+ Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.590 UNAFold: 0.543 Sensitivity Murlet(20): 0.438 UNAFold: 0.475 Positive Predictive Value Murlet(20): 0.799 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.587 ProbKnot: 0.548 Sensitivity Murlet(20): 0.435 ProbKnot: 0.484 Positive Predictive Value Murlet(20): 0.797 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.653 Cylofold: 0.642 Sensitivity Murlet(20): 0.507 Cylofold: 0.543 Positive Predictive Value Murlet(20): 0.844 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.03850456744e-05	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.590 RNAfold: 0.540 Sensitivity Murlet(20): 0.438 RNAfold: 0.477 Positive Predictive Value Murlet(20): 0.799 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 Murlet(20): 0.447 Sensitivity RNASampler(seed): 0.353 Murlet(20): 0.329 Positive Predictive Value RNASampler(seed): 0.652 Murlet(20): 0.612 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.590 RNAsubopt: 0.534 Sensitivity Murlet(20): 0.438 RNAsubopt: 0.477 Positive Predictive Value Murlet(20): 0.799 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.597 Multilign(20): 0.534 Sensitivity Murlet(20): 0.455 Multilign(20): 0.449 Positive Predictive Value Murlet(20): 0.789 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.554 Afold: 0.511 Sensitivity Murlet(20): 0.408 Afold: 0.460 Positive Predictive Value Murlet(20): 0.758 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.590 RNAshapes: 0.517 Sensitivity Murlet(20): 0.438 RNAshapes: 0.453 Positive Predictive Value Murlet(20): 0.799 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.587 Fold: 0.531 Sensitivity Murlet(20): 0.435 Fold: 0.471 Positive Predictive Value Murlet(20): 0.797 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.590 McQFold: 0.506 Sensitivity Murlet(20): 0.438 McQFold: 0.433 Positive Predictive Value Murlet(20): 0.799 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.564 RNASLOpt: 0.463 Sensitivity Murlet(20): 0.418 RNASLOpt: 0.383 Positive Predictive Value Murlet(20): 0.765 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.590 Mastr(20): 0.500 Sensitivity Murlet(20): 0.438 Mastr(20): 0.336 Positive Predictive Value Murlet(20): 0.799 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.543 Multilign(seed): 0.497 Sensitivity Murlet(20): 0.394 Multilign(seed): 0.369 Positive Predictive Value Murlet(20): 0.755 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.605 Pknots: 0.481 Sensitivity Murlet(20): 0.456 Pknots: 0.433 Positive Predictive Value Murlet(20): 0.808 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.598 Vsfold4: 0.459 Sensitivity Murlet(20): 0.445 Vsfold4: 0.381 Positive Predictive Value Murlet(20): 0.808 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.568 CRWrnafold: 0.546 Sensitivity Murlet(20): 0.428 CRWrnafold: 0.483 Positive Predictive Value Murlet(20): 0.759 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.510 Murlet(seed): 0.454 Sensitivity Murlet(20): 0.362 Murlet(seed): 0.241 Positive Predictive Value Murlet(20): 0.724 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.598 Vsfold5: 0.409 Sensitivity Murlet(20): 0.445 Vsfold5: 0.345 Positive Predictive Value Murlet(20): 0.808 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.602 MCFold: 0.402 Sensitivity Murlet(20): 0.461 MCFold: 0.418 Positive Predictive Value Murlet(20): 0.791 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.679 Alterna: 0.553 Sensitivity Murlet(20): 0.529 Alterna: 0.480 Positive Predictive Value Murlet(20): 0.877 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.669 RDfolder: 0.563 Sensitivity Murlet(20): 0.510 RDfolder: 0.447 Positive Predictive Value Murlet(20): 0.883 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.583 RNAwolf: 0.348 Sensitivity Murlet(20): 0.437 RNAwolf: 0.328 Positive Predictive Value Murlet(20): 0.784 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.607 NanoFolder: 0.269 Sensitivity Murlet(20): 0.457 NanoFolder: 0.280 Positive Predictive Value Murlet(20): 0.811 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.553 Carnac(seed): 0.110 Sensitivity Murlet(20): 0.404 Carnac(seed): 0.012 Positive Predictive Value Murlet(20): 0.762 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.589 RSpredict(seed): 0.174 Sensitivity Murlet(20): 0.441 RSpredict(seed): 0.068 Positive Predictive Value Murlet(20): 0.790 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.580 PPfold(seed): 0.072 Sensitivity Murlet(20): 0.439 PPfold(seed): 0.012 Positive Predictive Value Murlet(20): 0.772 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	? Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Murlet(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(seed): 0.946 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs DAFS(20) Matthews Correlation Coefficient Murlet(20): N/A DAFS(20): N/A Sensitivity Murlet(20): N/A DAFS(20): N/A Positive Predictive Value Murlet(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Murlet(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs DAFS(seed) Matthews Correlation Coefficient Murlet(20): N/A DAFS(seed): N/A Sensitivity Murlet(20): N/A DAFS(seed): N/A Positive Predictive Value Murlet(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.590 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.438 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.799 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	36 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 CentroidAlifold(seed): 0.587 Sensitivity CentroidAlifold(20): 0.529 CentroidAlifold(seed): 0.368 Positive Predictive Value CentroidAlifold(20): 0.882 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidAlifold(seed): 0.628 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidAlifold(seed): 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	36 RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.656 CentroidAlifold(seed): 0.587 Sensitivity RNAalifold(20): 0.513 CentroidAlifold(seed): 0.368 Positive Predictive Value RNAalifold(20): 0.841 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.644 CentroidAlifold(seed): 0.619 Sensitivity MXScarna(seed): 0.534 CentroidAlifold(seed): 0.427 Positive Predictive Value MXScarna(seed): 0.778 CentroidAlifold(seed): 0.899 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.663 CentroidAlifold(seed): 0.558 Sensitivity PPfold(20): 0.528 CentroidAlifold(seed): 0.330 Positive Predictive Value PPfold(20): 0.836 CentroidAlifold(seed): 0.949 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.670 CentroidAlifold(seed): 0.628 Sensitivity ContextFold: 0.552 CentroidAlifold(seed): 0.443 Positive Predictive Value ContextFold: 0.815 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	36 RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.613 CentroidAlifold(seed): 0.587 Sensitivity RNASampler(20): 0.475 CentroidAlifold(seed): 0.368 Positive Predictive Value RNASampler(20): 0.795 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidAlifold(seed): 0.533 Sensitivity PETfold_pre2.0(20): 0.530 CentroidAlifold(seed): 0.306 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.42071836373e-08	20 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 CentroidAlifold(seed): 0.558 Sensitivity TurboFold(20): 0.508 CentroidAlifold(seed): 0.330 Positive Predictive Value TurboFold(20): 0.752 CentroidAlifold(seed): 0.949 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	36 MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.611 CentroidAlifold(seed): 0.587 Sensitivity MXScarna(20): 0.510 CentroidAlifold(seed): 0.368 Positive Predictive Value MXScarna(20): 0.736 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.674 RNAalifold(seed): 0.606 Sensitivity CentroidAlifold(seed): 0.509 RNAalifold(seed): 0.428 Positive Predictive Value CentroidAlifold(seed): 0.892 RNAalifold(seed): 0.860 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	36 Murlet(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Murlet(20): 0.589 CentroidAlifold(seed): 0.587 Sensitivity Murlet(20): 0.439 CentroidAlifold(seed): 0.368 Positive Predictive Value Murlet(20): 0.795 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.382290189588		= Carnac(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Carnac(20): 0.592 CentroidAlifold(seed): 0.587 Sensitivity Carnac(20): 0.392 CentroidAlifold(seed): 0.368 Positive Predictive Value Carnac(20): 0.898 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.014979478926	+ CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 IPknot: 0.593 Sensitivity CentroidAlifold(seed): 0.445 IPknot: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.896 IPknot: 0.712 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 6.43400990727e-08	- CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.588 CentroidAlifold(seed): 0.566 Sensitivity CentroidHomfold‑LAST: 0.495 CentroidAlifold(seed): 0.341 Positive Predictive Value CentroidHomfold‑LAST: 0.704 CentroidAlifold(seed): 0.944 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 Contrafold: 0.568 Sensitivity CentroidAlifold(seed): 0.425 Contrafold: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.899 Contrafold: 0.641 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 Sfold: 0.538 Sensitivity CentroidAlifold(seed): 0.425 Sfold: 0.457 Positive Predictive Value CentroidAlifold(seed): 0.899 Sfold: 0.635 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 HotKnots: 0.537 Sensitivity CentroidAlifold(seed): 0.367 HotKnots: 0.485 Positive Predictive Value CentroidAlifold(seed): 0.923 HotKnots: 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 CentroidFold: 0.555 Sensitivity CentroidAlifold(seed): 0.425 CentroidFold: 0.474 Positive Predictive Value CentroidAlifold(seed): 0.899 CentroidFold: 0.653 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.614 TurboFold(seed): 0.529 Sensitivity CentroidAlifold(seed): 0.397 TurboFold(seed): 0.434 Positive Predictive Value CentroidAlifold(seed): 0.956 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 MaxExpect: 0.543 Sensitivity CentroidAlifold(seed): 0.427 MaxExpect: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.899 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.591 RSpredict(20): 0.549 Sensitivity CentroidAlifold(seed): 0.371 RSpredict(20): 0.434 Positive Predictive Value CentroidAlifold(seed): 0.945 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 PknotsRG: 0.560 Sensitivity CentroidAlifold(seed): 0.367 PknotsRG: 0.503 Positive Predictive Value CentroidAlifold(seed): 0.923 PknotsRG: 0.629 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 4.83792096436e-08	- CMfinder(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidAlifold(seed): 0.510 Sensitivity CMfinder(20): 0.366 CentroidAlifold(seed): 0.288 Positive Predictive Value CMfinder(20): 0.748 CentroidAlifold(seed): 0.908 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.73616572961e-05	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 UNAFold: 0.520 Sensitivity CentroidAlifold(seed): 0.425 UNAFold: 0.459 Positive Predictive Value CentroidAlifold(seed): 0.899 UNAFold: 0.590 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.621 ProbKnot: 0.535 Sensitivity CentroidAlifold(seed): 0.432 ProbKnot: 0.476 Positive Predictive Value CentroidAlifold(seed): 0.894 ProbKnot: 0.604 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.618 CentroidAlifold(seed): 0.593 Sensitivity Cylofold: 0.519 CentroidAlifold(seed): 0.370 Positive Predictive Value Cylofold: 0.741 CentroidAlifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 RNAfold: 0.528 Sensitivity CentroidAlifold(seed): 0.425 RNAfold: 0.469 Positive Predictive Value CentroidAlifold(seed): 0.899 RNAfold: 0.595 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 RNASampler(seed): 0.467 Sensitivity CentroidAlifold(seed): 0.407 RNASampler(seed): 0.328 Positive Predictive Value CentroidAlifold(seed): 0.949 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.31583660336e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 RNAsubopt: 0.537 Sensitivity CentroidAlifold(seed): 0.367 RNAsubopt: 0.485 Positive Predictive Value CentroidAlifold(seed): 0.923 RNAsubopt: 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.565 Multilign(20): 0.534 Sensitivity CentroidAlifold(seed): 0.338 Multilign(20): 0.449 Positive Predictive Value CentroidAlifold(seed): 0.950 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.572 Afold: 0.495 Sensitivity CentroidAlifold(seed): 0.366 Afold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.899 Afold: 0.539 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 RNAshapes: 0.521 Sensitivity CentroidAlifold(seed): 0.367 RNAshapes: 0.462 Positive Predictive Value CentroidAlifold(seed): 0.923 RNAshapes: 0.593 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.619 Fold: 0.519 Sensitivity CentroidAlifold(seed): 0.429 Fold: 0.464 Positive Predictive Value CentroidAlifold(seed): 0.895 Fold: 0.583 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 McQFold: 0.507 Sensitivity CentroidAlifold(seed): 0.425 McQFold: 0.437 Positive Predictive Value CentroidAlifold(seed): 0.899 McQFold: 0.591 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.558 RNASLOpt: 0.499 Sensitivity CentroidAlifold(seed): 0.334 RNASLOpt: 0.408 Positive Predictive Value CentroidAlifold(seed): 0.936 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.587 Mastr(20): 0.496 Sensitivity CentroidAlifold(seed): 0.368 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(seed): 0.941 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.653 Multilign(seed): 0.556 Sensitivity CentroidAlifold(seed): 0.451 Multilign(seed): 0.432 Positive Predictive Value CentroidAlifold(seed): 0.949 Multilign(seed): 0.723 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71210682542e-09	+ CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.585 Pknots: 0.529 Sensitivity CentroidAlifold(seed): 0.364 Pknots: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.945 Pknots: 0.596 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.576 Vsfold4: 0.481 Sensitivity CentroidAlifold(seed): 0.361 Vsfold4: 0.405 Positive Predictive Value CentroidAlifold(seed): 0.924 Vsfold4: 0.576 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.578 CRWrnafold: 0.536 Sensitivity CentroidAlifold(seed): 0.343 CRWrnafold: 0.472 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.677 Murlet(seed): 0.447 Sensitivity CentroidAlifold(seed): 0.481 Murlet(seed): 0.244 Positive Predictive Value CentroidAlifold(seed): 0.955 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.579 Vsfold5: 0.446 Sensitivity CentroidAlifold(seed): 0.365 Vsfold5: 0.381 Positive Predictive Value CentroidAlifold(seed): 0.923 Vsfold5: 0.528 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 MCFold: 0.414 Sensitivity CentroidAlifold(seed): 0.354 MCFold: 0.432 Positive Predictive Value CentroidAlifold(seed): 0.955 MCFold: 0.405 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.567 Alterna: 0.564 Sensitivity CentroidAlifold(seed): 0.337 Alterna: 0.492 Positive Predictive Value CentroidAlifold(seed): 0.960 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.228964554769	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.594 RDfolder: 0.504 Sensitivity CentroidAlifold(seed): 0.369 RDfolder: 0.407 Positive Predictive Value CentroidAlifold(seed): 0.963 RDfolder: 0.635 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 RNAwolf: 0.416 Sensitivity CentroidAlifold(seed): 0.445 RNAwolf: 0.385 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAwolf: 0.451 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.536 NanoFolder: 0.290 Sensitivity CentroidAlifold(seed): 0.308 NanoFolder: 0.301 Positive Predictive Value CentroidAlifold(seed): 0.940 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Carnac(seed): 0.385 Sensitivity CentroidAlifold(seed): 0.513 Carnac(seed): 0.167 Positive Predictive Value CentroidAlifold(seed): 0.909 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.621 RSpredict(seed): 0.334 Sensitivity CentroidAlifold(seed): 0.428 RSpredict(seed): 0.187 Positive Predictive Value CentroidAlifold(seed): 0.900 RSpredict(seed): 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.575 PPfold(seed): 0.148 Sensitivity CentroidAlifold(seed): 0.351 PPfold(seed): 0.032 Positive Predictive Value CentroidAlifold(seed): 0.947 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(seed): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidAlifold(seed): 0.618 Sensitivity PETfold_2.0(seed): 0.642 CentroidAlifold(seed): 0.432 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(20): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidAlifold(seed): 0.484 Sensitivity PETfold_2.0(20): 0.509 CentroidAlifold(seed): 0.281 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidAlifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs DAFS(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(seed): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 Mastr(seed): 0.024 Sensitivity CentroidAlifold(seed): 0.367 Mastr(seed): 0.002 Positive Predictive Value CentroidAlifold(seed): 0.923 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(20)	36 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Carnac(20): 0.592 Sensitivity CentroidAlifold(20): 0.529 Carnac(20): 0.392 Positive Predictive Value CentroidAlifold(20): 0.882 Carnac(20): 0.898 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(seed): 0.597 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.99051034341e-09	38 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Carnac(20): 0.590 Sensitivity RNAalifold(20): 0.511 Carnac(20): 0.389 Positive Predictive Value RNAalifold(20): 0.846 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 Carnac(20): 0.588 Sensitivity MXScarna(seed): 0.529 Carnac(20): 0.387 Positive Predictive Value MXScarna(seed): 0.791 Carnac(20): 0.897 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.663 Carnac(20): 0.565 Sensitivity PPfold(20): 0.528 Carnac(20): 0.372 Positive Predictive Value PPfold(20): 0.836 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.617 Carnac(20): 0.547 Sensitivity ContextFold: 0.499 Carnac(20): 0.351 Positive Predictive Value ContextFold: 0.767 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	38 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.612 Carnac(20): 0.590 Sensitivity RNASampler(20): 0.471 Carnac(20): 0.389 Positive Predictive Value RNASampler(20): 0.799 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Carnac(20): 0.547 Sensitivity PETfold_pre2.0(20): 0.530 Carnac(20): 0.351 Positive Predictive Value PETfold_pre2.0(20): 0.798 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	20 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.616 Carnac(20): 0.565 Sensitivity TurboFold(20): 0.508 Carnac(20): 0.372 Positive Predictive Value TurboFold(20): 0.752 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.611 Carnac(20): 0.590 Sensitivity MXScarna(20): 0.509 Carnac(20): 0.389 Positive Predictive Value MXScarna(20): 0.737 Carnac(20): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 Carnac(20): 0.517 Sensitivity RNAalifold(seed): 0.338 Carnac(20): 0.285 Positive Predictive Value RNAalifold(seed): 0.929 Carnac(20): 0.940 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	38 Carnac(20) vs Murlet(20) Matthews Correlation Coefficient Carnac(20): 0.590 Murlet(20): 0.590 Sensitivity Carnac(20): 0.389 Murlet(20): 0.438 Positive Predictive Value Carnac(20): 0.899 Murlet(20): 0.799 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.339915559821	36 Carnac(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient Carnac(20): 0.592 CentroidAlifold(seed): 0.587 Sensitivity Carnac(20): 0.392 CentroidAlifold(seed): 0.368 Positive Predictive Value Carnac(20): 0.898 CentroidAlifold(seed): 0.941 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.014979478926		+ Carnac(20) vs IPknot Matthews Correlation Coefficient Carnac(20): 0.565 IPknot: 0.526 Sensitivity Carnac(20): 0.371 IPknot: 0.433 Positive Predictive Value Carnac(20): 0.867 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	= CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Carnac(20): 0.580 Sensitivity CentroidHomfold‑LAST: 0.491 Carnac(20): 0.388 Positive Predictive Value CentroidHomfold‑LAST: 0.700 Carnac(20): 0.872 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.108666870025	+ Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.590 Contrafold: 0.536 Sensitivity Carnac(20): 0.389 Contrafold: 0.472 Positive Predictive Value Carnac(20): 0.899 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.590 Sfold: 0.560 Sensitivity Carnac(20): 0.389 Sfold: 0.466 Positive Predictive Value Carnac(20): 0.899 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.590 HotKnots: 0.533 Sensitivity Carnac(20): 0.389 HotKnots: 0.475 Positive Predictive Value Carnac(20): 0.899 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs CentroidFold Matthews Correlation Coefficient Carnac(20): 0.592 CentroidFold: 0.542 Sensitivity Carnac(20): 0.392 CentroidFold: 0.459 Positive Predictive Value Carnac(20): 0.898 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Carnac(20) vs TurboFold(seed) Matthews Correlation Coefficient Carnac(20): 0.485 TurboFold(seed): 0.484 Sensitivity Carnac(20): 0.272 TurboFold(seed): 0.393 Positive Predictive Value Carnac(20): 0.868 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.537823689986	+ Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.592 MaxExpect: 0.557 Sensitivity Carnac(20): 0.392 MaxExpect: 0.481 Positive Predictive Value Carnac(20): 0.898 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.594 RSpredict(20): 0.552 Sensitivity Carnac(20): 0.395 RSpredict(20): 0.436 Positive Predictive Value Carnac(20): 0.897 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.590 PknotsRG: 0.557 Sensitivity Carnac(20): 0.389 PknotsRG: 0.494 Positive Predictive Value Carnac(20): 0.899 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.574 CMfinder(20): 0.521 Sensitivity Carnac(20): 0.382 CMfinder(20): 0.366 Positive Predictive Value Carnac(20): 0.867 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.40200680498e-09	+ Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.590 UNAFold: 0.543 Sensitivity Carnac(20): 0.389 UNAFold: 0.475 Positive Predictive Value Carnac(20): 0.899 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.578 ProbKnot: 0.548 Sensitivity Carnac(20): 0.373 ProbKnot: 0.484 Positive Predictive Value Carnac(20): 0.899 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	- Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.642 Carnac(20): 0.619 Sensitivity Cylofold: 0.543 Carnac(20): 0.436 Positive Predictive Value Cylofold: 0.765 Carnac(20): 0.882 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.590 RNAfold: 0.540 Sensitivity Carnac(20): 0.389 RNAfold: 0.477 Positive Predictive Value Carnac(20): 0.899 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RNASampler(seed) Matthews Correlation Coefficient Carnac(20): 0.520 RNASampler(seed): 0.478 Sensitivity Carnac(20): 0.288 RNASampler(seed): 0.353 Positive Predictive Value Carnac(20): 0.942 RNASampler(seed): 0.652 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.590 RNAsubopt: 0.534 Sensitivity Carnac(20): 0.389 RNAsubopt: 0.477 Positive Predictive Value Carnac(20): 0.899 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Multilign(20) Matthews Correlation Coefficient Carnac(20): 0.580 Multilign(20): 0.534 Sensitivity Carnac(20): 0.391 Multilign(20): 0.449 Positive Predictive Value Carnac(20): 0.866 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.595 Afold: 0.511 Sensitivity Carnac(20): 0.382 Afold: 0.460 Positive Predictive Value Carnac(20): 0.928 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.590 RNAshapes: 0.517 Sensitivity Carnac(20): 0.389 RNAshapes: 0.453 Positive Predictive Value Carnac(20): 0.899 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.578 Fold: 0.531 Sensitivity Carnac(20): 0.373 Fold: 0.471 Positive Predictive Value Carnac(20): 0.899 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.590 McQFold: 0.506 Sensitivity Carnac(20): 0.389 McQFold: 0.433 Positive Predictive Value Carnac(20): 0.899 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.547 RNASLOpt: 0.463 Sensitivity Carnac(20): 0.351 RNASLOpt: 0.383 Positive Predictive Value Carnac(20): 0.858 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.590 Mastr(20): 0.500 Sensitivity Carnac(20): 0.389 Mastr(20): 0.336 Positive Predictive Value Carnac(20): 0.899 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.497 Carnac(20): 0.491 Sensitivity Multilign(seed): 0.369 Carnac(20): 0.281 Positive Predictive Value Multilign(seed): 0.676 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.600 Pknots: 0.481 Sensitivity Carnac(20): 0.404 Pknots: 0.433 Positive Predictive Value Carnac(20): 0.896 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.598 Vsfold4: 0.459 Sensitivity Carnac(20): 0.398 Vsfold4: 0.381 Positive Predictive Value Carnac(20): 0.902 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Carnac(20): 0.526 Sensitivity CRWrnafold: 0.483 Carnac(20): 0.335 Positive Predictive Value CRWrnafold: 0.623 Carnac(20): 0.832 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.526 Murlet(seed): 0.454 Sensitivity Carnac(20): 0.295 Murlet(seed): 0.241 Positive Predictive Value Carnac(20): 0.941 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.598 Vsfold5: 0.409 Sensitivity Carnac(20): 0.398 Vsfold5: 0.345 Positive Predictive Value Carnac(20): 0.902 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.609 MCFold: 0.402 Sensitivity Carnac(20): 0.417 MCFold: 0.418 Positive Predictive Value Carnac(20): 0.895 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.697 Alterna: 0.553 Sensitivity Carnac(20): 0.529 Alterna: 0.480 Positive Predictive Value Carnac(20): 0.924 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.01312059156e-09	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.652 RDfolder: 0.563 Sensitivity Carnac(20): 0.479 RDfolder: 0.447 Positive Predictive Value Carnac(20): 0.895 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.565 RNAwolf: 0.348 Sensitivity Carnac(20): 0.371 RNAwolf: 0.328 Positive Predictive Value Carnac(20): 0.867 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.576 NanoFolder: 0.269 Sensitivity Carnac(20): 0.383 NanoFolder: 0.280 Positive Predictive Value Carnac(20): 0.872 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.572 Carnac(seed): 0.110 Sensitivity Carnac(20): 0.355 Carnac(seed): 0.012 Positive Predictive Value Carnac(20): 0.927 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.594 RSpredict(seed): 0.174 Sensitivity Carnac(20): 0.395 RSpredict(seed): 0.068 Positive Predictive Value Carnac(20): 0.897 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.565 PPfold(seed): 0.072 Sensitivity Carnac(20): 0.372 PPfold(seed): 0.012 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	? CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(20): N/A Sensitivity CMfinder(seed): N/A Carnac(20): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Carnac(20): 0.576 Sensitivity PETfold_2.0(seed): 0.614 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(seed): 0.946 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs DAFS(20) Matthews Correlation Coefficient Carnac(20): N/A DAFS(20): N/A Sensitivity Carnac(20): N/A DAFS(20): N/A Positive Predictive Value Carnac(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Carnac(20): 0.576 Sensitivity PETfold_2.0(20): 0.509 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(20): 0.829 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Carnac(20) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(20): N/A Sensitivity DAFS(seed): N/A Carnac(20): N/A Positive Predictive Value DAFS(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.590 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.389 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.899 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08
IPknot	21 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.669 IPknot: 0.526 Sensitivity CentroidAlifold(20): 0.511 IPknot: 0.433 Positive Predictive Value CentroidAlifold(20): 0.880 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 IPknot: 0.587 Sensitivity PETfold_pre2.0(seed): 0.602 IPknot: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.850 IPknot: 0.703 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.644 IPknot: 0.526 Sensitivity RNAalifold(20): 0.503 IPknot: 0.433 Positive Predictive Value RNAalifold(20): 0.829 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.638 IPknot: 0.594 Sensitivity MXScarna(seed): 0.529 IPknot: 0.495 Positive Predictive Value MXScarna(seed): 0.770 IPknot: 0.714 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.663 IPknot: 0.535 Sensitivity PPfold(20): 0.528 IPknot: 0.443 Positive Predictive Value PPfold(20): 0.836 IPknot: 0.651 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	43 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.536 IPknot: 0.506 Sensitivity ContextFold: 0.440 IPknot: 0.406 Positive Predictive Value ContextFold: 0.654 IPknot: 0.633 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 4.83792096436e-08	21 RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.585 IPknot: 0.526 Sensitivity RNASampler(20): 0.448 IPknot: 0.433 Positive Predictive Value RNASampler(20): 0.768 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 IPknot: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 IPknot: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 IPknot: 0.614 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	20 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.616 IPknot: 0.535 Sensitivity TurboFold(20): 0.508 IPknot: 0.443 Positive Predictive Value TurboFold(20): 0.752 IPknot: 0.651 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	21 MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.590 IPknot: 0.526 Sensitivity MXScarna(20): 0.486 IPknot: 0.433 Positive Predictive Value MXScarna(20): 0.720 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	16 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.635 IPknot: 0.587 Sensitivity RNAalifold(seed): 0.475 IPknot: 0.489 Positive Predictive Value RNAalifold(seed): 0.849 IPknot: 0.706 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 4.61330405444e-08	21 Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.583 IPknot: 0.526 Sensitivity Murlet(20): 0.437 IPknot: 0.433 Positive Predictive Value Murlet(20): 0.784 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	29 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 IPknot: 0.593 Sensitivity CentroidAlifold(seed): 0.445 IPknot: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.896 IPknot: 0.712 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 6.43400990727e-08	21 Carnac(20) vs IPknot Matthews Correlation Coefficient Carnac(20): 0.565 IPknot: 0.526 Sensitivity Carnac(20): 0.371 IPknot: 0.433 Positive Predictive Value Carnac(20): 0.867 IPknot: 0.645 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.550 CentroidHomfold‑LAST: 0.513 Sensitivity IPknot: 0.453 CentroidHomfold‑LAST: 0.379 Positive Predictive Value IPknot: 0.672 CentroidHomfold‑LAST: 0.698 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.513 Contrafold: 0.459 Sensitivity IPknot: 0.411 Contrafold: 0.394 Positive Predictive Value IPknot: 0.641 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.513 Sfold: 0.468 Sensitivity IPknot: 0.411 Sfold: 0.393 Positive Predictive Value IPknot: 0.641 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.542 HotKnots: 0.501 Sensitivity IPknot: 0.445 HotKnots: 0.440 Positive Predictive Value IPknot: 0.665 HotKnots: 0.575 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.513 CentroidFold: 0.446 Sensitivity IPknot: 0.411 CentroidFold: 0.356 Positive Predictive Value IPknot: 0.641 CentroidFold: 0.560 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	= IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.535 TurboFold(seed): 0.529 Sensitivity IPknot: 0.431 TurboFold(seed): 0.434 Positive Predictive Value IPknot: 0.670 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00148733745706	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.513 MaxExpect: 0.446 Sensitivity IPknot: 0.411 MaxExpect: 0.384 Positive Predictive Value IPknot: 0.641 MaxExpect: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.535 RSpredict(20): 0.520 Sensitivity IPknot: 0.443 RSpredict(20): 0.398 Positive Predictive Value IPknot: 0.651 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.92531153888e-07	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.483 PknotsRG: 0.456 Sensitivity IPknot: 0.380 PknotsRG: 0.401 Positive Predictive Value IPknot: 0.616 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs IPknot Matthews Correlation Coefficient CMfinder(20): 0.521 IPknot: 0.488 Sensitivity CMfinder(20): 0.366 IPknot: 0.416 Positive Predictive Value CMfinder(20): 0.748 IPknot: 0.580 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.513 UNAFold: 0.446 Sensitivity IPknot: 0.411 UNAFold: 0.390 Positive Predictive Value IPknot: 0.641 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.513 ProbKnot: 0.444 Sensitivity IPknot: 0.411 ProbKnot: 0.388 Positive Predictive Value IPknot: 0.641 ProbKnot: 0.511 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.578 Cylofold: 0.490 Sensitivity IPknot: 0.481 Cylofold: 0.409 Positive Predictive Value IPknot: 0.701 Cylofold: 0.595 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.513 RNAfold: 0.449 Sensitivity IPknot: 0.411 RNAfold: 0.393 Positive Predictive Value IPknot: 0.641 RNAfold: 0.514 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.492 RNASampler(seed): 0.417 Sensitivity IPknot: 0.396 RNASampler(seed): 0.283 Positive Predictive Value IPknot: 0.617 RNASampler(seed): 0.619 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.542 RNAsubopt: 0.475 Sensitivity IPknot: 0.445 RNAsubopt: 0.417 Positive Predictive Value IPknot: 0.665 RNAsubopt: 0.546 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.544 Multilign(20): 0.534 Sensitivity IPknot: 0.461 Multilign(20): 0.449 Positive Predictive Value IPknot: 0.647 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.82922338419e-05	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.386 Afold: 0.348 Sensitivity IPknot: 0.290 Afold: 0.312 Positive Predictive Value IPknot: 0.514 Afold: 0.389 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.542 RNAshapes: 0.460 Sensitivity IPknot: 0.445 RNAshapes: 0.397 Positive Predictive Value IPknot: 0.665 RNAshapes: 0.537 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.513 Fold: 0.411 Sensitivity IPknot: 0.411 Fold: 0.364 Positive Predictive Value IPknot: 0.641 Fold: 0.467 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.513 McQFold: 0.380 Sensitivity IPknot: 0.411 McQFold: 0.322 Positive Predictive Value IPknot: 0.641 McQFold: 0.450 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.533 RNASLOpt: 0.427 Sensitivity IPknot: 0.439 RNASLOpt: 0.341 Positive Predictive Value IPknot: 0.652 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.526 Mastr(20): 0.496 Sensitivity IPknot: 0.433 Mastr(20): 0.341 Positive Predictive Value IPknot: 0.645 Mastr(20): 0.729 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 9.95914622767e-08	+ IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.604 Multilign(seed): 0.556 Sensitivity IPknot: 0.473 Multilign(seed): 0.432 Positive Predictive Value IPknot: 0.777 Multilign(seed): 0.723 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.93000771886e-09	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.561 Pknots: 0.446 Sensitivity IPknot: 0.465 Pknots: 0.400 Positive Predictive Value IPknot: 0.682 Pknots: 0.505 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.547 Vsfold4: 0.401 Sensitivity IPknot: 0.456 Vsfold4: 0.328 Positive Predictive Value IPknot: 0.662 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.541 CRWrnafold: 0.467 Sensitivity IPknot: 0.447 CRWrnafold: 0.410 Positive Predictive Value IPknot: 0.663 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.84765843136e-09	+ IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.555 Murlet(seed): 0.418 Sensitivity IPknot: 0.450 Murlet(seed): 0.227 Positive Predictive Value IPknot: 0.691 Murlet(seed): 0.777 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.541 Vsfold5: 0.368 Sensitivity IPknot: 0.450 Vsfold5: 0.315 Positive Predictive Value IPknot: 0.657 Vsfold5: 0.438 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.537 MCFold: 0.368 Sensitivity IPknot: 0.445 MCFold: 0.376 Positive Predictive Value IPknot: 0.653 MCFold: 0.369 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	? IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.577 Alterna: 0.500 Sensitivity IPknot: 0.449 Alterna: 0.432 Positive Predictive Value IPknot: 0.750 Alterna: 0.590 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.555 RDfolder: 0.403 Sensitivity IPknot: 0.444 RDfolder: 0.302 Positive Predictive Value IPknot: 0.704 RDfolder: 0.550 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.513 RNAwolf: 0.317 Sensitivity IPknot: 0.411 RNAwolf: 0.293 Positive Predictive Value IPknot: 0.641 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.533 NanoFolder: 0.272 Sensitivity IPknot: 0.446 NanoFolder: 0.284 Positive Predictive Value IPknot: 0.642 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.592 Carnac(seed): 0.452 Sensitivity IPknot: 0.492 Carnac(seed): 0.229 Positive Predictive Value IPknot: 0.712 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.45076534967e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.599 RSpredict(seed): 0.395 Sensitivity IPknot: 0.501 RSpredict(seed): 0.246 Positive Predictive Value IPknot: 0.717 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.589 PPfold(seed): 0.148 Sensitivity IPknot: 0.488 PPfold(seed): 0.032 Positive Predictive Value IPknot: 0.717 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 IPknot: 0.610 Sensitivity PETfold_2.0(seed): 0.642 IPknot: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 IPknot: 0.758 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? IPknot vs DAFS(20) Matthews Correlation Coefficient IPknot: N/A DAFS(20): N/A Sensitivity IPknot: N/A DAFS(20): N/A Positive Predictive Value IPknot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 IPknot: 0.401 Sensitivity PETfold_2.0(20): 0.509 IPknot: 0.298 Positive Predictive Value PETfold_2.0(20): 0.829 IPknot: 0.548 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs IPknot Matthews Correlation Coefficient DAFS(seed): N/A IPknot: N/A Sensitivity DAFS(seed): N/A IPknot: N/A Positive Predictive Value DAFS(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.580 Mastr(seed): 0.033 Sensitivity IPknot: 0.477 Mastr(seed): 0.003 Positive Predictive Value IPknot: 0.709 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08
CentroidHomfold‑LAST	20 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.686 CentroidHomfold‑LAST: 0.584 Sensitivity CentroidAlifold(20): 0.533 CentroidHomfold‑LAST: 0.491 Positive Predictive Value CentroidAlifold(20): 0.887 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	23 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidHomfold‑LAST: 0.574 Sensitivity PETfold_pre2.0(seed): 0.606 CentroidHomfold‑LAST: 0.489 Positive Predictive Value PETfold_pre2.0(seed): 0.882 CentroidHomfold‑LAST: 0.680 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	20 RNAalifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(20): 0.660 CentroidHomfold‑LAST: 0.584 Sensitivity RNAalifold(20): 0.519 CentroidHomfold‑LAST: 0.491 Positive Predictive Value RNAalifold(20): 0.844 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	25 MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.620 CentroidHomfold‑LAST: 0.584 Sensitivity MXScarna(seed): 0.503 CentroidHomfold‑LAST: 0.491 Positive Predictive Value MXScarna(seed): 0.770 CentroidHomfold‑LAST: 0.701 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	19 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.684 CentroidHomfold‑LAST: 0.589 Sensitivity PPfold(20): 0.552 CentroidHomfold‑LAST: 0.501 Positive Predictive Value PPfold(20): 0.851 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	35 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.597 CentroidHomfold‑LAST: 0.498 Sensitivity ContextFold: 0.485 CentroidHomfold‑LAST: 0.368 Positive Predictive Value ContextFold: 0.738 CentroidHomfold‑LAST: 0.679 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.605 CentroidHomfold‑LAST: 0.584 Sensitivity RNASampler(20): 0.466 CentroidHomfold‑LAST: 0.491 Positive Predictive Value RNASampler(20): 0.791 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.14303126762e-07	17 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 CentroidHomfold‑LAST: 0.565 Sensitivity PETfold_pre2.0(20): 0.559 CentroidHomfold‑LAST: 0.482 Positive Predictive Value PETfold_pre2.0(20): 0.826 CentroidHomfold‑LAST: 0.668 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52609899389e-08	19 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.631 CentroidHomfold‑LAST: 0.589 Sensitivity TurboFold(20): 0.526 CentroidHomfold‑LAST: 0.501 Positive Predictive Value TurboFold(20): 0.762 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	20 MXScarna(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(20): 0.606 CentroidHomfold‑LAST: 0.584 Sensitivity MXScarna(20): 0.505 CentroidHomfold‑LAST: 0.491 Positive Predictive Value MXScarna(20): 0.733 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	13 RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.553 CentroidHomfold‑LAST: 0.496 Sensitivity RNAalifold(seed): 0.350 CentroidHomfold‑LAST: 0.415 Positive Predictive Value RNAalifold(seed): 0.880 CentroidHomfold‑LAST: 0.599 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	20 Murlet(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Murlet(20): 0.599 CentroidHomfold‑LAST: 0.584 Sensitivity Murlet(20): 0.451 CentroidHomfold‑LAST: 0.491 Positive Predictive Value Murlet(20): 0.800 CentroidHomfold‑LAST: 0.700 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 2.40326410557e-07	26 CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.588 CentroidAlifold(seed): 0.566 Sensitivity CentroidHomfold‑LAST: 0.495 CentroidAlifold(seed): 0.341 Positive Predictive Value CentroidHomfold‑LAST: 0.704 CentroidAlifold(seed): 0.944 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	20 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Carnac(20): 0.580 Sensitivity CentroidHomfold‑LAST: 0.491 Carnac(20): 0.388 Positive Predictive Value CentroidHomfold‑LAST: 0.700 Carnac(20): 0.872 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.108666870025	38 IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.550 CentroidHomfold‑LAST: 0.513 Sensitivity IPknot: 0.453 CentroidHomfold‑LAST: 0.379 Positive Predictive Value IPknot: 0.672 CentroidHomfold‑LAST: 0.698 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 Contrafold: 0.497 Sensitivity CentroidHomfold‑LAST: 0.378 Contrafold: 0.426 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.76761760679e-06	- Sfold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Sfold: 0.526 CentroidHomfold‑LAST: 0.512 Sensitivity Sfold: 0.431 CentroidHomfold‑LAST: 0.378 Positive Predictive Value Sfold: 0.646 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.00036811921398	- HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.518 CentroidHomfold‑LAST: 0.512 Sensitivity HotKnots: 0.450 CentroidHomfold‑LAST: 0.378 Positive Predictive Value HotKnots: 0.602 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000609097173132	+ CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 CentroidFold: 0.473 Sensitivity CentroidHomfold‑LAST: 0.378 CentroidFold: 0.386 Positive Predictive Value CentroidHomfold‑LAST: 0.699 CentroidFold: 0.585 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.509 CentroidHomfold‑LAST: 0.492 Sensitivity TurboFold(seed): 0.421 CentroidHomfold‑LAST: 0.404 Positive Predictive Value TurboFold(seed): 0.622 CentroidHomfold‑LAST: 0.605 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.17451270932e-06	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 MaxExpect: 0.476 Sensitivity CentroidHomfold‑LAST: 0.378 MaxExpect: 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.699 MaxExpect: 0.566 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.589 RSpredict(20): 0.539 Sensitivity CentroidHomfold‑LAST: 0.501 RSpredict(20): 0.414 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RSpredict(20): 0.709 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	= PknotsRG vs CentroidHomfold‑LAST Matthews Correlation Coefficient PknotsRG: 0.516 CentroidHomfold‑LAST: 0.512 Sensitivity PknotsRG: 0.446 CentroidHomfold‑LAST: 0.378 Positive Predictive Value PknotsRG: 0.601 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.00911763231782	+ CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.538 CMfinder(20): 0.521 Sensitivity CentroidHomfold‑LAST: 0.465 CMfinder(20): 0.366 Positive Predictive Value CentroidHomfold‑LAST: 0.627 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.35948134614e-05	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 UNAFold: 0.491 Sensitivity CentroidHomfold‑LAST: 0.378 UNAFold: 0.422 Positive Predictive Value CentroidHomfold‑LAST: 0.699 UNAFold: 0.577 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 ProbKnot: 0.478 Sensitivity CentroidHomfold‑LAST: 0.378 ProbKnot: 0.415 Positive Predictive Value CentroidHomfold‑LAST: 0.699 ProbKnot: 0.554 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 Cylofold: 0.483 Sensitivity CentroidHomfold‑LAST: 0.380 Cylofold: 0.401 Positive Predictive Value CentroidHomfold‑LAST: 0.696 Cylofold: 0.590 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 RNAfold: 0.502 Sensitivity CentroidHomfold‑LAST: 0.378 RNAfold: 0.431 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RNAfold: 0.590 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 9.77069178155e-06	? CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.472 RNASampler(seed): 0.434 Sensitivity CentroidHomfold‑LAST: 0.383 RNASampler(seed): 0.301 Positive Predictive Value CentroidHomfold‑LAST: 0.589 RNASampler(seed): 0.633 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 RNAsubopt: 0.482 Sensitivity CentroidHomfold‑LAST: 0.378 RNAsubopt: 0.420 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RNAsubopt: 0.559 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.589 Multilign(20): 0.534 Sensitivity CentroidHomfold‑LAST: 0.501 Multilign(20): 0.449 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.61939086268e-08	- Afold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Afold: 0.424 CentroidHomfold‑LAST: 0.388 Sensitivity Afold: 0.373 CentroidHomfold‑LAST: 0.263 Positive Predictive Value Afold: 0.490 CentroidHomfold‑LAST: 0.579 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.57172654109e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 RNAshapes: 0.466 Sensitivity CentroidHomfold‑LAST: 0.378 RNAshapes: 0.398 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RNAshapes: 0.551 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 Fold: 0.448 Sensitivity CentroidHomfold‑LAST: 0.378 Fold: 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Fold: 0.522 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 McQFold: 0.454 Sensitivity CentroidHomfold‑LAST: 0.378 McQFold: 0.381 Positive Predictive Value CentroidHomfold‑LAST: 0.699 McQFold: 0.547 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.498 RNASLOpt: 0.437 Sensitivity CentroidHomfold‑LAST: 0.368 RNASLOpt: 0.347 Positive Predictive Value CentroidHomfold‑LAST: 0.679 RNASLOpt: 0.555 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Mastr(20): 0.513 Sensitivity CentroidHomfold‑LAST: 0.491 Mastr(20): 0.364 Positive Predictive Value CentroidHomfold‑LAST: 0.700 Mastr(20): 0.729 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	? CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.549 Multilign(seed): 0.534 Sensitivity CentroidHomfold‑LAST: 0.435 Multilign(seed): 0.414 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Multilign(seed): 0.697 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.572 Pknots: 0.471 Sensitivity CentroidHomfold‑LAST: 0.458 Pknots: 0.415 Positive Predictive Value CentroidHomfold‑LAST: 0.720 Pknots: 0.543 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.539 Vsfold4: 0.402 Sensitivity CentroidHomfold‑LAST: 0.411 Vsfold4: 0.327 Positive Predictive Value CentroidHomfold‑LAST: 0.711 Vsfold4: 0.501 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.531 CRWrnafold: 0.467 Sensitivity CentroidHomfold‑LAST: 0.380 CRWrnafold: 0.410 Positive Predictive Value CentroidHomfold‑LAST: 0.749 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.496 Murlet(seed): 0.424 Sensitivity CentroidHomfold‑LAST: 0.415 Murlet(seed): 0.240 Positive Predictive Value CentroidHomfold‑LAST: 0.599 Murlet(seed): 0.758 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.518 Vsfold5: 0.362 Sensitivity CentroidHomfold‑LAST: 0.399 Vsfold5: 0.309 Positive Predictive Value CentroidHomfold‑LAST: 0.677 Vsfold5: 0.433 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.544 MCFold: 0.377 Sensitivity CentroidHomfold‑LAST: 0.438 MCFold: 0.383 Positive Predictive Value CentroidHomfold‑LAST: 0.682 MCFold: 0.380 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.596 Alterna: 0.496 Sensitivity CentroidHomfold‑LAST: 0.427 Alterna: 0.419 Positive Predictive Value CentroidHomfold‑LAST: 0.840 Alterna: 0.599 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.21584974784e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.624 RDfolder: 0.400 Sensitivity CentroidHomfold‑LAST: 0.483 RDfolder: 0.298 Positive Predictive Value CentroidHomfold‑LAST: 0.815 RDfolder: 0.550 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.513 RNAwolf: 0.341 Sensitivity CentroidHomfold‑LAST: 0.379 RNAwolf: 0.315 Positive Predictive Value CentroidHomfold‑LAST: 0.698 RNAwolf: 0.375 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.557 NanoFolder: 0.268 Sensitivity CentroidHomfold‑LAST: 0.439 NanoFolder: 0.280 Positive Predictive Value CentroidHomfold‑LAST: 0.712 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.516 Carnac(seed): 0.220 Sensitivity CentroidHomfold‑LAST: 0.431 Carnac(seed): 0.049 Positive Predictive Value CentroidHomfold‑LAST: 0.625 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.592 RSpredict(seed): 0.128 Sensitivity CentroidHomfold‑LAST: 0.503 RSpredict(seed): 0.051 Positive Predictive Value CentroidHomfold‑LAST: 0.703 RSpredict(seed): 0.328 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.592 PPfold(seed): 0.149 Sensitivity CentroidHomfold‑LAST: 0.503 PPfold(seed): 0.031 Positive Predictive Value CentroidHomfold‑LAST: 0.703 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(seed): 0.614 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs DAFS(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(20): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(20): 0.509 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs DAFS(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.588 Mastr(seed): 0.034 Sensitivity CentroidHomfold‑LAST: 0.495 Mastr(seed): 0.003 Positive Predictive Value CentroidHomfold‑LAST: 0.704 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08
Contrafold	36 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Contrafold: 0.541 Sensitivity CentroidAlifold(20): 0.529 Contrafold: 0.478 Positive Predictive Value CentroidAlifold(20): 0.882 Contrafold: 0.617 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Contrafold: 0.565 Sensitivity PETfold_pre2.0(seed): 0.602 Contrafold: 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Contrafold: 0.650 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	38 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.656 Contrafold: 0.536 Sensitivity RNAalifold(20): 0.511 Contrafold: 0.472 Positive Predictive Value RNAalifold(20): 0.846 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.646 Contrafold: 0.568 Sensitivity MXScarna(seed): 0.536 Contrafold: 0.504 Positive Predictive Value MXScarna(seed): 0.779 Contrafold: 0.642 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.663 Contrafold: 0.523 Sensitivity PPfold(20): 0.528 Contrafold: 0.460 Positive Predictive Value PPfold(20): 0.836 Contrafold: 0.602 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	43 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.536 Contrafold: 0.453 Sensitivity ContextFold: 0.440 Contrafold: 0.389 Positive Predictive Value ContextFold: 0.654 Contrafold: 0.528 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.612 Contrafold: 0.536 Sensitivity RNASampler(20): 0.471 Contrafold: 0.472 Positive Predictive Value RNASampler(20): 0.799 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Contrafold: 0.503 Sensitivity PETfold_pre2.0(20): 0.530 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.798 Contrafold: 0.579 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	20 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.616 Contrafold: 0.523 Sensitivity TurboFold(20): 0.508 Contrafold: 0.460 Positive Predictive Value TurboFold(20): 0.752 Contrafold: 0.602 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.611 Contrafold: 0.536 Sensitivity MXScarna(20): 0.509 Contrafold: 0.472 Positive Predictive Value MXScarna(20): 0.737 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.606 Contrafold: 0.565 Sensitivity RNAalifold(seed): 0.427 Contrafold: 0.499 Positive Predictive Value RNAalifold(seed): 0.861 Contrafold: 0.642 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.10039559051e-07	38 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.590 Contrafold: 0.536 Sensitivity Murlet(20): 0.438 Contrafold: 0.472 Positive Predictive Value Murlet(20): 0.799 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	51 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 Contrafold: 0.568 Sensitivity CentroidAlifold(seed): 0.425 Contrafold: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.899 Contrafold: 0.641 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.590 Contrafold: 0.536 Sensitivity Carnac(20): 0.389 Contrafold: 0.472 Positive Predictive Value Carnac(20): 0.899 Contrafold: 0.613 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.513 Contrafold: 0.459 Sensitivity IPknot: 0.411 Contrafold: 0.394 Positive Predictive Value IPknot: 0.641 Contrafold: 0.537 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 Contrafold: 0.497 Sensitivity CentroidHomfold‑LAST: 0.378 Contrafold: 0.426 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.76761760679e-06		+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.500 Sfold: 0.462 Sensitivity Contrafold: 0.437 Sfold: 0.387 Positive Predictive Value Contrafold: 0.573 Sfold: 0.552 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.535 Contrafold: 0.530 Sensitivity HotKnots: 0.474 Contrafold: 0.462 Positive Predictive Value HotKnots: 0.610 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 1.1061772363e-05	+ Contrafold vs CentroidFold Matthews Correlation Coefficient Contrafold: 0.488 CentroidFold: 0.483 Sensitivity Contrafold: 0.430 CentroidFold: 0.397 Positive Predictive Value Contrafold: 0.556 CentroidFold: 0.587 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 5.21776328505e-08	- TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.529 Contrafold: 0.515 Sensitivity TurboFold(seed): 0.434 Contrafold: 0.438 Positive Predictive Value TurboFold(seed): 0.650 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.509 MaxExpect: 0.503 Sensitivity Contrafold: 0.439 MaxExpect: 0.432 Positive Predictive Value Contrafold: 0.591 MaxExpect: 0.586 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 1.1061772363e-05	- RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.552 Contrafold: 0.547 Sensitivity RSpredict(20): 0.436 Contrafold: 0.485 Positive Predictive Value RSpredict(20): 0.703 Contrafold: 0.621 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.000741474702242	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.493 PknotsRG: 0.433 Sensitivity Contrafold: 0.430 PknotsRG: 0.387 Positive Predictive Value Contrafold: 0.565 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.85233844192e-08	- CMfinder(20) vs Contrafold Matthews Correlation Coefficient CMfinder(20): 0.521 Contrafold: 0.497 Sensitivity CMfinder(20): 0.366 Contrafold: 0.445 Positive Predictive Value CMfinder(20): 0.748 Contrafold: 0.563 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.40919803867e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.500 UNAFold: 0.442 Sensitivity Contrafold: 0.437 UNAFold: 0.390 Positive Predictive Value Contrafold: 0.573 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.488 ProbKnot: 0.478 Sensitivity Contrafold: 0.424 ProbKnot: 0.423 Positive Predictive Value Contrafold: 0.562 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 5.84585956207e-05	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.596 Cylofold: 0.554 Sensitivity Contrafold: 0.522 Cylofold: 0.463 Positive Predictive Value Contrafold: 0.688 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.500 RNAfold: 0.438 Sensitivity Contrafold: 0.437 RNAfold: 0.390 Positive Predictive Value Contrafold: 0.573 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.491 RNASampler(seed): 0.482 Sensitivity Contrafold: 0.429 RNASampler(seed): 0.342 Positive Predictive Value Contrafold: 0.566 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00243391354489	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.530 RNAsubopt: 0.509 Sensitivity Contrafold: 0.462 RNAsubopt: 0.452 Positive Predictive Value Contrafold: 0.611 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.539 Multilign(20): 0.534 Sensitivity Contrafold: 0.479 Multilign(20): 0.449 Positive Predictive Value Contrafold: 0.614 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00064555593904	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.481 Afold: 0.408 Sensitivity Contrafold: 0.422 Afold: 0.368 Positive Predictive Value Contrafold: 0.548 Afold: 0.453 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.530 RNAshapes: 0.499 Sensitivity Contrafold: 0.462 RNAshapes: 0.434 Positive Predictive Value Contrafold: 0.611 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.495 Fold: 0.457 Sensitivity Contrafold: 0.431 Fold: 0.406 Positive Predictive Value Contrafold: 0.569 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.500 McQFold: 0.363 Sensitivity Contrafold: 0.437 McQFold: 0.287 Positive Predictive Value Contrafold: 0.573 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.481 RNASLOpt: 0.427 Sensitivity Contrafold: 0.415 RNASLOpt: 0.341 Positive Predictive Value Contrafold: 0.562 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.536 Mastr(20): 0.500 Sensitivity Contrafold: 0.472 Mastr(20): 0.336 Positive Predictive Value Contrafold: 0.613 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.581 Multilign(seed): 0.556 Sensitivity Contrafold: 0.478 Multilign(seed): 0.432 Positive Predictive Value Contrafold: 0.713 Multilign(seed): 0.723 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.49320234536e-07	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.557 Pknots: 0.507 Sensitivity Contrafold: 0.485 Pknots: 0.454 Positive Predictive Value Contrafold: 0.645 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.542 Vsfold4: 0.451 Sensitivity Contrafold: 0.476 Vsfold4: 0.373 Positive Predictive Value Contrafold: 0.622 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.517 CRWrnafold: 0.467 Sensitivity Contrafold: 0.442 CRWrnafold: 0.410 Positive Predictive Value Contrafold: 0.612 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.586 Murlet(seed): 0.448 Sensitivity Contrafold: 0.505 Murlet(seed): 0.245 Positive Predictive Value Contrafold: 0.684 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.550 Vsfold5: 0.409 Sensitivity Contrafold: 0.483 Vsfold5: 0.346 Positive Predictive Value Contrafold: 0.632 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.533 MCFold: 0.385 Sensitivity Contrafold: 0.466 MCFold: 0.396 Positive Predictive Value Contrafold: 0.615 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.608 Alterna: 0.523 Sensitivity Contrafold: 0.512 Alterna: 0.449 Positive Predictive Value Contrafold: 0.732 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.603 RDfolder: 0.461 Sensitivity Contrafold: 0.512 RDfolder: 0.358 Positive Predictive Value Contrafold: 0.720 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.459 RNAwolf: 0.317 Sensitivity Contrafold: 0.394 RNAwolf: 0.293 Positive Predictive Value Contrafold: 0.537 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.483 NanoFolder: 0.272 Sensitivity Contrafold: 0.423 NanoFolder: 0.284 Positive Predictive Value Contrafold: 0.557 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.588 Carnac(seed): 0.392 Sensitivity Contrafold: 0.514 Carnac(seed): 0.172 Positive Predictive Value Contrafold: 0.673 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.571 RSpredict(seed): 0.337 Sensitivity Contrafold: 0.508 RSpredict(seed): 0.189 Positive Predictive Value Contrafold: 0.643 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.568 PPfold(seed): 0.148 Sensitivity Contrafold: 0.494 PPfold(seed): 0.032 Positive Predictive Value Contrafold: 0.659 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Contrafold: 0.649 Sensitivity PETfold_2.0(seed): 0.642 Contrafold: 0.547 Positive Predictive Value PETfold_2.0(seed): 0.924 Contrafold: 0.776 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs DAFS(20) Matthews Correlation Coefficient Contrafold: N/A DAFS(20): N/A Sensitivity Contrafold: N/A DAFS(20): N/A Positive Predictive Value Contrafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Contrafold: 0.482 Sensitivity PETfold_2.0(20): 0.509 Contrafold: 0.386 Positive Predictive Value PETfold_2.0(20): 0.829 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Contrafold Matthews Correlation Coefficient DAFS(seed): N/A Contrafold: N/A Sensitivity DAFS(seed): N/A Contrafold: N/A Positive Predictive Value DAFS(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.559 Mastr(seed): 0.023 Sensitivity Contrafold: 0.498 Mastr(seed): 0.002 Positive Predictive Value Contrafold: 0.632 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
Sfold	36 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Sfold: 0.558 Sensitivity CentroidAlifold(20): 0.529 Sfold: 0.466 Positive Predictive Value CentroidAlifold(20): 0.882 Sfold: 0.673 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Sfold: 0.505 Sensitivity PETfold_pre2.0(seed): 0.602 Sfold: 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Sfold: 0.601 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.656 Sfold: 0.560 Sensitivity RNAalifold(20): 0.511 Sfold: 0.466 Positive Predictive Value RNAalifold(20): 0.846 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.646 Sfold: 0.542 Sensitivity MXScarna(seed): 0.536 Sfold: 0.461 Positive Predictive Value MXScarna(seed): 0.779 Sfold: 0.638 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.663 Sfold: 0.526 Sensitivity PPfold(20): 0.528 Sfold: 0.439 Positive Predictive Value PPfold(20): 0.836 Sfold: 0.635 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	43 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.536 Sfold: 0.460 Sensitivity ContextFold: 0.440 Sfold: 0.387 Positive Predictive Value ContextFold: 0.654 Sfold: 0.548 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.612 Sfold: 0.560 Sensitivity RNASampler(20): 0.471 Sfold: 0.466 Positive Predictive Value RNASampler(20): 0.799 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Sfold: 0.500 Sensitivity PETfold_pre2.0(20): 0.530 Sfold: 0.416 Positive Predictive Value PETfold_pre2.0(20): 0.798 Sfold: 0.606 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	20 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.616 Sfold: 0.526 Sensitivity TurboFold(20): 0.508 Sfold: 0.439 Positive Predictive Value TurboFold(20): 0.752 Sfold: 0.635 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	38 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.611 Sfold: 0.560 Sensitivity MXScarna(20): 0.509 Sfold: 0.466 Positive Predictive Value MXScarna(20): 0.737 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.606 Sfold: 0.526 Sensitivity RNAalifold(seed): 0.427 Sfold: 0.446 Positive Predictive Value RNAalifold(seed): 0.861 Sfold: 0.622 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 7.51223576774e-08	38 Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.590 Sfold: 0.560 Sensitivity Murlet(20): 0.438 Sfold: 0.466 Positive Predictive Value Murlet(20): 0.799 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 Sfold: 0.538 Sensitivity CentroidAlifold(seed): 0.425 Sfold: 0.457 Positive Predictive Value CentroidAlifold(seed): 0.899 Sfold: 0.635 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.590 Sfold: 0.560 Sensitivity Carnac(20): 0.389 Sfold: 0.466 Positive Predictive Value Carnac(20): 0.899 Sfold: 0.677 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.513 Sfold: 0.468 Sensitivity IPknot: 0.411 Sfold: 0.393 Positive Predictive Value IPknot: 0.641 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Sfold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Sfold: 0.526 CentroidHomfold‑LAST: 0.512 Sensitivity Sfold: 0.431 CentroidHomfold‑LAST: 0.378 Positive Predictive Value Sfold: 0.646 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.00036811921398	87 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.500 Sfold: 0.462 Sensitivity Contrafold: 0.437 Sfold: 0.387 Positive Predictive Value Contrafold: 0.573 Sfold: 0.552 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.552 HotKnots: 0.535 Sensitivity Sfold: 0.459 HotKnots: 0.474 Positive Predictive Value Sfold: 0.669 HotKnots: 0.610 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.483 Sfold: 0.471 Sensitivity CentroidFold: 0.397 Sfold: 0.397 Positive Predictive Value CentroidFold: 0.587 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 8.67590017402e-07	= TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.529 Sfold: 0.524 Sensitivity TurboFold(seed): 0.434 Sfold: 0.423 Positive Predictive Value TurboFold(seed): 0.650 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00422458200172	- MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.503 Sfold: 0.490 Sensitivity MaxExpect: 0.432 Sfold: 0.407 Positive Predictive Value MaxExpect: 0.586 Sfold: 0.590 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.563 RSpredict(20): 0.552 Sensitivity Sfold: 0.473 RSpredict(20): 0.436 Positive Predictive Value Sfold: 0.675 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.000207424631753	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.461 PknotsRG: 0.433 Sensitivity Sfold: 0.385 PknotsRG: 0.387 Positive Predictive Value Sfold: 0.552 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs Sfold Matthews Correlation Coefficient CMfinder(20): 0.521 Sfold: 0.502 Sensitivity CMfinder(20): 0.366 Sfold: 0.427 Positive Predictive Value CMfinder(20): 0.748 Sfold: 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.23704939182e-05	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.462 UNAFold: 0.442 Sensitivity Sfold: 0.387 UNAFold: 0.390 Positive Predictive Value Sfold: 0.552 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.497 ProbKnot: 0.478 Sensitivity Sfold: 0.420 ProbKnot: 0.423 Positive Predictive Value Sfold: 0.589 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.570 Cylofold: 0.554 Sensitivity Sfold: 0.474 Cylofold: 0.463 Positive Predictive Value Sfold: 0.693 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.462 RNAfold: 0.438 Sensitivity Sfold: 0.387 RNAfold: 0.390 Positive Predictive Value Sfold: 0.552 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.505 RNASampler(seed): 0.482 Sensitivity Sfold: 0.421 RNASampler(seed): 0.342 Positive Predictive Value Sfold: 0.610 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.552 RNAsubopt: 0.509 Sensitivity Sfold: 0.459 RNAsubopt: 0.452 Positive Predictive Value Sfold: 0.669 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.539 Multilign(20): 0.534 Sensitivity Sfold: 0.457 Multilign(20): 0.449 Positive Predictive Value Sfold: 0.643 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00419758437992	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.429 Afold: 0.408 Sensitivity Sfold: 0.361 Afold: 0.368 Positive Predictive Value Sfold: 0.511 Afold: 0.453 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.552 RNAshapes: 0.499 Sensitivity Sfold: 0.459 RNAshapes: 0.434 Positive Predictive Value Sfold: 0.669 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.501 Fold: 0.457 Sensitivity Sfold: 0.424 Fold: 0.406 Positive Predictive Value Sfold: 0.593 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.462 McQFold: 0.363 Sensitivity Sfold: 0.387 McQFold: 0.287 Positive Predictive Value Sfold: 0.552 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.508 RNASLOpt: 0.427 Sensitivity Sfold: 0.418 RNASLOpt: 0.341 Positive Predictive Value Sfold: 0.623 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.560 Mastr(20): 0.500 Sensitivity Sfold: 0.466 Mastr(20): 0.336 Positive Predictive Value Sfold: 0.677 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.556 Sfold: 0.556 Sensitivity Multilign(seed): 0.432 Sfold: 0.446 Positive Predictive Value Multilign(seed): 0.723 Sfold: 0.701 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0300471658456	+ Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.574 Pknots: 0.507 Sensitivity Sfold: 0.476 Pknots: 0.454 Positive Predictive Value Sfold: 0.697 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.552 Vsfold4: 0.451 Sensitivity Sfold: 0.462 Vsfold4: 0.373 Positive Predictive Value Sfold: 0.664 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.508 CRWrnafold: 0.467 Sensitivity Sfold: 0.421 CRWrnafold: 0.410 Positive Predictive Value Sfold: 0.621 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 8.18166149643e-09	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.587 Murlet(seed): 0.448 Sensitivity Sfold: 0.478 Murlet(seed): 0.245 Positive Predictive Value Sfold: 0.725 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.546 Vsfold5: 0.409 Sensitivity Sfold: 0.455 Vsfold5: 0.346 Positive Predictive Value Sfold: 0.659 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.569 MCFold: 0.385 Sensitivity Sfold: 0.475 MCFold: 0.396 Positive Predictive Value Sfold: 0.689 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.585 Alterna: 0.523 Sensitivity Sfold: 0.474 Alterna: 0.449 Positive Predictive Value Sfold: 0.732 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.567 RDfolder: 0.461 Sensitivity Sfold: 0.460 RDfolder: 0.358 Positive Predictive Value Sfold: 0.707 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.468 RNAwolf: 0.317 Sensitivity Sfold: 0.393 RNAwolf: 0.293 Positive Predictive Value Sfold: 0.559 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.491 NanoFolder: 0.272 Sensitivity Sfold: 0.411 NanoFolder: 0.284 Positive Predictive Value Sfold: 0.594 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.554 Carnac(seed): 0.392 Sensitivity Sfold: 0.469 Carnac(seed): 0.172 Positive Predictive Value Sfold: 0.657 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.541 RSpredict(seed): 0.337 Sensitivity Sfold: 0.461 RSpredict(seed): 0.189 Positive Predictive Value Sfold: 0.635 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.544 PPfold(seed): 0.148 Sensitivity Sfold: 0.450 PPfold(seed): 0.032 Positive Predictive Value Sfold: 0.664 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Sfold: 0.673 Sensitivity PETfold_2.0(seed): 0.642 Sfold: 0.537 Positive Predictive Value PETfold_2.0(seed): 0.924 Sfold: 0.850 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Sfold vs DAFS(20) Matthews Correlation Coefficient Sfold: N/A DAFS(20): N/A Sensitivity Sfold: N/A DAFS(20): N/A Positive Predictive Value Sfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Sfold: 0.514 Sensitivity PETfold_2.0(20): 0.509 Sfold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs Sfold Matthews Correlation Coefficient DAFS(seed): N/A Sfold: N/A Sensitivity DAFS(seed): N/A Sfold: N/A Positive Predictive Value DAFS(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.560 Mastr(seed): 0.023 Sensitivity Sfold: 0.472 Mastr(seed): 0.002 Positive Predictive Value Sfold: 0.669 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
HotKnots	36 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.682 HotKnots: 0.531 Sensitivity CentroidAlifold(20): 0.529 HotKnots: 0.475 Positive Predictive Value CentroidAlifold(20): 0.882 HotKnots: 0.599 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 HotKnots: 0.504 Sensitivity PETfold_pre2.0(seed): 0.595 HotKnots: 0.450 Positive Predictive Value PETfold_pre2.0(seed): 0.879 HotKnots: 0.570 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.656 HotKnots: 0.533 Sensitivity RNAalifold(20): 0.511 HotKnots: 0.475 Positive Predictive Value RNAalifold(20): 0.846 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.638 HotKnots: 0.543 Sensitivity MXScarna(seed): 0.522 HotKnots: 0.491 Positive Predictive Value MXScarna(seed): 0.783 HotKnots: 0.606 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.663 HotKnots: 0.497 Sensitivity PPfold(20): 0.528 HotKnots: 0.443 Positive Predictive Value PPfold(20): 0.836 HotKnots: 0.564 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	41 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.578 HotKnots: 0.489 Sensitivity ContextFold: 0.471 HotKnots: 0.432 Positive Predictive Value ContextFold: 0.713 HotKnots: 0.559 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.612 HotKnots: 0.533 Sensitivity RNASampler(20): 0.471 HotKnots: 0.475 Positive Predictive Value RNASampler(20): 0.799 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 HotKnots: 0.474 Sensitivity PETfold_pre2.0(20): 0.530 HotKnots: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.798 HotKnots: 0.535 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.30549897711e-08	20 TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.616 HotKnots: 0.497 Sensitivity TurboFold(20): 0.508 HotKnots: 0.443 Positive Predictive Value TurboFold(20): 0.752 HotKnots: 0.564 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.611 HotKnots: 0.533 Sensitivity MXScarna(20): 0.509 HotKnots: 0.475 Positive Predictive Value MXScarna(20): 0.737 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.549 HotKnots: 0.518 Sensitivity RNAalifold(seed): 0.338 HotKnots: 0.474 Positive Predictive Value RNAalifold(seed): 0.895 HotKnots: 0.571 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.6410608252e-08	38 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.590 HotKnots: 0.533 Sensitivity Murlet(20): 0.438 HotKnots: 0.475 Positive Predictive Value Murlet(20): 0.799 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 HotKnots: 0.537 Sensitivity CentroidAlifold(seed): 0.367 HotKnots: 0.485 Positive Predictive Value CentroidAlifold(seed): 0.923 HotKnots: 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.590 HotKnots: 0.533 Sensitivity Carnac(20): 0.389 HotKnots: 0.475 Positive Predictive Value Carnac(20): 0.899 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.542 HotKnots: 0.501 Sensitivity IPknot: 0.445 HotKnots: 0.440 Positive Predictive Value IPknot: 0.665 HotKnots: 0.575 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.518 CentroidHomfold‑LAST: 0.512 Sensitivity HotKnots: 0.450 CentroidHomfold‑LAST: 0.378 Positive Predictive Value HotKnots: 0.602 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.000609097173132	82 HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.535 Contrafold: 0.530 Sensitivity HotKnots: 0.474 Contrafold: 0.462 Positive Predictive Value HotKnots: 0.610 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 1.1061772363e-05	82 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.552 HotKnots: 0.535 Sensitivity Sfold: 0.459 HotKnots: 0.474 Positive Predictive Value Sfold: 0.669 HotKnots: 0.610 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ HotKnots vs CentroidFold Matthews Correlation Coefficient HotKnots: 0.537 CentroidFold: 0.527 Sensitivity HotKnots: 0.478 CentroidFold: 0.442 Positive Predictive Value HotKnots: 0.608 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 1.02208072244e-07	- TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.529 HotKnots: 0.502 Sensitivity TurboFold(seed): 0.434 HotKnots: 0.452 Positive Predictive Value TurboFold(seed): 0.650 HotKnots: 0.564 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.17605609581e-07	= HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.534 MaxExpect: 0.529 Sensitivity HotKnots: 0.475 MaxExpect: 0.458 Positive Predictive Value HotKnots: 0.604 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.00238364898467	- RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.552 HotKnots: 0.535 Sensitivity RSpredict(20): 0.436 HotKnots: 0.480 Positive Predictive Value RSpredict(20): 0.703 HotKnots: 0.600 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.535 PknotsRG: 0.530 Sensitivity HotKnots: 0.474 PknotsRG: 0.468 Positive Predictive Value HotKnots: 0.610 PknotsRG: 0.605 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 4.32815307575e-07	- CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.521 HotKnots: 0.486 Sensitivity CMfinder(20): 0.366 HotKnots: 0.431 Positive Predictive Value CMfinder(20): 0.748 HotKnots: 0.555 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ HotKnots vs UNAFold Matthews Correlation Coefficient HotKnots: 0.535 UNAFold: 0.534 Sensitivity HotKnots: 0.474 UNAFold: 0.466 Positive Predictive Value HotKnots: 0.610 UNAFold: 0.617 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.000857786362802	+ HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.528 ProbKnot: 0.515 Sensitivity HotKnots: 0.471 ProbKnot: 0.458 Positive Predictive Value HotKnots: 0.596 ProbKnot: 0.583 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 2.23046259944e-06	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.571 Cylofold: 0.554 Sensitivity HotKnots: 0.505 Cylofold: 0.463 Positive Predictive Value HotKnots: 0.653 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.535 RNAfold: 0.524 Sensitivity HotKnots: 0.474 RNAfold: 0.460 Positive Predictive Value HotKnots: 0.610 RNAfold: 0.601 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.482 HotKnots: 0.441 Sensitivity RNASampler(seed): 0.342 HotKnots: 0.410 Positive Predictive Value RNASampler(seed): 0.684 HotKnots: 0.479 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.535 RNAsubopt: 0.509 Sensitivity HotKnots: 0.474 RNAsubopt: 0.452 Positive Predictive Value HotKnots: 0.610 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.538 Multilign(20): 0.534 Sensitivity HotKnots: 0.477 Multilign(20): 0.449 Positive Predictive Value HotKnots: 0.613 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000108864879631	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.515 Afold: 0.488 Sensitivity HotKnots: 0.464 Afold: 0.439 Positive Predictive Value HotKnots: 0.577 Afold: 0.547 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.535 RNAshapes: 0.499 Sensitivity HotKnots: 0.474 RNAshapes: 0.434 Positive Predictive Value HotKnots: 0.610 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.535 Fold: 0.501 Sensitivity HotKnots: 0.477 Fold: 0.444 Positive Predictive Value HotKnots: 0.603 Fold: 0.570 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.535 McQFold: 0.481 Sensitivity HotKnots: 0.474 McQFold: 0.409 Positive Predictive Value HotKnots: 0.610 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.489 RNASLOpt: 0.427 Sensitivity HotKnots: 0.432 RNASLOpt: 0.341 Positive Predictive Value HotKnots: 0.559 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.533 Mastr(20): 0.500 Sensitivity HotKnots: 0.475 Mastr(20): 0.336 Positive Predictive Value HotKnots: 0.604 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.48494289621e-08	- Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.556 HotKnots: 0.503 Sensitivity Multilign(seed): 0.432 HotKnots: 0.443 Positive Predictive Value Multilign(seed): 0.723 HotKnots: 0.578 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.08682696847e-09	+ HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.556 Pknots: 0.507 Sensitivity HotKnots: 0.491 Pknots: 0.454 Positive Predictive Value HotKnots: 0.635 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.543 Vsfold4: 0.451 Sensitivity HotKnots: 0.482 Vsfold4: 0.373 Positive Predictive Value HotKnots: 0.617 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.534 CRWrnafold: 0.467 Sensitivity HotKnots: 0.481 CRWrnafold: 0.410 Positive Predictive Value HotKnots: 0.599 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.539 Murlet(seed): 0.448 Sensitivity HotKnots: 0.481 Murlet(seed): 0.245 Positive Predictive Value HotKnots: 0.609 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.540 Vsfold5: 0.409 Sensitivity HotKnots: 0.480 Vsfold5: 0.346 Positive Predictive Value HotKnots: 0.613 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.545 MCFold: 0.385 Sensitivity HotKnots: 0.486 MCFold: 0.396 Positive Predictive Value HotKnots: 0.617 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.588 Alterna: 0.523 Sensitivity HotKnots: 0.504 Alterna: 0.449 Positive Predictive Value HotKnots: 0.694 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.579 RDfolder: 0.461 Sensitivity HotKnots: 0.502 RDfolder: 0.358 Positive Predictive Value HotKnots: 0.677 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.501 RNAwolf: 0.323 Sensitivity HotKnots: 0.440 RNAwolf: 0.301 Positive Predictive Value HotKnots: 0.575 RNAwolf: 0.354 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.499 NanoFolder: 0.272 Sensitivity HotKnots: 0.443 NanoFolder: 0.284 Positive Predictive Value HotKnots: 0.569 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.564 Carnac(seed): 0.179 Sensitivity HotKnots: 0.506 Carnac(seed): 0.032 Positive Predictive Value HotKnots: 0.634 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.539 RSpredict(seed): 0.178 Sensitivity HotKnots: 0.489 RSpredict(seed): 0.075 Positive Predictive Value HotKnots: 0.600 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.520 PPfold(seed): 0.148 Sensitivity HotKnots: 0.463 PPfold(seed): 0.032 Positive Predictive Value HotKnots: 0.591 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 HotKnots: 0.682 Sensitivity PETfold_2.0(seed): 0.642 HotKnots: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 HotKnots: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs DAFS(20) Matthews Correlation Coefficient HotKnots: N/A DAFS(20): N/A Sensitivity HotKnots: N/A DAFS(20): N/A Positive Predictive Value HotKnots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 HotKnots: 0.541 Sensitivity PETfold_2.0(20): 0.509 HotKnots: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 HotKnots: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs DAFS(seed) Matthews Correlation Coefficient HotKnots: N/A DAFS(seed): N/A Sensitivity HotKnots: N/A DAFS(seed): N/A Positive Predictive Value HotKnots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.538 Mastr(seed): 0.023 Sensitivity HotKnots: 0.485 Mastr(seed): 0.002 Positive Predictive Value HotKnots: 0.603 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidFold	36 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 CentroidFold: 0.542 Sensitivity CentroidAlifold(20): 0.529 CentroidFold: 0.459 Positive Predictive Value CentroidAlifold(20): 0.882 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 CentroidFold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.602 CentroidFold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 CentroidFold: 0.625 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	36 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.656 CentroidFold: 0.542 Sensitivity RNAalifold(20): 0.513 CentroidFold: 0.459 Positive Predictive Value RNAalifold(20): 0.841 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.644 CentroidFold: 0.556 Sensitivity MXScarna(seed): 0.534 CentroidFold: 0.474 Positive Predictive Value MXScarna(seed): 0.778 CentroidFold: 0.654 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.663 CentroidFold: 0.474 Sensitivity PPfold(20): 0.528 CentroidFold: 0.400 Positive Predictive Value PPfold(20): 0.836 CentroidFold: 0.568 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	43 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.536 CentroidFold: 0.437 Sensitivity ContextFold: 0.440 CentroidFold: 0.349 Positive Predictive Value ContextFold: 0.654 CentroidFold: 0.550 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.613 CentroidFold: 0.542 Sensitivity RNASampler(20): 0.475 CentroidFold: 0.459 Positive Predictive Value RNASampler(20): 0.795 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 CentroidFold: 0.445 Sensitivity PETfold_pre2.0(20): 0.530 CentroidFold: 0.376 Positive Predictive Value PETfold_pre2.0(20): 0.798 CentroidFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.91763127434e-08	20 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.616 CentroidFold: 0.474 Sensitivity TurboFold(20): 0.508 CentroidFold: 0.400 Positive Predictive Value TurboFold(20): 0.752 CentroidFold: 0.568 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	36 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.611 CentroidFold: 0.542 Sensitivity MXScarna(20): 0.510 CentroidFold: 0.459 Positive Predictive Value MXScarna(20): 0.736 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs CentroidFold Matthews Correlation Coefficient RNAalifold(seed): 0.606 CentroidFold: 0.554 Sensitivity RNAalifold(seed): 0.428 CentroidFold: 0.466 Positive Predictive Value RNAalifold(seed): 0.860 CentroidFold: 0.658 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	36 Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.589 CentroidFold: 0.542 Sensitivity Murlet(20): 0.439 CentroidFold: 0.459 Positive Predictive Value Murlet(20): 0.795 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 CentroidFold: 0.555 Sensitivity CentroidAlifold(seed): 0.425 CentroidFold: 0.474 Positive Predictive Value CentroidAlifold(seed): 0.899 CentroidFold: 0.653 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 Carnac(20) vs CentroidFold Matthews Correlation Coefficient Carnac(20): 0.592 CentroidFold: 0.542 Sensitivity Carnac(20): 0.392 CentroidFold: 0.459 Positive Predictive Value Carnac(20): 0.898 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.513 CentroidFold: 0.446 Sensitivity IPknot: 0.411 CentroidFold: 0.356 Positive Predictive Value IPknot: 0.641 CentroidFold: 0.560 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 CentroidFold: 0.473 Sensitivity CentroidHomfold‑LAST: 0.378 CentroidFold: 0.386 Positive Predictive Value CentroidHomfold‑LAST: 0.699 CentroidFold: 0.585 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 Contrafold vs CentroidFold Matthews Correlation Coefficient Contrafold: 0.488 CentroidFold: 0.483 Sensitivity Contrafold: 0.430 CentroidFold: 0.397 Positive Predictive Value Contrafold: 0.556 CentroidFold: 0.587 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 5.21776328505e-08	81 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.483 Sfold: 0.471 Sensitivity CentroidFold: 0.397 Sfold: 0.397 Positive Predictive Value CentroidFold: 0.587 Sfold: 0.559 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 8.67590017402e-07	77 HotKnots vs CentroidFold Matthews Correlation Coefficient HotKnots: 0.537 CentroidFold: 0.527 Sensitivity HotKnots: 0.478 CentroidFold: 0.442 Positive Predictive Value HotKnots: 0.608 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 1.02208072244e-07		- TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.529 CentroidFold: 0.494 Sensitivity TurboFold(seed): 0.434 CentroidFold: 0.393 Positive Predictive Value TurboFold(seed): 0.650 CentroidFold: 0.627 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.10032755566e-08	= CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.503 MaxExpect: 0.503 Sensitivity CentroidFold: 0.406 MaxExpect: 0.432 Positive Predictive Value CentroidFold: 0.625 MaxExpect: 0.586 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 0.686772471119	= RSpredict(20) vs CentroidFold Matthews Correlation Coefficient RSpredict(20): 0.549 CentroidFold: 0.545 Sensitivity RSpredict(20): 0.434 CentroidFold: 0.463 Positive Predictive Value RSpredict(20): 0.700 CentroidFold: 0.646 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.484584865998	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.473 PknotsRG: 0.439 Sensitivity CentroidFold: 0.388 PknotsRG: 0.396 Positive Predictive Value CentroidFold: 0.577 PknotsRG: 0.487 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidFold: 0.393 Sensitivity CMfinder(20): 0.366 CentroidFold: 0.344 Positive Predictive Value CMfinder(20): 0.748 CentroidFold: 0.458 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.483 UNAFold: 0.449 Sensitivity CentroidFold: 0.397 UNAFold: 0.400 Positive Predictive Value CentroidFold: 0.587 UNAFold: 0.504 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.482 ProbKnot: 0.478 Sensitivity CentroidFold: 0.393 ProbKnot: 0.423 Positive Predictive Value CentroidFold: 0.594 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.13872543599e-05	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.583 Cylofold: 0.554 Sensitivity CentroidFold: 0.491 Cylofold: 0.463 Positive Predictive Value CentroidFold: 0.699 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.483 RNAfold: 0.442 Sensitivity CentroidFold: 0.397 RNAfold: 0.397 Positive Predictive Value CentroidFold: 0.587 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.514 RNASampler(seed): 0.467 Sensitivity CentroidFold: 0.420 RNASampler(seed): 0.328 Positive Predictive Value CentroidFold: 0.634 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.527 RNAsubopt: 0.514 Sensitivity CentroidFold: 0.442 RNAsubopt: 0.458 Positive Predictive Value CentroidFold: 0.634 RNAsubopt: 0.581 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.534 CentroidFold: 0.476 Sensitivity Multilign(20): 0.449 CentroidFold: 0.410 Positive Predictive Value Multilign(20): 0.642 CentroidFold: 0.559 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.462 Afold: 0.402 Sensitivity CentroidFold: 0.381 Afold: 0.369 Positive Predictive Value CentroidFold: 0.561 Afold: 0.439 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.527 RNAshapes: 0.501 Sensitivity CentroidFold: 0.442 RNAshapes: 0.439 Positive Predictive Value CentroidFold: 0.634 RNAshapes: 0.577 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.490 Fold: 0.457 Sensitivity CentroidFold: 0.400 Fold: 0.406 Positive Predictive Value CentroidFold: 0.602 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.483 McQFold: 0.373 Sensitivity CentroidFold: 0.397 McQFold: 0.293 Positive Predictive Value CentroidFold: 0.587 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.447 RNASLOpt: 0.427 Sensitivity CentroidFold: 0.365 RNASLOpt: 0.341 Positive Predictive Value CentroidFold: 0.553 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.542 Mastr(20): 0.496 Sensitivity CentroidFold: 0.459 Mastr(20): 0.333 Positive Predictive Value CentroidFold: 0.644 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.556 CentroidFold: 0.546 Sensitivity Multilign(seed): 0.432 CentroidFold: 0.418 Positive Predictive Value Multilign(seed): 0.723 CentroidFold: 0.720 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0325256581203	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.555 Pknots: 0.514 Sensitivity CentroidFold: 0.466 Pknots: 0.462 Positive Predictive Value CentroidFold: 0.666 Pknots: 0.579 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.549 Vsfold4: 0.451 Sensitivity CentroidFold: 0.467 Vsfold4: 0.375 Positive Predictive Value CentroidFold: 0.650 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.522 CRWrnafold: 0.467 Sensitivity CentroidFold: 0.428 CRWrnafold: 0.410 Positive Predictive Value CentroidFold: 0.645 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.565 Murlet(seed): 0.447 Sensitivity CentroidFold: 0.461 Murlet(seed): 0.244 Positive Predictive Value CentroidFold: 0.697 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.552 Vsfold5: 0.412 Sensitivity CentroidFold: 0.470 Vsfold5: 0.350 Positive Predictive Value CentroidFold: 0.654 Vsfold5: 0.492 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.534 MCFold: 0.385 Sensitivity CentroidFold: 0.449 MCFold: 0.398 Positive Predictive Value CentroidFold: 0.642 MCFold: 0.381 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.634 Alterna: 0.518 Sensitivity CentroidFold: 0.522 Alterna: 0.452 Positive Predictive Value CentroidFold: 0.778 Alterna: 0.605 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.629 RDfolder: 0.453 Sensitivity CentroidFold: 0.521 RDfolder: 0.354 Positive Predictive Value CentroidFold: 0.768 RDfolder: 0.589 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.446 RNAwolf: 0.317 Sensitivity CentroidFold: 0.356 RNAwolf: 0.293 Positive Predictive Value CentroidFold: 0.560 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.469 NanoFolder: 0.272 Sensitivity CentroidFold: 0.393 NanoFolder: 0.284 Positive Predictive Value CentroidFold: 0.565 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.574 Carnac(seed): 0.385 Sensitivity CentroidFold: 0.480 Carnac(seed): 0.167 Positive Predictive Value CentroidFold: 0.687 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.557 RSpredict(seed): 0.334 Sensitivity CentroidFold: 0.476 RSpredict(seed): 0.187 Positive Predictive Value CentroidFold: 0.654 RSpredict(seed): 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.511 PPfold(seed): 0.148 Sensitivity CentroidFold: 0.426 PPfold(seed): 0.032 Positive Predictive Value CentroidFold: 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	? CMfinder(seed) vs CentroidFold Matthews Correlation Coefficient CMfinder(seed): N/A CentroidFold: N/A Sensitivity CMfinder(seed): N/A CentroidFold: N/A Positive Predictive Value CMfinder(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidFold: 0.506 Sensitivity PETfold_2.0(seed): 0.642 CentroidFold: 0.421 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidFold: 0.615 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs DAFS(20) Matthews Correlation Coefficient CentroidFold: N/A DAFS(20): N/A Sensitivity CentroidFold: N/A DAFS(20): N/A Positive Predictive Value CentroidFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidFold: 0.467 Sensitivity PETfold_2.0(20): 0.509 CentroidFold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CentroidFold Matthews Correlation Coefficient DAFS(seed): N/A CentroidFold: N/A Sensitivity DAFS(seed): N/A CentroidFold: N/A Positive Predictive Value DAFS(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.551 Mastr(seed): 0.024 Sensitivity CentroidFold: 0.472 Mastr(seed): 0.002 Positive Predictive Value CentroidFold: 0.649 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(seed)	10 CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.567 TurboFold(seed): 0.484 Sensitivity CentroidAlifold(20): 0.382 TurboFold(seed): 0.393 Positive Predictive Value CentroidAlifold(20): 0.848 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	12 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.645 TurboFold(seed): 0.504 Sensitivity PETfold_pre2.0(seed): 0.511 TurboFold(seed): 0.416 Positive Predictive Value PETfold_pre2.0(seed): 0.818 TurboFold(seed): 0.616 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08	10 RNAalifold(20) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.527 TurboFold(seed): 0.484 Sensitivity RNAalifold(20): 0.393 TurboFold(seed): 0.393 Positive Predictive Value RNAalifold(20): 0.711 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.22791024781e-09	14 MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.539 TurboFold(seed): 0.529 Sensitivity MXScarna(seed): 0.413 TurboFold(seed): 0.434 Positive Predictive Value MXScarna(seed): 0.709 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.10997767043e-07	10 PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.531 TurboFold(seed): 0.484 Sensitivity PPfold(20): 0.393 TurboFold(seed): 0.393 Positive Predictive Value PPfold(20): 0.722 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	12 TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.504 ContextFold: 0.480 Sensitivity TurboFold(seed): 0.416 ContextFold: 0.385 Positive Predictive Value TurboFold(seed): 0.616 ContextFold: 0.605 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.58782420473e-08	10 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.498 TurboFold(seed): 0.484 Sensitivity RNASampler(20): 0.371 TurboFold(seed): 0.393 Positive Predictive Value RNASampler(20): 0.675 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.29209047668e-09	8 PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.488 TurboFold(seed): 0.437 Sensitivity PETfold_pre2.0(20): 0.375 TurboFold(seed): 0.358 Positive Predictive Value PETfold_pre2.0(20): 0.639 TurboFold(seed): 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.491 TurboFold(seed): 0.484 Sensitivity TurboFold(20): 0.393 TurboFold(seed): 0.393 Positive Predictive Value TurboFold(20): 0.619 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.10218298521e-08	10 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.484 MXScarna(20): 0.478 Sensitivity TurboFold(seed): 0.393 MXScarna(20): 0.371 Positive Predictive Value TurboFold(seed): 0.601 MXScarna(20): 0.622 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.34181747534e-06	13 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.527 TurboFold(seed): 0.508 Sensitivity RNAalifold(seed): 0.320 TurboFold(seed): 0.416 Positive Predictive Value RNAalifold(seed): 0.874 TurboFold(seed): 0.626 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.45609004183e-07	10 Murlet(20) vs TurboFold(seed) Matthews Correlation Coefficient Murlet(20): 0.494 TurboFold(seed): 0.484 Sensitivity Murlet(20): 0.354 TurboFold(seed): 0.393 Positive Predictive Value Murlet(20): 0.694 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.2838375299e-05	14 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.614 TurboFold(seed): 0.529 Sensitivity CentroidAlifold(seed): 0.397 TurboFold(seed): 0.434 Positive Predictive Value CentroidAlifold(seed): 0.956 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	10 Carnac(20) vs TurboFold(seed) Matthews Correlation Coefficient Carnac(20): 0.485 TurboFold(seed): 0.484 Sensitivity Carnac(20): 0.272 TurboFold(seed): 0.393 Positive Predictive Value Carnac(20): 0.868 TurboFold(seed): 0.601 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.537823689986	14 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.535 TurboFold(seed): 0.529 Sensitivity IPknot: 0.431 TurboFold(seed): 0.434 Positive Predictive Value IPknot: 0.670 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00148733745706	12 TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.509 CentroidHomfold‑LAST: 0.492 Sensitivity TurboFold(seed): 0.421 CentroidHomfold‑LAST: 0.404 Positive Predictive Value TurboFold(seed): 0.622 CentroidHomfold‑LAST: 0.605 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.17451270932e-06	14 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.529 Contrafold: 0.515 Sensitivity TurboFold(seed): 0.434 Contrafold: 0.438 Positive Predictive Value TurboFold(seed): 0.650 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	14 TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.529 Sfold: 0.524 Sensitivity TurboFold(seed): 0.434 Sfold: 0.423 Positive Predictive Value TurboFold(seed): 0.650 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00422458200172	14 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.529 HotKnots: 0.502 Sensitivity TurboFold(seed): 0.434 HotKnots: 0.452 Positive Predictive Value TurboFold(seed): 0.650 HotKnots: 0.564 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.17605609581e-07	14 TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.529 CentroidFold: 0.494 Sensitivity TurboFold(seed): 0.434 CentroidFold: 0.393 Positive Predictive Value TurboFold(seed): 0.650 CentroidFold: 0.627 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.10032755566e-08		+ TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.529 MaxExpect: 0.484 Sensitivity TurboFold(seed): 0.434 MaxExpect: 0.405 Positive Predictive Value TurboFold(seed): 0.650 MaxExpect: 0.584 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.484 RSpredict(20): 0.394 Sensitivity TurboFold(seed): 0.393 RSpredict(20): 0.302 Positive Predictive Value TurboFold(seed): 0.601 RSpredict(20): 0.521 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	- PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.532 TurboFold(seed): 0.529 Sensitivity PknotsRG: 0.472 TurboFold(seed): 0.434 Positive Predictive Value PknotsRG: 0.605 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00020716383404	? CMfinder(20) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(20): 0.296 TurboFold(seed): 0.290 Sensitivity CMfinder(20): 0.203 TurboFold(seed): 0.261 Positive Predictive Value CMfinder(20): 0.438 TurboFold(seed): 0.327 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.529 UNAFold: 0.466 Sensitivity TurboFold(seed): 0.434 UNAFold: 0.407 Positive Predictive Value TurboFold(seed): 0.650 UNAFold: 0.541 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.529 ProbKnot: 0.479 Sensitivity TurboFold(seed): 0.434 ProbKnot: 0.423 Positive Predictive Value TurboFold(seed): 0.650 ProbKnot: 0.549 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.02533530638e-08	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.580 TurboFold(seed): 0.578 Sensitivity Cylofold: 0.462 TurboFold(seed): 0.448 Positive Predictive Value Cylofold: 0.737 TurboFold(seed): 0.754 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAfold: 0.502 Sensitivity TurboFold(seed): 0.434 RNAfold: 0.440 Positive Predictive Value TurboFold(seed): 0.650 RNAfold: 0.580 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.45805449719e-08	? TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.409 RNASampler(seed): 0.404 Sensitivity TurboFold(seed): 0.342 RNASampler(seed): 0.281 Positive Predictive Value TurboFold(seed): 0.495 RNASampler(seed): 0.585 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAsubopt: 0.467 Sensitivity TurboFold(seed): 0.434 RNAsubopt: 0.413 Positive Predictive Value TurboFold(seed): 0.650 RNAsubopt: 0.534 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.498 Multilign(20): 0.460 Sensitivity TurboFold(seed): 0.413 Multilign(20): 0.388 Positive Predictive Value TurboFold(seed): 0.606 Multilign(20): 0.553 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.414 TurboFold(seed): 0.326 Sensitivity Afold: 0.374 TurboFold(seed): 0.281 Positive Predictive Value Afold: 0.464 TurboFold(seed): 0.386 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAshapes: 0.499 Sensitivity TurboFold(seed): 0.434 RNAshapes: 0.438 Positive Predictive Value TurboFold(seed): 0.650 RNAshapes: 0.575 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.529 Fold: 0.432 Sensitivity TurboFold(seed): 0.434 Fold: 0.380 Positive Predictive Value TurboFold(seed): 0.650 Fold: 0.497 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.529 McQFold: 0.490 Sensitivity TurboFold(seed): 0.434 McQFold: 0.425 Positive Predictive Value TurboFold(seed): 0.650 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.96094765137e-08	+ TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.504 RNASLOpt: 0.430 Sensitivity TurboFold(seed): 0.416 RNASLOpt: 0.356 Positive Predictive Value TurboFold(seed): 0.616 RNASLOpt: 0.525 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.38194587311e-08	+ TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.484 Mastr(20): 0.443 Sensitivity TurboFold(seed): 0.393 Mastr(20): 0.245 Positive Predictive Value TurboFold(seed): 0.601 Mastr(20): 0.809 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.26497248087e-08	? TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.555 Multilign(seed): 0.518 Sensitivity TurboFold(seed): 0.442 Multilign(seed): 0.396 Positive Predictive Value TurboFold(seed): 0.704 Multilign(seed): 0.684 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.529 Pknots: 0.455 Sensitivity TurboFold(seed): 0.434 Pknots: 0.413 Positive Predictive Value TurboFold(seed): 0.650 Pknots: 0.508 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.492 Vsfold4: 0.369 Sensitivity TurboFold(seed): 0.408 Vsfold4: 0.303 Positive Predictive Value TurboFold(seed): 0.599 Vsfold4: 0.458 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.4651262096e-08	? CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 TurboFold(seed): 0.483 Sensitivity CRWrnafold: 0.428 TurboFold(seed): 0.397 Positive Predictive Value CRWrnafold: 0.554 TurboFold(seed): 0.595 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.508 Murlet(seed): 0.442 Sensitivity TurboFold(seed): 0.416 Murlet(seed): 0.237 Positive Predictive Value TurboFold(seed): 0.626 Murlet(seed): 0.831 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.12262428713e-08	+ TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.509 Vsfold5: 0.355 Sensitivity TurboFold(seed): 0.421 Vsfold5: 0.311 Positive Predictive Value TurboFold(seed): 0.622 Vsfold5: 0.413 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.491 MCFold: 0.355 Sensitivity TurboFold(seed): 0.403 MCFold: 0.369 Positive Predictive Value TurboFold(seed): 0.604 MCFold: 0.350 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.67657656842e-08	? Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.540 TurboFold(seed): 0.514 Sensitivity Alterna: 0.448 TurboFold(seed): 0.417 Positive Predictive Value Alterna: 0.662 TurboFold(seed): 0.645 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.553 RDfolder: 0.392 Sensitivity TurboFold(seed): 0.426 RDfolder: 0.284 Positive Predictive Value TurboFold(seed): 0.728 RDfolder: 0.556 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAwolf: 0.297 Sensitivity TurboFold(seed): 0.434 RNAwolf: 0.282 Positive Predictive Value TurboFold(seed): 0.650 RNAwolf: 0.321 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.435 NanoFolder: 0.306 Sensitivity TurboFold(seed): 0.369 NanoFolder: 0.328 Positive Predictive Value TurboFold(seed): 0.518 NanoFolder: 0.293 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 Carnac(seed): 0.216 Sensitivity TurboFold(seed): 0.434 Carnac(seed): 0.047 Positive Predictive Value TurboFold(seed): 0.650 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 RSpredict(seed): 0.213 Sensitivity TurboFold(seed): 0.434 RSpredict(seed): 0.092 Positive Predictive Value TurboFold(seed): 0.650 RSpredict(seed): 0.500 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.00475527001e-08	+ TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 PPfold(seed): 0.208 Sensitivity TurboFold(seed): 0.434 PPfold(seed): 0.063 Positive Predictive Value TurboFold(seed): 0.650 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.75835195567e-08	? TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity TurboFold(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value TurboFold(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs DAFS(20) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(20): N/A Sensitivity TurboFold(seed): N/A DAFS(20): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(seed): N/A Sensitivity TurboFold(seed): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 Mastr(seed): 0.047 Sensitivity TurboFold(seed): 0.434 Mastr(seed): 0.006 Positive Predictive Value TurboFold(seed): 0.650 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08
MaxExpect	36 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.682 MaxExpect: 0.557 Sensitivity CentroidAlifold(20): 0.529 MaxExpect: 0.481 Positive Predictive Value CentroidAlifold(20): 0.882 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 MaxExpect: 0.509 Sensitivity PETfold_pre2.0(seed): 0.602 MaxExpect: 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.850 MaxExpect: 0.592 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	36 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.656 MaxExpect: 0.557 Sensitivity RNAalifold(20): 0.513 MaxExpect: 0.481 Positive Predictive Value RNAalifold(20): 0.841 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.641 MaxExpect: 0.544 Sensitivity MXScarna(seed): 0.531 MaxExpect: 0.476 Positive Predictive Value MXScarna(seed): 0.773 MaxExpect: 0.624 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.663 MaxExpect: 0.503 Sensitivity PPfold(20): 0.528 MaxExpect: 0.431 Positive Predictive Value PPfold(20): 0.836 MaxExpect: 0.594 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	43 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.536 MaxExpect: 0.439 Sensitivity ContextFold: 0.440 MaxExpect: 0.378 Positive Predictive Value ContextFold: 0.654 MaxExpect: 0.511 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.613 MaxExpect: 0.557 Sensitivity RNASampler(20): 0.475 MaxExpect: 0.481 Positive Predictive Value RNASampler(20): 0.795 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 MaxExpect: 0.481 Sensitivity PETfold_pre2.0(20): 0.530 MaxExpect: 0.412 Positive Predictive Value PETfold_pre2.0(20): 0.798 MaxExpect: 0.568 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	20 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.616 MaxExpect: 0.503 Sensitivity TurboFold(20): 0.508 MaxExpect: 0.431 Positive Predictive Value TurboFold(20): 0.752 MaxExpect: 0.594 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	36 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.611 MaxExpect: 0.557 Sensitivity MXScarna(20): 0.510 MaxExpect: 0.481 Positive Predictive Value MXScarna(20): 0.736 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.604 MaxExpect: 0.510 Sensitivity RNAalifold(seed): 0.426 MaxExpect: 0.446 Positive Predictive Value RNAalifold(seed): 0.857 MaxExpect: 0.585 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	36 Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.589 MaxExpect: 0.557 Sensitivity Murlet(20): 0.439 MaxExpect: 0.481 Positive Predictive Value Murlet(20): 0.795 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 MaxExpect: 0.543 Sensitivity CentroidAlifold(seed): 0.427 MaxExpect: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.899 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.592 MaxExpect: 0.557 Sensitivity Carnac(20): 0.392 MaxExpect: 0.481 Positive Predictive Value Carnac(20): 0.898 MaxExpect: 0.649 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.513 MaxExpect: 0.446 Sensitivity IPknot: 0.411 MaxExpect: 0.384 Positive Predictive Value IPknot: 0.641 MaxExpect: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 MaxExpect: 0.476 Sensitivity CentroidHomfold‑LAST: 0.378 MaxExpect: 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.699 MaxExpect: 0.566 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.509 MaxExpect: 0.503 Sensitivity Contrafold: 0.439 MaxExpect: 0.432 Positive Predictive Value Contrafold: 0.591 MaxExpect: 0.586 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 1.1061772363e-05	77 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.503 Sfold: 0.490 Sensitivity MaxExpect: 0.432 Sfold: 0.407 Positive Predictive Value MaxExpect: 0.586 Sfold: 0.590 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 4.48494289621e-08	74 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.534 MaxExpect: 0.529 Sensitivity HotKnots: 0.475 MaxExpect: 0.458 Positive Predictive Value HotKnots: 0.604 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.00238364898467	77 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.503 MaxExpect: 0.503 Sensitivity CentroidFold: 0.406 MaxExpect: 0.432 Positive Predictive Value CentroidFold: 0.625 MaxExpect: 0.586 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 0.686772471119	14 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.529 MaxExpect: 0.484 Sensitivity TurboFold(seed): 0.434 MaxExpect: 0.405 Positive Predictive Value TurboFold(seed): 0.650 MaxExpect: 0.584 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08		+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.559 RSpredict(20): 0.549 Sensitivity MaxExpect: 0.484 RSpredict(20): 0.434 Positive Predictive Value MaxExpect: 0.650 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 1.49438993542e-06	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.504 PknotsRG: 0.462 Sensitivity MaxExpect: 0.432 PknotsRG: 0.407 Positive Predictive Value MaxExpect: 0.590 PknotsRG: 0.527 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(20) vs MaxExpect Matthews Correlation Coefficient CMfinder(20): 0.521 MaxExpect: 0.476 Sensitivity CMfinder(20): 0.366 MaxExpect: 0.413 Positive Predictive Value CMfinder(20): 0.748 MaxExpect: 0.554 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.503 UNAFold: 0.473 Sensitivity MaxExpect: 0.432 UNAFold: 0.412 Positive Predictive Value MaxExpect: 0.586 UNAFold: 0.544 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.482 ProbKnot: 0.478 Sensitivity MaxExpect: 0.419 ProbKnot: 0.423 Positive Predictive Value MaxExpect: 0.557 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.570 Cylofold: 0.554 Sensitivity MaxExpect: 0.491 Cylofold: 0.463 Positive Predictive Value MaxExpect: 0.667 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.26115971074e-07	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.503 RNAfold: 0.464 Sensitivity MaxExpect: 0.432 RNAfold: 0.407 Positive Predictive Value MaxExpect: 0.586 RNAfold: 0.530 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.447 RNASampler(seed): 0.447 Sensitivity MaxExpect: 0.388 RNASampler(seed): 0.314 Positive Predictive Value MaxExpect: 0.521 RNASampler(seed): 0.641 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.551554687255	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.529 RNAsubopt: 0.513 Sensitivity MaxExpect: 0.458 RNAsubopt: 0.457 Positive Predictive Value MaxExpect: 0.616 RNAsubopt: 0.580 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.534 MaxExpect: 0.510 Sensitivity Multilign(20): 0.449 MaxExpect: 0.443 Positive Predictive Value Multilign(20): 0.642 MaxExpect: 0.592 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.484 Afold: 0.431 Sensitivity MaxExpect: 0.419 Afold: 0.383 Positive Predictive Value MaxExpect: 0.561 Afold: 0.487 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.529 RNAshapes: 0.501 Sensitivity MaxExpect: 0.458 RNAshapes: 0.438 Positive Predictive Value MaxExpect: 0.616 RNAshapes: 0.577 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.488 Fold: 0.457 Sensitivity MaxExpect: 0.424 Fold: 0.406 Positive Predictive Value MaxExpect: 0.563 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.503 McQFold: 0.398 Sensitivity MaxExpect: 0.432 McQFold: 0.337 Positive Predictive Value MaxExpect: 0.586 McQFold: 0.471 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.464 RNASLOpt: 0.427 Sensitivity MaxExpect: 0.395 RNASLOpt: 0.341 Positive Predictive Value MaxExpect: 0.550 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.557 Mastr(20): 0.496 Sensitivity MaxExpect: 0.481 Mastr(20): 0.333 Positive Predictive Value MaxExpect: 0.649 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.556 MaxExpect: 0.555 Sensitivity Multilign(seed): 0.432 MaxExpect: 0.451 Positive Predictive Value Multilign(seed): 0.723 MaxExpect: 0.689 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.140151831921	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.569 Pknots: 0.509 Sensitivity MaxExpect: 0.492 Pknots: 0.457 Positive Predictive Value MaxExpect: 0.664 Pknots: 0.573 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.546 Vsfold4: 0.443 Sensitivity MaxExpect: 0.477 Vsfold4: 0.368 Positive Predictive Value MaxExpect: 0.631 Vsfold4: 0.540 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.467 MaxExpect: 0.445 Sensitivity CRWrnafold: 0.410 MaxExpect: 0.387 Positive Predictive Value CRWrnafold: 0.540 MaxExpect: 0.522 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.70236007792e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.542 Murlet(seed): 0.441 Sensitivity MaxExpect: 0.457 Murlet(seed): 0.241 Positive Predictive Value MaxExpect: 0.647 Murlet(seed): 0.814 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.538 Vsfold5: 0.404 Sensitivity MaxExpect: 0.469 Vsfold5: 0.342 Positive Predictive Value MaxExpect: 0.622 Vsfold5: 0.483 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.542 MCFold: 0.373 Sensitivity MaxExpect: 0.470 MCFold: 0.385 Positive Predictive Value MaxExpect: 0.632 MCFold: 0.369 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.602 Alterna: 0.508 Sensitivity MaxExpect: 0.512 Alterna: 0.443 Positive Predictive Value MaxExpect: 0.717 Alterna: 0.593 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.581 RDfolder: 0.450 Sensitivity MaxExpect: 0.496 RDfolder: 0.349 Positive Predictive Value MaxExpect: 0.691 RDfolder: 0.591 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.446 RNAwolf: 0.317 Sensitivity MaxExpect: 0.384 RNAwolf: 0.293 Positive Predictive Value MaxExpect: 0.520 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.491 NanoFolder: 0.272 Sensitivity MaxExpect: 0.424 NanoFolder: 0.284 Positive Predictive Value MaxExpect: 0.575 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.541 Carnac(seed): 0.390 Sensitivity MaxExpect: 0.468 Carnac(seed): 0.171 Positive Predictive Value MaxExpect: 0.626 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.544 RSpredict(seed): 0.334 Sensitivity MaxExpect: 0.477 RSpredict(seed): 0.187 Positive Predictive Value MaxExpect: 0.622 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.534 PPfold(seed): 0.148 Sensitivity MaxExpect: 0.455 PPfold(seed): 0.032 Positive Predictive Value MaxExpect: 0.633 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(seed): N/A Sensitivity MaxExpect: N/A CMfinder(seed): N/A Positive Predictive Value MaxExpect: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MaxExpect: 0.657 Sensitivity PETfold_2.0(seed): 0.642 MaxExpect: 0.558 Positive Predictive Value PETfold_2.0(seed): 0.924 MaxExpect: 0.779 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs DAFS(20) Matthews Correlation Coefficient MaxExpect: N/A DAFS(20): N/A Sensitivity MaxExpect: N/A DAFS(20): N/A Positive Predictive Value MaxExpect: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MaxExpect: 0.498 Sensitivity PETfold_2.0(20): 0.509 MaxExpect: 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs DAFS(seed) Matthews Correlation Coefficient MaxExpect: N/A DAFS(seed): N/A Sensitivity MaxExpect: N/A DAFS(seed): N/A Positive Predictive Value MaxExpect: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.559 Mastr(seed): 0.024 Sensitivity MaxExpect: 0.489 Mastr(seed): 0.002 Positive Predictive Value MaxExpect: 0.644 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(20)	35 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.683 RSpredict(20): 0.549 Sensitivity CentroidAlifold(20): 0.532 RSpredict(20): 0.434 Positive Predictive Value CentroidAlifold(20): 0.880 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.669 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.534 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(seed): 0.841 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	36 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.655 RSpredict(20): 0.552 Sensitivity RNAalifold(20): 0.513 RSpredict(20): 0.436 Positive Predictive Value RNAalifold(20): 0.841 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.649 RSpredict(20): 0.547 Sensitivity MXScarna(seed): 0.532 RSpredict(20): 0.432 Positive Predictive Value MXScarna(seed): 0.795 RSpredict(20): 0.698 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	20 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(20): 0.520 Sensitivity PPfold(20): 0.528 RSpredict(20): 0.398 Positive Predictive Value PPfold(20): 0.836 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.605 RSpredict(20): 0.491 Sensitivity ContextFold: 0.492 RSpredict(20): 0.373 Positive Predictive Value ContextFold: 0.749 RSpredict(20): 0.653 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	36 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.616 RSpredict(20): 0.552 Sensitivity RNASampler(20): 0.481 RSpredict(20): 0.436 Positive Predictive Value RNASampler(20): 0.792 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(20): 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(20): 0.675 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.64318034126e-08	20 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.616 RSpredict(20): 0.520 Sensitivity TurboFold(20): 0.508 RSpredict(20): 0.398 Positive Predictive Value TurboFold(20): 0.752 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	36 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.609 RSpredict(20): 0.552 Sensitivity MXScarna(20): 0.509 RSpredict(20): 0.436 Positive Predictive Value MXScarna(20): 0.732 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 RSpredict(20): 0.440 Sensitivity RNAalifold(seed): 0.338 RSpredict(20): 0.338 Positive Predictive Value RNAalifold(seed): 0.929 RSpredict(20): 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	36 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.589 RSpredict(20): 0.552 Sensitivity Murlet(20): 0.441 RSpredict(20): 0.436 Positive Predictive Value Murlet(20): 0.790 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.591 RSpredict(20): 0.549 Sensitivity CentroidAlifold(seed): 0.371 RSpredict(20): 0.434 Positive Predictive Value CentroidAlifold(seed): 0.945 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.594 RSpredict(20): 0.552 Sensitivity Carnac(20): 0.395 RSpredict(20): 0.436 Positive Predictive Value Carnac(20): 0.897 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.535 RSpredict(20): 0.520 Sensitivity IPknot: 0.443 RSpredict(20): 0.398 Positive Predictive Value IPknot: 0.651 RSpredict(20): 0.685 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 1.92531153888e-07	19 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.589 RSpredict(20): 0.539 Sensitivity CentroidHomfold‑LAST: 0.501 RSpredict(20): 0.414 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RSpredict(20): 0.709 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	36 RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.552 Contrafold: 0.547 Sensitivity RSpredict(20): 0.436 Contrafold: 0.485 Positive Predictive Value RSpredict(20): 0.703 Contrafold: 0.621 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.000741474702242	36 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.563 RSpredict(20): 0.552 Sensitivity Sfold: 0.473 RSpredict(20): 0.436 Positive Predictive Value Sfold: 0.675 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 0.000207424631753	36 RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.552 HotKnots: 0.535 Sensitivity RSpredict(20): 0.436 HotKnots: 0.480 Positive Predictive Value RSpredict(20): 0.703 HotKnots: 0.600 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.62644058675e-08	35 RSpredict(20) vs CentroidFold Matthews Correlation Coefficient RSpredict(20): 0.549 CentroidFold: 0.545 Sensitivity RSpredict(20): 0.434 CentroidFold: 0.463 Positive Predictive Value RSpredict(20): 0.700 CentroidFold: 0.646 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.484584865998	10 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.484 RSpredict(20): 0.394 Sensitivity TurboFold(seed): 0.393 RSpredict(20): 0.302 Positive Predictive Value TurboFold(seed): 0.601 RSpredict(20): 0.521 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	35 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.559 RSpredict(20): 0.549 Sensitivity MaxExpect: 0.484 RSpredict(20): 0.434 Positive Predictive Value MaxExpect: 0.650 RSpredict(20): 0.700 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 1.49438993542e-06		- PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.558 RSpredict(20): 0.552 Sensitivity PknotsRG: 0.499 RSpredict(20): 0.436 Positive Predictive Value PknotsRG: 0.629 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.90626908729e-06	+ RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.566 CMfinder(20): 0.539 Sensitivity RSpredict(20): 0.443 CMfinder(20): 0.389 Positive Predictive Value RSpredict(20): 0.729 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.552 UNAFold: 0.545 Sensitivity RSpredict(20): 0.436 UNAFold: 0.481 Positive Predictive Value RSpredict(20): 0.703 UNAFold: 0.623 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 1.5875416339e-07	- ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.549 RSpredict(20): 0.538 Sensitivity ProbKnot: 0.487 RSpredict(20): 0.421 Positive Predictive Value ProbKnot: 0.624 RSpredict(20): 0.691 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 7.61266898416e-07	- Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.642 RSpredict(20): 0.611 Sensitivity Cylofold: 0.543 RSpredict(20): 0.480 Positive Predictive Value Cylofold: 0.765 RSpredict(20): 0.784 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.552 RNAfold: 0.541 Sensitivity RSpredict(20): 0.436 RNAfold: 0.483 Positive Predictive Value RSpredict(20): 0.703 RNAfold: 0.612 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 2.71856013146e-06	- RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 RSpredict(20): 0.415 Sensitivity RNASampler(seed): 0.353 RSpredict(20): 0.362 Positive Predictive Value RNASampler(seed): 0.652 RSpredict(20): 0.480 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.61680779366e-09	+ RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.552 RNAsubopt: 0.544 Sensitivity RSpredict(20): 0.436 RNAsubopt: 0.489 Positive Predictive Value RSpredict(20): 0.703 RNAsubopt: 0.609 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 1.97386617324e-07	+ RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.539 Multilign(20): 0.534 Sensitivity RSpredict(20): 0.414 Multilign(20): 0.449 Positive Predictive Value RSpredict(20): 0.709 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.93966096077e-06	+ RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.549 Afold: 0.514 Sensitivity RSpredict(20): 0.462 Afold: 0.469 Positive Predictive Value RSpredict(20): 0.655 Afold: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.552 RNAshapes: 0.533 Sensitivity RSpredict(20): 0.436 RNAshapes: 0.471 Positive Predictive Value RSpredict(20): 0.703 RNAshapes: 0.608 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RSpredict(20) vs Fold Matthews Correlation Coefficient RSpredict(20): 0.538 Fold: 0.532 Sensitivity RSpredict(20): 0.421 Fold: 0.473 Positive Predictive Value RSpredict(20): 0.691 Fold: 0.602 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000322134726257	+ RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.552 McQFold: 0.516 Sensitivity RSpredict(20): 0.436 McQFold: 0.446 Positive Predictive Value RSpredict(20): 0.703 McQFold: 0.602 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.491 RNASLOpt: 0.464 Sensitivity RSpredict(20): 0.373 RNASLOpt: 0.387 Positive Predictive Value RSpredict(20): 0.653 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.86366296137e-06	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.552 Mastr(20): 0.513 Sensitivity RSpredict(20): 0.436 Mastr(20): 0.346 Positive Predictive Value RSpredict(20): 0.703 Mastr(20): 0.765 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.497 RSpredict(20): 0.409 Sensitivity Multilign(seed): 0.369 RSpredict(20): 0.305 Positive Predictive Value Multilign(seed): 0.676 RSpredict(20): 0.554 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.554 Pknots: 0.494 Sensitivity RSpredict(20): 0.436 Pknots: 0.448 Positive Predictive Value RSpredict(20): 0.709 Pknots: 0.551 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.562 Vsfold4: 0.476 Sensitivity RSpredict(20): 0.445 Vsfold4: 0.398 Positive Predictive Value RSpredict(20): 0.715 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.546 RSpredict(20): 0.446 Sensitivity CRWrnafold: 0.483 RSpredict(20): 0.331 Positive Predictive Value CRWrnafold: 0.623 RSpredict(20): 0.609 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.454 RSpredict(20): 0.420 Sensitivity Murlet(seed): 0.241 RSpredict(20): 0.318 Positive Predictive Value Murlet(seed): 0.861 RSpredict(20): 0.562 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.562 Vsfold5: 0.432 Sensitivity RSpredict(20): 0.445 Vsfold5: 0.366 Positive Predictive Value RSpredict(20): 0.715 Vsfold5: 0.516 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.573 MCFold: 0.402 Sensitivity RSpredict(20): 0.464 MCFold: 0.418 Positive Predictive Value RSpredict(20): 0.714 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.703 Alterna: 0.553 Sensitivity RSpredict(20): 0.560 Alterna: 0.480 Positive Predictive Value RSpredict(20): 0.887 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.665 RDfolder: 0.563 Sensitivity RSpredict(20): 0.514 RDfolder: 0.447 Positive Predictive Value RSpredict(20): 0.868 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.520 RNAwolf: 0.343 Sensitivity RSpredict(20): 0.398 RNAwolf: 0.325 Positive Predictive Value RSpredict(20): 0.685 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.511 NanoFolder: 0.271 Sensitivity RSpredict(20): 0.394 NanoFolder: 0.286 Positive Predictive Value RSpredict(20): 0.667 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.473 Carnac(seed): 0.110 Sensitivity RSpredict(20): 0.367 Carnac(seed): 0.012 Positive Predictive Value RSpredict(20): 0.616 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.540 RSpredict(seed): 0.274 Sensitivity RSpredict(20): 0.416 RSpredict(seed): 0.127 Positive Predictive Value RSpredict(20): 0.705 RSpredict(seed): 0.593 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.520 PPfold(seed): 0.072 Sensitivity RSpredict(20): 0.398 PPfold(seed): 0.012 Positive Predictive Value RSpredict(20): 0.685 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	? RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(seed): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs DAFS(20) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(20): N/A Sensitivity RSpredict(20): N/A DAFS(20): N/A Positive Predictive Value RSpredict(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(seed): N/A Sensitivity RSpredict(20): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.552 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.436 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.703 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	36 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.682 PknotsRG: 0.555 Sensitivity CentroidAlifold(20): 0.529 PknotsRG: 0.494 Positive Predictive Value CentroidAlifold(20): 0.882 PknotsRG: 0.628 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(seed): 0.595 PknotsRG: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.879 PknotsRG: 0.636 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	38 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.656 PknotsRG: 0.557 Sensitivity RNAalifold(20): 0.511 PknotsRG: 0.494 Positive Predictive Value RNAalifold(20): 0.846 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.638 PknotsRG: 0.562 Sensitivity MXScarna(seed): 0.522 PknotsRG: 0.505 Positive Predictive Value MXScarna(seed): 0.783 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.663 PknotsRG: 0.541 Sensitivity PPfold(20): 0.528 PknotsRG: 0.479 Positive Predictive Value PPfold(20): 0.836 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	42 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.478 PknotsRG: 0.446 Sensitivity ContextFold: 0.389 PknotsRG: 0.394 Positive Predictive Value ContextFold: 0.588 PknotsRG: 0.508 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.85233844192e-08	38 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.612 PknotsRG: 0.557 Sensitivity RNASampler(20): 0.471 PknotsRG: 0.494 Positive Predictive Value RNASampler(20): 0.799 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PknotsRG: 0.522 Sensitivity PETfold_pre2.0(20): 0.530 PknotsRG: 0.464 Positive Predictive Value PETfold_pre2.0(20): 0.798 PknotsRG: 0.593 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	20 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.616 PknotsRG: 0.541 Sensitivity TurboFold(20): 0.508 PknotsRG: 0.479 Positive Predictive Value TurboFold(20): 0.752 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.611 PknotsRG: 0.557 Sensitivity MXScarna(20): 0.509 PknotsRG: 0.494 Positive Predictive Value MXScarna(20): 0.737 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs PknotsRG Matthews Correlation Coefficient RNAalifold(seed): 0.549 PknotsRG: 0.544 Sensitivity RNAalifold(seed): 0.338 PknotsRG: 0.494 Positive Predictive Value RNAalifold(seed): 0.895 PknotsRG: 0.603 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000552293176012	38 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.590 PknotsRG: 0.557 Sensitivity Murlet(20): 0.438 PknotsRG: 0.494 Positive Predictive Value Murlet(20): 0.799 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 PknotsRG: 0.560 Sensitivity CentroidAlifold(seed): 0.367 PknotsRG: 0.503 Positive Predictive Value CentroidAlifold(seed): 0.923 PknotsRG: 0.629 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 4.83792096436e-08	38 Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.590 PknotsRG: 0.557 Sensitivity Carnac(20): 0.389 PknotsRG: 0.494 Positive Predictive Value Carnac(20): 0.899 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.483 PknotsRG: 0.456 Sensitivity IPknot: 0.380 PknotsRG: 0.401 Positive Predictive Value IPknot: 0.616 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 PknotsRG vs CentroidHomfold‑LAST Matthews Correlation Coefficient PknotsRG: 0.516 CentroidHomfold‑LAST: 0.512 Sensitivity PknotsRG: 0.446 CentroidHomfold‑LAST: 0.378 Positive Predictive Value PknotsRG: 0.601 CentroidHomfold‑LAST: 0.699 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.00911763231782	86 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.493 PknotsRG: 0.433 Sensitivity Contrafold: 0.430 PknotsRG: 0.387 Positive Predictive Value Contrafold: 0.565 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.85233844192e-08	86 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.461 PknotsRG: 0.433 Sensitivity Sfold: 0.385 PknotsRG: 0.387 Positive Predictive Value Sfold: 0.552 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.535 PknotsRG: 0.530 Sensitivity HotKnots: 0.474 PknotsRG: 0.468 Positive Predictive Value HotKnots: 0.610 PknotsRG: 0.605 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 4.32815307575e-07	80 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.473 PknotsRG: 0.439 Sensitivity CentroidFold: 0.388 PknotsRG: 0.396 Positive Predictive Value CentroidFold: 0.577 PknotsRG: 0.487 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.532 TurboFold(seed): 0.529 Sensitivity PknotsRG: 0.472 TurboFold(seed): 0.434 Positive Predictive Value PknotsRG: 0.605 TurboFold(seed): 0.650 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00020716383404	76 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.504 PknotsRG: 0.462 Sensitivity MaxExpect: 0.432 PknotsRG: 0.407 Positive Predictive Value MaxExpect: 0.590 PknotsRG: 0.527 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.558 RSpredict(20): 0.552 Sensitivity PknotsRG: 0.499 RSpredict(20): 0.436 Positive Predictive Value PknotsRG: 0.629 RSpredict(20): 0.703 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.90626908729e-06		= CMfinder(20) vs PknotsRG Matthews Correlation Coefficient CMfinder(20): 0.521 PknotsRG: 0.518 Sensitivity CMfinder(20): 0.366 PknotsRG: 0.456 Positive Predictive Value CMfinder(20): 0.748 PknotsRG: 0.594 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.144482071027	- UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.440 PknotsRG: 0.433 Sensitivity UNAFold: 0.388 PknotsRG: 0.387 Positive Predictive Value UNAFold: 0.498 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.487 ProbKnot: 0.474 Sensitivity PknotsRG: 0.434 ProbKnot: 0.421 Positive Predictive Value PknotsRG: 0.549 ProbKnot: 0.536 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.561 Cylofold: 0.554 Sensitivity PknotsRG: 0.495 Cylofold: 0.463 Positive Predictive Value PknotsRG: 0.642 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 5.90626908729e-06	- RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.436 PknotsRG: 0.433 Sensitivity RNAfold: 0.389 PknotsRG: 0.387 Positive Predictive Value RNAfold: 0.489 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 1.02208072244e-07	= PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.484 RNASampler(seed): 0.482 Sensitivity PknotsRG: 0.440 RNASampler(seed): 0.342 Positive Predictive Value PknotsRG: 0.538 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0786965679238	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.530 RNAsubopt: 0.509 Sensitivity PknotsRG: 0.468 RNAsubopt: 0.452 Positive Predictive Value PknotsRG: 0.605 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.563 Multilign(20): 0.534 Sensitivity PknotsRG: 0.499 Multilign(20): 0.449 Positive Predictive Value PknotsRG: 0.642 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.1413769576e-08	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.408 PknotsRG: 0.401 Sensitivity Afold: 0.368 PknotsRG: 0.362 Positive Predictive Value Afold: 0.453 PknotsRG: 0.444 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 0.000639955457467	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.530 RNAshapes: 0.499 Sensitivity PknotsRG: 0.468 RNAshapes: 0.434 Positive Predictive Value PknotsRG: 0.605 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.488 Fold: 0.458 Sensitivity PknotsRG: 0.435 Fold: 0.407 Positive Predictive Value PknotsRG: 0.549 Fold: 0.518 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.433 McQFold: 0.353 Sensitivity PknotsRG: 0.387 McQFold: 0.278 Positive Predictive Value PknotsRG: 0.485 McQFold: 0.450 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.497 RNASLOpt: 0.427 Sensitivity PknotsRG: 0.436 RNASLOpt: 0.341 Positive Predictive Value PknotsRG: 0.572 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.557 Mastr(20): 0.500 Sensitivity PknotsRG: 0.494 Mastr(20): 0.336 Positive Predictive Value PknotsRG: 0.633 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.556 PknotsRG: 0.549 Sensitivity Multilign(seed): 0.432 PknotsRG: 0.473 Positive Predictive Value Multilign(seed): 0.723 PknotsRG: 0.644 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00117233828523	+ PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.558 Pknots: 0.507 Sensitivity PknotsRG: 0.491 Pknots: 0.454 Positive Predictive Value PknotsRG: 0.640 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.540 Vsfold4: 0.451 Sensitivity PknotsRG: 0.478 Vsfold4: 0.373 Positive Predictive Value PknotsRG: 0.614 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.529 CRWrnafold: 0.467 Sensitivity PknotsRG: 0.472 CRWrnafold: 0.410 Positive Predictive Value PknotsRG: 0.600 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.574 Murlet(seed): 0.448 Sensitivity PknotsRG: 0.507 Murlet(seed): 0.245 Positive Predictive Value PknotsRG: 0.656 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.539 Vsfold5: 0.409 Sensitivity PknotsRG: 0.478 Vsfold5: 0.346 Positive Predictive Value PknotsRG: 0.613 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.551 MCFold: 0.385 Sensitivity PknotsRG: 0.488 MCFold: 0.396 Positive Predictive Value PknotsRG: 0.628 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.568 Alterna: 0.523 Sensitivity PknotsRG: 0.485 Alterna: 0.449 Positive Predictive Value PknotsRG: 0.674 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.573 RDfolder: 0.461 Sensitivity PknotsRG: 0.494 RDfolder: 0.358 Positive Predictive Value PknotsRG: 0.674 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.456 RNAwolf: 0.278 Sensitivity PknotsRG: 0.401 RNAwolf: 0.258 Positive Predictive Value PknotsRG: 0.521 RNAwolf: 0.303 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.525 NanoFolder: 0.272 Sensitivity PknotsRG: 0.460 NanoFolder: 0.284 Positive Predictive Value PknotsRG: 0.606 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.583 Carnac(seed): 0.179 Sensitivity PknotsRG: 0.519 Carnac(seed): 0.032 Positive Predictive Value PknotsRG: 0.659 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.563 RSpredict(seed): 0.178 Sensitivity PknotsRG: 0.507 RSpredict(seed): 0.075 Positive Predictive Value PknotsRG: 0.630 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.568 PPfold(seed): 0.148 Sensitivity PknotsRG: 0.499 PPfold(seed): 0.032 Positive Predictive Value PknotsRG: 0.652 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	? PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(seed): N/A Sensitivity PknotsRG: N/A CMfinder(seed): N/A Positive Predictive Value PknotsRG: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 PknotsRG: 0.687 Sensitivity PETfold_2.0(seed): 0.642 PknotsRG: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 PknotsRG: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs DAFS(20) Matthews Correlation Coefficient PknotsRG: N/A DAFS(20): N/A Sensitivity PknotsRG: N/A DAFS(20): N/A Positive Predictive Value PknotsRG: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(20): 0.647 PknotsRG: 0.549 Sensitivity PETfold_2.0(20): 0.509 PknotsRG: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 PknotsRG: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs DAFS(seed) Matthews Correlation Coefficient PknotsRG: N/A DAFS(seed): N/A Sensitivity PknotsRG: N/A DAFS(seed): N/A Positive Predictive Value PknotsRG: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.562 Mastr(seed): 0.023 Sensitivity PknotsRG: 0.503 Mastr(seed): 0.002 Positive Predictive Value PknotsRG: 0.633 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(20)	11 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.667 CMfinder(20): 0.521 Sensitivity CentroidAlifold(20): 0.524 CMfinder(20): 0.366 Positive Predictive Value CentroidAlifold(20): 0.853 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.38194587311e-08	11 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.741 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(seed): 0.622 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(seed): 0.885 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	11 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.662 CMfinder(20): 0.521 Sensitivity RNAalifold(20): 0.521 CMfinder(20): 0.366 Positive Predictive Value RNAalifold(20): 0.844 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	10 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.603 CMfinder(20): 0.504 Sensitivity MXScarna(seed): 0.494 CMfinder(20): 0.350 Positive Predictive Value MXScarna(seed): 0.741 CMfinder(20): 0.730 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.43692248862e-08	10 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.678 CMfinder(20): 0.539 Sensitivity PPfold(20): 0.554 CMfinder(20): 0.389 Positive Predictive Value PPfold(20): 0.833 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.39551335374e-08	11 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.641 CMfinder(20): 0.521 Sensitivity ContextFold: 0.528 CMfinder(20): 0.366 Positive Predictive Value ContextFold: 0.783 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.04409141234e-08	11 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.565 CMfinder(20): 0.521 Sensitivity RNASampler(20): 0.436 CMfinder(20): 0.366 Positive Predictive Value RNASampler(20): 0.738 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.5281770229e-09	11 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 CMfinder(20): 0.521 Sensitivity PETfold_pre2.0(20): 0.564 CMfinder(20): 0.366 Positive Predictive Value PETfold_pre2.0(20): 0.826 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	10 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.634 CMfinder(20): 0.539 Sensitivity TurboFold(20): 0.541 CMfinder(20): 0.389 Positive Predictive Value TurboFold(20): 0.747 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.58287649515e-08	11 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.600 CMfinder(20): 0.521 Sensitivity MXScarna(20): 0.506 CMfinder(20): 0.366 Positive Predictive Value MXScarna(20): 0.717 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	3 RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): 0.507 CMfinder(20): 0.333 Sensitivity RNAalifold(seed): 0.257 CMfinder(20): 0.208 Positive Predictive Value RNAalifold(seed): 1.000 CMfinder(20): 0.538 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	11 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.606 CMfinder(20): 0.521 Sensitivity Murlet(20): 0.456 CMfinder(20): 0.366 Positive Predictive Value Murlet(20): 0.809 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.68522644707e-09	11 CMfinder(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidAlifold(seed): 0.510 Sensitivity CMfinder(20): 0.366 CentroidAlifold(seed): 0.288 Positive Predictive Value CMfinder(20): 0.748 CentroidAlifold(seed): 0.908 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.73616572961e-05	11 Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.574 CMfinder(20): 0.521 Sensitivity Carnac(20): 0.382 CMfinder(20): 0.366 Positive Predictive Value Carnac(20): 0.867 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.40200680498e-09	11 CMfinder(20) vs IPknot Matthews Correlation Coefficient CMfinder(20): 0.521 IPknot: 0.488 Sensitivity CMfinder(20): 0.366 IPknot: 0.416 Positive Predictive Value CMfinder(20): 0.748 IPknot: 0.580 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.58287649515e-08	11 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.538 CMfinder(20): 0.521 Sensitivity CentroidHomfold‑LAST: 0.465 CMfinder(20): 0.366 Positive Predictive Value CentroidHomfold‑LAST: 0.627 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.35948134614e-05	11 CMfinder(20) vs Contrafold Matthews Correlation Coefficient CMfinder(20): 0.521 Contrafold: 0.497 Sensitivity CMfinder(20): 0.366 Contrafold: 0.445 Positive Predictive Value CMfinder(20): 0.748 Contrafold: 0.563 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.40919803867e-08	11 CMfinder(20) vs Sfold Matthews Correlation Coefficient CMfinder(20): 0.521 Sfold: 0.502 Sensitivity CMfinder(20): 0.366 Sfold: 0.427 Positive Predictive Value CMfinder(20): 0.748 Sfold: 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.23704939182e-05	11 CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.521 HotKnots: 0.486 Sensitivity CMfinder(20): 0.366 HotKnots: 0.431 Positive Predictive Value CMfinder(20): 0.748 HotKnots: 0.555 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.98760236454e-08	11 CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.521 CentroidFold: 0.393 Sensitivity CMfinder(20): 0.366 CentroidFold: 0.344 Positive Predictive Value CMfinder(20): 0.748 CentroidFold: 0.458 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	2 CMfinder(20) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(20): 0.296 TurboFold(seed): 0.290 Sensitivity CMfinder(20): 0.203 TurboFold(seed): 0.261 Positive Predictive Value CMfinder(20): 0.438 TurboFold(seed): 0.327 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	11 CMfinder(20) vs MaxExpect Matthews Correlation Coefficient CMfinder(20): 0.521 MaxExpect: 0.476 Sensitivity CMfinder(20): 0.366 MaxExpect: 0.413 Positive Predictive Value CMfinder(20): 0.748 MaxExpect: 0.554 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	10 RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.566 CMfinder(20): 0.539 Sensitivity RSpredict(20): 0.443 CMfinder(20): 0.389 Positive Predictive Value RSpredict(20): 0.729 CMfinder(20): 0.751 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	11 CMfinder(20) vs PknotsRG Matthews Correlation Coefficient CMfinder(20): 0.521 PknotsRG: 0.518 Sensitivity CMfinder(20): 0.366 PknotsRG: 0.456 Positive Predictive Value CMfinder(20): 0.748 PknotsRG: 0.594 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.144482071027		+ CMfinder(20) vs UNAFold Matthews Correlation Coefficient CMfinder(20): 0.521 UNAFold: 0.467 Sensitivity CMfinder(20): 0.366 UNAFold: 0.411 Positive Predictive Value CMfinder(20): 0.748 UNAFold: 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.49298650753e-09	+ CMfinder(20) vs ProbKnot Matthews Correlation Coefficient CMfinder(20): 0.521 ProbKnot: 0.481 Sensitivity CMfinder(20): 0.366 ProbKnot: 0.416 Positive Predictive Value CMfinder(20): 0.748 ProbKnot: 0.564 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: 0.596 CMfinder(20): 0.530 Sensitivity Cylofold: 0.503 CMfinder(20): 0.369 Positive Predictive Value Cylofold: 0.712 CMfinder(20): 0.767 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RNAfold Matthews Correlation Coefficient CMfinder(20): 0.521 RNAfold: 0.487 Sensitivity CMfinder(20): 0.366 RNAfold: 0.431 Positive Predictive Value CMfinder(20): 0.748 RNAfold: 0.557 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	? CMfinder(20) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(20): 0.296 RNASampler(seed): 0.287 Sensitivity CMfinder(20): 0.203 RNASampler(seed): 0.217 Positive Predictive Value CMfinder(20): 0.438 RNASampler(seed): 0.385 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	= CMfinder(20) vs RNAsubopt Matthews Correlation Coefficient CMfinder(20): 0.521 RNAsubopt: 0.521 Sensitivity CMfinder(20): 0.366 RNAsubopt: 0.465 Positive Predictive Value CMfinder(20): 0.748 RNAsubopt: 0.590 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0128883198586	+ CMfinder(20) vs Multilign(20) Matthews Correlation Coefficient CMfinder(20): 0.539 Multilign(20): 0.502 Sensitivity CMfinder(20): 0.389 Multilign(20): 0.418 Positive Predictive Value CMfinder(20): 0.751 Multilign(20): 0.609 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.5677163434e-08	? Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.492 CMfinder(20): 0.396 Sensitivity Afold: 0.427 CMfinder(20): 0.256 Positive Predictive Value Afold: 0.574 CMfinder(20): 0.618 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.521 RNAshapes: 0.446 Sensitivity CMfinder(20): 0.366 RNAshapes: 0.393 Positive Predictive Value CMfinder(20): 0.748 RNAshapes: 0.513 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ CMfinder(20) vs Fold Matthews Correlation Coefficient CMfinder(20): 0.521 Fold: 0.470 Sensitivity CMfinder(20): 0.366 Fold: 0.416 Positive Predictive Value CMfinder(20): 0.748 Fold: 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.521 McQFold: 0.456 Sensitivity CMfinder(20): 0.366 McQFold: 0.382 Positive Predictive Value CMfinder(20): 0.748 McQFold: 0.550 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.521 RNASLOpt: 0.455 Sensitivity CMfinder(20): 0.366 RNASLOpt: 0.375 Positive Predictive Value CMfinder(20): 0.748 RNASLOpt: 0.559 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.5281770229e-09	+ CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.521 Mastr(20): 0.499 Sensitivity CMfinder(20): 0.366 Mastr(20): 0.357 Positive Predictive Value CMfinder(20): 0.748 Mastr(20): 0.704 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.80287361792e-07	? Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): 0.128 CMfinder(20): 0.098 Sensitivity Multilign(seed): 0.091 CMfinder(20): 0.061 Positive Predictive Value Multilign(seed): 0.188 CMfinder(20): 0.167 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.521 Pknots: 0.395 Sensitivity CMfinder(20): 0.366 Pknots: 0.346 Positive Predictive Value CMfinder(20): 0.748 Pknots: 0.460 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.521 Vsfold4: 0.411 Sensitivity CMfinder(20): 0.366 Vsfold4: 0.337 Positive Predictive Value CMfinder(20): 0.748 Vsfold4: 0.508 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.54892753461e-09	? CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.333 Murlet(seed): 0.259 Sensitivity CMfinder(20): 0.208 Murlet(seed): 0.119 Positive Predictive Value CMfinder(20): 0.538 Murlet(seed): 0.571 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.521 Vsfold5: 0.355 Sensitivity CMfinder(20): 0.366 Vsfold5: 0.299 Positive Predictive Value CMfinder(20): 0.748 Vsfold5: 0.430 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.64686604905e-09	+ CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.539 MCFold: 0.378 Sensitivity CMfinder(20): 0.389 MCFold: 0.392 Positive Predictive Value CMfinder(20): 0.751 MCFold: 0.373 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	? Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.753 RDfolder: 0.722 Sensitivity CMfinder(20): 0.586 RDfolder: 0.586 Positive Predictive Value CMfinder(20): 0.971 RDfolder: 0.895 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.521 RNAwolf: 0.370 Sensitivity CMfinder(20): 0.366 RNAwolf: 0.346 Positive Predictive Value CMfinder(20): 0.748 RNAwolf: 0.403 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.99051034341e-09	? CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.508 NanoFolder: 0.241 Sensitivity CMfinder(20): 0.363 NanoFolder: 0.251 Positive Predictive Value CMfinder(20): 0.716 NanoFolder: 0.241 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.333 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.208 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.538 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.539 RSpredict(seed): 0.015 Sensitivity CMfinder(20): 0.389 RSpredict(seed): 0.005 Positive Predictive Value CMfinder(20): 0.751 RSpredict(seed): 0.053 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.00780879471e-09	+ CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.539 PPfold(seed): 0.071 Sensitivity CMfinder(20): 0.389 PPfold(seed): 0.010 Positive Predictive Value CMfinder(20): 0.751 PPfold(seed): 0.500 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.42300079339e-08	? CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CMfinder(20): 0.383 Sensitivity PETfold_2.0(seed): 0.614 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.946 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(20) vs CMfinder(20) Matthews Correlation Coefficient DAFS(20): N/A CMfinder(20): N/A Sensitivity DAFS(20): N/A CMfinder(20): N/A Positive Predictive Value DAFS(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CMfinder(20): 0.383 Sensitivity PETfold_2.0(20): 0.509 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(20): 0.829 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs CMfinder(20) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(20): N/A Sensitivity DAFS(seed): N/A CMfinder(20): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.521 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.366 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.52214427071e-09
UNAFold	36 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 UNAFold: 0.542 Sensitivity CentroidAlifold(20): 0.529 UNAFold: 0.476 Positive Predictive Value CentroidAlifold(20): 0.882 UNAFold: 0.621 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 UNAFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.602 UNAFold: 0.414 Positive Predictive Value PETfold_pre2.0(seed): 0.850 UNAFold: 0.544 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	38 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.656 UNAFold: 0.543 Sensitivity RNAalifold(20): 0.511 UNAFold: 0.475 Positive Predictive Value RNAalifold(20): 0.846 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.646 UNAFold: 0.524 Sensitivity MXScarna(seed): 0.536 UNAFold: 0.464 Positive Predictive Value MXScarna(seed): 0.779 UNAFold: 0.595 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.663 UNAFold: 0.487 Sensitivity PPfold(20): 0.528 UNAFold: 0.427 Positive Predictive Value PPfold(20): 0.836 UNAFold: 0.561 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	43 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.536 UNAFold: 0.438 Sensitivity ContextFold: 0.440 UNAFold: 0.383 Positive Predictive Value ContextFold: 0.654 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.612 UNAFold: 0.543 Sensitivity RNASampler(20): 0.471 UNAFold: 0.475 Positive Predictive Value RNASampler(20): 0.799 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 UNAFold: 0.462 Sensitivity PETfold_pre2.0(20): 0.530 UNAFold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 UNAFold: 0.531 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	20 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.616 UNAFold: 0.487 Sensitivity TurboFold(20): 0.508 UNAFold: 0.427 Positive Predictive Value TurboFold(20): 0.752 UNAFold: 0.561 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.611 UNAFold: 0.543 Sensitivity MXScarna(20): 0.509 UNAFold: 0.475 Positive Predictive Value MXScarna(20): 0.737 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.606 UNAFold: 0.499 Sensitivity RNAalifold(seed): 0.427 UNAFold: 0.442 Positive Predictive Value RNAalifold(seed): 0.861 UNAFold: 0.564 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	38 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.590 UNAFold: 0.543 Sensitivity Murlet(20): 0.438 UNAFold: 0.475 Positive Predictive Value Murlet(20): 0.799 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 UNAFold: 0.520 Sensitivity CentroidAlifold(seed): 0.425 UNAFold: 0.459 Positive Predictive Value CentroidAlifold(seed): 0.899 UNAFold: 0.590 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.590 UNAFold: 0.543 Sensitivity Carnac(20): 0.389 UNAFold: 0.475 Positive Predictive Value Carnac(20): 0.899 UNAFold: 0.626 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.513 UNAFold: 0.446 Sensitivity IPknot: 0.411 UNAFold: 0.390 Positive Predictive Value IPknot: 0.641 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 UNAFold: 0.491 Sensitivity CentroidHomfold‑LAST: 0.378 UNAFold: 0.422 Positive Predictive Value CentroidHomfold‑LAST: 0.699 UNAFold: 0.577 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.500 UNAFold: 0.442 Sensitivity Contrafold: 0.437 UNAFold: 0.390 Positive Predictive Value Contrafold: 0.573 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.462 UNAFold: 0.442 Sensitivity Sfold: 0.387 UNAFold: 0.390 Positive Predictive Value Sfold: 0.552 UNAFold: 0.501 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 HotKnots vs UNAFold Matthews Correlation Coefficient HotKnots: 0.535 UNAFold: 0.534 Sensitivity HotKnots: 0.474 UNAFold: 0.466 Positive Predictive Value HotKnots: 0.610 UNAFold: 0.617 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.000857786362802	81 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.483 UNAFold: 0.449 Sensitivity CentroidFold: 0.397 UNAFold: 0.400 Positive Predictive Value CentroidFold: 0.587 UNAFold: 0.504 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.529 UNAFold: 0.466 Sensitivity TurboFold(seed): 0.434 UNAFold: 0.407 Positive Predictive Value TurboFold(seed): 0.650 UNAFold: 0.541 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.61939086268e-08	77 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.503 UNAFold: 0.473 Sensitivity MaxExpect: 0.432 UNAFold: 0.412 Positive Predictive Value MaxExpect: 0.586 UNAFold: 0.544 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.552 UNAFold: 0.545 Sensitivity RSpredict(20): 0.436 UNAFold: 0.481 Positive Predictive Value RSpredict(20): 0.703 UNAFold: 0.623 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 1.5875416339e-07	86 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.440 PknotsRG: 0.433 Sensitivity UNAFold: 0.388 PknotsRG: 0.387 Positive Predictive Value UNAFold: 0.498 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs UNAFold Matthews Correlation Coefficient CMfinder(20): 0.521 UNAFold: 0.467 Sensitivity CMfinder(20): 0.366 UNAFold: 0.411 Positive Predictive Value CMfinder(20): 0.748 UNAFold: 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.49298650753e-09		= UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.478 ProbKnot: 0.478 Sensitivity UNAFold: 0.421 ProbKnot: 0.423 Positive Predictive Value UNAFold: 0.545 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.989275719324	= UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.556 Cylofold: 0.554 Sensitivity UNAFold: 0.485 Cylofold: 0.463 Positive Predictive Value UNAFold: 0.644 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.115804103359	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.442 RNAfold: 0.438 Sensitivity UNAFold: 0.390 RNAfold: 0.390 Positive Predictive Value UNAFold: 0.501 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.482 UNAFold: 0.452 Sensitivity RNASampler(seed): 0.342 UNAFold: 0.406 Positive Predictive Value RNASampler(seed): 0.684 UNAFold: 0.509 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.534 RNAsubopt: 0.509 Sensitivity UNAFold: 0.466 RNAsubopt: 0.452 Positive Predictive Value UNAFold: 0.617 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.534 UNAFold: 0.505 Sensitivity Multilign(20): 0.449 UNAFold: 0.443 Positive Predictive Value Multilign(20): 0.642 UNAFold: 0.582 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.412 Afold: 0.408 Sensitivity UNAFold: 0.367 Afold: 0.368 Positive Predictive Value UNAFold: 0.463 Afold: 0.453 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 1.10039559051e-07	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.534 RNAshapes: 0.499 Sensitivity UNAFold: 0.466 RNAshapes: 0.434 Positive Predictive Value UNAFold: 0.617 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.484 Fold: 0.457 Sensitivity UNAFold: 0.426 Fold: 0.406 Positive Predictive Value UNAFold: 0.551 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.442 McQFold: 0.363 Sensitivity UNAFold: 0.390 McQFold: 0.287 Positive Predictive Value UNAFold: 0.501 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.470 RNASLOpt: 0.427 Sensitivity UNAFold: 0.409 RNASLOpt: 0.341 Positive Predictive Value UNAFold: 0.545 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.543 Mastr(20): 0.500 Sensitivity UNAFold: 0.475 Mastr(20): 0.336 Positive Predictive Value UNAFold: 0.626 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.556 UNAFold: 0.496 Sensitivity Multilign(seed): 0.432 UNAFold: 0.421 Positive Predictive Value Multilign(seed): 0.723 UNAFold: 0.592 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.47941000302e-08	+ UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.560 Pknots: 0.507 Sensitivity UNAFold: 0.487 Pknots: 0.454 Positive Predictive Value UNAFold: 0.650 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.541 Vsfold4: 0.451 Sensitivity UNAFold: 0.473 Vsfold4: 0.373 Positive Predictive Value UNAFold: 0.624 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.481 CRWrnafold: 0.467 Sensitivity UNAFold: 0.426 CRWrnafold: 0.410 Positive Predictive Value UNAFold: 0.551 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000803342806742	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.536 Murlet(seed): 0.448 Sensitivity UNAFold: 0.466 Murlet(seed): 0.245 Positive Predictive Value UNAFold: 0.622 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.534 Vsfold5: 0.409 Sensitivity UNAFold: 0.467 Vsfold5: 0.346 Positive Predictive Value UNAFold: 0.616 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.549 MCFold: 0.385 Sensitivity UNAFold: 0.481 MCFold: 0.396 Positive Predictive Value UNAFold: 0.634 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.593 Alterna: 0.523 Sensitivity UNAFold: 0.502 Alterna: 0.449 Positive Predictive Value UNAFold: 0.710 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.567 RDfolder: 0.461 Sensitivity UNAFold: 0.483 RDfolder: 0.358 Positive Predictive Value UNAFold: 0.674 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.446 RNAwolf: 0.317 Sensitivity UNAFold: 0.390 RNAwolf: 0.293 Positive Predictive Value UNAFold: 0.512 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.472 NanoFolder: 0.272 Sensitivity UNAFold: 0.411 NanoFolder: 0.284 Positive Predictive Value UNAFold: 0.549 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.527 Carnac(seed): 0.392 Sensitivity UNAFold: 0.462 Carnac(seed): 0.172 Positive Predictive Value UNAFold: 0.603 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.521 RSpredict(seed): 0.337 Sensitivity UNAFold: 0.462 RSpredict(seed): 0.189 Positive Predictive Value UNAFold: 0.590 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.494 PPfold(seed): 0.148 Sensitivity UNAFold: 0.431 PPfold(seed): 0.032 Positive Predictive Value UNAFold: 0.573 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: N/A CMfinder(seed): N/A Sensitivity UNAFold: N/A CMfinder(seed): N/A Positive Predictive Value UNAFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 UNAFold: 0.687 Sensitivity PETfold_2.0(seed): 0.642 UNAFold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 UNAFold: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs DAFS(20) Matthews Correlation Coefficient UNAFold: N/A DAFS(20): N/A Sensitivity UNAFold: N/A DAFS(20): N/A Positive Predictive Value UNAFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 UNAFold: 0.549 Sensitivity PETfold_2.0(20): 0.509 UNAFold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 UNAFold: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs DAFS(seed) Matthews Correlation Coefficient UNAFold: N/A DAFS(seed): N/A Sensitivity UNAFold: N/A DAFS(seed): N/A Positive Predictive Value UNAFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.537 Mastr(seed): 0.023 Sensitivity UNAFold: 0.475 Mastr(seed): 0.002 Positive Predictive Value UNAFold: 0.611 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	28 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.677 ProbKnot: 0.548 Sensitivity CentroidAlifold(20): 0.518 ProbKnot: 0.484 Positive Predictive Value CentroidAlifold(20): 0.887 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 ProbKnot: 0.513 Sensitivity PETfold_pre2.0(seed): 0.602 ProbKnot: 0.447 Positive Predictive Value PETfold_pre2.0(seed): 0.850 ProbKnot: 0.590 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.649 ProbKnot: 0.548 Sensitivity RNAalifold(20): 0.503 ProbKnot: 0.484 Positive Predictive Value RNAalifold(20): 0.840 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.640 ProbKnot: 0.536 Sensitivity MXScarna(seed): 0.531 ProbKnot: 0.476 Positive Predictive Value MXScarna(seed): 0.773 ProbKnot: 0.605 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.663 ProbKnot: 0.502 Sensitivity PPfold(20): 0.528 ProbKnot: 0.441 Positive Predictive Value PPfold(20): 0.836 ProbKnot: 0.578 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	43 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.536 ProbKnot: 0.438 Sensitivity ContextFold: 0.440 ProbKnot: 0.382 Positive Predictive Value ContextFold: 0.654 ProbKnot: 0.502 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.600 ProbKnot: 0.548 Sensitivity RNASampler(20): 0.458 ProbKnot: 0.484 Positive Predictive Value RNASampler(20): 0.790 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 ProbKnot: 0.484 Sensitivity PETfold_pre2.0(20): 0.530 ProbKnot: 0.424 Positive Predictive Value PETfold_pre2.0(20): 0.798 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	20 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.616 ProbKnot: 0.502 Sensitivity TurboFold(20): 0.508 ProbKnot: 0.441 Positive Predictive Value TurboFold(20): 0.752 ProbKnot: 0.578 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.606 ProbKnot: 0.548 Sensitivity MXScarna(20): 0.503 ProbKnot: 0.484 Positive Predictive Value MXScarna(20): 0.734 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	22 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.602 ProbKnot: 0.495 Sensitivity RNAalifold(seed): 0.425 ProbKnot: 0.442 Positive Predictive Value RNAalifold(seed): 0.854 ProbKnot: 0.556 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.587 ProbKnot: 0.548 Sensitivity Murlet(20): 0.435 ProbKnot: 0.484 Positive Predictive Value Murlet(20): 0.797 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	39 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.621 ProbKnot: 0.535 Sensitivity CentroidAlifold(seed): 0.432 ProbKnot: 0.476 Positive Predictive Value CentroidAlifold(seed): 0.894 ProbKnot: 0.604 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.578 ProbKnot: 0.548 Sensitivity Carnac(20): 0.373 ProbKnot: 0.484 Positive Predictive Value Carnac(20): 0.899 ProbKnot: 0.626 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	46 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.513 ProbKnot: 0.444 Sensitivity IPknot: 0.411 ProbKnot: 0.388 Positive Predictive Value IPknot: 0.641 ProbKnot: 0.511 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 ProbKnot: 0.478 Sensitivity CentroidHomfold‑LAST: 0.378 ProbKnot: 0.415 Positive Predictive Value CentroidHomfold‑LAST: 0.699 ProbKnot: 0.554 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.488 ProbKnot: 0.478 Sensitivity Contrafold: 0.424 ProbKnot: 0.423 Positive Predictive Value Contrafold: 0.562 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 5.84585956207e-05	61 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.497 ProbKnot: 0.478 Sensitivity Sfold: 0.420 ProbKnot: 0.423 Positive Predictive Value Sfold: 0.589 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.528 ProbKnot: 0.515 Sensitivity HotKnots: 0.471 ProbKnot: 0.458 Positive Predictive Value HotKnots: 0.596 ProbKnot: 0.583 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 2.23046259944e-06	61 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.482 ProbKnot: 0.478 Sensitivity CentroidFold: 0.393 ProbKnot: 0.423 Positive Predictive Value CentroidFold: 0.594 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.13872543599e-05	14 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.529 ProbKnot: 0.479 Sensitivity TurboFold(seed): 0.434 ProbKnot: 0.423 Positive Predictive Value TurboFold(seed): 0.650 ProbKnot: 0.549 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.02533530638e-08	61 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.482 ProbKnot: 0.478 Sensitivity MaxExpect: 0.419 ProbKnot: 0.423 Positive Predictive Value MaxExpect: 0.557 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.549 RSpredict(20): 0.538 Sensitivity ProbKnot: 0.487 RSpredict(20): 0.421 Positive Predictive Value ProbKnot: 0.624 RSpredict(20): 0.691 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 7.61266898416e-07	60 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.487 ProbKnot: 0.474 Sensitivity PknotsRG: 0.434 ProbKnot: 0.421 Positive Predictive Value PknotsRG: 0.549 ProbKnot: 0.536 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.85233844192e-08	11 CMfinder(20) vs ProbKnot Matthews Correlation Coefficient CMfinder(20): 0.521 ProbKnot: 0.481 Sensitivity CMfinder(20): 0.366 ProbKnot: 0.416 Positive Predictive Value CMfinder(20): 0.748 ProbKnot: 0.564 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	61 UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.478 ProbKnot: 0.478 Sensitivity UNAFold: 0.421 ProbKnot: 0.423 Positive Predictive Value UNAFold: 0.545 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.989275719324		+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.558 Cylofold: 0.547 Sensitivity ProbKnot: 0.498 Cylofold: 0.456 Positive Predictive Value ProbKnot: 0.631 Cylofold: 0.662 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 1.35125075749e-05	= ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.478 RNAfold: 0.476 Sensitivity ProbKnot: 0.423 RNAfold: 0.422 Positive Predictive Value ProbKnot: 0.542 RNAfold: 0.540 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.0655545093322	= ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.421 RNASampler(seed): 0.421 Sensitivity ProbKnot: 0.390 RNASampler(seed): 0.289 Positive Predictive Value ProbKnot: 0.460 RNASampler(seed): 0.617 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.775607734133	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.515 RNAsubopt: 0.510 Sensitivity ProbKnot: 0.458 RNAsubopt: 0.454 Positive Predictive Value ProbKnot: 0.583 RNAsubopt: 0.576 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 5.62644058675e-08	- Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.534 ProbKnot: 0.511 Sensitivity Multilign(20): 0.449 ProbKnot: 0.451 Positive Predictive Value Multilign(20): 0.642 ProbKnot: 0.585 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.424 Afold: 0.414 Sensitivity ProbKnot: 0.385 Afold: 0.378 Positive Predictive Value ProbKnot: 0.468 Afold: 0.455 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.515 RNAshapes: 0.493 Sensitivity ProbKnot: 0.458 RNAshapes: 0.432 Positive Predictive Value ProbKnot: 0.583 RNAshapes: 0.568 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.478 Fold: 0.451 Sensitivity ProbKnot: 0.423 Fold: 0.401 Positive Predictive Value ProbKnot: 0.542 Fold: 0.509 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.478 McQFold: 0.421 Sensitivity ProbKnot: 0.423 McQFold: 0.360 Positive Predictive Value ProbKnot: 0.542 McQFold: 0.493 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.464 RNASLOpt: 0.427 Sensitivity ProbKnot: 0.405 RNASLOpt: 0.341 Positive Predictive Value ProbKnot: 0.537 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.548 Mastr(20): 0.471 Sensitivity ProbKnot: 0.484 Mastr(20): 0.305 Positive Predictive Value ProbKnot: 0.626 Mastr(20): 0.734 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	- Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.556 ProbKnot: 0.540 Sensitivity Multilign(seed): 0.432 ProbKnot: 0.462 Positive Predictive Value Multilign(seed): 0.723 ProbKnot: 0.637 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32348179894e-08	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.562 Pknots: 0.510 Sensitivity ProbKnot: 0.499 Pknots: 0.457 Positive Predictive Value ProbKnot: 0.639 Pknots: 0.577 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.535 Vsfold4: 0.433 Sensitivity ProbKnot: 0.481 Vsfold4: 0.360 Positive Predictive Value ProbKnot: 0.600 Vsfold4: 0.526 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.467 ProbKnot: 0.460 Sensitivity CRWrnafold: 0.410 ProbKnot: 0.417 Positive Predictive Value CRWrnafold: 0.540 ProbKnot: 0.516 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.33528019466e-05	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.513 Murlet(seed): 0.426 Sensitivity ProbKnot: 0.458 Murlet(seed): 0.226 Positive Predictive Value ProbKnot: 0.580 Murlet(seed): 0.810 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.525 Vsfold5: 0.405 Sensitivity ProbKnot: 0.472 Vsfold5: 0.346 Positive Predictive Value ProbKnot: 0.589 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.535 MCFold: 0.395 Sensitivity ProbKnot: 0.478 MCFold: 0.404 Positive Predictive Value ProbKnot: 0.604 MCFold: 0.395 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.586 Alterna: 0.522 Sensitivity ProbKnot: 0.529 Alterna: 0.455 Positive Predictive Value ProbKnot: 0.659 Alterna: 0.609 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.561 RDfolder: 0.455 Sensitivity ProbKnot: 0.502 RDfolder: 0.354 Positive Predictive Value ProbKnot: 0.638 RDfolder: 0.598 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.444 RNAwolf: 0.317 Sensitivity ProbKnot: 0.388 RNAwolf: 0.293 Positive Predictive Value ProbKnot: 0.511 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.492 NanoFolder: 0.272 Sensitivity ProbKnot: 0.434 NanoFolder: 0.284 Positive Predictive Value ProbKnot: 0.565 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.529 Carnac(seed): 0.411 Sensitivity ProbKnot: 0.465 Carnac(seed): 0.190 Positive Predictive Value ProbKnot: 0.602 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.535 RSpredict(seed): 0.338 Sensitivity ProbKnot: 0.477 RSpredict(seed): 0.193 Positive Predictive Value ProbKnot: 0.602 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.534 PPfold(seed): 0.148 Sensitivity ProbKnot: 0.469 PPfold(seed): 0.032 Positive Predictive Value ProbKnot: 0.614 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	? ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 ProbKnot: 0.675 Sensitivity PETfold_2.0(seed): 0.642 ProbKnot: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 ProbKnot: 0.806 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs DAFS(20) Matthews Correlation Coefficient ProbKnot: N/A DAFS(20): N/A Sensitivity ProbKnot: N/A DAFS(20): N/A Positive Predictive Value ProbKnot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 ProbKnot: 0.527 Sensitivity PETfold_2.0(20): 0.509 ProbKnot: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 ProbKnot: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs DAFS(seed) Matthews Correlation Coefficient ProbKnot: N/A DAFS(seed): N/A Sensitivity ProbKnot: N/A DAFS(seed): N/A Positive Predictive Value ProbKnot: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.550 Mastr(seed): 0.027 Sensitivity ProbKnot: 0.494 Mastr(seed): 0.002 Positive Predictive Value ProbKnot: 0.615 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08
Cylofold	17 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.746 Cylofold: 0.642 Sensitivity CentroidAlifold(20): 0.603 Cylofold: 0.543 Positive Predictive Value CentroidAlifold(20): 0.928 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	14 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.726 Cylofold: 0.563 Sensitivity PETfold_pre2.0(seed): 0.609 Cylofold: 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.871 Cylofold: 0.681 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	17 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.720 Cylofold: 0.642 Sensitivity RNAalifold(20): 0.577 Cylofold: 0.543 Positive Predictive Value RNAalifold(20): 0.902 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	24 MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.658 Cylofold: 0.618 Sensitivity MXScarna(seed): 0.545 Cylofold: 0.519 Positive Predictive Value MXScarna(seed): 0.800 Cylofold: 0.741 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	12 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.743 Cylofold: 0.628 Sensitivity PPfold(20): 0.608 Cylofold: 0.529 Positive Predictive Value PPfold(20): 0.912 Cylofold: 0.751 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.86109605532e-08	25 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.595 Cylofold: 0.466 Sensitivity ContextFold: 0.491 Cylofold: 0.390 Positive Predictive Value ContextFold: 0.726 Cylofold: 0.565 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.674 Cylofold: 0.642 Sensitivity RNASampler(20): 0.528 Cylofold: 0.543 Positive Predictive Value RNASampler(20): 0.865 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.80908287419e-08	9 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 Cylofold: 0.611 Sensitivity PETfold_pre2.0(20): 0.624 Cylofold: 0.521 Positive Predictive Value PETfold_pre2.0(20): 0.896 Cylofold: 0.722 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	12 TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.693 Cylofold: 0.628 Sensitivity TurboFold(20): 0.562 Cylofold: 0.529 Positive Predictive Value TurboFold(20): 0.860 Cylofold: 0.751 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.74172190343e-08	17 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.663 Cylofold: 0.642 Sensitivity MXScarna(20): 0.556 Cylofold: 0.543 Positive Predictive Value MXScarna(20): 0.796 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	12 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.600 RNAalifold(seed): 0.594 Sensitivity Cylofold: 0.491 RNAalifold(seed): 0.399 Positive Predictive Value Cylofold: 0.739 RNAalifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.311982599612	17 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.653 Cylofold: 0.642 Sensitivity Murlet(20): 0.507 Cylofold: 0.543 Positive Predictive Value Murlet(20): 0.844 Cylofold: 0.765 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.03850456744e-05	24 Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.618 CentroidAlifold(seed): 0.593 Sensitivity Cylofold: 0.519 CentroidAlifold(seed): 0.370 Positive Predictive Value Cylofold: 0.741 CentroidAlifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	17 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.642 Carnac(20): 0.619 Sensitivity Cylofold: 0.543 Carnac(20): 0.436 Positive Predictive Value Cylofold: 0.765 Carnac(20): 0.882 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	28 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.578 Cylofold: 0.490 Sensitivity IPknot: 0.481 Cylofold: 0.409 Positive Predictive Value IPknot: 0.701 Cylofold: 0.595 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 Cylofold: 0.483 Sensitivity CentroidHomfold‑LAST: 0.380 Cylofold: 0.401 Positive Predictive Value CentroidHomfold‑LAST: 0.696 Cylofold: 0.590 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	41 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.596 Cylofold: 0.554 Sensitivity Contrafold: 0.522 Cylofold: 0.463 Positive Predictive Value Contrafold: 0.688 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.570 Cylofold: 0.554 Sensitivity Sfold: 0.474 Cylofold: 0.463 Positive Predictive Value Sfold: 0.693 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 4.48494289621e-08	41 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.571 Cylofold: 0.554 Sensitivity HotKnots: 0.505 Cylofold: 0.463 Positive Predictive Value HotKnots: 0.653 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 5.21776328505e-08	41 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.583 Cylofold: 0.554 Sensitivity CentroidFold: 0.491 Cylofold: 0.463 Positive Predictive Value CentroidFold: 0.699 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.580 TurboFold(seed): 0.578 Sensitivity Cylofold: 0.462 TurboFold(seed): 0.448 Positive Predictive Value Cylofold: 0.737 TurboFold(seed): 0.754 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	41 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.570 Cylofold: 0.554 Sensitivity MaxExpect: 0.491 Cylofold: 0.463 Positive Predictive Value MaxExpect: 0.667 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.26115971074e-07	17 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.642 RSpredict(20): 0.611 Sensitivity Cylofold: 0.543 RSpredict(20): 0.480 Positive Predictive Value Cylofold: 0.765 RSpredict(20): 0.784 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.75835195567e-08	41 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.561 Cylofold: 0.554 Sensitivity PknotsRG: 0.495 Cylofold: 0.463 Positive Predictive Value PknotsRG: 0.642 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 5.90626908729e-06	5 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: 0.596 CMfinder(20): 0.530 Sensitivity Cylofold: 0.503 CMfinder(20): 0.369 Positive Predictive Value Cylofold: 0.712 CMfinder(20): 0.767 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	41 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.556 Cylofold: 0.554 Sensitivity UNAFold: 0.485 Cylofold: 0.463 Positive Predictive Value UNAFold: 0.644 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.115804103359	40 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.558 Cylofold: 0.547 Sensitivity ProbKnot: 0.498 Cylofold: 0.456 Positive Predictive Value ProbKnot: 0.631 Cylofold: 0.662 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 1.35125075749e-05		+ Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.554 RNAfold: 0.548 Sensitivity Cylofold: 0.463 RNAfold: 0.480 Positive Predictive Value Cylofold: 0.669 RNAfold: 0.633 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.00026990691477	? Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.540 RNASampler(seed): 0.514 Sensitivity Cylofold: 0.462 RNASampler(seed): 0.351 Positive Predictive Value Cylofold: 0.637 RNASampler(seed): 0.759 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	= RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.560 Cylofold: 0.554 Sensitivity RNAsubopt: 0.492 Cylofold: 0.463 Positive Predictive Value RNAsubopt: 0.645 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.028456752624	+ Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.628 Multilign(20): 0.592 Sensitivity Cylofold: 0.529 Multilign(20): 0.496 Positive Predictive Value Cylofold: 0.751 Multilign(20): 0.714 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 5.4618626652e-08	- Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.559 Cylofold: 0.535 Sensitivity Afold: 0.497 Cylofold: 0.451 Positive Predictive Value Afold: 0.634 Cylofold: 0.641 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 6.07491858776e-08	+ Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.554 RNAshapes: 0.539 Sensitivity Cylofold: 0.463 RNAshapes: 0.470 Positive Predictive Value Cylofold: 0.669 RNAshapes: 0.625 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 5.62644058675e-08	- Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.563 Cylofold: 0.554 Sensitivity Fold: 0.496 Cylofold: 0.463 Positive Predictive Value Fold: 0.646 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 1.95308298399e-06	- McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.585 Cylofold: 0.554 Sensitivity McQFold: 0.493 Cylofold: 0.463 Positive Predictive Value McQFold: 0.700 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.466 RNASLOpt: 0.454 Sensitivity Cylofold: 0.390 RNASLOpt: 0.373 Positive Predictive Value Cylofold: 0.565 RNASLOpt: 0.559 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.24386558293e-07	+ Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.642 Mastr(20): 0.529 Sensitivity Cylofold: 0.543 Mastr(20): 0.373 Positive Predictive Value Cylofold: 0.765 Mastr(20): 0.755 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	? Multilign(seed) vs Cylofold Matthews Correlation Coefficient Multilign(seed): 0.554 Cylofold: 0.492 Sensitivity Multilign(seed): 0.435 Cylofold: 0.388 Positive Predictive Value Multilign(seed): 0.715 Cylofold: 0.634 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	= Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.593 Pknots: 0.590 Sensitivity Cylofold: 0.498 Pknots: 0.523 Positive Predictive Value Cylofold: 0.711 Pknots: 0.672 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.545273100092	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.560 Vsfold4: 0.504 Sensitivity Cylofold: 0.471 Vsfold4: 0.418 Positive Predictive Value Cylofold: 0.672 Vsfold4: 0.614 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.526 CRWrnafold: 0.473 Sensitivity Cylofold: 0.449 CRWrnafold: 0.406 Positive Predictive Value Cylofold: 0.625 CRWrnafold: 0.560 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.582 Murlet(seed): 0.429 Sensitivity Cylofold: 0.473 Murlet(seed): 0.246 Positive Predictive Value Cylofold: 0.723 Murlet(seed): 0.756 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.552 Vsfold5: 0.446 Sensitivity Cylofold: 0.463 Vsfold5: 0.378 Positive Predictive Value Cylofold: 0.666 Vsfold5: 0.535 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.598 MCFold: 0.431 Sensitivity Cylofold: 0.501 MCFold: 0.447 Positive Predictive Value Cylofold: 0.721 MCFold: 0.425 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.629 Alterna: 0.528 Sensitivity Cylofold: 0.531 Alterna: 0.464 Positive Predictive Value Cylofold: 0.753 Alterna: 0.612 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.629 RDfolder: 0.425 Sensitivity Cylofold: 0.532 RDfolder: 0.331 Positive Predictive Value Cylofold: 0.752 RDfolder: 0.558 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.490 RNAwolf: 0.382 Sensitivity Cylofold: 0.409 RNAwolf: 0.354 Positive Predictive Value Cylofold: 0.595 RNAwolf: 0.422 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.455 NanoFolder: 0.283 Sensitivity Cylofold: 0.384 NanoFolder: 0.295 Positive Predictive Value Cylofold: 0.547 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.611 Carnac(seed): 0.091 Sensitivity Cylofold: 0.499 Carnac(seed): 0.008 Positive Predictive Value Cylofold: 0.753 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.618 RSpredict(seed): 0.137 Sensitivity Cylofold: 0.519 RSpredict(seed): 0.056 Positive Predictive Value Cylofold: 0.741 RSpredict(seed): 0.348 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.584 PPfold(seed): 0.089 Sensitivity Cylofold: 0.486 PPfold(seed): 0.011 Positive Predictive Value Cylofold: 0.709 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	? Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs DAFS(20) Matthews Correlation Coefficient Cylofold: N/A DAFS(20): N/A Sensitivity Cylofold: N/A DAFS(20): N/A Positive Predictive Value Cylofold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(20): N/A Sensitivity Cylofold: N/A PETfold_2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs DAFS(seed) Matthews Correlation Coefficient Cylofold: N/A DAFS(seed): N/A Sensitivity Cylofold: N/A DAFS(seed): N/A Positive Predictive Value Cylofold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.618 Mastr(seed): 0.000 Sensitivity Cylofold: 0.519 Mastr(seed): 0.000 Positive Predictive Value Cylofold: 0.741 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08
RNAfold	36 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAfold: 0.538 Sensitivity CentroidAlifold(20): 0.529 RNAfold: 0.478 Positive Predictive Value CentroidAlifold(20): 0.882 RNAfold: 0.610 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAfold: 0.500 Sensitivity PETfold_pre2.0(seed): 0.602 RNAfold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAfold: 0.573 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAfold: 0.540 Sensitivity RNAalifold(20): 0.511 RNAfold: 0.477 Positive Predictive Value RNAalifold(20): 0.846 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.646 RNAfold: 0.533 Sensitivity MXScarna(seed): 0.536 RNAfold: 0.474 Positive Predictive Value MXScarna(seed): 0.779 RNAfold: 0.600 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.663 RNAfold: 0.506 Sensitivity PPfold(20): 0.528 RNAfold: 0.446 Positive Predictive Value PPfold(20): 0.836 RNAfold: 0.581 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	43 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.536 RNAfold: 0.440 Sensitivity ContextFold: 0.440 RNAfold: 0.386 Positive Predictive Value ContextFold: 0.654 RNAfold: 0.503 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.612 RNAfold: 0.540 Sensitivity RNASampler(20): 0.471 RNAfold: 0.477 Positive Predictive Value RNASampler(20): 0.799 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAfold: 0.483 Sensitivity PETfold_pre2.0(20): 0.530 RNAfold: 0.428 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAfold: 0.552 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	20 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.616 RNAfold: 0.506 Sensitivity TurboFold(20): 0.508 RNAfold: 0.446 Positive Predictive Value TurboFold(20): 0.752 RNAfold: 0.581 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.611 RNAfold: 0.540 Sensitivity MXScarna(20): 0.509 RNAfold: 0.477 Positive Predictive Value MXScarna(20): 0.737 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.606 RNAfold: 0.508 Sensitivity RNAalifold(seed): 0.427 RNAfold: 0.453 Positive Predictive Value RNAalifold(seed): 0.861 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.590 RNAfold: 0.540 Sensitivity Murlet(20): 0.438 RNAfold: 0.477 Positive Predictive Value Murlet(20): 0.799 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 RNAfold: 0.528 Sensitivity CentroidAlifold(seed): 0.425 RNAfold: 0.469 Positive Predictive Value CentroidAlifold(seed): 0.899 RNAfold: 0.595 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.590 RNAfold: 0.540 Sensitivity Carnac(20): 0.389 RNAfold: 0.477 Positive Predictive Value Carnac(20): 0.899 RNAfold: 0.616 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.513 RNAfold: 0.449 Sensitivity IPknot: 0.411 RNAfold: 0.393 Positive Predictive Value IPknot: 0.641 RNAfold: 0.514 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 RNAfold: 0.502 Sensitivity CentroidHomfold‑LAST: 0.378 RNAfold: 0.431 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RNAfold: 0.590 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 9.77069178155e-06	87 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.500 RNAfold: 0.438 Sensitivity Contrafold: 0.437 RNAfold: 0.390 Positive Predictive Value Contrafold: 0.573 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.462 RNAfold: 0.438 Sensitivity Sfold: 0.387 RNAfold: 0.390 Positive Predictive Value Sfold: 0.552 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.535 RNAfold: 0.524 Sensitivity HotKnots: 0.474 RNAfold: 0.460 Positive Predictive Value HotKnots: 0.610 RNAfold: 0.601 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.483 RNAfold: 0.442 Sensitivity CentroidFold: 0.397 RNAfold: 0.397 Positive Predictive Value CentroidFold: 0.587 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAfold: 0.502 Sensitivity TurboFold(seed): 0.434 RNAfold: 0.440 Positive Predictive Value TurboFold(seed): 0.650 RNAfold: 0.580 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.45805449719e-08	77 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.503 RNAfold: 0.464 Sensitivity MaxExpect: 0.432 RNAfold: 0.407 Positive Predictive Value MaxExpect: 0.586 RNAfold: 0.530 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.552 RNAfold: 0.541 Sensitivity RSpredict(20): 0.436 RNAfold: 0.483 Positive Predictive Value RSpredict(20): 0.703 RNAfold: 0.612 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 2.71856013146e-06	86 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.436 PknotsRG: 0.433 Sensitivity RNAfold: 0.389 PknotsRG: 0.387 Positive Predictive Value RNAfold: 0.489 PknotsRG: 0.485 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 1.02208072244e-07	11 CMfinder(20) vs RNAfold Matthews Correlation Coefficient CMfinder(20): 0.521 RNAfold: 0.487 Sensitivity CMfinder(20): 0.366 RNAfold: 0.431 Positive Predictive Value CMfinder(20): 0.748 RNAfold: 0.557 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	87 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.442 RNAfold: 0.438 Sensitivity UNAFold: 0.390 RNAfold: 0.390 Positive Predictive Value UNAFold: 0.501 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.478 RNAfold: 0.476 Sensitivity ProbKnot: 0.423 RNAfold: 0.422 Positive Predictive Value ProbKnot: 0.542 RNAfold: 0.540 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.0655545093322	41 Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.554 RNAfold: 0.548 Sensitivity Cylofold: 0.463 RNAfold: 0.480 Positive Predictive Value Cylofold: 0.669 RNAfold: 0.633 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.00026990691477		- RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.482 RNAfold: 0.480 Sensitivity RNASampler(seed): 0.342 RNAfold: 0.434 Positive Predictive Value RNASampler(seed): 0.684 RNAfold: 0.536 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.000195761842109	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.524 RNAsubopt: 0.509 Sensitivity RNAfold: 0.460 RNAsubopt: 0.452 Positive Predictive Value RNAfold: 0.601 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.534 RNAfold: 0.526 Sensitivity Multilign(20): 0.449 RNAfold: 0.464 Positive Predictive Value Multilign(20): 0.642 RNAfold: 0.603 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.21488232292e-05	= Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.408 RNAfold: 0.407 Sensitivity Afold: 0.368 RNAfold: 0.367 Positive Predictive Value Afold: 0.453 RNAfold: 0.451 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 0.109706356059	+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.524 RNAshapes: 0.499 Sensitivity RNAfold: 0.460 RNAshapes: 0.434 Positive Predictive Value RNAfold: 0.601 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.477 Fold: 0.457 Sensitivity RNAfold: 0.423 Fold: 0.406 Positive Predictive Value RNAfold: 0.540 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.438 McQFold: 0.363 Sensitivity RNAfold: 0.390 McQFold: 0.287 Positive Predictive Value RNAfold: 0.493 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.481 RNASLOpt: 0.427 Sensitivity RNAfold: 0.418 RNASLOpt: 0.341 Positive Predictive Value RNAfold: 0.557 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.540 Mastr(20): 0.500 Sensitivity RNAfold: 0.477 Mastr(20): 0.336 Positive Predictive Value RNAfold: 0.616 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.556 RNAfold: 0.543 Sensitivity Multilign(seed): 0.432 RNAfold: 0.465 Positive Predictive Value Multilign(seed): 0.723 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0201340087366	+ RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.548 Pknots: 0.507 Sensitivity RNAfold: 0.480 Pknots: 0.454 Positive Predictive Value RNAfold: 0.633 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.532 Vsfold4: 0.451 Sensitivity RNAfold: 0.469 Vsfold4: 0.373 Positive Predictive Value RNAfold: 0.609 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.511 CRWrnafold: 0.467 Sensitivity RNAfold: 0.447 CRWrnafold: 0.410 Positive Predictive Value RNAfold: 0.592 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.556 Murlet(seed): 0.448 Sensitivity RNAfold: 0.487 Murlet(seed): 0.245 Positive Predictive Value RNAfold: 0.641 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.528 Vsfold5: 0.409 Sensitivity RNAfold: 0.466 Vsfold5: 0.346 Positive Predictive Value RNAfold: 0.605 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.540 MCFold: 0.385 Sensitivity RNAfold: 0.476 MCFold: 0.396 Positive Predictive Value RNAfold: 0.620 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.569 Alterna: 0.523 Sensitivity RNAfold: 0.484 Alterna: 0.449 Positive Predictive Value RNAfold: 0.680 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.547 RDfolder: 0.461 Sensitivity RNAfold: 0.468 RDfolder: 0.358 Positive Predictive Value RNAfold: 0.649 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.449 RNAwolf: 0.317 Sensitivity RNAfold: 0.393 RNAwolf: 0.293 Positive Predictive Value RNAfold: 0.514 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.503 NanoFolder: 0.272 Sensitivity RNAfold: 0.439 NanoFolder: 0.284 Positive Predictive Value RNAfold: 0.583 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.529 Carnac(seed): 0.392 Sensitivity RNAfold: 0.466 Carnac(seed): 0.172 Positive Predictive Value RNAfold: 0.603 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.530 RSpredict(seed): 0.337 Sensitivity RNAfold: 0.472 RSpredict(seed): 0.189 Positive Predictive Value RNAfold: 0.596 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.539 PPfold(seed): 0.148 Sensitivity RNAfold: 0.470 PPfold(seed): 0.032 Positive Predictive Value RNAfold: 0.623 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAfold: 0.682 Sensitivity PETfold_2.0(seed): 0.642 RNAfold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAfold: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs DAFS(20) Matthews Correlation Coefficient RNAfold: N/A DAFS(20): N/A Sensitivity RNAfold: N/A DAFS(20): N/A Positive Predictive Value RNAfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAfold: 0.541 Sensitivity PETfold_2.0(20): 0.509 RNAfold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 RNAfold: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAfold Matthews Correlation Coefficient DAFS(seed): N/A RNAfold: N/A Sensitivity DAFS(seed): N/A RNAfold: N/A Positive Predictive Value DAFS(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.548 Mastr(seed): 0.023 Sensitivity RNAfold: 0.489 Mastr(seed): 0.002 Positive Predictive Value RNAfold: 0.619 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(seed)	9 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.495 RNASampler(seed): 0.458 Sensitivity CentroidAlifold(20): 0.319 RNASampler(seed): 0.334 Positive Predictive Value CentroidAlifold(20): 0.772 RNASampler(seed): 0.632 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.594 RNASampler(seed): 0.333 Sensitivity PETfold_pre2.0(seed): 0.453 RNASampler(seed): 0.224 Positive Predictive Value PETfold_pre2.0(seed): 0.782 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	10 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 RNAalifold(20): 0.466 Sensitivity RNASampler(seed): 0.353 RNAalifold(20): 0.356 Positive Predictive Value RNASampler(seed): 0.652 RNAalifold(20): 0.614 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71178597147e-06	14 MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.506 RNASampler(seed): 0.482 Sensitivity MXScarna(seed): 0.380 RNASampler(seed): 0.342 Positive Predictive Value MXScarna(seed): 0.677 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	6 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.423 PPfold(20): 0.419 Sensitivity RNASampler(seed): 0.300 PPfold(20): 0.300 Positive Predictive Value RNASampler(seed): 0.600 PPfold(20): 0.590 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.394 RNASampler(seed): 0.333 Sensitivity ContextFold: 0.322 RNASampler(seed): 0.224 Positive Predictive Value ContextFold: 0.488 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	10 RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 RNASampler(20): 0.449 Sensitivity RNASampler(seed): 0.353 RNASampler(20): 0.356 Positive Predictive Value RNASampler(seed): 0.652 RNASampler(20): 0.571 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	4 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.299 PETfold_pre2.0(20): 0.262 Sensitivity RNASampler(seed): 0.214 PETfold_pre2.0(20): 0.195 Positive Predictive Value RNASampler(seed): 0.423 PETfold_pre2.0(20): 0.357 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): 0.423 TurboFold(20): 0.408 Sensitivity RNASampler(seed): 0.300 TurboFold(20): 0.335 Positive Predictive Value RNASampler(seed): 0.600 TurboFold(20): 0.503 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	10 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 MXScarna(20): 0.464 Sensitivity RNASampler(seed): 0.353 MXScarna(20): 0.368 Positive Predictive Value RNASampler(seed): 0.652 MXScarna(20): 0.590 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.43284180886e-08	14 RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.503 RNASampler(seed): 0.482 Sensitivity RNAalifold(seed): 0.295 RNASampler(seed): 0.342 Positive Predictive Value RNAalifold(seed): 0.863 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.32883086441e-08	10 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 Murlet(20): 0.447 Sensitivity RNASampler(seed): 0.353 Murlet(20): 0.329 Positive Predictive Value RNASampler(seed): 0.652 Murlet(20): 0.612 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.22797000563e-08	13 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.620 RNASampler(seed): 0.467 Sensitivity CentroidAlifold(seed): 0.407 RNASampler(seed): 0.328 Positive Predictive Value CentroidAlifold(seed): 0.949 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.31583660336e-08	10 Carnac(20) vs RNASampler(seed) Matthews Correlation Coefficient Carnac(20): 0.520 RNASampler(seed): 0.478 Sensitivity Carnac(20): 0.288 RNASampler(seed): 0.353 Positive Predictive Value Carnac(20): 0.942 RNASampler(seed): 0.652 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.45096400029e-08	9 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.492 RNASampler(seed): 0.417 Sensitivity IPknot: 0.396 RNASampler(seed): 0.283 Positive Predictive Value IPknot: 0.617 RNASampler(seed): 0.619 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.472 RNASampler(seed): 0.434 Sensitivity CentroidHomfold‑LAST: 0.383 RNASampler(seed): 0.301 Positive Predictive Value CentroidHomfold‑LAST: 0.589 RNASampler(seed): 0.633 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.491 RNASampler(seed): 0.482 Sensitivity Contrafold: 0.429 RNASampler(seed): 0.342 Positive Predictive Value Contrafold: 0.566 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00243391354489	14 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.505 RNASampler(seed): 0.482 Sensitivity Sfold: 0.421 RNASampler(seed): 0.342 Positive Predictive Value Sfold: 0.610 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.78993384543e-08	14 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.482 HotKnots: 0.441 Sensitivity RNASampler(seed): 0.342 HotKnots: 0.410 Positive Predictive Value RNASampler(seed): 0.684 HotKnots: 0.479 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	13 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.514 RNASampler(seed): 0.467 Sensitivity CentroidFold: 0.420 RNASampler(seed): 0.328 Positive Predictive Value CentroidFold: 0.634 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	8 TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.409 RNASampler(seed): 0.404 Sensitivity TurboFold(seed): 0.342 RNASampler(seed): 0.281 Positive Predictive Value TurboFold(seed): 0.495 RNASampler(seed): 0.585 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	12 MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.447 RNASampler(seed): 0.447 Sensitivity MaxExpect: 0.388 RNASampler(seed): 0.314 Positive Predictive Value MaxExpect: 0.521 RNASampler(seed): 0.641 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.551554687255	10 RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 RSpredict(20): 0.415 Sensitivity RNASampler(seed): 0.353 RSpredict(20): 0.362 Positive Predictive Value RNASampler(seed): 0.652 RSpredict(20): 0.480 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.61680779366e-09	14 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.484 RNASampler(seed): 0.482 Sensitivity PknotsRG: 0.440 RNASampler(seed): 0.342 Positive Predictive Value PknotsRG: 0.538 RNASampler(seed): 0.684 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0786965679238	2 CMfinder(20) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(20): 0.296 RNASampler(seed): 0.287 Sensitivity CMfinder(20): 0.203 RNASampler(seed): 0.217 Positive Predictive Value CMfinder(20): 0.438 RNASampler(seed): 0.385 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	14 RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.482 UNAFold: 0.452 Sensitivity RNASampler(seed): 0.342 UNAFold: 0.406 Positive Predictive Value RNASampler(seed): 0.684 UNAFold: 0.509 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.67657656842e-08	10 ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.421 RNASampler(seed): 0.421 Sensitivity ProbKnot: 0.390 RNASampler(seed): 0.289 Positive Predictive Value ProbKnot: 0.460 RNASampler(seed): 0.617 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.775607734133	5 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.540 RNASampler(seed): 0.514 Sensitivity Cylofold: 0.462 RNASampler(seed): 0.351 Positive Predictive Value Cylofold: 0.637 RNASampler(seed): 0.759 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	14 RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.482 RNAfold: 0.480 Sensitivity RNASampler(seed): 0.342 RNAfold: 0.434 Positive Predictive Value RNASampler(seed): 0.684 RNAfold: 0.536 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.000195761842109		+ RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.482 RNAsubopt: 0.454 Sensitivity RNASampler(seed): 0.342 RNAsubopt: 0.419 Positive Predictive Value RNASampler(seed): 0.684 RNAsubopt: 0.499 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.450 Multilign(20): 0.378 Sensitivity RNASampler(seed): 0.331 Multilign(20): 0.331 Positive Predictive Value RNASampler(seed): 0.615 Multilign(20): 0.437 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	= RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.493 Afold: 0.487 Sensitivity RNASampler(seed): 0.365 Afold: 0.443 Positive Predictive Value RNASampler(seed): 0.671 Afold: 0.540 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0806085266796	+ RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.482 RNAshapes: 0.468 Sensitivity RNASampler(seed): 0.342 RNAshapes: 0.423 Positive Predictive Value RNASampler(seed): 0.684 RNAshapes: 0.524 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 9.60786361713e-08	+ RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.421 Fold: 0.385 Sensitivity RNASampler(seed): 0.289 Fold: 0.354 Positive Predictive Value RNASampler(seed): 0.617 Fold: 0.426 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.26710183075e-09	+ RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.482 McQFold: 0.465 Sensitivity RNASampler(seed): 0.342 McQFold: 0.419 Positive Predictive Value RNASampler(seed): 0.684 McQFold: 0.521 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.87872347734e-08	? RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.399 RNASampler(seed): 0.333 Sensitivity RNASLOpt: 0.347 RNASampler(seed): 0.224 Positive Predictive Value RNASLOpt: 0.464 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 Mastr(20): 0.422 Sensitivity RNASampler(seed): 0.353 Mastr(20): 0.200 Positive Predictive Value RNASampler(seed): 0.652 Mastr(20): 0.895 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.77512146924e-08	? Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.534 RNASampler(seed): 0.432 Sensitivity Multilign(seed): 0.413 RNASampler(seed): 0.282 Positive Predictive Value Multilign(seed): 0.698 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	= RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.482 Pknots: 0.471 Sensitivity RNASampler(seed): 0.342 Pknots: 0.449 Positive Predictive Value RNASampler(seed): 0.684 Pknots: 0.500 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00161539962317	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.500 Vsfold4: 0.421 Sensitivity RNASampler(seed): 0.361 Vsfold4: 0.358 Positive Predictive Value RNASampler(seed): 0.698 Vsfold4: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18141491686e-08	? RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.357 CRWrnafold: 0.262 Sensitivity RNASampler(seed): 0.253 CRWrnafold: 0.253 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.279 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 Murlet(seed): 0.411 Sensitivity RNASampler(seed): 0.342 Murlet(seed): 0.216 Positive Predictive Value RNASampler(seed): 0.684 Murlet(seed): 0.789 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.500 Vsfold5: 0.470 Sensitivity RNASampler(seed): 0.361 Vsfold5: 0.425 Positive Predictive Value RNASampler(seed): 0.698 Vsfold5: 0.525 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.69229414982e-08	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.478 MCFold: 0.361 Sensitivity RNASampler(seed): 0.346 MCFold: 0.381 Positive Predictive Value RNASampler(seed): 0.667 MCFold: 0.348 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.07229227445e-09	? Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.667 RNASampler(seed): 0.644 Sensitivity Alterna: 0.560 RNASampler(seed): 0.474 Positive Predictive Value Alterna: 0.803 RNASampler(seed): 0.883 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.627 RDfolder: 0.486 Sensitivity RNASampler(seed): 0.442 RDfolder: 0.372 Positive Predictive Value RNASampler(seed): 0.896 RDfolder: 0.645 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.417 RNAwolf: 0.340 Sensitivity RNASampler(seed): 0.283 RNAwolf: 0.333 Positive Predictive Value RNASampler(seed): 0.619 RNAwolf: 0.353 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.337 NanoFolder: 0.214 Sensitivity RNASampler(seed): 0.233 NanoFolder: 0.244 Positive Predictive Value RNASampler(seed): 0.495 NanoFolder: 0.195 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 Carnac(seed): 0.265 Sensitivity RNASampler(seed): 0.342 Carnac(seed): 0.071 Positive Predictive Value RNASampler(seed): 0.684 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 RSpredict(seed): 0.297 Sensitivity RNASampler(seed): 0.342 RSpredict(seed): 0.154 Positive Predictive Value RNASampler(seed): 0.684 RSpredict(seed): 0.581 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.417 PPfold(seed): 0.257 Sensitivity RNASampler(seed): 0.283 PPfold(seed): 0.097 Positive Predictive Value RNASampler(seed): 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs DAFS(20) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(20): N/A Sensitivity RNASampler(seed): N/A DAFS(20): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(seed): N/A Sensitivity RNASampler(seed): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 Mastr(seed): 0.048 Sensitivity RNASampler(seed): 0.342 Mastr(seed): 0.006 Positive Predictive Value RNASampler(seed): 0.684 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.78993384543e-08
RNAsubopt	36 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAsubopt: 0.540 Sensitivity CentroidAlifold(20): 0.529 RNAsubopt: 0.483 Positive Predictive Value CentroidAlifold(20): 0.882 RNAsubopt: 0.609 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAsubopt: 0.525 Sensitivity PETfold_pre2.0(seed): 0.595 RNAsubopt: 0.466 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAsubopt: 0.599 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAsubopt: 0.534 Sensitivity RNAalifold(20): 0.511 RNAsubopt: 0.477 Positive Predictive Value RNAalifold(20): 0.846 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAsubopt: 0.538 Sensitivity MXScarna(seed): 0.522 RNAsubopt: 0.486 Positive Predictive Value MXScarna(seed): 0.783 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.663 RNAsubopt: 0.526 Sensitivity PPfold(20): 0.528 RNAsubopt: 0.468 Positive Predictive Value PPfold(20): 0.836 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.81788725234e-08	41 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.578 RNAsubopt: 0.462 Sensitivity ContextFold: 0.471 RNAsubopt: 0.408 Positive Predictive Value ContextFold: 0.713 RNAsubopt: 0.529 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.612 RNAsubopt: 0.534 Sensitivity RNASampler(20): 0.471 RNAsubopt: 0.477 Positive Predictive Value RNASampler(20): 0.799 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAsubopt: 0.505 Sensitivity PETfold_pre2.0(20): 0.530 RNAsubopt: 0.451 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAsubopt: 0.572 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	20 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.616 RNAsubopt: 0.526 Sensitivity TurboFold(20): 0.508 RNAsubopt: 0.468 Positive Predictive Value TurboFold(20): 0.752 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.611 RNAsubopt: 0.534 Sensitivity MXScarna(20): 0.509 RNAsubopt: 0.477 Positive Predictive Value MXScarna(20): 0.737 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.549 RNAsubopt: 0.510 Sensitivity RNAalifold(seed): 0.338 RNAsubopt: 0.465 Positive Predictive Value RNAalifold(seed): 0.895 RNAsubopt: 0.564 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.590 RNAsubopt: 0.534 Sensitivity Murlet(20): 0.438 RNAsubopt: 0.477 Positive Predictive Value Murlet(20): 0.799 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 RNAsubopt: 0.537 Sensitivity CentroidAlifold(seed): 0.367 RNAsubopt: 0.485 Positive Predictive Value CentroidAlifold(seed): 0.923 RNAsubopt: 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.590 RNAsubopt: 0.534 Sensitivity Carnac(20): 0.389 RNAsubopt: 0.477 Positive Predictive Value Carnac(20): 0.899 RNAsubopt: 0.604 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.542 RNAsubopt: 0.475 Sensitivity IPknot: 0.445 RNAsubopt: 0.417 Positive Predictive Value IPknot: 0.665 RNAsubopt: 0.546 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 RNAsubopt: 0.482 Sensitivity CentroidHomfold‑LAST: 0.378 RNAsubopt: 0.420 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RNAsubopt: 0.559 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.530 RNAsubopt: 0.509 Sensitivity Contrafold: 0.462 RNAsubopt: 0.452 Positive Predictive Value Contrafold: 0.611 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.552 RNAsubopt: 0.509 Sensitivity Sfold: 0.459 RNAsubopt: 0.452 Positive Predictive Value Sfold: 0.669 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.535 RNAsubopt: 0.509 Sensitivity HotKnots: 0.474 RNAsubopt: 0.452 Positive Predictive Value HotKnots: 0.610 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.527 RNAsubopt: 0.514 Sensitivity CentroidFold: 0.442 RNAsubopt: 0.458 Positive Predictive Value CentroidFold: 0.634 RNAsubopt: 0.581 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAsubopt: 0.467 Sensitivity TurboFold(seed): 0.434 RNAsubopt: 0.413 Positive Predictive Value TurboFold(seed): 0.650 RNAsubopt: 0.534 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	74 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.529 RNAsubopt: 0.513 Sensitivity MaxExpect: 0.458 RNAsubopt: 0.457 Positive Predictive Value MaxExpect: 0.616 RNAsubopt: 0.580 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.552 RNAsubopt: 0.544 Sensitivity RSpredict(20): 0.436 RNAsubopt: 0.489 Positive Predictive Value RSpredict(20): 0.703 RNAsubopt: 0.609 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 1.97386617324e-07	82 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.530 RNAsubopt: 0.509 Sensitivity PknotsRG: 0.468 RNAsubopt: 0.452 Positive Predictive Value PknotsRG: 0.605 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs RNAsubopt Matthews Correlation Coefficient CMfinder(20): 0.521 RNAsubopt: 0.521 Sensitivity CMfinder(20): 0.366 RNAsubopt: 0.465 Positive Predictive Value CMfinder(20): 0.748 RNAsubopt: 0.590 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0128883198586	82 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.534 RNAsubopt: 0.509 Sensitivity UNAFold: 0.466 RNAsubopt: 0.452 Positive Predictive Value UNAFold: 0.617 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.515 RNAsubopt: 0.510 Sensitivity ProbKnot: 0.458 RNAsubopt: 0.454 Positive Predictive Value ProbKnot: 0.583 RNAsubopt: 0.576 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 5.62644058675e-08	41 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.560 Cylofold: 0.554 Sensitivity RNAsubopt: 0.492 Cylofold: 0.463 Positive Predictive Value RNAsubopt: 0.645 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.028456752624	82 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.524 RNAsubopt: 0.509 Sensitivity RNAfold: 0.460 RNAsubopt: 0.452 Positive Predictive Value RNAfold: 0.601 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.482 RNAsubopt: 0.454 Sensitivity RNASampler(seed): 0.342 RNAsubopt: 0.419 Positive Predictive Value RNASampler(seed): 0.684 RNAsubopt: 0.499 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08		+ RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.547 Multilign(20): 0.534 Sensitivity RNAsubopt: 0.488 Multilign(20): 0.449 Positive Predictive Value RNAsubopt: 0.619 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.32662850847e-07	+ RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.496 Afold: 0.488 Sensitivity RNAsubopt: 0.448 Afold: 0.439 Positive Predictive Value RNAsubopt: 0.553 Afold: 0.547 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 1.97386617324e-07	+ RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.509 RNAshapes: 0.499 Sensitivity RNAsubopt: 0.452 RNAshapes: 0.434 Positive Predictive Value RNAsubopt: 0.579 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ RNAsubopt vs Fold Matthews Correlation Coefficient RNAsubopt: 0.519 Fold: 0.501 Sensitivity RNAsubopt: 0.463 Fold: 0.444 Positive Predictive Value RNAsubopt: 0.586 Fold: 0.570 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.509 McQFold: 0.481 Sensitivity RNAsubopt: 0.452 McQFold: 0.409 Positive Predictive Value RNAsubopt: 0.579 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.462 RNASLOpt: 0.427 Sensitivity RNAsubopt: 0.408 RNASLOpt: 0.341 Positive Predictive Value RNAsubopt: 0.529 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.534 Mastr(20): 0.500 Sensitivity RNAsubopt: 0.477 Mastr(20): 0.336 Positive Predictive Value RNAsubopt: 0.604 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.1569883686e-08	- Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.556 RNAsubopt: 0.530 Sensitivity Multilign(seed): 0.432 RNAsubopt: 0.457 Positive Predictive Value Multilign(seed): 0.723 RNAsubopt: 0.622 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.00475527001e-08	+ RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.537 Pknots: 0.507 Sensitivity RNAsubopt: 0.474 Pknots: 0.454 Positive Predictive Value RNAsubopt: 0.614 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.521 Vsfold4: 0.451 Sensitivity RNAsubopt: 0.463 Vsfold4: 0.373 Positive Predictive Value RNAsubopt: 0.591 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.467 RNAsubopt: 0.454 Sensitivity CRWrnafold: 0.410 RNAsubopt: 0.403 Positive Predictive Value CRWrnafold: 0.540 RNAsubopt: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.07671381975e-06	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.527 Murlet(seed): 0.448 Sensitivity RNAsubopt: 0.468 Murlet(seed): 0.245 Positive Predictive Value RNAsubopt: 0.598 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.522 Vsfold5: 0.409 Sensitivity RNAsubopt: 0.464 Vsfold5: 0.346 Positive Predictive Value RNAsubopt: 0.593 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.520 MCFold: 0.385 Sensitivity RNAsubopt: 0.463 MCFold: 0.396 Positive Predictive Value RNAsubopt: 0.591 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.550 Alterna: 0.523 Sensitivity RNAsubopt: 0.468 Alterna: 0.449 Positive Predictive Value RNAsubopt: 0.655 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.552 RDfolder: 0.461 Sensitivity RNAsubopt: 0.474 RDfolder: 0.358 Positive Predictive Value RNAsubopt: 0.653 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.475 RNAwolf: 0.323 Sensitivity RNAsubopt: 0.417 RNAwolf: 0.301 Positive Predictive Value RNAsubopt: 0.546 RNAwolf: 0.354 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.489 NanoFolder: 0.272 Sensitivity RNAsubopt: 0.433 NanoFolder: 0.284 Positive Predictive Value RNAsubopt: 0.559 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.555 Carnac(seed): 0.179 Sensitivity RNAsubopt: 0.497 Carnac(seed): 0.032 Positive Predictive Value RNAsubopt: 0.625 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.540 RSpredict(seed): 0.178 Sensitivity RNAsubopt: 0.489 RSpredict(seed): 0.075 Positive Predictive Value RNAsubopt: 0.600 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.540 PPfold(seed): 0.148 Sensitivity RNAsubopt: 0.478 PPfold(seed): 0.032 Positive Predictive Value RNAsubopt: 0.616 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): N/A RNAsubopt: N/A Sensitivity CMfinder(seed): N/A RNAsubopt: N/A Positive Predictive Value CMfinder(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAsubopt: 0.685 Sensitivity PETfold_2.0(seed): 0.642 RNAsubopt: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAsubopt: 0.831 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs DAFS(20) Matthews Correlation Coefficient RNAsubopt: N/A DAFS(20): N/A Sensitivity RNAsubopt: N/A DAFS(20): N/A Positive Predictive Value RNAsubopt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAsubopt: 0.542 Sensitivity PETfold_2.0(20): 0.509 RNAsubopt: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAsubopt Matthews Correlation Coefficient DAFS(seed): N/A RNAsubopt: N/A Sensitivity DAFS(seed): N/A RNAsubopt: N/A Positive Predictive Value DAFS(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.533 Mastr(seed): 0.023 Sensitivity RNAsubopt: 0.480 Mastr(seed): 0.002 Positive Predictive Value RNAsubopt: 0.596 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(20)	19 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.688 Multilign(20): 0.534 Sensitivity CentroidAlifold(20): 0.537 Multilign(20): 0.449 Positive Predictive Value CentroidAlifold(20): 0.884 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	16 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(seed): 0.616 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.86595104665e-08	19 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Multilign(20): 0.534 Sensitivity RNAalifold(20): 0.521 Multilign(20): 0.449 Positive Predictive Value RNAalifold(20): 0.841 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	18 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.634 Multilign(20): 0.521 Sensitivity MXScarna(seed): 0.518 Multilign(20): 0.438 Positive Predictive Value MXScarna(seed): 0.782 Multilign(20): 0.627 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	19 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.684 Multilign(20): 0.534 Sensitivity PPfold(20): 0.552 Multilign(20): 0.449 Positive Predictive Value PPfold(20): 0.851 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	16 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.628 Multilign(20): 0.514 Sensitivity ContextFold: 0.514 Multilign(20): 0.433 Positive Predictive Value ContextFold: 0.771 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.7402423548e-08	19 RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.604 Multilign(20): 0.534 Sensitivity RNASampler(20): 0.470 Multilign(20): 0.449 Positive Predictive Value RNASampler(20): 0.780 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.02344513449e-08	16 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.681 Multilign(20): 0.514 Sensitivity PETfold_pre2.0(20): 0.564 Multilign(20): 0.433 Positive Predictive Value PETfold_pre2.0(20): 0.825 Multilign(20): 0.617 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.87872347734e-08	19 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.631 Multilign(20): 0.534 Sensitivity TurboFold(20): 0.526 Multilign(20): 0.449 Positive Predictive Value TurboFold(20): 0.762 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	19 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.595 Multilign(20): 0.534 Sensitivity MXScarna(20): 0.496 Multilign(20): 0.449 Positive Predictive Value MXScarna(20): 0.719 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	9 RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.563 Multilign(20): 0.380 Sensitivity RNAalifold(seed): 0.338 Multilign(20): 0.317 Positive Predictive Value RNAalifold(seed): 0.942 Multilign(20): 0.462 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.597 Multilign(20): 0.534 Sensitivity Murlet(20): 0.455 Multilign(20): 0.449 Positive Predictive Value Murlet(20): 0.789 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	19 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.565 Multilign(20): 0.534 Sensitivity CentroidAlifold(seed): 0.338 Multilign(20): 0.449 Positive Predictive Value CentroidAlifold(seed): 0.950 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	19 Carnac(20) vs Multilign(20) Matthews Correlation Coefficient Carnac(20): 0.580 Multilign(20): 0.534 Sensitivity Carnac(20): 0.391 Multilign(20): 0.449 Positive Predictive Value Carnac(20): 0.866 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	19 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.544 Multilign(20): 0.534 Sensitivity IPknot: 0.461 Multilign(20): 0.449 Positive Predictive Value IPknot: 0.647 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.82922338419e-05	19 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.589 Multilign(20): 0.534 Sensitivity CentroidHomfold‑LAST: 0.501 Multilign(20): 0.449 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.61939086268e-08	19 Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.539 Multilign(20): 0.534 Sensitivity Contrafold: 0.479 Multilign(20): 0.449 Positive Predictive Value Contrafold: 0.614 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00064555593904	19 Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.539 Multilign(20): 0.534 Sensitivity Sfold: 0.457 Multilign(20): 0.449 Positive Predictive Value Sfold: 0.643 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.00419758437992	19 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.538 Multilign(20): 0.534 Sensitivity HotKnots: 0.477 Multilign(20): 0.449 Positive Predictive Value HotKnots: 0.613 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000108864879631	19 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.534 CentroidFold: 0.476 Sensitivity Multilign(20): 0.449 CentroidFold: 0.410 Positive Predictive Value Multilign(20): 0.642 CentroidFold: 0.559 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	9 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.498 Multilign(20): 0.460 Sensitivity TurboFold(seed): 0.413 Multilign(20): 0.388 Positive Predictive Value TurboFold(seed): 0.606 Multilign(20): 0.553 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.534 MaxExpect: 0.510 Sensitivity Multilign(20): 0.449 MaxExpect: 0.443 Positive Predictive Value Multilign(20): 0.642 MaxExpect: 0.592 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.95070920198e-08	19 RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.539 Multilign(20): 0.534 Sensitivity RSpredict(20): 0.414 Multilign(20): 0.449 Positive Predictive Value RSpredict(20): 0.709 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.93966096077e-06	19 PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.563 Multilign(20): 0.534 Sensitivity PknotsRG: 0.499 Multilign(20): 0.449 Positive Predictive Value PknotsRG: 0.642 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.1413769576e-08	10 CMfinder(20) vs Multilign(20) Matthews Correlation Coefficient CMfinder(20): 0.539 Multilign(20): 0.502 Sensitivity CMfinder(20): 0.389 Multilign(20): 0.418 Positive Predictive Value CMfinder(20): 0.751 Multilign(20): 0.609 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.5677163434e-08	19 Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.534 UNAFold: 0.505 Sensitivity Multilign(20): 0.449 UNAFold: 0.443 Positive Predictive Value Multilign(20): 0.642 UNAFold: 0.582 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	19 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.534 ProbKnot: 0.511 Sensitivity Multilign(20): 0.449 ProbKnot: 0.451 Positive Predictive Value Multilign(20): 0.642 ProbKnot: 0.585 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	12 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.628 Multilign(20): 0.592 Sensitivity Cylofold: 0.529 Multilign(20): 0.496 Positive Predictive Value Cylofold: 0.751 Multilign(20): 0.714 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 5.4618626652e-08	19 Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.534 RNAfold: 0.526 Sensitivity Multilign(20): 0.449 RNAfold: 0.464 Positive Predictive Value Multilign(20): 0.642 RNAfold: 0.603 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.21488232292e-05	5 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.450 Multilign(20): 0.378 Sensitivity RNASampler(seed): 0.331 Multilign(20): 0.331 Positive Predictive Value RNASampler(seed): 0.615 Multilign(20): 0.437 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	19 RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.547 Multilign(20): 0.534 Sensitivity RNAsubopt: 0.488 Multilign(20): 0.449 Positive Predictive Value RNAsubopt: 0.619 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.32662850847e-07		? Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.476 Multilign(20): 0.430 Sensitivity Afold: 0.423 Multilign(20): 0.375 Positive Predictive Value Afold: 0.542 Multilign(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.534 RNAshapes: 0.525 Sensitivity Multilign(20): 0.449 RNAshapes: 0.461 Positive Predictive Value Multilign(20): 0.642 RNAshapes: 0.604 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8055779522e-08	+ Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.534 Fold: 0.500 Sensitivity Multilign(20): 0.449 Fold: 0.442 Positive Predictive Value Multilign(20): 0.642 Fold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.534 McQFold: 0.500 Sensitivity Multilign(20): 0.449 McQFold: 0.432 Positive Predictive Value Multilign(20): 0.642 McQFold: 0.587 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.56567380563e-08	+ Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.514 RNASLOpt: 0.481 Sensitivity Multilign(20): 0.433 RNASLOpt: 0.403 Positive Predictive Value Multilign(20): 0.617 RNASLOpt: 0.581 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	= Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.538 Multilign(20): 0.534 Sensitivity Mastr(20): 0.385 Multilign(20): 0.449 Positive Predictive Value Mastr(20): 0.757 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.290704005595	? Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.529 Multilign(20): 0.465 Sensitivity Multilign(seed): 0.404 Multilign(20): 0.377 Positive Predictive Value Multilign(seed): 0.701 Multilign(20): 0.582 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.534 Pknots: 0.458 Sensitivity Multilign(20): 0.449 Pknots: 0.404 Positive Predictive Value Multilign(20): 0.642 Pknots: 0.527 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.534 Vsfold4: 0.451 Sensitivity Multilign(20): 0.449 Vsfold4: 0.374 Positive Predictive Value Multilign(20): 0.642 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	? CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Multilign(20): 0.509 Sensitivity CRWrnafold: 0.483 Multilign(20): 0.432 Positive Predictive Value CRWrnafold: 0.623 Multilign(20): 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.439 Multilign(20): 0.380 Sensitivity Murlet(seed): 0.234 Multilign(20): 0.317 Positive Predictive Value Murlet(seed): 0.829 Multilign(20): 0.462 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.534 Vsfold5: 0.410 Sensitivity Multilign(20): 0.449 Vsfold5: 0.352 Positive Predictive Value Multilign(20): 0.642 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.519 MCFold: 0.408 Sensitivity Multilign(20): 0.437 MCFold: 0.422 Positive Predictive Value Multilign(20): 0.624 MCFold: 0.402 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	? Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.647 Alterna: 0.584 Sensitivity Multilign(20): 0.544 Alterna: 0.495 Positive Predictive Value Multilign(20): 0.778 Alterna: 0.699 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.614 RDfolder: 0.489 Sensitivity Multilign(20): 0.506 RDfolder: 0.365 Positive Predictive Value Multilign(20): 0.753 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.534 RNAwolf: 0.366 Sensitivity Multilign(20): 0.449 RNAwolf: 0.345 Positive Predictive Value Multilign(20): 0.642 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.537 NanoFolder: 0.271 Sensitivity Multilign(20): 0.455 NanoFolder: 0.286 Positive Predictive Value Multilign(20): 0.640 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.431 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.360 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.523 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.64686604905e-09	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.534 RSpredict(seed): 0.132 Sensitivity Multilign(20): 0.449 RSpredict(seed): 0.048 Positive Predictive Value Multilign(20): 0.642 RSpredict(seed): 0.371 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.534 PPfold(seed): 0.052 Sensitivity Multilign(20): 0.449 PPfold(seed): 0.007 Positive Predictive Value Multilign(20): 0.642 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	? CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A Multilign(20): N/A Sensitivity PETfold_2.0(seed): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(20) vs DAFS(20) Matthews Correlation Coefficient Multilign(20): N/A DAFS(20): N/A Sensitivity Multilign(20): N/A DAFS(20): N/A Positive Predictive Value Multilign(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A Multilign(20): N/A Sensitivity PETfold_2.0(20): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(20): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Multilign(20) Matthews Correlation Coefficient DAFS(seed): N/A Multilign(20): N/A Sensitivity DAFS(seed): N/A Multilign(20): N/A Positive Predictive Value DAFS(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.534 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.449 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.642 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08
Afold	17 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.647 Afold: 0.507 Sensitivity CentroidAlifold(20): 0.492 Afold: 0.462 Positive Predictive Value CentroidAlifold(20): 0.853 Afold: 0.559 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	6 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.639 Afold: 0.453 Sensitivity PETfold_pre2.0(seed): 0.521 Afold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Afold: 0.503 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	19 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.609 Afold: 0.511 Sensitivity RNAalifold(20): 0.468 Afold: 0.460 Positive Predictive Value RNAalifold(20): 0.795 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.08252958266e-08	26 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.623 Afold: 0.500 Sensitivity MXScarna(seed): 0.507 Afold: 0.463 Positive Predictive Value MXScarna(seed): 0.767 Afold: 0.544 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	5 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.541 Afold: 0.476 Sensitivity PPfold(20): 0.411 Afold: 0.423 Positive Predictive Value PPfold(20): 0.719 Afold: 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	18 Afold vs ContextFold Matthews Correlation Coefficient Afold: 0.337 ContextFold: 0.326 Sensitivity Afold: 0.303 ContextFold: 0.268 Positive Predictive Value Afold: 0.376 ContextFold: 0.398 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.0017973759e-06	19 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.585 Afold: 0.511 Sensitivity RNASampler(20): 0.447 Afold: 0.460 Positive Predictive Value RNASampler(20): 0.769 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	4 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.526 Afold: 0.416 Sensitivity PETfold_pre2.0(20): 0.410 Afold: 0.381 Positive Predictive Value PETfold_pre2.0(20): 0.679 Afold: 0.459 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.510 Afold: 0.476 Sensitivity TurboFold(20): 0.417 Afold: 0.423 Positive Predictive Value TurboFold(20): 0.631 Afold: 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	19 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.575 Afold: 0.511 Sensitivity MXScarna(20): 0.479 Afold: 0.460 Positive Predictive Value MXScarna(20): 0.694 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	16 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.501 RNAalifold(seed): 0.484 Sensitivity Afold: 0.466 RNAalifold(seed): 0.283 Positive Predictive Value Afold: 0.541 RNAalifold(seed): 0.829 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.81039766894e-08	19 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.554 Afold: 0.511 Sensitivity Murlet(20): 0.408 Afold: 0.460 Positive Predictive Value Murlet(20): 0.758 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	25 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.572 Afold: 0.495 Sensitivity CentroidAlifold(seed): 0.366 Afold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.899 Afold: 0.539 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	19 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.595 Afold: 0.511 Sensitivity Carnac(20): 0.382 Afold: 0.460 Positive Predictive Value Carnac(20): 0.928 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	19 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.386 Afold: 0.348 Sensitivity IPknot: 0.290 Afold: 0.312 Positive Predictive Value IPknot: 0.514 Afold: 0.389 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	14 Afold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Afold: 0.424 CentroidHomfold‑LAST: 0.388 Sensitivity Afold: 0.373 CentroidHomfold‑LAST: 0.263 Positive Predictive Value Afold: 0.490 CentroidHomfold‑LAST: 0.579 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.57172654109e-08	54 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.481 Afold: 0.408 Sensitivity Contrafold: 0.422 Afold: 0.368 Positive Predictive Value Contrafold: 0.548 Afold: 0.453 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	54 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.429 Afold: 0.408 Sensitivity Sfold: 0.361 Afold: 0.368 Positive Predictive Value Sfold: 0.511 Afold: 0.453 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.515 Afold: 0.488 Sensitivity HotKnots: 0.464 Afold: 0.439 Positive Predictive Value HotKnots: 0.577 Afold: 0.547 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.462 Afold: 0.402 Sensitivity CentroidFold: 0.381 Afold: 0.369 Positive Predictive Value CentroidFold: 0.561 Afold: 0.439 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.414 TurboFold(seed): 0.326 Sensitivity Afold: 0.374 TurboFold(seed): 0.281 Positive Predictive Value Afold: 0.464 TurboFold(seed): 0.386 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	44 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.484 Afold: 0.431 Sensitivity MaxExpect: 0.419 Afold: 0.383 Positive Predictive Value MaxExpect: 0.561 Afold: 0.487 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.549 Afold: 0.514 Sensitivity RSpredict(20): 0.462 Afold: 0.469 Positive Predictive Value RSpredict(20): 0.655 Afold: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	54 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.408 PknotsRG: 0.401 Sensitivity Afold: 0.368 PknotsRG: 0.362 Positive Predictive Value Afold: 0.453 PknotsRG: 0.444 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 0.000639955457467	2 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.492 CMfinder(20): 0.396 Sensitivity Afold: 0.427 CMfinder(20): 0.256 Positive Predictive Value Afold: 0.574 CMfinder(20): 0.618 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	54 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.412 Afold: 0.408 Sensitivity UNAFold: 0.367 Afold: 0.368 Positive Predictive Value UNAFold: 0.463 Afold: 0.453 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 1.10039559051e-07	30 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.424 Afold: 0.414 Sensitivity ProbKnot: 0.385 Afold: 0.378 Positive Predictive Value ProbKnot: 0.468 Afold: 0.455 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 6.53888633552e-08	22 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.559 Cylofold: 0.535 Sensitivity Afold: 0.497 Cylofold: 0.451 Positive Predictive Value Afold: 0.634 Cylofold: 0.641 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 6.07491858776e-08	54 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.408 RNAfold: 0.407 Sensitivity Afold: 0.368 RNAfold: 0.367 Positive Predictive Value Afold: 0.453 RNAfold: 0.451 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 0.109706356059	10 RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.493 Afold: 0.487 Sensitivity RNASampler(seed): 0.365 Afold: 0.443 Positive Predictive Value RNASampler(seed): 0.671 Afold: 0.540 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0806085266796	50 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.496 Afold: 0.488 Sensitivity RNAsubopt: 0.448 Afold: 0.439 Positive Predictive Value RNAsubopt: 0.553 Afold: 0.547 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 1.97386617324e-07	5 Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.476 Multilign(20): 0.430 Sensitivity Afold: 0.423 Multilign(20): 0.375 Positive Predictive Value Afold: 0.542 Multilign(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		+ Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.488 RNAshapes: 0.479 Sensitivity Afold: 0.439 RNAshapes: 0.425 Positive Predictive Value Afold: 0.547 RNAshapes: 0.545 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 1.18450348589e-07	= Afold vs Fold Matthews Correlation Coefficient Afold: 0.422 Fold: 0.419 Sensitivity Afold: 0.386 Fold: 0.381 Positive Predictive Value Afold: 0.463 Fold: 0.463 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.00108987668019	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.408 McQFold: 0.319 Sensitivity Afold: 0.368 McQFold: 0.248 Positive Predictive Value Afold: 0.453 McQFold: 0.412 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs Afold Matthews Correlation Coefficient RNASLOpt: 0.393 Afold: 0.383 Sensitivity RNASLOpt: 0.331 Afold: 0.344 Positive Predictive Value RNASLOpt: 0.474 Afold: 0.434 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.26278708866e-06	- Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.528 Afold: 0.511 Sensitivity Mastr(20): 0.350 Afold: 0.460 Positive Predictive Value Mastr(20): 0.800 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	? Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.520 Afold: 0.491 Sensitivity Multilign(seed): 0.409 Afold: 0.425 Positive Predictive Value Multilign(seed): 0.667 Afold: 0.574 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	= Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.529 Afold: 0.526 Sensitivity Pknots: 0.481 Afold: 0.468 Positive Predictive Value Pknots: 0.588 Afold: 0.598 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0982739791036	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.497 Vsfold4: 0.438 Sensitivity Afold: 0.447 Vsfold4: 0.366 Positive Predictive Value Afold: 0.559 Vsfold4: 0.531 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.475 CRWrnafold: 0.299 Sensitivity Afold: 0.442 CRWrnafold: 0.273 Positive Predictive Value Afold: 0.518 CRWrnafold: 0.336 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.543 Murlet(seed): 0.435 Sensitivity Afold: 0.483 Murlet(seed): 0.246 Positive Predictive Value Afold: 0.616 Murlet(seed): 0.775 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.497 Vsfold5: 0.388 Sensitivity Afold: 0.447 Vsfold5: 0.330 Positive Predictive Value Afold: 0.559 Vsfold5: 0.462 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.521 MCFold: 0.385 Sensitivity Afold: 0.468 MCFold: 0.406 Positive Predictive Value Afold: 0.588 MCFold: 0.374 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Alterna Matthews Correlation Coefficient Afold: 0.546 Alterna: 0.518 Sensitivity Afold: 0.475 Alterna: 0.447 Positive Predictive Value Afold: 0.637 Alterna: 0.612 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.92687381315e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.534 RDfolder: 0.458 Sensitivity Afold: 0.466 RDfolder: 0.362 Positive Predictive Value Afold: 0.622 RDfolder: 0.593 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.348 RNAwolf: 0.218 Sensitivity Afold: 0.312 RNAwolf: 0.203 Positive Predictive Value Afold: 0.389 RNAwolf: 0.235 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.380 NanoFolder: 0.230 Sensitivity Afold: 0.339 NanoFolder: 0.249 Positive Predictive Value Afold: 0.432 NanoFolder: 0.221 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.563 Carnac(seed): 0.163 Sensitivity Afold: 0.509 Carnac(seed): 0.027 Positive Predictive Value Afold: 0.628 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.36849473644e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.500 RSpredict(seed): 0.242 Sensitivity Afold: 0.463 RSpredict(seed): 0.112 Positive Predictive Value Afold: 0.544 RSpredict(seed): 0.526 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.492 PPfold(seed): 0.127 Sensitivity Afold: 0.439 PPfold(seed): 0.031 Positive Predictive Value Afold: 0.559 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): N/A Afold: N/A Sensitivity CMfinder(seed): N/A Afold: N/A Positive Predictive Value CMfinder(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs PETfold_2.0(seed) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(seed): N/A Sensitivity Afold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Afold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs DAFS(20) Matthews Correlation Coefficient Afold: N/A DAFS(20): N/A Sensitivity Afold: N/A DAFS(20): N/A Positive Predictive Value Afold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs PETfold_2.0(20) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(20): N/A Sensitivity Afold: N/A PETfold_2.0(20): N/A Positive Predictive Value Afold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Afold Matthews Correlation Coefficient DAFS(seed): N/A Afold: N/A Sensitivity DAFS(seed): N/A Afold: N/A Positive Predictive Value DAFS(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.499 Mastr(seed): 0.000 Sensitivity Afold: 0.457 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.548 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08
RNAshapes	36 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.682 RNAshapes: 0.517 Sensitivity CentroidAlifold(20): 0.529 RNAshapes: 0.455 Positive Predictive Value CentroidAlifold(20): 0.882 RNAshapes: 0.594 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNAshapes: 0.491 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNAshapes: 0.567 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.656 RNAshapes: 0.517 Sensitivity RNAalifold(20): 0.511 RNAshapes: 0.453 Positive Predictive Value RNAalifold(20): 0.846 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAshapes: 0.523 Sensitivity MXScarna(seed): 0.522 RNAshapes: 0.464 Positive Predictive Value MXScarna(seed): 0.783 RNAshapes: 0.594 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.663 RNAshapes: 0.503 Sensitivity PPfold(20): 0.528 RNAshapes: 0.443 Positive Predictive Value PPfold(20): 0.836 RNAshapes: 0.576 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	41 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.578 RNAshapes: 0.445 Sensitivity ContextFold: 0.471 RNAshapes: 0.386 Positive Predictive Value ContextFold: 0.713 RNAshapes: 0.519 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.612 RNAshapes: 0.517 Sensitivity RNASampler(20): 0.471 RNAshapes: 0.453 Positive Predictive Value RNASampler(20): 0.799 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAshapes: 0.454 Sensitivity PETfold_pre2.0(20): 0.530 RNAshapes: 0.402 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.7402423548e-08	20 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.616 RNAshapes: 0.503 Sensitivity TurboFold(20): 0.508 RNAshapes: 0.443 Positive Predictive Value TurboFold(20): 0.752 RNAshapes: 0.576 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	38 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.611 RNAshapes: 0.517 Sensitivity MXScarna(20): 0.509 RNAshapes: 0.453 Positive Predictive Value MXScarna(20): 0.737 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.549 RNAshapes: 0.515 Sensitivity RNAalifold(seed): 0.338 RNAshapes: 0.460 Positive Predictive Value RNAalifold(seed): 0.895 RNAshapes: 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.590 RNAshapes: 0.517 Sensitivity Murlet(20): 0.438 RNAshapes: 0.453 Positive Predictive Value Murlet(20): 0.799 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 RNAshapes: 0.521 Sensitivity CentroidAlifold(seed): 0.367 RNAshapes: 0.462 Positive Predictive Value CentroidAlifold(seed): 0.923 RNAshapes: 0.593 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.590 RNAshapes: 0.517 Sensitivity Carnac(20): 0.389 RNAshapes: 0.453 Positive Predictive Value Carnac(20): 0.899 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.542 RNAshapes: 0.460 Sensitivity IPknot: 0.445 RNAshapes: 0.397 Positive Predictive Value IPknot: 0.665 RNAshapes: 0.537 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 RNAshapes: 0.466 Sensitivity CentroidHomfold‑LAST: 0.378 RNAshapes: 0.398 Positive Predictive Value CentroidHomfold‑LAST: 0.699 RNAshapes: 0.551 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.530 RNAshapes: 0.499 Sensitivity Contrafold: 0.462 RNAshapes: 0.434 Positive Predictive Value Contrafold: 0.611 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.552 RNAshapes: 0.499 Sensitivity Sfold: 0.459 RNAshapes: 0.434 Positive Predictive Value Sfold: 0.669 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.535 RNAshapes: 0.499 Sensitivity HotKnots: 0.474 RNAshapes: 0.434 Positive Predictive Value HotKnots: 0.610 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.527 RNAshapes: 0.501 Sensitivity CentroidFold: 0.442 RNAshapes: 0.439 Positive Predictive Value CentroidFold: 0.634 RNAshapes: 0.577 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAshapes: 0.499 Sensitivity TurboFold(seed): 0.434 RNAshapes: 0.438 Positive Predictive Value TurboFold(seed): 0.650 RNAshapes: 0.575 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.77512146924e-08	74 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.529 RNAshapes: 0.501 Sensitivity MaxExpect: 0.458 RNAshapes: 0.438 Positive Predictive Value MaxExpect: 0.616 RNAshapes: 0.577 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.552 RNAshapes: 0.533 Sensitivity RSpredict(20): 0.436 RNAshapes: 0.471 Positive Predictive Value RSpredict(20): 0.703 RNAshapes: 0.608 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.85233844192e-08	82 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.530 RNAshapes: 0.499 Sensitivity PknotsRG: 0.468 RNAshapes: 0.434 Positive Predictive Value PknotsRG: 0.605 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.521 RNAshapes: 0.446 Sensitivity CMfinder(20): 0.366 RNAshapes: 0.393 Positive Predictive Value CMfinder(20): 0.748 RNAshapes: 0.513 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.08252958266e-08	82 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.534 RNAshapes: 0.499 Sensitivity UNAFold: 0.466 RNAshapes: 0.434 Positive Predictive Value UNAFold: 0.617 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.515 RNAshapes: 0.493 Sensitivity ProbKnot: 0.458 RNAshapes: 0.432 Positive Predictive Value ProbKnot: 0.583 RNAshapes: 0.568 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.554 RNAshapes: 0.539 Sensitivity Cylofold: 0.463 RNAshapes: 0.470 Positive Predictive Value Cylofold: 0.669 RNAshapes: 0.625 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 5.62644058675e-08	82 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.524 RNAshapes: 0.499 Sensitivity RNAfold: 0.460 RNAshapes: 0.434 Positive Predictive Value RNAfold: 0.601 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.482 RNAshapes: 0.468 Sensitivity RNASampler(seed): 0.342 RNAshapes: 0.423 Positive Predictive Value RNASampler(seed): 0.684 RNAshapes: 0.524 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 9.60786361713e-08	82 RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.509 RNAshapes: 0.499 Sensitivity RNAsubopt: 0.452 RNAshapes: 0.434 Positive Predictive Value RNAsubopt: 0.579 RNAshapes: 0.579 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 4.48494289621e-08	19 Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.534 RNAshapes: 0.525 Sensitivity Multilign(20): 0.449 RNAshapes: 0.461 Positive Predictive Value Multilign(20): 0.642 RNAshapes: 0.604 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8055779522e-08	50 Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.488 RNAshapes: 0.479 Sensitivity Afold: 0.439 RNAshapes: 0.425 Positive Predictive Value Afold: 0.547 RNAshapes: 0.545 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 1.18450348589e-07		= Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.501 RNAshapes: 0.499 Sensitivity Fold: 0.444 RNAshapes: 0.438 Positive Predictive Value Fold: 0.570 RNAshapes: 0.574 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.231589081714	+ RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.499 McQFold: 0.481 Sensitivity RNAshapes: 0.434 McQFold: 0.409 Positive Predictive Value RNAshapes: 0.579 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.445 RNASLOpt: 0.427 Sensitivity RNAshapes: 0.386 RNASLOpt: 0.341 Positive Predictive Value RNAshapes: 0.519 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.517 Mastr(20): 0.500 Sensitivity RNAshapes: 0.453 Mastr(20): 0.336 Positive Predictive Value RNAshapes: 0.595 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.53079410487e-06	= Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.556 RNAshapes: 0.540 Sensitivity Multilign(seed): 0.432 RNAshapes: 0.462 Positive Predictive Value Multilign(seed): 0.723 RNAshapes: 0.637 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00137673878406	+ RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.529 Pknots: 0.507 Sensitivity RNAshapes: 0.460 Pknots: 0.454 Positive Predictive Value RNAshapes: 0.615 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.507 Vsfold4: 0.451 Sensitivity RNAshapes: 0.442 Vsfold4: 0.373 Positive Predictive Value RNAshapes: 0.586 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.508 CRWrnafold: 0.467 Sensitivity RNAshapes: 0.442 CRWrnafold: 0.410 Positive Predictive Value RNAshapes: 0.591 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.542 Murlet(seed): 0.448 Sensitivity RNAshapes: 0.473 Murlet(seed): 0.245 Positive Predictive Value RNAshapes: 0.626 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.506 Vsfold5: 0.409 Sensitivity RNAshapes: 0.442 Vsfold5: 0.346 Positive Predictive Value RNAshapes: 0.586 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.526 MCFold: 0.385 Sensitivity RNAshapes: 0.461 MCFold: 0.396 Positive Predictive Value RNAshapes: 0.608 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.554 Alterna: 0.523 Sensitivity RNAshapes: 0.466 Alterna: 0.449 Positive Predictive Value RNAshapes: 0.669 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.546 RDfolder: 0.461 Sensitivity RNAshapes: 0.461 RDfolder: 0.358 Positive Predictive Value RNAshapes: 0.655 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.460 RNAwolf: 0.323 Sensitivity RNAshapes: 0.397 RNAwolf: 0.301 Positive Predictive Value RNAshapes: 0.537 RNAwolf: 0.354 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.463 NanoFolder: 0.272 Sensitivity RNAshapes: 0.403 NanoFolder: 0.284 Positive Predictive Value RNAshapes: 0.538 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.556 Carnac(seed): 0.179 Sensitivity RNAshapes: 0.490 Carnac(seed): 0.032 Positive Predictive Value RNAshapes: 0.636 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.532 RSpredict(seed): 0.178 Sensitivity RNAshapes: 0.474 RSpredict(seed): 0.075 Positive Predictive Value RNAshapes: 0.603 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.526 PPfold(seed): 0.148 Sensitivity RNAshapes: 0.460 PPfold(seed): 0.032 Positive Predictive Value RNAshapes: 0.608 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAshapes: 0.493 Sensitivity PETfold_2.0(seed): 0.642 RNAshapes: 0.411 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAshapes: 0.600 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs DAFS(20) Matthews Correlation Coefficient RNAshapes: N/A DAFS(20): N/A Sensitivity RNAshapes: N/A DAFS(20): N/A Positive Predictive Value RNAshapes: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAshapes: 0.199 Sensitivity PETfold_2.0(20): 0.509 RNAshapes: 0.158 Positive Predictive Value PETfold_2.0(20): 0.829 RNAshapes: 0.265 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAshapes Matthews Correlation Coefficient DAFS(seed): N/A RNAshapes: N/A Sensitivity DAFS(seed): N/A RNAshapes: N/A Positive Predictive Value DAFS(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.521 Mastr(seed): 0.023 Sensitivity RNAshapes: 0.461 Mastr(seed): 0.002 Positive Predictive Value RNAshapes: 0.594 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	28 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.677 Fold: 0.531 Sensitivity CentroidAlifold(20): 0.518 Fold: 0.471 Positive Predictive Value CentroidAlifold(20): 0.887 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 Fold: 0.486 Sensitivity PETfold_pre2.0(seed): 0.602 Fold: 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.850 Fold: 0.551 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.649 Fold: 0.531 Sensitivity RNAalifold(20): 0.503 Fold: 0.471 Positive Predictive Value RNAalifold(20): 0.840 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	39 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.639 Fold: 0.520 Sensitivity MXScarna(seed): 0.530 Fold: 0.464 Positive Predictive Value MXScarna(seed): 0.772 Fold: 0.584 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.663 Fold: 0.479 Sensitivity PPfold(20): 0.528 Fold: 0.426 Positive Predictive Value PPfold(20): 0.836 Fold: 0.546 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	43 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.536 Fold: 0.403 Sensitivity ContextFold: 0.440 Fold: 0.357 Positive Predictive Value ContextFold: 0.654 Fold: 0.457 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.600 Fold: 0.531 Sensitivity RNASampler(20): 0.458 Fold: 0.471 Positive Predictive Value RNASampler(20): 0.790 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Fold: 0.458 Sensitivity PETfold_pre2.0(20): 0.530 Fold: 0.408 Positive Predictive Value PETfold_pre2.0(20): 0.798 Fold: 0.521 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	20 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.616 Fold: 0.479 Sensitivity TurboFold(20): 0.508 Fold: 0.426 Positive Predictive Value TurboFold(20): 0.752 Fold: 0.546 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.606 Fold: 0.531 Sensitivity MXScarna(20): 0.503 Fold: 0.471 Positive Predictive Value MXScarna(20): 0.734 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.02343278931e-08	22 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.602 Fold: 0.461 Sensitivity RNAalifold(seed): 0.425 Fold: 0.416 Positive Predictive Value RNAalifold(seed): 0.854 Fold: 0.513 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.587 Fold: 0.531 Sensitivity Murlet(20): 0.435 Fold: 0.471 Positive Predictive Value Murlet(20): 0.797 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	40 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.619 Fold: 0.519 Sensitivity CentroidAlifold(seed): 0.429 Fold: 0.464 Positive Predictive Value CentroidAlifold(seed): 0.895 Fold: 0.583 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.578 Fold: 0.531 Sensitivity Carnac(20): 0.373 Fold: 0.471 Positive Predictive Value Carnac(20): 0.899 Fold: 0.604 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	46 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.513 Fold: 0.411 Sensitivity IPknot: 0.411 Fold: 0.364 Positive Predictive Value IPknot: 0.641 Fold: 0.467 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 Fold: 0.448 Sensitivity CentroidHomfold‑LAST: 0.378 Fold: 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Fold: 0.522 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.495 Fold: 0.457 Sensitivity Contrafold: 0.431 Fold: 0.406 Positive Predictive Value Contrafold: 0.569 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.501 Fold: 0.457 Sensitivity Sfold: 0.424 Fold: 0.406 Positive Predictive Value Sfold: 0.593 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.535 Fold: 0.501 Sensitivity HotKnots: 0.477 Fold: 0.444 Positive Predictive Value HotKnots: 0.603 Fold: 0.570 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.85233844192e-08	63 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.490 Fold: 0.457 Sensitivity CentroidFold: 0.400 Fold: 0.406 Positive Predictive Value CentroidFold: 0.602 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.529 Fold: 0.432 Sensitivity TurboFold(seed): 0.434 Fold: 0.380 Positive Predictive Value TurboFold(seed): 0.650 Fold: 0.497 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.34821445183e-08	63 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.488 Fold: 0.457 Sensitivity MaxExpect: 0.424 Fold: 0.406 Positive Predictive Value MaxExpect: 0.563 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RSpredict(20) vs Fold Matthews Correlation Coefficient RSpredict(20): 0.538 Fold: 0.532 Sensitivity RSpredict(20): 0.421 Fold: 0.473 Positive Predictive Value RSpredict(20): 0.691 Fold: 0.602 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000322134726257	62 PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.488 Fold: 0.458 Sensitivity PknotsRG: 0.435 Fold: 0.407 Positive Predictive Value PknotsRG: 0.549 Fold: 0.518 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs Fold Matthews Correlation Coefficient CMfinder(20): 0.521 Fold: 0.470 Sensitivity CMfinder(20): 0.366 Fold: 0.416 Positive Predictive Value CMfinder(20): 0.748 Fold: 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-08	63 UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.484 Fold: 0.457 Sensitivity UNAFold: 0.426 Fold: 0.406 Positive Predictive Value UNAFold: 0.551 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.85233844192e-08	61 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.478 Fold: 0.451 Sensitivity ProbKnot: 0.423 Fold: 0.401 Positive Predictive Value ProbKnot: 0.542 Fold: 0.509 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.563 Cylofold: 0.554 Sensitivity Fold: 0.496 Cylofold: 0.463 Positive Predictive Value Fold: 0.646 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 1.95308298399e-06	63 RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.477 Fold: 0.457 Sensitivity RNAfold: 0.423 Fold: 0.406 Positive Predictive Value RNAfold: 0.540 Fold: 0.516 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.421 Fold: 0.385 Sensitivity RNASampler(seed): 0.289 Fold: 0.354 Positive Predictive Value RNASampler(seed): 0.617 Fold: 0.426 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.26710183075e-09	61 RNAsubopt vs Fold Matthews Correlation Coefficient RNAsubopt: 0.519 Fold: 0.501 Sensitivity RNAsubopt: 0.463 Fold: 0.444 Positive Predictive Value RNAsubopt: 0.586 Fold: 0.570 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 4.83792096436e-08	19 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.534 Fold: 0.500 Sensitivity Multilign(20): 0.449 Fold: 0.442 Positive Predictive Value Multilign(20): 0.642 Fold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	31 Afold vs Fold Matthews Correlation Coefficient Afold: 0.422 Fold: 0.419 Sensitivity Afold: 0.386 Fold: 0.381 Positive Predictive Value Afold: 0.463 Fold: 0.463 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.00108987668019	61 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.501 RNAshapes: 0.499 Sensitivity Fold: 0.444 RNAshapes: 0.438 Positive Predictive Value Fold: 0.570 RNAshapes: 0.574 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 0.231589081714		+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.457 McQFold: 0.425 Sensitivity Fold: 0.406 McQFold: 0.363 Positive Predictive Value Fold: 0.516 McQFold: 0.499 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.431 RNASLOpt: 0.427 Sensitivity Fold: 0.378 RNASLOpt: 0.341 Positive Predictive Value Fold: 0.496 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.0529232299595	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.531 Mastr(20): 0.471 Sensitivity Fold: 0.471 Mastr(20): 0.305 Positive Predictive Value Fold: 0.604 Mastr(20): 0.734 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	- Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.556 Fold: 0.505 Sensitivity Multilign(seed): 0.432 Fold: 0.435 Positive Predictive Value Multilign(seed): 0.723 Fold: 0.593 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.560 Pknots: 0.515 Sensitivity Fold: 0.495 Pknots: 0.461 Positive Predictive Value Fold: 0.640 Pknots: 0.582 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.539 Vsfold4: 0.444 Sensitivity Fold: 0.479 Vsfold4: 0.370 Positive Predictive Value Fold: 0.613 Vsfold4: 0.539 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.467 Fold: 0.446 Sensitivity CRWrnafold: 0.410 Fold: 0.394 Positive Predictive Value CRWrnafold: 0.540 Fold: 0.514 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.471 Murlet(seed): 0.426 Sensitivity Fold: 0.420 Murlet(seed): 0.226 Positive Predictive Value Fold: 0.536 Murlet(seed): 0.810 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.82974185391e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.530 Vsfold5: 0.413 Sensitivity Fold: 0.471 Vsfold5: 0.352 Positive Predictive Value Fold: 0.601 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.523 MCFold: 0.390 Sensitivity Fold: 0.465 MCFold: 0.399 Positive Predictive Value Fold: 0.594 MCFold: 0.390 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.624 Alterna: 0.543 Sensitivity Fold: 0.538 Alterna: 0.478 Positive Predictive Value Fold: 0.732 Alterna: 0.628 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.572 RDfolder: 0.463 Sensitivity Fold: 0.495 RDfolder: 0.363 Positive Predictive Value Fold: 0.670 RDfolder: 0.603 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.411 RNAwolf: 0.317 Sensitivity Fold: 0.364 RNAwolf: 0.293 Positive Predictive Value Fold: 0.467 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.503 NanoFolder: 0.272 Sensitivity Fold: 0.439 NanoFolder: 0.284 Positive Predictive Value Fold: 0.582 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.487 Carnac(seed): 0.411 Sensitivity Fold: 0.433 Carnac(seed): 0.190 Positive Predictive Value Fold: 0.548 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.520 RSpredict(seed): 0.335 Sensitivity Fold: 0.465 RSpredict(seed): 0.190 Positive Predictive Value Fold: 0.582 RSpredict(seed): 0.591 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.521 PPfold(seed): 0.148 Sensitivity Fold: 0.459 PPfold(seed): 0.032 Positive Predictive Value Fold: 0.599 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Fold: 0.665 Sensitivity PETfold_2.0(seed): 0.642 Fold: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 Fold: 0.783 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Fold vs DAFS(20) Matthews Correlation Coefficient Fold: N/A DAFS(20): N/A Sensitivity Fold: N/A DAFS(20): N/A Positive Predictive Value Fold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Fold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Fold: 0.513 Sensitivity PETfold_2.0(20): 0.509 Fold: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 Fold: 0.632 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Fold vs DAFS(seed) Matthews Correlation Coefficient Fold: N/A DAFS(seed): N/A Sensitivity Fold: N/A DAFS(seed): N/A Positive Predictive Value Fold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.545 Mastr(seed): 0.026 Sensitivity Fold: 0.487 Mastr(seed): 0.002 Positive Predictive Value Fold: 0.614 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08
McQFold	36 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.682 McQFold: 0.511 Sensitivity CentroidAlifold(20): 0.529 McQFold: 0.438 Positive Predictive Value CentroidAlifold(20): 0.882 McQFold: 0.601 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 McQFold: 0.484 Sensitivity PETfold_pre2.0(seed): 0.602 McQFold: 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.850 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	38 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.656 McQFold: 0.506 Sensitivity RNAalifold(20): 0.511 McQFold: 0.433 Positive Predictive Value RNAalifold(20): 0.846 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.646 McQFold: 0.506 Sensitivity MXScarna(seed): 0.536 McQFold: 0.436 Positive Predictive Value MXScarna(seed): 0.779 McQFold: 0.589 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.663 McQFold: 0.485 Sensitivity PPfold(20): 0.528 McQFold: 0.416 Positive Predictive Value PPfold(20): 0.836 McQFold: 0.572 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	43 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.536 McQFold: 0.368 Sensitivity ContextFold: 0.440 McQFold: 0.312 Positive Predictive Value ContextFold: 0.654 McQFold: 0.434 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.612 McQFold: 0.506 Sensitivity RNASampler(20): 0.471 McQFold: 0.433 Positive Predictive Value RNASampler(20): 0.799 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 McQFold: 0.449 Sensitivity PETfold_pre2.0(20): 0.530 McQFold: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 McQFold: 0.533 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	20 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.616 McQFold: 0.485 Sensitivity TurboFold(20): 0.508 McQFold: 0.416 Positive Predictive Value TurboFold(20): 0.752 McQFold: 0.572 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.611 McQFold: 0.506 Sensitivity MXScarna(20): 0.509 McQFold: 0.433 Positive Predictive Value MXScarna(20): 0.737 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.606 McQFold: 0.500 Sensitivity RNAalifold(seed): 0.427 McQFold: 0.437 Positive Predictive Value RNAalifold(seed): 0.861 McQFold: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	38 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.590 McQFold: 0.506 Sensitivity Murlet(20): 0.438 McQFold: 0.433 Positive Predictive Value Murlet(20): 0.799 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	51 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.618 McQFold: 0.507 Sensitivity CentroidAlifold(seed): 0.425 McQFold: 0.437 Positive Predictive Value CentroidAlifold(seed): 0.899 McQFold: 0.591 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.590 McQFold: 0.506 Sensitivity Carnac(20): 0.389 McQFold: 0.433 Positive Predictive Value Carnac(20): 0.899 McQFold: 0.598 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.513 McQFold: 0.380 Sensitivity IPknot: 0.411 McQFold: 0.322 Positive Predictive Value IPknot: 0.641 McQFold: 0.450 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.512 McQFold: 0.454 Sensitivity CentroidHomfold‑LAST: 0.378 McQFold: 0.381 Positive Predictive Value CentroidHomfold‑LAST: 0.699 McQFold: 0.547 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.500 McQFold: 0.363 Sensitivity Contrafold: 0.437 McQFold: 0.287 Positive Predictive Value Contrafold: 0.573 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.462 McQFold: 0.363 Sensitivity Sfold: 0.387 McQFold: 0.287 Positive Predictive Value Sfold: 0.552 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.535 McQFold: 0.481 Sensitivity HotKnots: 0.474 McQFold: 0.409 Positive Predictive Value HotKnots: 0.610 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.483 McQFold: 0.373 Sensitivity CentroidFold: 0.397 McQFold: 0.293 Positive Predictive Value CentroidFold: 0.587 McQFold: 0.476 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.529 McQFold: 0.490 Sensitivity TurboFold(seed): 0.434 McQFold: 0.425 Positive Predictive Value TurboFold(seed): 0.650 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.96094765137e-08	77 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.503 McQFold: 0.398 Sensitivity MaxExpect: 0.432 McQFold: 0.337 Positive Predictive Value MaxExpect: 0.586 McQFold: 0.471 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.552 McQFold: 0.516 Sensitivity RSpredict(20): 0.436 McQFold: 0.446 Positive Predictive Value RSpredict(20): 0.703 McQFold: 0.602 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.433 McQFold: 0.353 Sensitivity PknotsRG: 0.387 McQFold: 0.278 Positive Predictive Value PknotsRG: 0.485 McQFold: 0.450 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.521 McQFold: 0.456 Sensitivity CMfinder(20): 0.366 McQFold: 0.382 Positive Predictive Value CMfinder(20): 0.748 McQFold: 0.550 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.93248927742e-08	87 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.442 McQFold: 0.363 Sensitivity UNAFold: 0.390 McQFold: 0.287 Positive Predictive Value UNAFold: 0.501 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.478 McQFold: 0.421 Sensitivity ProbKnot: 0.423 McQFold: 0.360 Positive Predictive Value ProbKnot: 0.542 McQFold: 0.493 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.585 Cylofold: 0.554 Sensitivity McQFold: 0.493 Cylofold: 0.463 Positive Predictive Value McQFold: 0.700 Cylofold: 0.669 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.438 McQFold: 0.363 Sensitivity RNAfold: 0.390 McQFold: 0.287 Positive Predictive Value RNAfold: 0.493 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.482 McQFold: 0.465 Sensitivity RNASampler(seed): 0.342 McQFold: 0.419 Positive Predictive Value RNASampler(seed): 0.684 McQFold: 0.521 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.87872347734e-08	82 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.509 McQFold: 0.481 Sensitivity RNAsubopt: 0.452 McQFold: 0.409 Positive Predictive Value RNAsubopt: 0.579 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.85233844192e-08	19 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.534 McQFold: 0.500 Sensitivity Multilign(20): 0.449 McQFold: 0.432 Positive Predictive Value Multilign(20): 0.642 McQFold: 0.587 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.56567380563e-08	54 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.408 McQFold: 0.319 Sensitivity Afold: 0.368 McQFold: 0.248 Positive Predictive Value Afold: 0.453 McQFold: 0.412 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.499 McQFold: 0.481 Sensitivity RNAshapes: 0.434 McQFold: 0.409 Positive Predictive Value RNAshapes: 0.579 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.457 McQFold: 0.425 Sensitivity Fold: 0.406 McQFold: 0.363 Positive Predictive Value Fold: 0.516 McQFold: 0.499 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.427 McQFold: 0.422 Sensitivity RNASLOpt: 0.341 McQFold: 0.356 Positive Predictive Value RNASLOpt: 0.541 McQFold: 0.506 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.000102525955954	= McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.506 Mastr(20): 0.500 Sensitivity McQFold: 0.433 Mastr(20): 0.336 Positive Predictive Value McQFold: 0.598 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.00636070127375	= Multilign(seed) vs McQFold Matthews Correlation Coefficient Multilign(seed): 0.556 McQFold: 0.541 Sensitivity Multilign(seed): 0.432 McQFold: 0.448 Positive Predictive Value Multilign(seed): 0.723 McQFold: 0.660 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00194962432759	+ McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.522 Pknots: 0.507 Sensitivity McQFold: 0.441 Pknots: 0.454 Positive Predictive Value McQFold: 0.624 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.500 Vsfold4: 0.451 Sensitivity McQFold: 0.427 Vsfold4: 0.373 Positive Predictive Value McQFold: 0.590 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.487 CRWrnafold: 0.467 Sensitivity McQFold: 0.417 CRWrnafold: 0.410 Positive Predictive Value McQFold: 0.577 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.25975249062e-07	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.565 Murlet(seed): 0.448 Sensitivity McQFold: 0.488 Murlet(seed): 0.245 Positive Predictive Value McQFold: 0.659 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.508 Vsfold5: 0.409 Sensitivity McQFold: 0.433 Vsfold5: 0.346 Positive Predictive Value McQFold: 0.600 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.513 MCFold: 0.385 Sensitivity McQFold: 0.435 MCFold: 0.396 Positive Predictive Value McQFold: 0.611 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.580 Alterna: 0.523 Sensitivity McQFold: 0.475 Alterna: 0.449 Positive Predictive Value McQFold: 0.719 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.595 RDfolder: 0.461 Sensitivity McQFold: 0.488 RDfolder: 0.358 Positive Predictive Value McQFold: 0.734 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.380 RNAwolf: 0.317 Sensitivity McQFold: 0.322 RNAwolf: 0.293 Positive Predictive Value McQFold: 0.450 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.431 NanoFolder: 0.272 Sensitivity McQFold: 0.369 NanoFolder: 0.284 Positive Predictive Value McQFold: 0.511 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.518 Carnac(seed): 0.392 Sensitivity McQFold: 0.446 Carnac(seed): 0.172 Positive Predictive Value McQFold: 0.603 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.510 RSpredict(seed): 0.337 Sensitivity McQFold: 0.441 RSpredict(seed): 0.189 Positive Predictive Value McQFold: 0.591 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.524 PPfold(seed): 0.148 Sensitivity McQFold: 0.448 PPfold(seed): 0.032 Positive Predictive Value McQFold: 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 McQFold: 0.616 Sensitivity PETfold_2.0(seed): 0.642 McQFold: 0.453 Positive Predictive Value PETfold_2.0(seed): 0.924 McQFold: 0.843 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? McQFold vs DAFS(20) Matthews Correlation Coefficient McQFold: N/A DAFS(20): N/A Sensitivity McQFold: N/A DAFS(20): N/A Positive Predictive Value McQFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 McQFold: 0.491 Sensitivity PETfold_2.0(20): 0.509 McQFold: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 McQFold: 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? McQFold vs DAFS(seed) Matthews Correlation Coefficient McQFold: N/A DAFS(seed): N/A Sensitivity McQFold: N/A DAFS(seed): N/A Positive Predictive Value McQFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.518 Mastr(seed): 0.023 Sensitivity McQFold: 0.447 Mastr(seed): 0.002 Positive Predictive Value McQFold: 0.604 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASLOpt	18 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.656 RNASLOpt: 0.463 Sensitivity CentroidAlifold(20): 0.501 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.864 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	25 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 RNASLOpt: 0.499 Sensitivity PETfold_pre2.0(seed): 0.595 RNASLOpt: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	18 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.629 RNASLOpt: 0.463 Sensitivity RNAalifold(20): 0.488 RNASLOpt: 0.383 Positive Predictive Value RNAalifold(20): 0.815 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.21671975982e-08	24 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.605 RNASLOpt: 0.488 Sensitivity MXScarna(seed): 0.487 RNASLOpt: 0.398 Positive Predictive Value MXScarna(seed): 0.757 RNASLOpt: 0.604 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	17 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.649 RNASLOpt: 0.464 Sensitivity PPfold(20): 0.517 RNASLOpt: 0.387 Positive Predictive Value PPfold(20): 0.819 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.72523032126e-08	41 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.578 RNASLOpt: 0.427 Sensitivity ContextFold: 0.471 RNASLOpt: 0.341 Positive Predictive Value ContextFold: 0.713 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.561 RNASLOpt: 0.463 Sensitivity RNASampler(20): 0.429 RNASLOpt: 0.383 Positive Predictive Value RNASampler(20): 0.738 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	18 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNASLOpt: 0.463 Sensitivity PETfold_pre2.0(20): 0.530 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.04409141234e-08	17 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.606 RNASLOpt: 0.464 Sensitivity TurboFold(20): 0.502 RNASLOpt: 0.387 Positive Predictive Value TurboFold(20): 0.737 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	18 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.570 RNASLOpt: 0.463 Sensitivity MXScarna(20): 0.470 RNASLOpt: 0.383 Positive Predictive Value MXScarna(20): 0.696 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.86595104665e-08	13 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.544 RNASLOpt: 0.449 Sensitivity RNAalifold(seed): 0.327 RNASLOpt: 0.376 Positive Predictive Value RNAalifold(seed): 0.910 RNASLOpt: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	18 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.564 RNASLOpt: 0.463 Sensitivity Murlet(20): 0.418 RNASLOpt: 0.383 Positive Predictive Value Murlet(20): 0.765 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64481516727e-08	25 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.558 RNASLOpt: 0.499 Sensitivity CentroidAlifold(seed): 0.334 RNASLOpt: 0.408 Positive Predictive Value CentroidAlifold(seed): 0.936 RNASLOpt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.547 RNASLOpt: 0.463 Sensitivity Carnac(20): 0.351 RNASLOpt: 0.383 Positive Predictive Value Carnac(20): 0.858 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	41 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.533 RNASLOpt: 0.427 Sensitivity IPknot: 0.439 RNASLOpt: 0.341 Positive Predictive Value IPknot: 0.652 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.498 RNASLOpt: 0.437 Sensitivity CentroidHomfold‑LAST: 0.368 RNASLOpt: 0.347 Positive Predictive Value CentroidHomfold‑LAST: 0.679 RNASLOpt: 0.555 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.481 RNASLOpt: 0.427 Sensitivity Contrafold: 0.415 RNASLOpt: 0.341 Positive Predictive Value Contrafold: 0.562 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.508 RNASLOpt: 0.427 Sensitivity Sfold: 0.418 RNASLOpt: 0.341 Positive Predictive Value Sfold: 0.623 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.489 RNASLOpt: 0.427 Sensitivity HotKnots: 0.432 RNASLOpt: 0.341 Positive Predictive Value HotKnots: 0.559 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.447 RNASLOpt: 0.427 Sensitivity CentroidFold: 0.365 RNASLOpt: 0.341 Positive Predictive Value CentroidFold: 0.553 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.504 RNASLOpt: 0.430 Sensitivity TurboFold(seed): 0.416 RNASLOpt: 0.356 Positive Predictive Value TurboFold(seed): 0.616 RNASLOpt: 0.525 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.38194587311e-08	41 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.464 RNASLOpt: 0.427 Sensitivity MaxExpect: 0.395 RNASLOpt: 0.341 Positive Predictive Value MaxExpect: 0.550 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.491 RNASLOpt: 0.464 Sensitivity RSpredict(20): 0.373 RNASLOpt: 0.387 Positive Predictive Value RSpredict(20): 0.653 RNASLOpt: 0.562 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.86366296137e-06	41 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.497 RNASLOpt: 0.427 Sensitivity PknotsRG: 0.436 RNASLOpt: 0.341 Positive Predictive Value PknotsRG: 0.572 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.521 RNASLOpt: 0.455 Sensitivity CMfinder(20): 0.366 RNASLOpt: 0.375 Positive Predictive Value CMfinder(20): 0.748 RNASLOpt: 0.559 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.5281770229e-09	41 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.470 RNASLOpt: 0.427 Sensitivity UNAFold: 0.409 RNASLOpt: 0.341 Positive Predictive Value UNAFold: 0.545 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.464 RNASLOpt: 0.427 Sensitivity ProbKnot: 0.405 RNASLOpt: 0.341 Positive Predictive Value ProbKnot: 0.537 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 4.48494289621e-08	25 Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.466 RNASLOpt: 0.454 Sensitivity Cylofold: 0.390 RNASLOpt: 0.373 Positive Predictive Value Cylofold: 0.565 RNASLOpt: 0.559 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.24386558293e-07	41 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.481 RNASLOpt: 0.427 Sensitivity RNAfold: 0.418 RNASLOpt: 0.341 Positive Predictive Value RNAfold: 0.557 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.399 RNASampler(seed): 0.333 Sensitivity RNASLOpt: 0.347 RNASampler(seed): 0.224 Positive Predictive Value RNASLOpt: 0.464 RNASampler(seed): 0.500 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	41 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.462 RNASLOpt: 0.427 Sensitivity RNAsubopt: 0.408 RNASLOpt: 0.341 Positive Predictive Value RNAsubopt: 0.529 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.514 RNASLOpt: 0.481 Sensitivity Multilign(20): 0.433 RNASLOpt: 0.403 Positive Predictive Value Multilign(20): 0.617 RNASLOpt: 0.581 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	17 RNASLOpt vs Afold Matthews Correlation Coefficient RNASLOpt: 0.393 Afold: 0.383 Sensitivity RNASLOpt: 0.331 Afold: 0.344 Positive Predictive Value RNASLOpt: 0.474 Afold: 0.434 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.26278708866e-06	41 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.445 RNASLOpt: 0.427 Sensitivity RNAshapes: 0.386 RNASLOpt: 0.341 Positive Predictive Value RNAshapes: 0.519 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.431 RNASLOpt: 0.427 Sensitivity Fold: 0.378 RNASLOpt: 0.341 Positive Predictive Value Fold: 0.496 RNASLOpt: 0.541 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.0529232299595	41 RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.427 McQFold: 0.422 Sensitivity RNASLOpt: 0.341 McQFold: 0.356 Positive Predictive Value RNASLOpt: 0.541 McQFold: 0.506 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.000102525955954		= Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.465 RNASLOpt: 0.463 Sensitivity Mastr(20): 0.313 RNASLOpt: 0.383 Positive Predictive Value Mastr(20): 0.698 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.371318546591	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.533 RNASLOpt: 0.458 Sensitivity Multilign(seed): 0.411 RNASLOpt: 0.366 Positive Predictive Value Multilign(seed): 0.698 RNASLOpt: 0.578 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.453 Pknots: 0.424 Sensitivity RNASLOpt: 0.363 Pknots: 0.382 Positive Predictive Value RNASLOpt: 0.571 Pknots: 0.477 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.452 Vsfold4: 0.393 Sensitivity RNASLOpt: 0.362 Vsfold4: 0.321 Positive Predictive Value RNASLOpt: 0.571 Vsfold4: 0.488 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.445 RNASLOpt: 0.441 Sensitivity CRWrnafold: 0.391 RNASLOpt: 0.369 Positive Predictive Value CRWrnafold: 0.514 RNASLOpt: 0.536 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0590663124617	+ RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.449 Murlet(seed): 0.403 Sensitivity RNASLOpt: 0.376 Murlet(seed): 0.213 Positive Predictive Value RNASLOpt: 0.542 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.458 Vsfold5: 0.358 Sensitivity RNASLOpt: 0.379 Vsfold5: 0.307 Positive Predictive Value RNASLOpt: 0.562 Vsfold5: 0.426 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.415 MCFold: 0.358 Sensitivity RNASLOpt: 0.334 MCFold: 0.366 Positive Predictive Value RNASLOpt: 0.522 MCFold: 0.357 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.432 RNASLOpt: 0.360 Sensitivity Alterna: 0.379 RNASLOpt: 0.274 Positive Predictive Value Alterna: 0.505 RNASLOpt: 0.486 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.556 RDfolder: 0.396 Sensitivity RNASLOpt: 0.450 RDfolder: 0.302 Positive Predictive Value RNASLOpt: 0.698 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.427 RNAwolf: 0.306 Sensitivity RNASLOpt: 0.341 RNAwolf: 0.285 Positive Predictive Value RNASLOpt: 0.541 RNAwolf: 0.335 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.441 NanoFolder: 0.272 Sensitivity RNASLOpt: 0.350 NanoFolder: 0.284 Positive Predictive Value RNASLOpt: 0.564 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.472 Carnac(seed): 0.217 Sensitivity RNASLOpt: 0.392 Carnac(seed): 0.047 Positive Predictive Value RNASLOpt: 0.574 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.501 RSpredict(seed): 0.115 Sensitivity RNASLOpt: 0.413 RSpredict(seed): 0.046 Positive Predictive Value RNASLOpt: 0.615 RSpredict(seed): 0.294 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.501 PPfold(seed): 0.156 Sensitivity RNASLOpt: 0.413 PPfold(seed): 0.036 Positive Predictive Value RNASLOpt: 0.615 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	? CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): N/A RNASLOpt: N/A Sensitivity CMfinder(seed): N/A RNASLOpt: N/A Positive Predictive Value CMfinder(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNASLOpt: 0.625 Sensitivity PETfold_2.0(seed): 0.642 RNASLOpt: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 RNASLOpt: 0.797 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs DAFS(20) Matthews Correlation Coefficient RNASLOpt: N/A DAFS(20): N/A Sensitivity RNASLOpt: N/A DAFS(20): N/A Positive Predictive Value RNASLOpt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASLOpt: 0.456 Sensitivity PETfold_2.0(20): 0.509 RNASLOpt: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 RNASLOpt: 0.633 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNASLOpt Matthews Correlation Coefficient DAFS(seed): N/A RNASLOpt: N/A Sensitivity DAFS(seed): N/A RNASLOpt: N/A Positive Predictive Value DAFS(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.499 Mastr(seed): 0.034 Sensitivity RNASLOpt: 0.408 Mastr(seed): 0.003 Positive Predictive Value RNASLOpt: 0.616 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08
Mastr(20)	36 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Mastr(20): 0.496 Sensitivity CentroidAlifold(20): 0.529 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(20): 0.882 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(seed): 0.597 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	38 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(20): 0.500 Sensitivity RNAalifold(20): 0.511 Mastr(20): 0.336 Positive Predictive Value RNAalifold(20): 0.846 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	36 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.646 Mastr(20): 0.493 Sensitivity MXScarna(seed): 0.529 Mastr(20): 0.330 Positive Predictive Value MXScarna(seed): 0.791 Mastr(20): 0.742 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(20): 0.518 Sensitivity PPfold(20): 0.528 Mastr(20): 0.357 Positive Predictive Value PPfold(20): 0.836 Mastr(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.617 Mastr(20): 0.465 Sensitivity ContextFold: 0.499 Mastr(20): 0.313 Positive Predictive Value ContextFold: 0.767 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	38 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.612 Mastr(20): 0.500 Sensitivity RNASampler(20): 0.471 Mastr(20): 0.336 Positive Predictive Value RNASampler(20): 0.799 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(20): 0.465 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(20): 0.313 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(20): 0.698 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	20 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.616 Mastr(20): 0.518 Sensitivity TurboFold(20): 0.508 Mastr(20): 0.357 Positive Predictive Value TurboFold(20): 0.752 Mastr(20): 0.757 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	38 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.611 Mastr(20): 0.500 Sensitivity MXScarna(20): 0.509 Mastr(20): 0.336 Positive Predictive Value MXScarna(20): 0.737 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.559 Mastr(20): 0.353 Sensitivity RNAalifold(seed): 0.338 Mastr(20): 0.166 Positive Predictive Value RNAalifold(seed): 0.929 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.02510705504e-08	38 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.590 Mastr(20): 0.500 Sensitivity Murlet(20): 0.438 Mastr(20): 0.336 Positive Predictive Value Murlet(20): 0.799 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.587 Mastr(20): 0.496 Sensitivity CentroidAlifold(seed): 0.368 Mastr(20): 0.333 Positive Predictive Value CentroidAlifold(seed): 0.941 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.590 Mastr(20): 0.500 Sensitivity Carnac(20): 0.389 Mastr(20): 0.336 Positive Predictive Value Carnac(20): 0.899 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.526 Mastr(20): 0.496 Sensitivity IPknot: 0.433 Mastr(20): 0.341 Positive Predictive Value IPknot: 0.645 Mastr(20): 0.729 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 9.95914622767e-08	20 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Mastr(20): 0.513 Sensitivity CentroidHomfold‑LAST: 0.491 Mastr(20): 0.364 Positive Predictive Value CentroidHomfold‑LAST: 0.700 Mastr(20): 0.729 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	38 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.536 Mastr(20): 0.500 Sensitivity Contrafold: 0.472 Mastr(20): 0.336 Positive Predictive Value Contrafold: 0.613 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.1569883686e-08	38 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.560 Mastr(20): 0.500 Sensitivity Sfold: 0.466 Mastr(20): 0.336 Positive Predictive Value Sfold: 0.677 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.533 Mastr(20): 0.500 Sensitivity HotKnots: 0.475 Mastr(20): 0.336 Positive Predictive Value HotKnots: 0.604 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.48494289621e-08	36 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.542 Mastr(20): 0.496 Sensitivity CentroidFold: 0.459 Mastr(20): 0.333 Positive Predictive Value CentroidFold: 0.644 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.484 Mastr(20): 0.443 Sensitivity TurboFold(seed): 0.393 Mastr(20): 0.245 Positive Predictive Value TurboFold(seed): 0.601 Mastr(20): 0.809 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.26497248087e-08	36 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.557 Mastr(20): 0.496 Sensitivity MaxExpect: 0.481 Mastr(20): 0.333 Positive Predictive Value MaxExpect: 0.649 Mastr(20): 0.745 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.552 Mastr(20): 0.513 Sensitivity RSpredict(20): 0.436 Mastr(20): 0.346 Positive Predictive Value RSpredict(20): 0.703 Mastr(20): 0.765 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.557 Mastr(20): 0.500 Sensitivity PknotsRG: 0.494 Mastr(20): 0.336 Positive Predictive Value PknotsRG: 0.633 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.521 Mastr(20): 0.499 Sensitivity CMfinder(20): 0.366 Mastr(20): 0.357 Positive Predictive Value CMfinder(20): 0.748 Mastr(20): 0.704 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.80287361792e-07	38 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.543 Mastr(20): 0.500 Sensitivity UNAFold: 0.475 Mastr(20): 0.336 Positive Predictive Value UNAFold: 0.626 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.548 Mastr(20): 0.471 Sensitivity ProbKnot: 0.484 Mastr(20): 0.305 Positive Predictive Value ProbKnot: 0.626 Mastr(20): 0.734 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	17 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.642 Mastr(20): 0.529 Sensitivity Cylofold: 0.543 Mastr(20): 0.373 Positive Predictive Value Cylofold: 0.765 Mastr(20): 0.755 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	38 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.540 Mastr(20): 0.500 Sensitivity RNAfold: 0.477 Mastr(20): 0.336 Positive Predictive Value RNAfold: 0.616 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.478 Mastr(20): 0.422 Sensitivity RNASampler(seed): 0.353 Mastr(20): 0.200 Positive Predictive Value RNASampler(seed): 0.652 Mastr(20): 0.895 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.77512146924e-08	38 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.534 Mastr(20): 0.500 Sensitivity RNAsubopt: 0.477 Mastr(20): 0.336 Positive Predictive Value RNAsubopt: 0.604 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.1569883686e-08	19 Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.538 Multilign(20): 0.534 Sensitivity Mastr(20): 0.385 Multilign(20): 0.449 Positive Predictive Value Mastr(20): 0.757 Multilign(20): 0.642 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.290704005595	19 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.528 Afold: 0.511 Sensitivity Mastr(20): 0.350 Afold: 0.460 Positive Predictive Value Mastr(20): 0.800 Afold: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	38 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.517 Mastr(20): 0.500 Sensitivity RNAshapes: 0.453 Mastr(20): 0.336 Positive Predictive Value RNAshapes: 0.595 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.53079410487e-06	28 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.531 Mastr(20): 0.471 Sensitivity Fold: 0.471 Mastr(20): 0.305 Positive Predictive Value Fold: 0.604 Mastr(20): 0.734 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.506 Mastr(20): 0.500 Sensitivity McQFold: 0.433 Mastr(20): 0.336 Positive Predictive Value McQFold: 0.598 Mastr(20): 0.749 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.00636070127375	18 Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.465 RNASLOpt: 0.463 Sensitivity Mastr(20): 0.313 RNASLOpt: 0.383 Positive Predictive Value Mastr(20): 0.698 RNASLOpt: 0.567 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.371318546591		? Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.497 Mastr(20): 0.428 Sensitivity Multilign(seed): 0.369 Mastr(20): 0.241 Positive Predictive Value Multilign(seed): 0.676 Mastr(20): 0.766 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.523 Pknots: 0.481 Sensitivity Mastr(20): 0.369 Pknots: 0.433 Positive Predictive Value Mastr(20): 0.749 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.509 Vsfold4: 0.459 Sensitivity Mastr(20): 0.348 Vsfold4: 0.381 Positive Predictive Value Mastr(20): 0.749 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Mastr(20) vs CRWrnafold Matthews Correlation Coefficient Mastr(20): 0.547 CRWrnafold: 0.546 Sensitivity Mastr(20): 0.373 CRWrnafold: 0.483 Positive Predictive Value Mastr(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.454 Mastr(20): 0.387 Sensitivity Murlet(seed): 0.241 Mastr(20): 0.200 Positive Predictive Value Murlet(seed): 0.861 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.509 Vsfold5: 0.409 Sensitivity Mastr(20): 0.348 Vsfold5: 0.345 Positive Predictive Value Mastr(20): 0.749 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.562 MCFold: 0.402 Sensitivity Mastr(20): 0.396 MCFold: 0.418 Positive Predictive Value Mastr(20): 0.804 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.701 Alterna: 0.553 Sensitivity Mastr(20): 0.570 Alterna: 0.480 Positive Predictive Value Mastr(20): 0.868 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.675 RDfolder: 0.563 Sensitivity Mastr(20): 0.529 RDfolder: 0.447 Positive Predictive Value Mastr(20): 0.868 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.496 RNAwolf: 0.348 Sensitivity Mastr(20): 0.341 RNAwolf: 0.328 Positive Predictive Value Mastr(20): 0.729 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.479 NanoFolder: 0.269 Sensitivity Mastr(20): 0.345 NanoFolder: 0.280 Positive Predictive Value Mastr(20): 0.673 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.471 Carnac(seed): 0.110 Sensitivity Mastr(20): 0.293 Carnac(seed): 0.012 Positive Predictive Value Mastr(20): 0.764 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.513 RSpredict(seed): 0.174 Sensitivity Mastr(20): 0.346 RSpredict(seed): 0.068 Positive Predictive Value Mastr(20): 0.765 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.518 PPfold(seed): 0.072 Sensitivity Mastr(20): 0.357 PPfold(seed): 0.012 Positive Predictive Value Mastr(20): 0.757 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Mastr(20): 0.189 Sensitivity PETfold_2.0(seed): 0.614 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs DAFS(20) Matthews Correlation Coefficient Mastr(20): N/A DAFS(20): N/A Sensitivity Mastr(20): N/A DAFS(20): N/A Positive Predictive Value Mastr(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(20): 0.189 Sensitivity PETfold_2.0(20): 0.509 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs DAFS(seed) Matthews Correlation Coefficient Mastr(20): N/A DAFS(seed): N/A Sensitivity Mastr(20): N/A DAFS(seed): N/A Positive Predictive Value Mastr(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.500 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.336 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.749 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(seed)	5 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.569 Multilign(seed): 0.497 Sensitivity CentroidAlifold(20): 0.369 Multilign(seed): 0.369 Positive Predictive Value CentroidAlifold(20): 0.882 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.658 Multilign(seed): 0.533 Sensitivity PETfold_pre2.0(seed): 0.510 Multilign(seed): 0.411 Positive Predictive Value PETfold_pre2.0(seed): 0.851 Multilign(seed): 0.698 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.556 Multilign(seed): 0.497 Sensitivity RNAalifold(20): 0.409 Multilign(seed): 0.369 Positive Predictive Value RNAalifold(20): 0.761 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 MXScarna(seed): 0.555 Sensitivity Multilign(seed): 0.432 MXScarna(seed): 0.432 Positive Predictive Value Multilign(seed): 0.723 MXScarna(seed): 0.719 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00343916605433	5 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.543 Multilign(seed): 0.497 Sensitivity PPfold(20): 0.394 Multilign(seed): 0.369 Positive Predictive Value PPfold(20): 0.755 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.533 ContextFold: 0.500 Sensitivity Multilign(seed): 0.411 ContextFold: 0.408 Positive Predictive Value Multilign(seed): 0.698 ContextFold: 0.620 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNASampler(20) Matthews Correlation Coefficient Multilign(seed): 0.497 RNASampler(20): 0.480 Sensitivity Multilign(seed): 0.369 RNASampler(20): 0.345 Positive Predictive Value Multilign(seed): 0.676 RNASampler(20): 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.443 Multilign(seed): 0.401 Sensitivity PETfold_pre2.0(20): 0.323 Multilign(seed): 0.283 Positive Predictive Value PETfold_pre2.0(20): 0.612 Multilign(seed): 0.571 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.497 TurboFold(20): 0.489 Sensitivity Multilign(seed): 0.369 TurboFold(20): 0.374 Positive Predictive Value Multilign(seed): 0.676 TurboFold(20): 0.644 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.502 Multilign(seed): 0.497 Sensitivity MXScarna(20): 0.384 Multilign(seed): 0.369 Positive Predictive Value MXScarna(20): 0.661 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 RNAalifold(seed): 0.554 Sensitivity Multilign(seed): 0.432 RNAalifold(seed): 0.356 Positive Predictive Value Multilign(seed): 0.723 RNAalifold(seed): 0.868 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.304583021065	5 Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.543 Multilign(seed): 0.497 Sensitivity Murlet(20): 0.394 Multilign(seed): 0.369 Positive Predictive Value Murlet(20): 0.755 Multilign(seed): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.653 Multilign(seed): 0.556 Sensitivity CentroidAlifold(seed): 0.451 Multilign(seed): 0.432 Positive Predictive Value CentroidAlifold(seed): 0.949 Multilign(seed): 0.723 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.71210682542e-09	5 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.497 Carnac(20): 0.491 Sensitivity Multilign(seed): 0.369 Carnac(20): 0.281 Positive Predictive Value Multilign(seed): 0.676 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.604 Multilign(seed): 0.556 Sensitivity IPknot: 0.473 Multilign(seed): 0.432 Positive Predictive Value IPknot: 0.777 Multilign(seed): 0.723 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.93000771886e-09	8 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.549 Multilign(seed): 0.534 Sensitivity CentroidHomfold‑LAST: 0.435 Multilign(seed): 0.414 Positive Predictive Value CentroidHomfold‑LAST: 0.699 Multilign(seed): 0.697 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.581 Multilign(seed): 0.556 Sensitivity Contrafold: 0.478 Multilign(seed): 0.432 Positive Predictive Value Contrafold: 0.713 Multilign(seed): 0.723 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.49320234536e-07	10 Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.556 Sfold: 0.556 Sensitivity Multilign(seed): 0.432 Sfold: 0.446 Positive Predictive Value Multilign(seed): 0.723 Sfold: 0.701 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0300471658456	10 Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.556 HotKnots: 0.503 Sensitivity Multilign(seed): 0.432 HotKnots: 0.443 Positive Predictive Value Multilign(seed): 0.723 HotKnots: 0.578 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.08682696847e-09	10 Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.556 CentroidFold: 0.546 Sensitivity Multilign(seed): 0.432 CentroidFold: 0.418 Positive Predictive Value Multilign(seed): 0.723 CentroidFold: 0.720 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0325256581203	9 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.555 Multilign(seed): 0.518 Sensitivity TurboFold(seed): 0.442 Multilign(seed): 0.396 Positive Predictive Value TurboFold(seed): 0.704 Multilign(seed): 0.684 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.556 MaxExpect: 0.555 Sensitivity Multilign(seed): 0.432 MaxExpect: 0.451 Positive Predictive Value Multilign(seed): 0.723 MaxExpect: 0.689 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.140151831921	5 Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.497 RSpredict(20): 0.409 Sensitivity Multilign(seed): 0.369 RSpredict(20): 0.305 Positive Predictive Value Multilign(seed): 0.676 RSpredict(20): 0.554 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.556 PknotsRG: 0.549 Sensitivity Multilign(seed): 0.432 PknotsRG: 0.473 Positive Predictive Value Multilign(seed): 0.723 PknotsRG: 0.644 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00117233828523	1 Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): 0.128 CMfinder(20): 0.098 Sensitivity Multilign(seed): 0.091 CMfinder(20): 0.061 Positive Predictive Value Multilign(seed): 0.188 CMfinder(20): 0.167 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.556 UNAFold: 0.496 Sensitivity Multilign(seed): 0.432 UNAFold: 0.421 Positive Predictive Value Multilign(seed): 0.723 UNAFold: 0.592 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.47941000302e-08	10 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.556 ProbKnot: 0.540 Sensitivity Multilign(seed): 0.432 ProbKnot: 0.462 Positive Predictive Value Multilign(seed): 0.723 ProbKnot: 0.637 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32348179894e-08	6 Multilign(seed) vs Cylofold Matthews Correlation Coefficient Multilign(seed): 0.554 Cylofold: 0.492 Sensitivity Multilign(seed): 0.435 Cylofold: 0.388 Positive Predictive Value Multilign(seed): 0.715 Cylofold: 0.634 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.556 RNAfold: 0.543 Sensitivity Multilign(seed): 0.432 RNAfold: 0.465 Positive Predictive Value Multilign(seed): 0.723 RNAfold: 0.640 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0201340087366	7 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.534 RNASampler(seed): 0.432 Sensitivity Multilign(seed): 0.413 RNASampler(seed): 0.282 Positive Predictive Value Multilign(seed): 0.698 RNASampler(seed): 0.670 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.556 RNAsubopt: 0.530 Sensitivity Multilign(seed): 0.432 RNAsubopt: 0.457 Positive Predictive Value Multilign(seed): 0.723 RNAsubopt: 0.622 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.00475527001e-08	4 Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.529 Multilign(20): 0.465 Sensitivity Multilign(seed): 0.404 Multilign(20): 0.377 Positive Predictive Value Multilign(seed): 0.701 Multilign(20): 0.582 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.520 Afold: 0.491 Sensitivity Multilign(seed): 0.409 Afold: 0.425 Positive Predictive Value Multilign(seed): 0.667 Afold: 0.574 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.556 RNAshapes: 0.540 Sensitivity Multilign(seed): 0.432 RNAshapes: 0.462 Positive Predictive Value Multilign(seed): 0.723 RNAshapes: 0.637 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00137673878406	10 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.556 Fold: 0.505 Sensitivity Multilign(seed): 0.432 Fold: 0.435 Positive Predictive Value Multilign(seed): 0.723 Fold: 0.593 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	10 Multilign(seed) vs McQFold Matthews Correlation Coefficient Multilign(seed): 0.556 McQFold: 0.541 Sensitivity Multilign(seed): 0.432 McQFold: 0.448 Positive Predictive Value Multilign(seed): 0.723 McQFold: 0.660 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00194962432759	8 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.533 RNASLOpt: 0.458 Sensitivity Multilign(seed): 0.411 RNASLOpt: 0.366 Positive Predictive Value Multilign(seed): 0.698 RNASLOpt: 0.578 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.497 Mastr(20): 0.428 Sensitivity Multilign(seed): 0.369 Mastr(20): 0.241 Positive Predictive Value Multilign(seed): 0.676 Mastr(20): 0.766 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		+ Multilign(seed) vs Pknots Matthews Correlation Coefficient Multilign(seed): 0.556 Pknots: 0.501 Sensitivity Multilign(seed): 0.432 Pknots: 0.446 Positive Predictive Value Multilign(seed): 0.723 Pknots: 0.569 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.9854753845e-09	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.573 Vsfold4: 0.415 Sensitivity Multilign(seed): 0.450 Vsfold4: 0.339 Positive Predictive Value Multilign(seed): 0.736 Vsfold4: 0.519 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.465 CRWrnafold: 0.443 Sensitivity Multilign(seed): 0.365 CRWrnafold: 0.375 Positive Predictive Value Multilign(seed): 0.603 CRWrnafold: 0.534 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 Murlet(seed): 0.425 Sensitivity Multilign(seed): 0.432 Murlet(seed): 0.234 Positive Predictive Value Multilign(seed): 0.723 Murlet(seed): 0.782 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.16590079822e-09	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.534 Vsfold5: 0.380 Sensitivity Multilign(seed): 0.414 Vsfold5: 0.324 Positive Predictive Value Multilign(seed): 0.697 Vsfold5: 0.457 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.438 MCFold: 0.350 Sensitivity Multilign(seed): 0.327 MCFold: 0.347 Positive Predictive Value Multilign(seed): 0.596 MCFold: 0.361 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.540 Multilign(seed): 0.509 Sensitivity Alterna: 0.448 Multilign(seed): 0.406 Positive Predictive Value Alterna: 0.662 Multilign(seed): 0.650 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.610 RDfolder: 0.353 Sensitivity Multilign(seed): 0.489 RDfolder: 0.264 Positive Predictive Value Multilign(seed): 0.770 RDfolder: 0.485 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.556 RNAwolf: 0.374 Sensitivity Multilign(seed): 0.432 RNAwolf: 0.348 Positive Predictive Value Multilign(seed): 0.723 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.3765112512e-09	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.541 NanoFolder: 0.278 Sensitivity Multilign(seed): 0.422 NanoFolder: 0.283 Positive Predictive Value Multilign(seed): 0.700 NanoFolder: 0.285 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 Carnac(seed): 0.249 Sensitivity Multilign(seed): 0.432 Carnac(seed): 0.063 Positive Predictive Value Multilign(seed): 0.723 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 RSpredict(seed): 0.272 Sensitivity Multilign(seed): 0.432 RSpredict(seed): 0.133 Positive Predictive Value Multilign(seed): 0.723 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.07842257011e-08	+ Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 PPfold(seed): 0.238 Sensitivity Multilign(seed): 0.432 PPfold(seed): 0.071 Positive Predictive Value Multilign(seed): 0.723 PPfold(seed): 0.813 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08	? Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient Multilign(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity Multilign(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value Multilign(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs DAFS(20) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(20): N/A Sensitivity Multilign(seed): N/A DAFS(20): N/A Positive Predictive Value Multilign(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_2.0(20): N/A Sensitivity Multilign(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Multilign(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs DAFS(seed) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(seed): N/A Sensitivity Multilign(seed): N/A DAFS(seed): N/A Positive Predictive Value Multilign(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 Mastr(seed): 0.054 Sensitivity Multilign(seed): 0.432 Mastr(seed): 0.008 Positive Predictive Value Multilign(seed): 0.723 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.61358433984e-08
Pknots	35 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Pknots: 0.486 Sensitivity CentroidAlifold(20): 0.544 Pknots: 0.439 Positive Predictive Value CentroidAlifold(20): 0.882 Pknots: 0.546 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Pknots: 0.457 Sensitivity PETfold_pre2.0(seed): 0.595 Pknots: 0.408 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Pknots: 0.519 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	37 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.667 Pknots: 0.481 Sensitivity RNAalifold(20): 0.527 Pknots: 0.433 Positive Predictive Value RNAalifold(20): 0.848 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.644 Pknots: 0.533 Sensitivity MXScarna(seed): 0.528 Pknots: 0.478 Positive Predictive Value MXScarna(seed): 0.791 Pknots: 0.600 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.663 Pknots: 0.426 Sensitivity PPfold(20): 0.528 Pknots: 0.381 Positive Predictive Value PPfold(20): 0.836 Pknots: 0.484 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.571 Pknots: 0.424 Sensitivity ContextFold: 0.469 Pknots: 0.382 Positive Predictive Value ContextFold: 0.702 Pknots: 0.477 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.624 Pknots: 0.481 Sensitivity RNASampler(20): 0.485 Pknots: 0.433 Positive Predictive Value RNASampler(20): 0.807 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Pknots: 0.381 Sensitivity PETfold_pre2.0(20): 0.530 Pknots: 0.342 Positive Predictive Value PETfold_pre2.0(20): 0.798 Pknots: 0.431 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	20 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.616 Pknots: 0.426 Sensitivity TurboFold(20): 0.508 Pknots: 0.381 Positive Predictive Value TurboFold(20): 0.752 Pknots: 0.484 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	37 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.620 Pknots: 0.481 Sensitivity MXScarna(20): 0.519 Pknots: 0.433 Positive Predictive Value MXScarna(20): 0.746 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.581 Pknots: 0.535 Sensitivity RNAalifold(seed): 0.370 Pknots: 0.486 Positive Predictive Value RNAalifold(seed): 0.917 Pknots: 0.594 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	37 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.605 Pknots: 0.481 Sensitivity Murlet(20): 0.456 Pknots: 0.433 Positive Predictive Value Murlet(20): 0.808 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.585 Pknots: 0.529 Sensitivity CentroidAlifold(seed): 0.364 Pknots: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.945 Pknots: 0.596 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.600 Pknots: 0.481 Sensitivity Carnac(20): 0.404 Pknots: 0.433 Positive Predictive Value Carnac(20): 0.896 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.561 Pknots: 0.446 Sensitivity IPknot: 0.465 Pknots: 0.400 Positive Predictive Value IPknot: 0.682 Pknots: 0.505 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.572 Pknots: 0.471 Sensitivity CentroidHomfold‑LAST: 0.458 Pknots: 0.415 Positive Predictive Value CentroidHomfold‑LAST: 0.720 Pknots: 0.543 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.557 Pknots: 0.507 Sensitivity Contrafold: 0.485 Pknots: 0.454 Positive Predictive Value Contrafold: 0.645 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.574 Pknots: 0.507 Sensitivity Sfold: 0.476 Pknots: 0.454 Positive Predictive Value Sfold: 0.697 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.556 Pknots: 0.507 Sensitivity HotKnots: 0.491 Pknots: 0.454 Positive Predictive Value HotKnots: 0.635 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	72 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.555 Pknots: 0.514 Sensitivity CentroidFold: 0.466 Pknots: 0.462 Positive Predictive Value CentroidFold: 0.666 Pknots: 0.579 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.529 Pknots: 0.455 Sensitivity TurboFold(seed): 0.434 Pknots: 0.413 Positive Predictive Value TurboFold(seed): 0.650 Pknots: 0.508 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.66715895098e-08	69 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.569 Pknots: 0.509 Sensitivity MaxExpect: 0.492 Pknots: 0.457 Positive Predictive Value MaxExpect: 0.664 Pknots: 0.573 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.554 Pknots: 0.494 Sensitivity RSpredict(20): 0.436 Pknots: 0.448 Positive Predictive Value RSpredict(20): 0.709 Pknots: 0.551 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.558 Pknots: 0.507 Sensitivity PknotsRG: 0.491 Pknots: 0.454 Positive Predictive Value PknotsRG: 0.640 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.521 Pknots: 0.395 Sensitivity CMfinder(20): 0.366 Pknots: 0.346 Positive Predictive Value CMfinder(20): 0.748 Pknots: 0.460 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.86109605532e-08	77 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.560 Pknots: 0.507 Sensitivity UNAFold: 0.487 Pknots: 0.454 Positive Predictive Value UNAFold: 0.650 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	54 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.562 Pknots: 0.510 Sensitivity ProbKnot: 0.499 Pknots: 0.457 Positive Predictive Value ProbKnot: 0.639 Pknots: 0.577 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.593 Pknots: 0.590 Sensitivity Cylofold: 0.498 Pknots: 0.523 Positive Predictive Value Cylofold: 0.711 Pknots: 0.672 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 0.545273100092	77 RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.548 Pknots: 0.507 Sensitivity RNAfold: 0.480 Pknots: 0.454 Positive Predictive Value RNAfold: 0.633 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.482 Pknots: 0.471 Sensitivity RNASampler(seed): 0.342 Pknots: 0.449 Positive Predictive Value RNASampler(seed): 0.684 Pknots: 0.500 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.00161539962317	77 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.537 Pknots: 0.507 Sensitivity RNAsubopt: 0.474 Pknots: 0.454 Positive Predictive Value RNAsubopt: 0.614 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.534 Pknots: 0.458 Sensitivity Multilign(20): 0.449 Pknots: 0.404 Positive Predictive Value Multilign(20): 0.642 Pknots: 0.527 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.69132796717e-08	46 Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.529 Afold: 0.526 Sensitivity Pknots: 0.481 Afold: 0.468 Positive Predictive Value Pknots: 0.588 Afold: 0.598 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0982739791036	77 RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.529 Pknots: 0.507 Sensitivity RNAshapes: 0.460 Pknots: 0.454 Positive Predictive Value RNAshapes: 0.615 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.560 Pknots: 0.515 Sensitivity Fold: 0.495 Pknots: 0.461 Positive Predictive Value Fold: 0.640 Pknots: 0.582 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.522 Pknots: 0.507 Sensitivity McQFold: 0.441 Pknots: 0.454 Positive Predictive Value McQFold: 0.624 Pknots: 0.574 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 4.48494289621e-08	38 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.453 Pknots: 0.424 Sensitivity RNASLOpt: 0.363 Pknots: 0.382 Positive Predictive Value RNASLOpt: 0.571 Pknots: 0.477 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.523 Pknots: 0.481 Sensitivity Mastr(20): 0.369 Pknots: 0.433 Positive Predictive Value Mastr(20): 0.749 Pknots: 0.541 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs Pknots Matthews Correlation Coefficient Multilign(seed): 0.556 Pknots: 0.501 Sensitivity Multilign(seed): 0.432 Pknots: 0.446 Positive Predictive Value Multilign(seed): 0.723 Pknots: 0.569 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.9854753845e-09		+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.525 Vsfold4: 0.479 Sensitivity Pknots: 0.467 Vsfold4: 0.394 Positive Predictive Value Pknots: 0.596 Vsfold4: 0.592 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.467 Pknots: 0.430 Sensitivity CRWrnafold: 0.410 Pknots: 0.391 Positive Predictive Value CRWrnafold: 0.540 Pknots: 0.481 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.15570126439e-07	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.526 Murlet(seed): 0.448 Sensitivity Pknots: 0.478 Murlet(seed): 0.245 Positive Predictive Value Pknots: 0.585 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.530 Vsfold5: 0.434 Sensitivity Pknots: 0.471 Vsfold5: 0.366 Positive Predictive Value Pknots: 0.603 Vsfold5: 0.523 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.492 MCFold: 0.385 Sensitivity Pknots: 0.443 MCFold: 0.396 Positive Predictive Value Pknots: 0.553 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.612 Alterna: 0.523 Sensitivity Pknots: 0.532 Alterna: 0.449 Positive Predictive Value Pknots: 0.714 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.607 RDfolder: 0.461 Sensitivity Pknots: 0.530 RDfolder: 0.358 Positive Predictive Value Pknots: 0.703 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.446 RNAwolf: 0.359 Sensitivity Pknots: 0.400 RNAwolf: 0.335 Positive Predictive Value Pknots: 0.505 RNAwolf: 0.393 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.434 NanoFolder: 0.293 Sensitivity Pknots: 0.387 NanoFolder: 0.305 Positive Predictive Value Pknots: 0.495 NanoFolder: 0.290 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.525 Carnac(seed): 0.179 Sensitivity Pknots: 0.478 Carnac(seed): 0.032 Positive Predictive Value Pknots: 0.583 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.536 RSpredict(seed): 0.178 Sensitivity Pknots: 0.483 RSpredict(seed): 0.075 Positive Predictive Value Pknots: 0.601 RSpredict(seed): 0.434 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.488 PPfold(seed): 0.148 Sensitivity Pknots: 0.434 PPfold(seed): 0.032 Positive Predictive Value Pknots: 0.556 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Pknots: 0.607 Sensitivity PETfold_2.0(seed): 0.642 Pknots: 0.516 Positive Predictive Value PETfold_2.0(seed): 0.924 Pknots: 0.721 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Pknots vs DAFS(20) Matthews Correlation Coefficient Pknots: N/A DAFS(20): N/A Sensitivity Pknots: N/A DAFS(20): N/A Positive Predictive Value Pknots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Pknots: 0.410 Sensitivity PETfold_2.0(20): 0.509 Pknots: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 Pknots: 0.514 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs DAFS(seed) Matthews Correlation Coefficient Pknots: N/A DAFS(seed): N/A Sensitivity Pknots: N/A DAFS(seed): N/A Positive Predictive Value Pknots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.523 Mastr(seed): 0.025 Sensitivity Pknots: 0.469 Mastr(seed): 0.002 Positive Predictive Value Pknots: 0.590 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold4	35 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Vsfold4: 0.460 Sensitivity CentroidAlifold(20): 0.541 Vsfold4: 0.383 Positive Predictive Value CentroidAlifold(20): 0.885 Vsfold4: 0.559 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold4: 0.452 Sensitivity PETfold_pre2.0(seed): 0.605 Vsfold4: 0.371 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold4: 0.559 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	37 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.665 Vsfold4: 0.459 Sensitivity RNAalifold(20): 0.520 Vsfold4: 0.381 Positive Predictive Value RNAalifold(20): 0.854 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.19332990918e-08	47 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.641 Vsfold4: 0.485 Sensitivity MXScarna(seed): 0.526 Vsfold4: 0.408 Positive Predictive Value MXScarna(seed): 0.784 Vsfold4: 0.581 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.684 Vsfold4: 0.451 Sensitivity PPfold(20): 0.552 Vsfold4: 0.374 Positive Predictive Value PPfold(20): 0.851 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.7968284078e-08	34 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.578 Vsfold4: 0.393 Sensitivity ContextFold: 0.471 Vsfold4: 0.321 Positive Predictive Value ContextFold: 0.714 Vsfold4: 0.488 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.623 Vsfold4: 0.459 Sensitivity RNASampler(20): 0.481 Vsfold4: 0.381 Positive Predictive Value RNASampler(20): 0.812 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold4: 0.421 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold4: 0.346 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold4: 0.519 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	19 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.631 Vsfold4: 0.451 Sensitivity TurboFold(20): 0.526 Vsfold4: 0.374 Positive Predictive Value TurboFold(20): 0.762 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30280588002e-08	37 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.620 Vsfold4: 0.459 Sensitivity MXScarna(20): 0.520 Vsfold4: 0.381 Positive Predictive Value MXScarna(20): 0.743 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.542 Vsfold4: 0.457 Sensitivity RNAalifold(seed): 0.333 Vsfold4: 0.388 Positive Predictive Value RNAalifold(seed): 0.887 Vsfold4: 0.542 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	37 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.598 Vsfold4: 0.459 Sensitivity Murlet(20): 0.445 Vsfold4: 0.381 Positive Predictive Value Murlet(20): 0.808 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.576 Vsfold4: 0.481 Sensitivity CentroidAlifold(seed): 0.361 Vsfold4: 0.405 Positive Predictive Value CentroidAlifold(seed): 0.924 Vsfold4: 0.576 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.598 Vsfold4: 0.459 Sensitivity Carnac(20): 0.398 Vsfold4: 0.381 Positive Predictive Value Carnac(20): 0.902 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.547 Vsfold4: 0.401 Sensitivity IPknot: 0.456 Vsfold4: 0.328 Positive Predictive Value IPknot: 0.662 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.539 Vsfold4: 0.402 Sensitivity CentroidHomfold‑LAST: 0.411 Vsfold4: 0.327 Positive Predictive Value CentroidHomfold‑LAST: 0.711 Vsfold4: 0.501 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.542 Vsfold4: 0.451 Sensitivity Contrafold: 0.476 Vsfold4: 0.373 Positive Predictive Value Contrafold: 0.622 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.552 Vsfold4: 0.451 Sensitivity Sfold: 0.462 Vsfold4: 0.373 Positive Predictive Value Sfold: 0.664 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.543 Vsfold4: 0.451 Sensitivity HotKnots: 0.482 Vsfold4: 0.373 Positive Predictive Value HotKnots: 0.617 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	70 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.549 Vsfold4: 0.451 Sensitivity CentroidFold: 0.467 Vsfold4: 0.375 Positive Predictive Value CentroidFold: 0.650 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.492 Vsfold4: 0.369 Sensitivity TurboFold(seed): 0.408 Vsfold4: 0.303 Positive Predictive Value TurboFold(seed): 0.599 Vsfold4: 0.458 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.4651262096e-08	67 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.546 Vsfold4: 0.443 Sensitivity MaxExpect: 0.477 Vsfold4: 0.368 Positive Predictive Value MaxExpect: 0.631 Vsfold4: 0.540 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.562 Vsfold4: 0.476 Sensitivity RSpredict(20): 0.445 Vsfold4: 0.398 Positive Predictive Value RSpredict(20): 0.715 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.540 Vsfold4: 0.451 Sensitivity PknotsRG: 0.478 Vsfold4: 0.373 Positive Predictive Value PknotsRG: 0.614 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.521 Vsfold4: 0.411 Sensitivity CMfinder(20): 0.366 Vsfold4: 0.337 Positive Predictive Value CMfinder(20): 0.748 Vsfold4: 0.508 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.54892753461e-09	75 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.541 Vsfold4: 0.451 Sensitivity UNAFold: 0.473 Vsfold4: 0.373 Positive Predictive Value UNAFold: 0.624 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.535 Vsfold4: 0.433 Sensitivity ProbKnot: 0.481 Vsfold4: 0.360 Positive Predictive Value ProbKnot: 0.600 Vsfold4: 0.526 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.560 Vsfold4: 0.504 Sensitivity Cylofold: 0.471 Vsfold4: 0.418 Positive Predictive Value Cylofold: 0.672 Vsfold4: 0.614 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.532 Vsfold4: 0.451 Sensitivity RNAfold: 0.469 Vsfold4: 0.373 Positive Predictive Value RNAfold: 0.609 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.500 Vsfold4: 0.421 Sensitivity RNASampler(seed): 0.361 Vsfold4: 0.358 Positive Predictive Value RNASampler(seed): 0.698 Vsfold4: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18141491686e-08	75 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.521 Vsfold4: 0.451 Sensitivity RNAsubopt: 0.463 Vsfold4: 0.373 Positive Predictive Value RNAsubopt: 0.591 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.534 Vsfold4: 0.451 Sensitivity Multilign(20): 0.449 Vsfold4: 0.374 Positive Predictive Value Multilign(20): 0.642 Vsfold4: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	47 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.497 Vsfold4: 0.438 Sensitivity Afold: 0.447 Vsfold4: 0.366 Positive Predictive Value Afold: 0.559 Vsfold4: 0.531 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.507 Vsfold4: 0.451 Sensitivity RNAshapes: 0.442 Vsfold4: 0.373 Positive Predictive Value RNAshapes: 0.586 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	54 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.539 Vsfold4: 0.444 Sensitivity Fold: 0.479 Vsfold4: 0.370 Positive Predictive Value Fold: 0.613 Vsfold4: 0.539 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.500 Vsfold4: 0.451 Sensitivity McQFold: 0.427 Vsfold4: 0.373 Positive Predictive Value McQFold: 0.590 Vsfold4: 0.552 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.452 Vsfold4: 0.393 Sensitivity RNASLOpt: 0.362 Vsfold4: 0.321 Positive Predictive Value RNASLOpt: 0.571 Vsfold4: 0.488 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.509 Vsfold4: 0.459 Sensitivity Mastr(20): 0.348 Vsfold4: 0.381 Positive Predictive Value Mastr(20): 0.749 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.573 Vsfold4: 0.415 Sensitivity Multilign(seed): 0.450 Vsfold4: 0.339 Positive Predictive Value Multilign(seed): 0.736 Vsfold4: 0.519 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	71 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.525 Vsfold4: 0.479 Sensitivity Pknots: 0.467 Vsfold4: 0.394 Positive Predictive Value Pknots: 0.596 Vsfold4: 0.592 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.467 Vsfold4: 0.393 Sensitivity CRWrnafold: 0.410 Vsfold4: 0.331 Positive Predictive Value CRWrnafold: 0.540 Vsfold4: 0.475 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.488 Murlet(seed): 0.447 Sensitivity Vsfold4: 0.403 Murlet(seed): 0.247 Positive Predictive Value Vsfold4: 0.597 Murlet(seed): 0.813 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.85839946686e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.455 Vsfold5: 0.413 Sensitivity Vsfold4: 0.377 Vsfold5: 0.349 Positive Predictive Value Vsfold4: 0.556 Vsfold5: 0.495 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.475 MCFold: 0.399 Sensitivity Vsfold4: 0.391 MCFold: 0.409 Positive Predictive Value Vsfold4: 0.586 MCFold: 0.398 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.570 Alterna: 0.523 Sensitivity Vsfold4: 0.463 Alterna: 0.449 Positive Predictive Value Vsfold4: 0.711 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.570 RDfolder: 0.461 Sensitivity Vsfold4: 0.464 RDfolder: 0.358 Positive Predictive Value Vsfold4: 0.709 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.401 RNAwolf: 0.371 Sensitivity Vsfold4: 0.328 RNAwolf: 0.345 Positive Predictive Value Vsfold4: 0.498 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.372 NanoFolder: 0.272 Sensitivity Vsfold4: 0.303 NanoFolder: 0.284 Positive Predictive Value Vsfold4: 0.465 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.489 Carnac(seed): 0.192 Sensitivity Vsfold4: 0.406 Carnac(seed): 0.037 Positive Predictive Value Vsfold4: 0.594 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.493 RSpredict(seed): 0.173 Sensitivity Vsfold4: 0.417 RSpredict(seed): 0.073 Positive Predictive Value Vsfold4: 0.587 RSpredict(seed): 0.420 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.474 PPfold(seed): 0.152 Sensitivity Vsfold4: 0.392 PPfold(seed): 0.032 Positive Predictive Value Vsfold4: 0.581 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold4: 0.167 Sensitivity PETfold_2.0(seed): 0.614 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs DAFS(20) Matthews Correlation Coefficient Vsfold4: N/A DAFS(20): N/A Sensitivity Vsfold4: N/A DAFS(20): N/A Positive Predictive Value Vsfold4: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold4: 0.167 Sensitivity PETfold_2.0(20): 0.509 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs DAFS(seed) Matthews Correlation Coefficient Vsfold4: N/A DAFS(seed): N/A Sensitivity Vsfold4: N/A DAFS(seed): N/A Positive Predictive Value Vsfold4: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.479 Mastr(seed): 0.024 Sensitivity Vsfold4: 0.402 Mastr(seed): 0.002 Positive Predictive Value Vsfold4: 0.575 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08
CRWrnafold	7 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.687 CRWrnafold: 0.546 Sensitivity CentroidAlifold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value CentroidAlifold(20): 0.924 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.675 CRWrnafold: 0.522 Sensitivity PETfold_pre2.0(seed): 0.553 CRWrnafold: 0.461 Positive Predictive Value PETfold_pre2.0(seed): 0.828 CRWrnafold: 0.599 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.620 CRWrnafold: 0.546 Sensitivity RNAalifold(20): 0.479 CRWrnafold: 0.483 Positive Predictive Value RNAalifold(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.610 CRWrnafold: 0.536 Sensitivity MXScarna(seed): 0.490 CRWrnafold: 0.472 Positive Predictive Value MXScarna(seed): 0.765 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.657 CRWrnafold: 0.546 Sensitivity PPfold(20): 0.513 CRWrnafold: 0.483 Positive Predictive Value PPfold(20): 0.846 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	13 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.590 CRWrnafold: 0.445 Sensitivity ContextFold: 0.477 CRWrnafold: 0.391 Positive Predictive Value ContextFold: 0.736 CRWrnafold: 0.514 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.01312059156e-09	7 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.618 CRWrnafold: 0.546 Sensitivity RNASampler(20): 0.462 CRWrnafold: 0.483 Positive Predictive Value RNASampler(20): 0.832 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CRWrnafold: 0.531 Sensitivity PETfold_pre2.0(20): 0.497 CRWrnafold: 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 CRWrnafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.570 CRWrnafold: 0.546 Sensitivity TurboFold(20): 0.453 CRWrnafold: 0.483 Positive Predictive Value TurboFold(20): 0.723 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.569 CRWrnafold: 0.546 Sensitivity MXScarna(20): 0.466 CRWrnafold: 0.483 Positive Predictive Value MXScarna(20): 0.701 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.500 CRWrnafold: 0.419 Sensitivity RNAalifold(seed): 0.320 CRWrnafold: 0.377 Positive Predictive Value RNAalifold(seed): 0.789 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.568 CRWrnafold: 0.546 Sensitivity Murlet(20): 0.428 CRWrnafold: 0.483 Positive Predictive Value Murlet(20): 0.759 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.578 CRWrnafold: 0.536 Sensitivity CentroidAlifold(seed): 0.343 CRWrnafold: 0.472 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.616 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Carnac(20): 0.526 Sensitivity CRWrnafold: 0.483 Carnac(20): 0.335 Positive Predictive Value CRWrnafold: 0.623 Carnac(20): 0.832 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	15 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.541 CRWrnafold: 0.467 Sensitivity IPknot: 0.447 CRWrnafold: 0.410 Positive Predictive Value IPknot: 0.663 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.84765843136e-09	15 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.531 CRWrnafold: 0.467 Sensitivity CentroidHomfold‑LAST: 0.380 CRWrnafold: 0.410 Positive Predictive Value CentroidHomfold‑LAST: 0.749 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	15 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.517 CRWrnafold: 0.467 Sensitivity Contrafold: 0.442 CRWrnafold: 0.410 Positive Predictive Value Contrafold: 0.612 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	15 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.508 CRWrnafold: 0.467 Sensitivity Sfold: 0.421 CRWrnafold: 0.410 Positive Predictive Value Sfold: 0.621 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 8.18166149643e-09	15 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.534 CRWrnafold: 0.467 Sensitivity HotKnots: 0.481 CRWrnafold: 0.410 Positive Predictive Value HotKnots: 0.599 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.43692248862e-08	15 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.522 CRWrnafold: 0.467 Sensitivity CentroidFold: 0.428 CRWrnafold: 0.410 Positive Predictive Value CentroidFold: 0.645 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	7 CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 TurboFold(seed): 0.483 Sensitivity CRWrnafold: 0.428 TurboFold(seed): 0.397 Positive Predictive Value CRWrnafold: 0.554 TurboFold(seed): 0.595 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	15 CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.467 MaxExpect: 0.445 Sensitivity CRWrnafold: 0.410 MaxExpect: 0.387 Positive Predictive Value CRWrnafold: 0.540 MaxExpect: 0.522 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.70236007792e-08	7 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.546 RSpredict(20): 0.446 Sensitivity CRWrnafold: 0.483 RSpredict(20): 0.331 Positive Predictive Value CRWrnafold: 0.623 RSpredict(20): 0.609 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	15 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.529 CRWrnafold: 0.467 Sensitivity PknotsRG: 0.472 CRWrnafold: 0.410 Positive Predictive Value PknotsRG: 0.600 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.50834591464e-08	0 CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	15 UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.481 CRWrnafold: 0.467 Sensitivity UNAFold: 0.426 CRWrnafold: 0.410 Positive Predictive Value UNAFold: 0.551 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000803342806742	15 CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.467 ProbKnot: 0.460 Sensitivity CRWrnafold: 0.410 ProbKnot: 0.417 Positive Predictive Value CRWrnafold: 0.540 ProbKnot: 0.516 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.33528019466e-05	13 Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.526 CRWrnafold: 0.473 Sensitivity Cylofold: 0.449 CRWrnafold: 0.406 Positive Predictive Value Cylofold: 0.625 CRWrnafold: 0.560 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.10198558684e-08	15 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.511 CRWrnafold: 0.467 Sensitivity RNAfold: 0.447 CRWrnafold: 0.410 Positive Predictive Value RNAfold: 0.592 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	3 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.357 CRWrnafold: 0.262 Sensitivity RNASampler(seed): 0.253 CRWrnafold: 0.253 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.279 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	15 CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.467 RNAsubopt: 0.454 Sensitivity CRWrnafold: 0.410 RNAsubopt: 0.403 Positive Predictive Value CRWrnafold: 0.540 RNAsubopt: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.07671381975e-06	7 CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.546 Multilign(20): 0.509 Sensitivity CRWrnafold: 0.483 Multilign(20): 0.432 Positive Predictive Value CRWrnafold: 0.623 Multilign(20): 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.475 CRWrnafold: 0.299 Sensitivity Afold: 0.442 CRWrnafold: 0.273 Positive Predictive Value Afold: 0.518 CRWrnafold: 0.336 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	15 RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.508 CRWrnafold: 0.467 Sensitivity RNAshapes: 0.442 CRWrnafold: 0.410 Positive Predictive Value RNAshapes: 0.591 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	15 CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.467 Fold: 0.446 Sensitivity CRWrnafold: 0.410 Fold: 0.394 Positive Predictive Value CRWrnafold: 0.540 Fold: 0.514 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	15 McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.487 CRWrnafold: 0.467 Sensitivity McQFold: 0.417 CRWrnafold: 0.410 Positive Predictive Value McQFold: 0.577 CRWrnafold: 0.540 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.25975249062e-07	13 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.445 RNASLOpt: 0.441 Sensitivity CRWrnafold: 0.391 RNASLOpt: 0.369 Positive Predictive Value CRWrnafold: 0.514 RNASLOpt: 0.536 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0590663124617	7 Mastr(20) vs CRWrnafold Matthews Correlation Coefficient Mastr(20): 0.547 CRWrnafold: 0.546 Sensitivity Mastr(20): 0.373 CRWrnafold: 0.483 Positive Predictive Value Mastr(20): 0.807 CRWrnafold: 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.465 CRWrnafold: 0.443 Sensitivity Multilign(seed): 0.365 CRWrnafold: 0.375 Positive Predictive Value Multilign(seed): 0.603 CRWrnafold: 0.534 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	15 CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.467 Pknots: 0.430 Sensitivity CRWrnafold: 0.410 Pknots: 0.391 Positive Predictive Value CRWrnafold: 0.540 Pknots: 0.481 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.15570126439e-07	15 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.467 Vsfold4: 0.393 Sensitivity CRWrnafold: 0.410 Vsfold4: 0.331 Positive Predictive Value CRWrnafold: 0.540 Vsfold4: 0.475 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.59816551561e-08		? Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.435 CRWrnafold: 0.419 Sensitivity Murlet(seed): 0.251 CRWrnafold: 0.377 Positive Predictive Value Murlet(seed): 0.759 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.467 Vsfold5: 0.356 Sensitivity CRWrnafold: 0.410 Vsfold5: 0.308 Positive Predictive Value CRWrnafold: 0.540 Vsfold5: 0.421 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.455 MCFold: 0.431 Sensitivity CRWrnafold: 0.403 MCFold: 0.459 Positive Predictive Value CRWrnafold: 0.522 MCFold: 0.412 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18866702221e-08	? Alterna vs CRWrnafold Matthews Correlation Coefficient Alterna: 0.457 CRWrnafold: 0.450 Sensitivity Alterna: 0.404 CRWrnafold: 0.391 Positive Predictive Value Alterna: 0.529 CRWrnafold: 0.530 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.513 RDfolder: 0.230 Sensitivity CRWrnafold: 0.436 RDfolder: 0.165 Positive Predictive Value CRWrnafold: 0.613 RDfolder: 0.336 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.60513176667e-09	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.467 RNAwolf: 0.352 Sensitivity CRWrnafold: 0.410 RNAwolf: 0.329 Positive Predictive Value CRWrnafold: 0.540 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	? CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.492 NanoFolder: 0.366 Sensitivity CRWrnafold: 0.431 NanoFolder: 0.380 Positive Predictive Value CRWrnafold: 0.570 NanoFolder: 0.362 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 Carnac(seed): 0.132 Sensitivity CRWrnafold: 0.428 Carnac(seed): 0.017 Positive Predictive Value CRWrnafold: 0.554 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 RSpredict(seed): 0.108 Sensitivity CRWrnafold: 0.472 RSpredict(seed): 0.042 Positive Predictive Value CRWrnafold: 0.616 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 PPfold(seed): 0.114 Sensitivity CRWrnafold: 0.472 PPfold(seed): 0.024 Positive Predictive Value CRWrnafold: 0.616 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(seed): N/A Sensitivity CRWrnafold: N/A CMfinder(seed): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs PETfold_2.0(seed) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(seed): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(seed): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs DAFS(20) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(20): N/A Sensitivity CRWrnafold: N/A DAFS(20): N/A Positive Predictive Value CRWrnafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs PETfold_2.0(20) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(20): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(20): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs DAFS(seed) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(seed): N/A Sensitivity CRWrnafold: N/A DAFS(seed): N/A Positive Predictive Value CRWrnafold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.472 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.616 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
Murlet(seed)	17 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.618 Murlet(seed): 0.453 Sensitivity CentroidAlifold(20): 0.438 Murlet(seed): 0.240 Positive Predictive Value CentroidAlifold(20): 0.877 Murlet(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	13 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.640 Murlet(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.508 Murlet(seed): 0.213 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.77512146924e-08	18 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.579 Murlet(seed): 0.454 Sensitivity RNAalifold(20): 0.433 Murlet(seed): 0.241 Positive Predictive Value RNAalifold(20): 0.779 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.84041289224e-08	24 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.581 Murlet(seed): 0.448 Sensitivity MXScarna(seed): 0.456 Murlet(seed): 0.245 Positive Predictive Value MXScarna(seed): 0.745 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	10 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.509 Murlet(seed): 0.429 Sensitivity PPfold(20): 0.371 Murlet(seed): 0.219 Positive Predictive Value PPfold(20): 0.702 Murlet(seed): 0.843 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.31583660336e-08	13 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.491 Murlet(seed): 0.403 Sensitivity ContextFold: 0.397 Murlet(seed): 0.213 Positive Predictive Value ContextFold: 0.613 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.27752322258e-08	18 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.551 Murlet(seed): 0.454 Sensitivity RNASampler(20): 0.421 Murlet(seed): 0.241 Positive Predictive Value RNASampler(20): 0.727 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.54229534325e-08	8 PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.449 Murlet(seed): 0.407 Sensitivity PETfold_pre2.0(20): 0.342 Murlet(seed): 0.195 Positive Predictive Value PETfold_pre2.0(20): 0.595 Murlet(seed): 0.852 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.488 Murlet(seed): 0.429 Sensitivity TurboFold(20): 0.389 Murlet(seed): 0.219 Positive Predictive Value TurboFold(20): 0.619 Murlet(seed): 0.843 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12659692944e-08	18 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.555 Murlet(seed): 0.454 Sensitivity MXScarna(20): 0.439 Murlet(seed): 0.241 Positive Predictive Value MXScarna(20): 0.706 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	24 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.588 Murlet(seed): 0.448 Sensitivity RNAalifold(seed): 0.378 Murlet(seed): 0.245 Positive Predictive Value RNAalifold(seed): 0.917 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.510 Murlet(seed): 0.454 Sensitivity Murlet(20): 0.362 Murlet(seed): 0.241 Positive Predictive Value Murlet(20): 0.724 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.50323628132e-08	23 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.677 Murlet(seed): 0.447 Sensitivity CentroidAlifold(seed): 0.481 Murlet(seed): 0.244 Positive Predictive Value CentroidAlifold(seed): 0.955 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	18 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.526 Murlet(seed): 0.454 Sensitivity Carnac(20): 0.295 Murlet(seed): 0.241 Positive Predictive Value Carnac(20): 0.941 Murlet(seed): 0.861 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.10198558684e-08	15 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.555 Murlet(seed): 0.418 Sensitivity IPknot: 0.450 Murlet(seed): 0.227 Positive Predictive Value IPknot: 0.691 Murlet(seed): 0.777 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	13 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.496 Murlet(seed): 0.424 Sensitivity CentroidHomfold‑LAST: 0.415 Murlet(seed): 0.240 Positive Predictive Value CentroidHomfold‑LAST: 0.599 Murlet(seed): 0.758 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	24 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.586 Murlet(seed): 0.448 Sensitivity Contrafold: 0.505 Murlet(seed): 0.245 Positive Predictive Value Contrafold: 0.684 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	24 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.587 Murlet(seed): 0.448 Sensitivity Sfold: 0.478 Murlet(seed): 0.245 Positive Predictive Value Sfold: 0.725 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.539 Murlet(seed): 0.448 Sensitivity HotKnots: 0.481 Murlet(seed): 0.245 Positive Predictive Value HotKnots: 0.609 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	23 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.565 Murlet(seed): 0.447 Sensitivity CentroidFold: 0.461 Murlet(seed): 0.244 Positive Predictive Value CentroidFold: 0.697 Murlet(seed): 0.823 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	13 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.508 Murlet(seed): 0.442 Sensitivity TurboFold(seed): 0.416 Murlet(seed): 0.237 Positive Predictive Value TurboFold(seed): 0.626 Murlet(seed): 0.831 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.12262428713e-08	22 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.542 Murlet(seed): 0.441 Sensitivity MaxExpect: 0.457 Murlet(seed): 0.241 Positive Predictive Value MaxExpect: 0.647 Murlet(seed): 0.814 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.454 RSpredict(20): 0.420 Sensitivity Murlet(seed): 0.241 RSpredict(20): 0.318 Positive Predictive Value Murlet(seed): 0.861 RSpredict(20): 0.562 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	24 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.574 Murlet(seed): 0.448 Sensitivity PknotsRG: 0.507 Murlet(seed): 0.245 Positive Predictive Value PknotsRG: 0.656 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	3 CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.333 Murlet(seed): 0.259 Sensitivity CMfinder(20): 0.208 Murlet(seed): 0.119 Positive Predictive Value CMfinder(20): 0.538 Murlet(seed): 0.571 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	24 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.536 Murlet(seed): 0.448 Sensitivity UNAFold: 0.466 Murlet(seed): 0.245 Positive Predictive Value UNAFold: 0.622 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	18 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.513 Murlet(seed): 0.426 Sensitivity ProbKnot: 0.458 Murlet(seed): 0.226 Positive Predictive Value ProbKnot: 0.580 Murlet(seed): 0.810 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.36983135185e-08	11 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.582 Murlet(seed): 0.429 Sensitivity Cylofold: 0.473 Murlet(seed): 0.246 Positive Predictive Value Cylofold: 0.723 Murlet(seed): 0.756 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	24 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.556 Murlet(seed): 0.448 Sensitivity RNAfold: 0.487 Murlet(seed): 0.245 Positive Predictive Value RNAfold: 0.641 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 Murlet(seed): 0.411 Sensitivity RNASampler(seed): 0.342 Murlet(seed): 0.216 Positive Predictive Value RNASampler(seed): 0.684 Murlet(seed): 0.789 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.7402423548e-08	24 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.527 Murlet(seed): 0.448 Sensitivity RNAsubopt: 0.468 Murlet(seed): 0.245 Positive Predictive Value RNAsubopt: 0.598 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	9 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.439 Multilign(20): 0.380 Sensitivity Murlet(seed): 0.234 Multilign(20): 0.317 Positive Predictive Value Murlet(seed): 0.829 Multilign(20): 0.462 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	13 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.543 Murlet(seed): 0.435 Sensitivity Afold: 0.483 Murlet(seed): 0.246 Positive Predictive Value Afold: 0.616 Murlet(seed): 0.775 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.62913390836e-08	24 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.542 Murlet(seed): 0.448 Sensitivity RNAshapes: 0.473 Murlet(seed): 0.245 Positive Predictive Value RNAshapes: 0.626 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	18 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.471 Murlet(seed): 0.426 Sensitivity Fold: 0.420 Murlet(seed): 0.226 Positive Predictive Value Fold: 0.536 Murlet(seed): 0.810 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.82974185391e-08	24 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.565 Murlet(seed): 0.448 Sensitivity McQFold: 0.488 Murlet(seed): 0.245 Positive Predictive Value McQFold: 0.659 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	13 RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.449 Murlet(seed): 0.403 Sensitivity RNASLOpt: 0.376 Murlet(seed): 0.213 Positive Predictive Value RNASLOpt: 0.542 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	18 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.454 Mastr(20): 0.387 Sensitivity Murlet(seed): 0.241 Mastr(20): 0.200 Positive Predictive Value Murlet(seed): 0.861 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	10 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 Murlet(seed): 0.425 Sensitivity Multilign(seed): 0.432 Murlet(seed): 0.234 Positive Predictive Value Multilign(seed): 0.723 Murlet(seed): 0.782 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.16590079822e-09	24 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.526 Murlet(seed): 0.448 Sensitivity Pknots: 0.478 Murlet(seed): 0.245 Positive Predictive Value Pknots: 0.585 Murlet(seed): 0.825 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	21 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.488 Murlet(seed): 0.447 Sensitivity Vsfold4: 0.403 Murlet(seed): 0.247 Positive Predictive Value Vsfold4: 0.597 Murlet(seed): 0.813 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.85839946686e-08	6 Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.435 CRWrnafold: 0.419 Sensitivity Murlet(seed): 0.251 CRWrnafold: 0.377 Positive Predictive Value Murlet(seed): 0.759 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0		= Vsfold5 vs Murlet(seed) Matthews Correlation Coefficient Vsfold5: 0.464 Murlet(seed): 0.454 Sensitivity Vsfold5: 0.398 Murlet(seed): 0.254 Positive Predictive Value Vsfold5: 0.548 Murlet(seed): 0.817 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.011312336181	+ Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.439 MCFold: 0.384 Sensitivity Murlet(seed): 0.240 MCFold: 0.399 Positive Predictive Value Murlet(seed): 0.811 MCFold: 0.376 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	? Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.651 Murlet(seed): 0.486 Sensitivity Alterna: 0.542 Murlet(seed): 0.313 Positive Predictive Value Alterna: 0.789 Murlet(seed): 0.765 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	= RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.495 Murlet(seed): 0.494 Sensitivity RDfolder: 0.379 Murlet(seed): 0.306 Positive Predictive Value RDfolder: 0.657 Murlet(seed): 0.807 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.317118147004	+ Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.418 RNAwolf: 0.348 Sensitivity Murlet(seed): 0.227 RNAwolf: 0.331 Positive Predictive Value Murlet(seed): 0.777 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.3551590886e-08	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.404 NanoFolder: 0.253 Sensitivity Murlet(seed): 0.213 NanoFolder: 0.276 Positive Predictive Value Murlet(seed): 0.771 NanoFolder: 0.241 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.448 Carnac(seed): 0.197 Sensitivity Murlet(seed): 0.245 Carnac(seed): 0.039 Positive Predictive Value Murlet(seed): 0.825 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.448 RSpredict(seed): 0.289 Sensitivity Murlet(seed): 0.245 RSpredict(seed): 0.139 Positive Predictive Value Murlet(seed): 0.825 RSpredict(seed): 0.608 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.418 PPfold(seed): 0.204 Sensitivity Murlet(seed): 0.227 PPfold(seed): 0.061 Positive Predictive Value Murlet(seed): 0.777 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	? CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Murlet(seed): 0.431 Sensitivity PETfold_2.0(seed): 0.684 Murlet(seed): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.897 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs DAFS(20) Matthews Correlation Coefficient Murlet(seed): N/A DAFS(20): N/A Sensitivity Murlet(seed): N/A DAFS(20): N/A Positive Predictive Value Murlet(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_2.0(20): N/A Sensitivity Murlet(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Murlet(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Murlet(seed) Matthews Correlation Coefficient DAFS(seed): N/A Murlet(seed): N/A Sensitivity DAFS(seed): N/A Murlet(seed): N/A Positive Predictive Value DAFS(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.448 Mastr(seed): 0.036 Sensitivity Murlet(seed): 0.245 Mastr(seed): 0.004 Positive Predictive Value Murlet(seed): 0.825 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08
Vsfold5	35 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Vsfold5: 0.418 Sensitivity CentroidAlifold(20): 0.541 Vsfold5: 0.353 Positive Predictive Value CentroidAlifold(20): 0.885 Vsfold5: 0.501 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold5: 0.403 Sensitivity PETfold_pre2.0(seed): 0.606 Vsfold5: 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.882 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	37 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.665 Vsfold5: 0.409 Sensitivity RNAalifold(20): 0.520 Vsfold5: 0.345 Positive Predictive Value RNAalifold(20): 0.854 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.640 Vsfold5: 0.446 Sensitivity MXScarna(seed): 0.526 Vsfold5: 0.381 Positive Predictive Value MXScarna(seed): 0.783 Vsfold5: 0.529 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.684 Vsfold5: 0.410 Sensitivity PPfold(20): 0.552 Vsfold5: 0.352 Positive Predictive Value PPfold(20): 0.851 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	34 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.592 Vsfold5: 0.358 Sensitivity ContextFold: 0.484 Vsfold5: 0.307 Positive Predictive Value ContextFold: 0.730 Vsfold5: 0.426 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.623 Vsfold5: 0.409 Sensitivity RNASampler(20): 0.481 Vsfold5: 0.345 Positive Predictive Value RNASampler(20): 0.812 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.678 Vsfold5: 0.378 Sensitivity PETfold_pre2.0(20): 0.559 Vsfold5: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.826 Vsfold5: 0.450 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	19 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.631 Vsfold5: 0.410 Sensitivity TurboFold(20): 0.526 Vsfold5: 0.352 Positive Predictive Value TurboFold(20): 0.762 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	37 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.620 Vsfold5: 0.409 Sensitivity MXScarna(20): 0.520 Vsfold5: 0.345 Positive Predictive Value MXScarna(20): 0.743 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.548 Vsfold5: 0.437 Sensitivity RNAalifold(seed): 0.340 Vsfold5: 0.377 Positive Predictive Value RNAalifold(seed): 0.888 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	37 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.598 Vsfold5: 0.409 Sensitivity Murlet(20): 0.445 Vsfold5: 0.345 Positive Predictive Value Murlet(20): 0.808 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.579 Vsfold5: 0.446 Sensitivity CentroidAlifold(seed): 0.365 Vsfold5: 0.381 Positive Predictive Value CentroidAlifold(seed): 0.923 Vsfold5: 0.528 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.598 Vsfold5: 0.409 Sensitivity Carnac(20): 0.398 Vsfold5: 0.345 Positive Predictive Value Carnac(20): 0.902 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.541 Vsfold5: 0.368 Sensitivity IPknot: 0.450 Vsfold5: 0.315 Positive Predictive Value IPknot: 0.657 Vsfold5: 0.438 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	37 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.518 Vsfold5: 0.362 Sensitivity CentroidHomfold‑LAST: 0.399 Vsfold5: 0.309 Positive Predictive Value CentroidHomfold‑LAST: 0.677 Vsfold5: 0.433 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.550 Vsfold5: 0.409 Sensitivity Contrafold: 0.483 Vsfold5: 0.346 Positive Predictive Value Contrafold: 0.632 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.546 Vsfold5: 0.409 Sensitivity Sfold: 0.455 Vsfold5: 0.346 Positive Predictive Value Sfold: 0.659 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.540 Vsfold5: 0.409 Sensitivity HotKnots: 0.480 Vsfold5: 0.346 Positive Predictive Value HotKnots: 0.613 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	70 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.552 Vsfold5: 0.412 Sensitivity CentroidFold: 0.470 Vsfold5: 0.350 Positive Predictive Value CentroidFold: 0.654 Vsfold5: 0.492 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.509 Vsfold5: 0.355 Sensitivity TurboFold(seed): 0.421 Vsfold5: 0.311 Positive Predictive Value TurboFold(seed): 0.622 Vsfold5: 0.413 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.52299983238e-08	67 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.538 Vsfold5: 0.404 Sensitivity MaxExpect: 0.469 Vsfold5: 0.342 Positive Predictive Value MaxExpect: 0.622 Vsfold5: 0.483 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.562 Vsfold5: 0.432 Sensitivity RSpredict(20): 0.445 Vsfold5: 0.366 Positive Predictive Value RSpredict(20): 0.715 Vsfold5: 0.516 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.539 Vsfold5: 0.409 Sensitivity PknotsRG: 0.478 Vsfold5: 0.346 Positive Predictive Value PknotsRG: 0.613 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.521 Vsfold5: 0.355 Sensitivity CMfinder(20): 0.366 Vsfold5: 0.299 Positive Predictive Value CMfinder(20): 0.748 Vsfold5: 0.430 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.64686604905e-09	75 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.534 Vsfold5: 0.409 Sensitivity UNAFold: 0.467 Vsfold5: 0.346 Positive Predictive Value UNAFold: 0.616 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.525 Vsfold5: 0.405 Sensitivity ProbKnot: 0.472 Vsfold5: 0.346 Positive Predictive Value ProbKnot: 0.589 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.552 Vsfold5: 0.446 Sensitivity Cylofold: 0.463 Vsfold5: 0.378 Positive Predictive Value Cylofold: 0.666 Vsfold5: 0.535 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.528 Vsfold5: 0.409 Sensitivity RNAfold: 0.466 Vsfold5: 0.346 Positive Predictive Value RNAfold: 0.605 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.500 Vsfold5: 0.470 Sensitivity RNASampler(seed): 0.361 Vsfold5: 0.425 Positive Predictive Value RNASampler(seed): 0.698 Vsfold5: 0.525 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.69229414982e-08	75 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.522 Vsfold5: 0.409 Sensitivity RNAsubopt: 0.464 Vsfold5: 0.346 Positive Predictive Value RNAsubopt: 0.593 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.534 Vsfold5: 0.410 Sensitivity Multilign(20): 0.449 Vsfold5: 0.352 Positive Predictive Value Multilign(20): 0.642 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	47 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.497 Vsfold5: 0.388 Sensitivity Afold: 0.447 Vsfold5: 0.330 Positive Predictive Value Afold: 0.559 Vsfold5: 0.462 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.506 Vsfold5: 0.409 Sensitivity RNAshapes: 0.442 Vsfold5: 0.346 Positive Predictive Value RNAshapes: 0.586 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	54 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.530 Vsfold5: 0.413 Sensitivity Fold: 0.471 Vsfold5: 0.352 Positive Predictive Value Fold: 0.601 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 54 Wilcoxon single-rank test P-value: 5.23657817852e-08	75 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.508 Vsfold5: 0.409 Sensitivity McQFold: 0.433 Vsfold5: 0.346 Positive Predictive Value McQFold: 0.600 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.458 Vsfold5: 0.358 Sensitivity RNASLOpt: 0.379 Vsfold5: 0.307 Positive Predictive Value RNASLOpt: 0.562 Vsfold5: 0.426 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.509 Vsfold5: 0.409 Sensitivity Mastr(20): 0.348 Vsfold5: 0.345 Positive Predictive Value Mastr(20): 0.749 Vsfold5: 0.491 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.534 Vsfold5: 0.380 Sensitivity Multilign(seed): 0.414 Vsfold5: 0.324 Positive Predictive Value Multilign(seed): 0.697 Vsfold5: 0.457 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	71 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.530 Vsfold5: 0.434 Sensitivity Pknots: 0.471 Vsfold5: 0.366 Positive Predictive Value Pknots: 0.603 Vsfold5: 0.523 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.455 Vsfold5: 0.413 Sensitivity Vsfold4: 0.377 Vsfold5: 0.349 Positive Predictive Value Vsfold4: 0.556 Vsfold5: 0.495 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.467 Vsfold5: 0.356 Sensitivity CRWrnafold: 0.410 Vsfold5: 0.308 Positive Predictive Value CRWrnafold: 0.540 Vsfold5: 0.421 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	22 Vsfold5 vs Murlet(seed) Matthews Correlation Coefficient Vsfold5: 0.464 Murlet(seed): 0.454 Sensitivity Vsfold5: 0.398 Murlet(seed): 0.254 Positive Predictive Value Vsfold5: 0.548 Murlet(seed): 0.817 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.011312336181		+ Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.445 MCFold: 0.403 Sensitivity Vsfold5: 0.376 MCFold: 0.421 Positive Predictive Value Vsfold5: 0.536 MCFold: 0.395 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.523 Vsfold5: 0.496 Sensitivity Alterna: 0.449 Vsfold5: 0.409 Positive Predictive Value Alterna: 0.620 Vsfold5: 0.613 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 1.01188337103e-07	+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.525 RDfolder: 0.461 Sensitivity Vsfold5: 0.437 RDfolder: 0.358 Positive Predictive Value Vsfold5: 0.640 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.370 Vsfold5: 0.368 Sensitivity RNAwolf: 0.345 Vsfold5: 0.315 Positive Predictive Value RNAwolf: 0.405 Vsfold5: 0.438 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.935722063919	+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.350 NanoFolder: 0.290 Sensitivity Vsfold5: 0.302 NanoFolder: 0.303 Positive Predictive Value Vsfold5: 0.415 NanoFolder: 0.287 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.456 Carnac(seed): 0.188 Sensitivity Vsfold5: 0.391 Carnac(seed): 0.036 Positive Predictive Value Vsfold5: 0.539 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.457 RSpredict(seed): 0.171 Sensitivity Vsfold5: 0.391 RSpredict(seed): 0.071 Positive Predictive Value Vsfold5: 0.539 RSpredict(seed): 0.416 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.427 PPfold(seed): 0.149 Sensitivity Vsfold5: 0.367 PPfold(seed): 0.031 Positive Predictive Value Vsfold5: 0.505 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(seed): N/A Sensitivity Vsfold5: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold5: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold5: 0.156 Sensitivity PETfold_2.0(seed): 0.614 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs DAFS(20) Matthews Correlation Coefficient Vsfold5: N/A DAFS(20): N/A Sensitivity Vsfold5: N/A DAFS(20): N/A Positive Predictive Value Vsfold5: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold5: 0.156 Sensitivity PETfold_2.0(20): 0.509 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs DAFS(seed) Matthews Correlation Coefficient Vsfold5: N/A DAFS(seed): N/A Sensitivity Vsfold5: N/A DAFS(seed): N/A Positive Predictive Value Vsfold5: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.438 Mastr(seed): 0.024 Sensitivity Vsfold5: 0.374 Mastr(seed): 0.002 Positive Predictive Value Vsfold5: 0.520 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08
MCFold	31 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.684 MCFold: 0.397 Sensitivity CentroidAlifold(20): 0.539 MCFold: 0.414 Positive Predictive Value CentroidAlifold(20): 0.872 MCFold: 0.388 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 MCFold: 0.384 Sensitivity PETfold_pre2.0(seed): 0.579 MCFold: 0.397 Positive Predictive Value PETfold_pre2.0(seed): 0.857 MCFold: 0.379 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.69265863073e-08	32 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.658 MCFold: 0.402 Sensitivity RNAalifold(20): 0.525 MCFold: 0.418 Positive Predictive Value RNAalifold(20): 0.829 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	40 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.634 MCFold: 0.418 Sensitivity MXScarna(seed): 0.517 MCFold: 0.436 Positive Predictive Value MXScarna(seed): 0.782 MCFold: 0.408 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.646 MCFold: 0.396 Sensitivity PPfold(20): 0.510 MCFold: 0.406 Positive Predictive Value PPfold(20): 0.822 MCFold: 0.394 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	32 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.530 MCFold: 0.358 Sensitivity ContextFold: 0.434 MCFold: 0.366 Positive Predictive Value ContextFold: 0.652 MCFold: 0.357 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.622 MCFold: 0.402 Sensitivity RNASampler(20): 0.493 MCFold: 0.418 Positive Predictive Value RNASampler(20): 0.788 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.628 MCFold: 0.382 Sensitivity PETfold_pre2.0(20): 0.512 MCFold: 0.393 Positive Predictive Value PETfold_pre2.0(20): 0.775 MCFold: 0.378 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	18 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.606 MCFold: 0.396 Sensitivity TurboFold(20): 0.500 MCFold: 0.406 Positive Predictive Value TurboFold(20): 0.739 MCFold: 0.394 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	32 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.609 MCFold: 0.402 Sensitivity MXScarna(20): 0.509 MCFold: 0.418 Positive Predictive Value MXScarna(20): 0.733 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.553 MCFold: 0.397 Sensitivity RNAalifold(seed): 0.342 MCFold: 0.411 Positive Predictive Value RNAalifold(seed): 0.898 MCFold: 0.389 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	32 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.602 MCFold: 0.402 Sensitivity Murlet(20): 0.461 MCFold: 0.418 Positive Predictive Value Murlet(20): 0.791 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 MCFold: 0.414 Sensitivity CentroidAlifold(seed): 0.354 MCFold: 0.432 Positive Predictive Value CentroidAlifold(seed): 0.955 MCFold: 0.405 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.609 MCFold: 0.402 Sensitivity Carnac(20): 0.417 MCFold: 0.418 Positive Predictive Value Carnac(20): 0.895 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.537 MCFold: 0.368 Sensitivity IPknot: 0.445 MCFold: 0.376 Positive Predictive Value IPknot: 0.653 MCFold: 0.369 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	31 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.544 MCFold: 0.377 Sensitivity CentroidHomfold‑LAST: 0.438 MCFold: 0.383 Positive Predictive Value CentroidHomfold‑LAST: 0.682 MCFold: 0.380 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.533 MCFold: 0.385 Sensitivity Contrafold: 0.466 MCFold: 0.396 Positive Predictive Value Contrafold: 0.615 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.569 MCFold: 0.385 Sensitivity Sfold: 0.475 MCFold: 0.396 Positive Predictive Value Sfold: 0.689 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.545 MCFold: 0.385 Sensitivity HotKnots: 0.486 MCFold: 0.396 Positive Predictive Value HotKnots: 0.617 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.534 MCFold: 0.385 Sensitivity CentroidFold: 0.449 MCFold: 0.398 Positive Predictive Value CentroidFold: 0.642 MCFold: 0.381 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.491 MCFold: 0.355 Sensitivity TurboFold(seed): 0.403 MCFold: 0.369 Positive Predictive Value TurboFold(seed): 0.604 MCFold: 0.350 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.67657656842e-08	60 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.542 MCFold: 0.373 Sensitivity MaxExpect: 0.470 MCFold: 0.385 Positive Predictive Value MaxExpect: 0.632 MCFold: 0.369 Number of pairs reference - predicted secondary structure: 60 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.573 MCFold: 0.402 Sensitivity RSpredict(20): 0.464 MCFold: 0.418 Positive Predictive Value RSpredict(20): 0.714 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.551 MCFold: 0.385 Sensitivity PknotsRG: 0.488 MCFold: 0.396 Positive Predictive Value PknotsRG: 0.628 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.539 MCFold: 0.378 Sensitivity CMfinder(20): 0.389 MCFold: 0.392 Positive Predictive Value CMfinder(20): 0.751 MCFold: 0.373 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	66 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.549 MCFold: 0.385 Sensitivity UNAFold: 0.481 MCFold: 0.396 Positive Predictive Value UNAFold: 0.634 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.535 MCFold: 0.395 Sensitivity ProbKnot: 0.478 MCFold: 0.404 Positive Predictive Value ProbKnot: 0.604 MCFold: 0.395 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.598 MCFold: 0.431 Sensitivity Cylofold: 0.501 MCFold: 0.447 Positive Predictive Value Cylofold: 0.721 MCFold: 0.425 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.540 MCFold: 0.385 Sensitivity RNAfold: 0.476 MCFold: 0.396 Positive Predictive Value RNAfold: 0.620 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.478 MCFold: 0.361 Sensitivity RNASampler(seed): 0.346 MCFold: 0.381 Positive Predictive Value RNASampler(seed): 0.667 MCFold: 0.348 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.07229227445e-09	66 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.520 MCFold: 0.385 Sensitivity RNAsubopt: 0.463 MCFold: 0.396 Positive Predictive Value RNAsubopt: 0.591 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.519 MCFold: 0.408 Sensitivity Multilign(20): 0.437 MCFold: 0.422 Positive Predictive Value Multilign(20): 0.624 MCFold: 0.402 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	41 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.521 MCFold: 0.385 Sensitivity Afold: 0.468 MCFold: 0.406 Positive Predictive Value Afold: 0.588 MCFold: 0.374 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.526 MCFold: 0.385 Sensitivity RNAshapes: 0.461 MCFold: 0.396 Positive Predictive Value RNAshapes: 0.608 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.523 MCFold: 0.390 Sensitivity Fold: 0.465 MCFold: 0.399 Positive Predictive Value Fold: 0.594 MCFold: 0.390 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.513 MCFold: 0.385 Sensitivity McQFold: 0.435 MCFold: 0.396 Positive Predictive Value McQFold: 0.611 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.415 MCFold: 0.358 Sensitivity RNASLOpt: 0.334 MCFold: 0.366 Positive Predictive Value RNASLOpt: 0.522 MCFold: 0.357 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.562 MCFold: 0.402 Sensitivity Mastr(20): 0.396 MCFold: 0.418 Positive Predictive Value Mastr(20): 0.804 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.438 MCFold: 0.350 Sensitivity Multilign(seed): 0.327 MCFold: 0.347 Positive Predictive Value Multilign(seed): 0.596 MCFold: 0.361 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	66 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.492 MCFold: 0.385 Sensitivity Pknots: 0.443 MCFold: 0.396 Positive Predictive Value Pknots: 0.553 MCFold: 0.383 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	61 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.475 MCFold: 0.399 Sensitivity Vsfold4: 0.391 MCFold: 0.409 Positive Predictive Value Vsfold4: 0.586 MCFold: 0.398 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.455 MCFold: 0.431 Sensitivity CRWrnafold: 0.403 MCFold: 0.459 Positive Predictive Value CRWrnafold: 0.522 MCFold: 0.412 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18866702221e-08	20 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.439 MCFold: 0.384 Sensitivity Murlet(seed): 0.240 MCFold: 0.399 Positive Predictive Value Murlet(seed): 0.811 MCFold: 0.376 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	61 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.445 MCFold: 0.403 Sensitivity Vsfold5: 0.376 MCFold: 0.421 Positive Predictive Value Vsfold5: 0.536 MCFold: 0.395 Number of pairs reference - predicted secondary structure: 61 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.537 MCFold: 0.401 Sensitivity Alterna: 0.460 MCFold: 0.415 Positive Predictive Value Alterna: 0.637 MCFold: 0.402 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.489 MCFold: 0.404 Sensitivity RDfolder: 0.376 MCFold: 0.416 Positive Predictive Value RDfolder: 0.649 MCFold: 0.405 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.368 RNAwolf: 0.324 Sensitivity MCFold: 0.376 RNAwolf: 0.305 Positive Predictive Value MCFold: 0.369 RNAwolf: 0.352 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.401 NanoFolder: 0.294 Sensitivity MCFold: 0.400 NanoFolder: 0.311 Positive Predictive Value MCFold: 0.409 NanoFolder: 0.286 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.412 Carnac(seed): 0.196 Sensitivity MCFold: 0.430 Carnac(seed): 0.039 Positive Predictive Value MCFold: 0.401 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.418 RSpredict(seed): 0.165 Sensitivity MCFold: 0.436 RSpredict(seed): 0.067 Positive Predictive Value MCFold: 0.409 RSpredict(seed): 0.414 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.396 PPfold(seed): 0.164 Sensitivity MCFold: 0.408 PPfold(seed): 0.039 Positive Predictive Value MCFold: 0.393 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_2.0(seed): N/A MCFold: N/A Sensitivity PETfold_2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MCFold vs DAFS(20) Matthews Correlation Coefficient MCFold: N/A DAFS(20): N/A Sensitivity MCFold: N/A DAFS(20): N/A Positive Predictive Value MCFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_2.0(20): N/A MCFold: N/A Sensitivity PETfold_2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs MCFold Matthews Correlation Coefficient DAFS(seed): N/A MCFold: N/A Sensitivity DAFS(seed): N/A MCFold: N/A Positive Predictive Value DAFS(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.418 Mastr(seed): 0.028 Sensitivity MCFold: 0.436 Mastr(seed): 0.002 Positive Predictive Value MCFold: 0.409 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08
Alterna	10 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.775 Alterna: 0.537 Sensitivity CentroidAlifold(20): 0.635 Alterna: 0.465 Positive Predictive Value CentroidAlifold(20): 0.952 Alterna: 0.630 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	3 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Alterna: 0.545 Sensitivity PETfold_pre2.0(seed): 0.540 Alterna: 0.460 Positive Predictive Value PETfold_pre2.0(seed): 0.870 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	11 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.757 Alterna: 0.553 Sensitivity RNAalifold(20): 0.619 Alterna: 0.480 Positive Predictive Value RNAalifold(20): 0.930 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	20 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.693 Alterna: 0.572 Sensitivity MXScarna(seed): 0.560 Alterna: 0.500 Positive Predictive Value MXScarna(seed): 0.864 Alterna: 0.664 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	3 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.743 Alterna: 0.584 Sensitivity PPfold(20): 0.592 Alterna: 0.495 Positive Predictive Value PPfold(20): 0.938 Alterna: 0.699 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.558 Alterna: 0.432 Sensitivity ContextFold: 0.452 Alterna: 0.379 Positive Predictive Value ContextFold: 0.700 Alterna: 0.505 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	11 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.772 Alterna: 0.553 Sensitivity RNASampler(20): 0.628 Alterna: 0.480 Positive Predictive Value RNASampler(20): 0.953 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.66062906821e-08	0 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	3 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.676 Alterna: 0.584 Sensitivity TurboFold(20): 0.544 Alterna: 0.495 Positive Predictive Value TurboFold(20): 0.848 Alterna: 0.699 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	11 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.738 Alterna: 0.553 Sensitivity MXScarna(20): 0.619 Alterna: 0.480 Positive Predictive Value MXScarna(20): 0.885 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.75835195567e-08	9 Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.668 RNAalifold(seed): 0.570 Sensitivity Alterna: 0.562 RNAalifold(seed): 0.404 Positive Predictive Value Alterna: 0.802 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.679 Alterna: 0.553 Sensitivity Murlet(20): 0.529 Alterna: 0.480 Positive Predictive Value Murlet(20): 0.877 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	19 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.567 Alterna: 0.564 Sensitivity CentroidAlifold(seed): 0.337 Alterna: 0.492 Positive Predictive Value CentroidAlifold(seed): 0.960 Alterna: 0.656 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.228964554769	11 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.697 Alterna: 0.553 Sensitivity Carnac(20): 0.529 Alterna: 0.480 Positive Predictive Value Carnac(20): 0.924 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.01312059156e-09	9 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.577 Alterna: 0.500 Sensitivity IPknot: 0.449 Alterna: 0.432 Positive Predictive Value IPknot: 0.750 Alterna: 0.590 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.596 Alterna: 0.496 Sensitivity CentroidHomfold‑LAST: 0.427 Alterna: 0.419 Positive Predictive Value CentroidHomfold‑LAST: 0.840 Alterna: 0.599 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.21584974784e-08	35 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.608 Alterna: 0.523 Sensitivity Contrafold: 0.512 Alterna: 0.449 Positive Predictive Value Contrafold: 0.732 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.585 Alterna: 0.523 Sensitivity Sfold: 0.474 Alterna: 0.449 Positive Predictive Value Sfold: 0.732 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.588 Alterna: 0.523 Sensitivity HotKnots: 0.504 Alterna: 0.449 Positive Predictive Value HotKnots: 0.694 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	31 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.634 Alterna: 0.518 Sensitivity CentroidFold: 0.522 Alterna: 0.452 Positive Predictive Value CentroidFold: 0.778 Alterna: 0.605 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.540 TurboFold(seed): 0.514 Sensitivity Alterna: 0.448 TurboFold(seed): 0.417 Positive Predictive Value Alterna: 0.662 TurboFold(seed): 0.645 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	28 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.602 Alterna: 0.508 Sensitivity MaxExpect: 0.512 Alterna: 0.443 Positive Predictive Value MaxExpect: 0.717 Alterna: 0.593 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	11 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.703 Alterna: 0.553 Sensitivity RSpredict(20): 0.560 Alterna: 0.480 Positive Predictive Value RSpredict(20): 0.887 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.70887622364e-08	35 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.568 Alterna: 0.523 Sensitivity PknotsRG: 0.485 Alterna: 0.449 Positive Predictive Value PknotsRG: 0.674 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	35 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.593 Alterna: 0.523 Sensitivity UNAFold: 0.502 Alterna: 0.449 Positive Predictive Value UNAFold: 0.710 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.586 Alterna: 0.522 Sensitivity ProbKnot: 0.529 Alterna: 0.455 Positive Predictive Value ProbKnot: 0.659 Alterna: 0.609 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.50323628132e-08	16 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.629 Alterna: 0.528 Sensitivity Cylofold: 0.531 Alterna: 0.464 Positive Predictive Value Cylofold: 0.753 Alterna: 0.612 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.71568867205e-08	35 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.569 Alterna: 0.523 Sensitivity RNAfold: 0.484 Alterna: 0.449 Positive Predictive Value RNAfold: 0.680 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.667 RNASampler(seed): 0.644 Sensitivity Alterna: 0.560 RNASampler(seed): 0.474 Positive Predictive Value Alterna: 0.803 RNASampler(seed): 0.883 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	35 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.550 Alterna: 0.523 Sensitivity RNAsubopt: 0.468 Alterna: 0.449 Positive Predictive Value RNAsubopt: 0.655 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.85233844192e-08	3 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.647 Alterna: 0.584 Sensitivity Multilign(20): 0.544 Alterna: 0.495 Positive Predictive Value Multilign(20): 0.778 Alterna: 0.699 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	25 Afold vs Alterna Matthews Correlation Coefficient Afold: 0.546 Alterna: 0.518 Sensitivity Afold: 0.475 Alterna: 0.447 Positive Predictive Value Afold: 0.637 Alterna: 0.612 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.92687381315e-08	35 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.554 Alterna: 0.523 Sensitivity RNAshapes: 0.466 Alterna: 0.449 Positive Predictive Value RNAshapes: 0.669 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.624 Alterna: 0.543 Sensitivity Fold: 0.538 Alterna: 0.478 Positive Predictive Value Fold: 0.732 Alterna: 0.628 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	35 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.580 Alterna: 0.523 Sensitivity McQFold: 0.475 Alterna: 0.449 Positive Predictive Value McQFold: 0.719 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.432 RNASLOpt: 0.360 Sensitivity Alterna: 0.379 RNASLOpt: 0.274 Positive Predictive Value Alterna: 0.505 RNASLOpt: 0.486 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	11 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.701 Alterna: 0.553 Sensitivity Mastr(20): 0.570 Alterna: 0.480 Positive Predictive Value Mastr(20): 0.868 Alterna: 0.646 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	3 Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.540 Multilign(seed): 0.509 Sensitivity Alterna: 0.448 Multilign(seed): 0.406 Positive Predictive Value Alterna: 0.662 Multilign(seed): 0.650 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	35 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.612 Alterna: 0.523 Sensitivity Pknots: 0.532 Alterna: 0.449 Positive Predictive Value Pknots: 0.714 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.570 Alterna: 0.523 Sensitivity Vsfold4: 0.463 Alterna: 0.449 Positive Predictive Value Vsfold4: 0.711 Alterna: 0.620 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Alterna vs CRWrnafold Matthews Correlation Coefficient Alterna: 0.457 CRWrnafold: 0.450 Sensitivity Alterna: 0.404 CRWrnafold: 0.391 Positive Predictive Value Alterna: 0.529 CRWrnafold: 0.530 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.651 Murlet(seed): 0.486 Sensitivity Alterna: 0.542 Murlet(seed): 0.313 Positive Predictive Value Alterna: 0.789 Murlet(seed): 0.765 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	35 Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.523 Vsfold5: 0.496 Sensitivity Alterna: 0.449 Vsfold5: 0.409 Positive Predictive Value Alterna: 0.620 Vsfold5: 0.613 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 1.01188337103e-07	32 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.537 MCFold: 0.401 Sensitivity Alterna: 0.460 MCFold: 0.415 Positive Predictive Value Alterna: 0.637 MCFold: 0.402 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.523 RDfolder: 0.448 Sensitivity Alterna: 0.450 RDfolder: 0.347 Positive Predictive Value Alterna: 0.619 RDfolder: 0.589 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.502 Alterna: 0.500 Sensitivity RNAwolf: 0.458 Alterna: 0.432 Positive Predictive Value RNAwolf: 0.562 Alterna: 0.590 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.545 NanoFolder: 0.398 Sensitivity Alterna: 0.460 NanoFolder: 0.402 Positive Predictive Value Alterna: 0.656 NanoFolder: 0.407 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.651 Carnac(seed): 0.236 Sensitivity Alterna: 0.542 Carnac(seed): 0.056 Positive Predictive Value Alterna: 0.789 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.572 RSpredict(seed): 0.286 Sensitivity Alterna: 0.500 RSpredict(seed): 0.140 Positive Predictive Value Alterna: 0.664 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.566 PPfold(seed): 0.153 Sensitivity Alterna: 0.479 PPfold(seed): 0.032 Positive Predictive Value Alterna: 0.679 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(seed): N/A Sensitivity Alterna: N/A PETfold_2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs DAFS(20) Matthews Correlation Coefficient Alterna: N/A DAFS(20): N/A Sensitivity Alterna: N/A DAFS(20): N/A Positive Predictive Value Alterna: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_2.0(20) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(20): N/A Sensitivity Alterna: N/A PETfold_2.0(20): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Alterna Matthews Correlation Coefficient DAFS(seed): N/A Alterna: N/A Sensitivity DAFS(seed): N/A Alterna: N/A Positive Predictive Value DAFS(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.572 Mastr(seed): 0.000 Sensitivity Alterna: 0.500 Mastr(seed): 0.000 Positive Predictive Value Alterna: 0.664 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08
RDfolder	15 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.771 RDfolder: 0.552 Sensitivity CentroidAlifold(20): 0.620 RDfolder: 0.436 Positive Predictive Value CentroidAlifold(20): 0.962 RDfolder: 0.708 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	8 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RDfolder: 0.395 Sensitivity PETfold_pre2.0(seed): 0.588 RDfolder: 0.311 Positive Predictive Value PETfold_pre2.0(seed): 0.865 RDfolder: 0.514 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	16 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.744 RDfolder: 0.563 Sensitivity RNAalifold(20): 0.590 RDfolder: 0.447 Positive Predictive Value RNAalifold(20): 0.944 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.52299983238e-08	24 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.685 RDfolder: 0.504 Sensitivity MXScarna(seed): 0.556 RDfolder: 0.407 Positive Predictive Value MXScarna(seed): 0.852 RDfolder: 0.634 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.737 RDfolder: 0.489 Sensitivity PPfold(20): 0.585 RDfolder: 0.365 Positive Predictive Value PPfold(20): 0.934 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	13 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.631 RDfolder: 0.396 Sensitivity ContextFold: 0.507 RDfolder: 0.302 Positive Predictive Value ContextFold: 0.795 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.69265863073e-08	16 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.754 RDfolder: 0.563 Sensitivity RNASampler(20): 0.603 RDfolder: 0.447 Positive Predictive Value RNASampler(20): 0.949 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.95070920198e-08	5 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.733 RDfolder: 0.535 Sensitivity PETfold_pre2.0(20): 0.587 RDfolder: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.920 RDfolder: 0.704 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.671 RDfolder: 0.489 Sensitivity TurboFold(20): 0.531 RDfolder: 0.365 Positive Predictive Value TurboFold(20): 0.853 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	16 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.718 RDfolder: 0.563 Sensitivity MXScarna(20): 0.590 RDfolder: 0.447 Positive Predictive Value MXScarna(20): 0.880 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.12160100812e-08	13 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.595 RDfolder: 0.515 Sensitivity RNAalifold(seed): 0.413 RDfolder: 0.398 Positive Predictive Value RNAalifold(seed): 0.865 RDfolder: 0.678 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.42300079339e-08	16 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.669 RDfolder: 0.563 Sensitivity Murlet(20): 0.510 RDfolder: 0.447 Positive Predictive Value Murlet(20): 0.883 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.20167918023e-08	24 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.594 RDfolder: 0.504 Sensitivity CentroidAlifold(seed): 0.369 RDfolder: 0.407 Positive Predictive Value CentroidAlifold(seed): 0.963 RDfolder: 0.635 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	16 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.652 RDfolder: 0.563 Sensitivity Carnac(20): 0.479 RDfolder: 0.447 Positive Predictive Value Carnac(20): 0.895 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	16 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.555 RDfolder: 0.403 Sensitivity IPknot: 0.444 RDfolder: 0.302 Positive Predictive Value IPknot: 0.704 RDfolder: 0.550 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.12160100812e-08	16 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.624 RDfolder: 0.400 Sensitivity CentroidHomfold‑LAST: 0.483 RDfolder: 0.298 Positive Predictive Value CentroidHomfold‑LAST: 0.815 RDfolder: 0.550 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.05041766982e-08	42 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.603 RDfolder: 0.461 Sensitivity Contrafold: 0.512 RDfolder: 0.358 Positive Predictive Value Contrafold: 0.720 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.567 RDfolder: 0.461 Sensitivity Sfold: 0.460 RDfolder: 0.358 Positive Predictive Value Sfold: 0.707 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.579 RDfolder: 0.461 Sensitivity HotKnots: 0.502 RDfolder: 0.358 Positive Predictive Value HotKnots: 0.677 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.629 RDfolder: 0.453 Sensitivity CentroidFold: 0.521 RDfolder: 0.354 Positive Predictive Value CentroidFold: 0.768 RDfolder: 0.589 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.553 RDfolder: 0.392 Sensitivity TurboFold(seed): 0.426 RDfolder: 0.284 Positive Predictive Value TurboFold(seed): 0.728 RDfolder: 0.556 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	35 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.581 RDfolder: 0.450 Sensitivity MaxExpect: 0.496 RDfolder: 0.349 Positive Predictive Value MaxExpect: 0.691 RDfolder: 0.591 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.665 RDfolder: 0.563 Sensitivity RSpredict(20): 0.514 RDfolder: 0.447 Positive Predictive Value RSpredict(20): 0.868 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	42 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.573 RDfolder: 0.461 Sensitivity PknotsRG: 0.494 RDfolder: 0.358 Positive Predictive Value PknotsRG: 0.674 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	2 CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.753 RDfolder: 0.722 Sensitivity CMfinder(20): 0.586 RDfolder: 0.586 Positive Predictive Value CMfinder(20): 0.971 RDfolder: 0.895 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	42 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.567 RDfolder: 0.461 Sensitivity UNAFold: 0.483 RDfolder: 0.358 Positive Predictive Value UNAFold: 0.674 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.561 RDfolder: 0.455 Sensitivity ProbKnot: 0.502 RDfolder: 0.354 Positive Predictive Value ProbKnot: 0.638 RDfolder: 0.598 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	21 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.629 RDfolder: 0.425 Sensitivity Cylofold: 0.532 RDfolder: 0.331 Positive Predictive Value Cylofold: 0.752 RDfolder: 0.558 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	42 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.547 RDfolder: 0.461 Sensitivity RNAfold: 0.468 RDfolder: 0.358 Positive Predictive Value RNAfold: 0.649 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.627 RDfolder: 0.486 Sensitivity RNASampler(seed): 0.442 RDfolder: 0.372 Positive Predictive Value RNASampler(seed): 0.896 RDfolder: 0.645 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	42 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.552 RDfolder: 0.461 Sensitivity RNAsubopt: 0.474 RDfolder: 0.358 Positive Predictive Value RNAsubopt: 0.653 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.614 RDfolder: 0.489 Sensitivity Multilign(20): 0.506 RDfolder: 0.365 Positive Predictive Value Multilign(20): 0.753 RDfolder: 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	29 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.534 RDfolder: 0.458 Sensitivity Afold: 0.466 RDfolder: 0.362 Positive Predictive Value Afold: 0.622 RDfolder: 0.593 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	42 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.546 RDfolder: 0.461 Sensitivity RNAshapes: 0.461 RDfolder: 0.358 Positive Predictive Value RNAshapes: 0.655 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.572 RDfolder: 0.463 Sensitivity Fold: 0.495 RDfolder: 0.363 Positive Predictive Value Fold: 0.670 RDfolder: 0.603 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	42 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.595 RDfolder: 0.461 Sensitivity McQFold: 0.488 RDfolder: 0.358 Positive Predictive Value McQFold: 0.734 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.556 RDfolder: 0.396 Sensitivity RNASLOpt: 0.450 RDfolder: 0.302 Positive Predictive Value RNASLOpt: 0.698 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.26346675981e-08	16 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.675 RDfolder: 0.563 Sensitivity Mastr(20): 0.529 RDfolder: 0.447 Positive Predictive Value Mastr(20): 0.868 RDfolder: 0.718 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	5 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.610 RDfolder: 0.353 Sensitivity Multilign(seed): 0.489 RDfolder: 0.264 Positive Predictive Value Multilign(seed): 0.770 RDfolder: 0.485 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	42 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.607 RDfolder: 0.461 Sensitivity Pknots: 0.530 RDfolder: 0.358 Positive Predictive Value Pknots: 0.703 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.570 RDfolder: 0.461 Sensitivity Vsfold4: 0.464 RDfolder: 0.358 Positive Predictive Value Vsfold4: 0.709 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.513 RDfolder: 0.230 Sensitivity CRWrnafold: 0.436 RDfolder: 0.165 Positive Predictive Value CRWrnafold: 0.613 RDfolder: 0.336 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.60513176667e-09	12 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.495 Murlet(seed): 0.494 Sensitivity RDfolder: 0.379 Murlet(seed): 0.306 Positive Predictive Value RDfolder: 0.657 Murlet(seed): 0.807 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.317118147004	42 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.525 RDfolder: 0.461 Sensitivity Vsfold5: 0.437 RDfolder: 0.358 Positive Predictive Value Vsfold5: 0.640 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.489 MCFold: 0.404 Sensitivity RDfolder: 0.376 MCFold: 0.416 Positive Predictive Value RDfolder: 0.649 MCFold: 0.405 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.523 RDfolder: 0.448 Sensitivity Alterna: 0.450 RDfolder: 0.347 Positive Predictive Value Alterna: 0.619 RDfolder: 0.589 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.466 RDfolder: 0.403 Sensitivity RNAwolf: 0.429 RDfolder: 0.302 Positive Predictive Value RNAwolf: 0.518 RDfolder: 0.550 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.76499031155e-08	? NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.425 RDfolder: 0.400 Sensitivity NanoFolder: 0.425 RDfolder: 0.316 Positive Predictive Value NanoFolder: 0.437 RDfolder: 0.519 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.495 Carnac(seed): 0.194 Sensitivity RDfolder: 0.379 Carnac(seed): 0.038 Positive Predictive Value RDfolder: 0.657 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.512 RSpredict(seed): 0.292 Sensitivity RDfolder: 0.415 RSpredict(seed): 0.146 Positive Predictive Value RDfolder: 0.643 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.403 PPfold(seed): 0.116 Sensitivity RDfolder: 0.308 PPfold(seed): 0.018 Positive Predictive Value RDfolder: 0.540 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	? RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs DAFS(20) Matthews Correlation Coefficient RDfolder: N/A DAFS(20): N/A Sensitivity RDfolder: N/A DAFS(20): N/A Positive Predictive Value RDfolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(20): N/A Sensitivity RDfolder: N/A PETfold_2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs DAFS(seed) Matthews Correlation Coefficient RDfolder: N/A DAFS(seed): N/A Sensitivity RDfolder: N/A DAFS(seed): N/A Positive Predictive Value RDfolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.512 Mastr(seed): 0.000 Sensitivity RDfolder: 0.415 Mastr(seed): 0.000 Positive Predictive Value RDfolder: 0.643 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08
RNAwolf	21 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.669 RNAwolf: 0.348 Sensitivity CentroidAlifold(20): 0.511 RNAwolf: 0.328 Positive Predictive Value CentroidAlifold(20): 0.880 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.715 RNAwolf: 0.404 Sensitivity PETfold_pre2.0(seed): 0.602 RNAwolf: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.850 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.644 RNAwolf: 0.348 Sensitivity RNAalifold(20): 0.503 RNAwolf: 0.328 Positive Predictive Value RNAalifold(20): 0.829 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.638 RNAwolf: 0.409 Sensitivity MXScarna(seed): 0.529 RNAwolf: 0.379 Positive Predictive Value MXScarna(seed): 0.770 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.663 RNAwolf: 0.343 Sensitivity PPfold(20): 0.528 RNAwolf: 0.325 Positive Predictive Value PPfold(20): 0.836 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	43 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.536 RNAwolf: 0.307 Sensitivity ContextFold: 0.440 RNAwolf: 0.284 Positive Predictive Value ContextFold: 0.654 RNAwolf: 0.333 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.585 RNAwolf: 0.348 Sensitivity RNASampler(20): 0.448 RNAwolf: 0.328 Positive Predictive Value RNASampler(20): 0.768 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 RNAwolf: 0.312 Sensitivity PETfold_pre2.0(20): 0.530 RNAwolf: 0.295 Positive Predictive Value PETfold_pre2.0(20): 0.798 RNAwolf: 0.338 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	20 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.616 RNAwolf: 0.343 Sensitivity TurboFold(20): 0.508 RNAwolf: 0.325 Positive Predictive Value TurboFold(20): 0.752 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	21 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.590 RNAwolf: 0.348 Sensitivity MXScarna(20): 0.486 RNAwolf: 0.328 Positive Predictive Value MXScarna(20): 0.720 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	16 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.635 RNAwolf: 0.408 Sensitivity RNAalifold(seed): 0.475 RNAwolf: 0.381 Positive Predictive Value RNAalifold(seed): 0.849 RNAwolf: 0.438 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.36983135185e-08	21 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.583 RNAwolf: 0.348 Sensitivity Murlet(20): 0.437 RNAwolf: 0.328 Positive Predictive Value Murlet(20): 0.784 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	29 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.631 RNAwolf: 0.416 Sensitivity CentroidAlifold(seed): 0.445 RNAwolf: 0.385 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAwolf: 0.451 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.565 RNAwolf: 0.348 Sensitivity Carnac(20): 0.371 RNAwolf: 0.328 Positive Predictive Value Carnac(20): 0.867 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	46 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.513 RNAwolf: 0.317 Sensitivity IPknot: 0.411 RNAwolf: 0.293 Positive Predictive Value IPknot: 0.641 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.513 RNAwolf: 0.341 Sensitivity CentroidHomfold‑LAST: 0.379 RNAwolf: 0.315 Positive Predictive Value CentroidHomfold‑LAST: 0.698 RNAwolf: 0.375 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.459 RNAwolf: 0.317 Sensitivity Contrafold: 0.394 RNAwolf: 0.293 Positive Predictive Value Contrafold: 0.537 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.468 RNAwolf: 0.317 Sensitivity Sfold: 0.393 RNAwolf: 0.293 Positive Predictive Value Sfold: 0.559 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.501 RNAwolf: 0.323 Sensitivity HotKnots: 0.440 RNAwolf: 0.301 Positive Predictive Value HotKnots: 0.575 RNAwolf: 0.354 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.446 RNAwolf: 0.317 Sensitivity CentroidFold: 0.356 RNAwolf: 0.293 Positive Predictive Value CentroidFold: 0.560 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.529 RNAwolf: 0.297 Sensitivity TurboFold(seed): 0.434 RNAwolf: 0.282 Positive Predictive Value TurboFold(seed): 0.650 RNAwolf: 0.321 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	46 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.446 RNAwolf: 0.317 Sensitivity MaxExpect: 0.384 RNAwolf: 0.293 Positive Predictive Value MaxExpect: 0.520 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.520 RNAwolf: 0.343 Sensitivity RSpredict(20): 0.398 RNAwolf: 0.325 Positive Predictive Value RSpredict(20): 0.685 RNAwolf: 0.370 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	45 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.456 RNAwolf: 0.278 Sensitivity PknotsRG: 0.401 RNAwolf: 0.258 Positive Predictive Value PknotsRG: 0.521 RNAwolf: 0.303 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.521 RNAwolf: 0.370 Sensitivity CMfinder(20): 0.366 RNAwolf: 0.346 Positive Predictive Value CMfinder(20): 0.748 RNAwolf: 0.403 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.99051034341e-09	46 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.446 RNAwolf: 0.317 Sensitivity UNAFold: 0.390 RNAwolf: 0.293 Positive Predictive Value UNAFold: 0.512 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.444 RNAwolf: 0.317 Sensitivity ProbKnot: 0.388 RNAwolf: 0.293 Positive Predictive Value ProbKnot: 0.511 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.490 RNAwolf: 0.382 Sensitivity Cylofold: 0.409 RNAwolf: 0.354 Positive Predictive Value Cylofold: 0.595 RNAwolf: 0.422 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.449 RNAwolf: 0.317 Sensitivity RNAfold: 0.393 RNAwolf: 0.293 Positive Predictive Value RNAfold: 0.514 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.417 RNAwolf: 0.340 Sensitivity RNASampler(seed): 0.283 RNAwolf: 0.333 Positive Predictive Value RNASampler(seed): 0.619 RNAwolf: 0.353 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	44 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.475 RNAwolf: 0.323 Sensitivity RNAsubopt: 0.417 RNAwolf: 0.301 Positive Predictive Value RNAsubopt: 0.546 RNAwolf: 0.354 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.534 RNAwolf: 0.366 Sensitivity Multilign(20): 0.449 RNAwolf: 0.345 Positive Predictive Value Multilign(20): 0.642 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	19 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.348 RNAwolf: 0.218 Sensitivity Afold: 0.312 RNAwolf: 0.203 Positive Predictive Value Afold: 0.389 RNAwolf: 0.235 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.30280588002e-08	44 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.460 RNAwolf: 0.323 Sensitivity RNAshapes: 0.397 RNAwolf: 0.301 Positive Predictive Value RNAshapes: 0.537 RNAwolf: 0.354 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.411 RNAwolf: 0.317 Sensitivity Fold: 0.364 RNAwolf: 0.293 Positive Predictive Value Fold: 0.467 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.380 RNAwolf: 0.317 Sensitivity McQFold: 0.322 RNAwolf: 0.293 Positive Predictive Value McQFold: 0.450 RNAwolf: 0.344 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.427 RNAwolf: 0.306 Sensitivity RNASLOpt: 0.341 RNAwolf: 0.285 Positive Predictive Value RNASLOpt: 0.541 RNAwolf: 0.335 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.496 RNAwolf: 0.348 Sensitivity Mastr(20): 0.341 RNAwolf: 0.328 Positive Predictive Value Mastr(20): 0.729 RNAwolf: 0.379 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	10 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.556 RNAwolf: 0.374 Sensitivity Multilign(seed): 0.432 RNAwolf: 0.348 Positive Predictive Value Multilign(seed): 0.723 RNAwolf: 0.410 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.3765112512e-09	41 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.446 RNAwolf: 0.359 Sensitivity Pknots: 0.400 RNAwolf: 0.335 Positive Predictive Value Pknots: 0.505 RNAwolf: 0.393 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.401 RNAwolf: 0.371 Sensitivity Vsfold4: 0.328 RNAwolf: 0.345 Positive Predictive Value Vsfold4: 0.498 RNAwolf: 0.408 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.467 RNAwolf: 0.352 Sensitivity CRWrnafold: 0.410 RNAwolf: 0.329 Positive Predictive Value CRWrnafold: 0.540 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	15 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.418 RNAwolf: 0.348 Sensitivity Murlet(seed): 0.227 RNAwolf: 0.331 Positive Predictive Value Murlet(seed): 0.777 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.3551590886e-08	37 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.370 Vsfold5: 0.368 Sensitivity RNAwolf: 0.345 Vsfold5: 0.315 Positive Predictive Value RNAwolf: 0.405 Vsfold5: 0.438 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.935722063919	35 MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.368 RNAwolf: 0.324 Sensitivity MCFold: 0.376 RNAwolf: 0.305 Positive Predictive Value MCFold: 0.369 RNAwolf: 0.352 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.502 Alterna: 0.500 Sensitivity RNAwolf: 0.458 Alterna: 0.432 Positive Predictive Value RNAwolf: 0.562 Alterna: 0.590 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	16 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.466 RDfolder: 0.403 Sensitivity RNAwolf: 0.429 RDfolder: 0.302 Positive Predictive Value RNAwolf: 0.518 RDfolder: 0.550 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.76499031155e-08		+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.360 NanoFolder: 0.272 Sensitivity RNAwolf: 0.333 NanoFolder: 0.284 Positive Predictive Value RNAwolf: 0.398 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.452 RNAwolf: 0.401 Sensitivity Carnac(seed): 0.229 RNAwolf: 0.373 Positive Predictive Value Carnac(seed): 0.890 RNAwolf: 0.432 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000233863577759	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.415 RSpredict(seed): 0.395 Sensitivity RNAwolf: 0.385 RSpredict(seed): 0.246 Positive Predictive Value RNAwolf: 0.449 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.387 PPfold(seed): 0.148 Sensitivity RNAwolf: 0.363 PPfold(seed): 0.032 Positive Predictive Value RNAwolf: 0.422 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAwolf: 0.549 Sensitivity PETfold_2.0(seed): 0.642 RNAwolf: 0.484 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAwolf: 0.630 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs DAFS(20) Matthews Correlation Coefficient RNAwolf: N/A DAFS(20): N/A Sensitivity RNAwolf: N/A DAFS(20): N/A Positive Predictive Value RNAwolf: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAwolf: 0.431 Sensitivity PETfold_2.0(20): 0.509 RNAwolf: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 RNAwolf: 0.512 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs RNAwolf Matthews Correlation Coefficient DAFS(seed): N/A RNAwolf: N/A Sensitivity DAFS(seed): N/A RNAwolf: N/A Positive Predictive Value DAFS(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.389 Mastr(seed): 0.033 Sensitivity RNAwolf: 0.363 Mastr(seed): 0.003 Positive Predictive Value RNAwolf: 0.426 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08
NanoFolder	14 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.664 NanoFolder: 0.269 Sensitivity CentroidAlifold(20): 0.516 NanoFolder: 0.280 Positive Predictive Value CentroidAlifold(20): 0.859 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.53777893337e-08	19 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.731 NanoFolder: 0.290 Sensitivity PETfold_pre2.0(seed): 0.605 NanoFolder: 0.301 Positive Predictive Value PETfold_pre2.0(seed): 0.885 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.7402423548e-08	14 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.637 NanoFolder: 0.269 Sensitivity RNAalifold(20): 0.504 NanoFolder: 0.280 Positive Predictive Value RNAalifold(20): 0.811 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	18 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.611 NanoFolder: 0.273 Sensitivity MXScarna(seed): 0.499 NanoFolder: 0.284 Positive Predictive Value MXScarna(seed): 0.754 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.24519439238e-08	13 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.664 NanoFolder: 0.271 Sensitivity PPfold(20): 0.541 NanoFolder: 0.286 Positive Predictive Value PPfold(20): 0.818 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	26 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.556 NanoFolder: 0.272 Sensitivity ContextFold: 0.451 NanoFolder: 0.284 Positive Predictive Value ContextFold: 0.691 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	14 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.572 NanoFolder: 0.269 Sensitivity RNASampler(20): 0.442 NanoFolder: 0.280 Positive Predictive Value RNASampler(20): 0.745 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	14 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.667 NanoFolder: 0.269 Sensitivity PETfold_pre2.0(20): 0.552 NanoFolder: 0.280 Positive Predictive Value PETfold_pre2.0(20): 0.810 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	13 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.608 NanoFolder: 0.271 Sensitivity TurboFold(20): 0.513 NanoFolder: 0.286 Positive Predictive Value TurboFold(20): 0.724 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	14 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.586 NanoFolder: 0.269 Sensitivity MXScarna(20): 0.498 NanoFolder: 0.280 Positive Predictive Value MXScarna(20): 0.695 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	8 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.488 NanoFolder: 0.253 Sensitivity RNAalifold(seed): 0.280 NanoFolder: 0.276 Positive Predictive Value RNAalifold(seed): 0.855 NanoFolder: 0.241 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.607 NanoFolder: 0.269 Sensitivity Murlet(20): 0.457 NanoFolder: 0.280 Positive Predictive Value Murlet(20): 0.811 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	19 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.536 NanoFolder: 0.290 Sensitivity CentroidAlifold(seed): 0.308 NanoFolder: 0.301 Positive Predictive Value CentroidAlifold(seed): 0.940 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	14 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.576 NanoFolder: 0.269 Sensitivity Carnac(20): 0.383 NanoFolder: 0.280 Positive Predictive Value Carnac(20): 0.872 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	26 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.533 NanoFolder: 0.272 Sensitivity IPknot: 0.446 NanoFolder: 0.284 Positive Predictive Value IPknot: 0.642 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.557 NanoFolder: 0.268 Sensitivity CentroidHomfold‑LAST: 0.439 NanoFolder: 0.280 Positive Predictive Value CentroidHomfold‑LAST: 0.712 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.483 NanoFolder: 0.272 Sensitivity Contrafold: 0.423 NanoFolder: 0.284 Positive Predictive Value Contrafold: 0.557 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.491 NanoFolder: 0.272 Sensitivity Sfold: 0.411 NanoFolder: 0.284 Positive Predictive Value Sfold: 0.594 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.499 NanoFolder: 0.272 Sensitivity HotKnots: 0.443 NanoFolder: 0.284 Positive Predictive Value HotKnots: 0.569 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.469 NanoFolder: 0.272 Sensitivity CentroidFold: 0.393 NanoFolder: 0.284 Positive Predictive Value CentroidFold: 0.565 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.435 NanoFolder: 0.306 Sensitivity TurboFold(seed): 0.369 NanoFolder: 0.328 Positive Predictive Value TurboFold(seed): 0.518 NanoFolder: 0.293 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.491 NanoFolder: 0.272 Sensitivity MaxExpect: 0.424 NanoFolder: 0.284 Positive Predictive Value MaxExpect: 0.575 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	13 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.511 NanoFolder: 0.271 Sensitivity RSpredict(20): 0.394 NanoFolder: 0.286 Positive Predictive Value RSpredict(20): 0.667 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08	26 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.525 NanoFolder: 0.272 Sensitivity PknotsRG: 0.460 NanoFolder: 0.284 Positive Predictive Value PknotsRG: 0.606 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	9 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.508 NanoFolder: 0.241 Sensitivity CMfinder(20): 0.363 NanoFolder: 0.251 Positive Predictive Value CMfinder(20): 0.716 NanoFolder: 0.241 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	26 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.472 NanoFolder: 0.272 Sensitivity UNAFold: 0.411 NanoFolder: 0.284 Positive Predictive Value UNAFold: 0.549 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.492 NanoFolder: 0.272 Sensitivity ProbKnot: 0.434 NanoFolder: 0.284 Positive Predictive Value ProbKnot: 0.565 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.455 NanoFolder: 0.283 Sensitivity Cylofold: 0.384 NanoFolder: 0.295 Positive Predictive Value Cylofold: 0.547 NanoFolder: 0.283 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	26 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.503 NanoFolder: 0.272 Sensitivity RNAfold: 0.439 NanoFolder: 0.284 Positive Predictive Value RNAfold: 0.583 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	6 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.337 NanoFolder: 0.214 Sensitivity RNASampler(seed): 0.233 NanoFolder: 0.244 Positive Predictive Value RNASampler(seed): 0.495 NanoFolder: 0.195 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	26 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.489 NanoFolder: 0.272 Sensitivity RNAsubopt: 0.433 NanoFolder: 0.284 Positive Predictive Value RNAsubopt: 0.559 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	13 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.537 NanoFolder: 0.271 Sensitivity Multilign(20): 0.455 NanoFolder: 0.286 Positive Predictive Value Multilign(20): 0.640 NanoFolder: 0.266 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.62913390836e-08	11 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.380 NanoFolder: 0.230 Sensitivity Afold: 0.339 NanoFolder: 0.249 Positive Predictive Value Afold: 0.432 NanoFolder: 0.221 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	26 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.463 NanoFolder: 0.272 Sensitivity RNAshapes: 0.403 NanoFolder: 0.284 Positive Predictive Value RNAshapes: 0.538 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.503 NanoFolder: 0.272 Sensitivity Fold: 0.439 NanoFolder: 0.284 Positive Predictive Value Fold: 0.582 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.431 NanoFolder: 0.272 Sensitivity McQFold: 0.369 NanoFolder: 0.284 Positive Predictive Value McQFold: 0.511 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.441 NanoFolder: 0.272 Sensitivity RNASLOpt: 0.350 NanoFolder: 0.284 Positive Predictive Value RNASLOpt: 0.564 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.479 NanoFolder: 0.269 Sensitivity Mastr(20): 0.345 NanoFolder: 0.280 Positive Predictive Value Mastr(20): 0.673 NanoFolder: 0.267 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.50323628132e-08	5 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.541 NanoFolder: 0.278 Sensitivity Multilign(seed): 0.422 NanoFolder: 0.283 Positive Predictive Value Multilign(seed): 0.700 NanoFolder: 0.285 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	25 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.434 NanoFolder: 0.293 Sensitivity Pknots: 0.387 NanoFolder: 0.305 Positive Predictive Value Pknots: 0.495 NanoFolder: 0.290 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.372 NanoFolder: 0.272 Sensitivity Vsfold4: 0.303 NanoFolder: 0.284 Positive Predictive Value Vsfold4: 0.465 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	8 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.492 NanoFolder: 0.366 Sensitivity CRWrnafold: 0.431 NanoFolder: 0.380 Positive Predictive Value CRWrnafold: 0.570 NanoFolder: 0.362 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.404 NanoFolder: 0.253 Sensitivity Murlet(seed): 0.213 NanoFolder: 0.276 Positive Predictive Value Murlet(seed): 0.771 NanoFolder: 0.241 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	25 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.350 NanoFolder: 0.290 Sensitivity Vsfold5: 0.302 NanoFolder: 0.303 Positive Predictive Value Vsfold5: 0.415 NanoFolder: 0.287 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	20 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.401 NanoFolder: 0.294 Sensitivity MCFold: 0.400 NanoFolder: 0.311 Positive Predictive Value MCFold: 0.409 NanoFolder: 0.286 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	3 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.545 NanoFolder: 0.398 Sensitivity Alterna: 0.460 NanoFolder: 0.402 Positive Predictive Value Alterna: 0.656 NanoFolder: 0.407 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.425 RDfolder: 0.400 Sensitivity NanoFolder: 0.425 RDfolder: 0.316 Positive Predictive Value NanoFolder: 0.437 RDfolder: 0.519 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.360 NanoFolder: 0.272 Sensitivity RNAwolf: 0.333 NanoFolder: 0.284 Positive Predictive Value RNAwolf: 0.398 NanoFolder: 0.269 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08		? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.289 Carnac(seed): 0.273 Sensitivity NanoFolder: 0.308 Carnac(seed): 0.075 Positive Predictive Value NanoFolder: 0.279 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.293 RSpredict(seed): 0.091 Sensitivity NanoFolder: 0.307 RSpredict(seed): 0.037 Positive Predictive Value NanoFolder: 0.290 RSpredict(seed): 0.235 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.293 PPfold(seed): 0.172 Sensitivity NanoFolder: 0.307 PPfold(seed): 0.041 Positive Predictive Value NanoFolder: 0.290 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	? NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 NanoFolder: 0.243 Sensitivity PETfold_2.0(seed): 0.614 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(seed): 0.946 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs DAFS(20) Matthews Correlation Coefficient NanoFolder: N/A DAFS(20): N/A Sensitivity NanoFolder: N/A DAFS(20): N/A Positive Predictive Value NanoFolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(20): 0.647 NanoFolder: 0.243 Sensitivity PETfold_2.0(20): 0.509 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(20): 0.829 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs DAFS(seed) Matthews Correlation Coefficient NanoFolder: N/A DAFS(seed): N/A Sensitivity NanoFolder: N/A DAFS(seed): N/A Positive Predictive Value NanoFolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.290 Mastr(seed): 0.039 Sensitivity NanoFolder: 0.301 Mastr(seed): 0.004 Positive Predictive Value NanoFolder: 0.288 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08
Carnac(seed)	21 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.645 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.481 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.868 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	15 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.687 Carnac(seed): 0.467 Sensitivity PETfold_pre2.0(seed): 0.577 Carnac(seed): 0.245 Positive Predictive Value PETfold_pre2.0(seed): 0.820 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	22 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.612 Carnac(seed): 0.110 Sensitivity RNAalifold(20): 0.471 Carnac(seed): 0.012 Positive Predictive Value RNAalifold(20): 0.799 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	29 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.630 Carnac(seed): 0.392 Sensitivity MXScarna(seed): 0.522 Carnac(seed): 0.172 Positive Predictive Value MXScarna(seed): 0.760 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	11 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.547 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.407 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.742 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.28433927253e-09	15 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.642 Carnac(seed): 0.467 Sensitivity ContextFold: 0.530 Carnac(seed): 0.245 Positive Predictive Value ContextFold: 0.778 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08	22 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.590 Carnac(seed): 0.110 Sensitivity RNASampler(20): 0.454 Carnac(seed): 0.012 Positive Predictive Value RNASampler(20): 0.770 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.516 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.400 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.670 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.517 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.414 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.651 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08	22 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.578 Carnac(seed): 0.110 Sensitivity MXScarna(20): 0.474 Carnac(seed): 0.012 Positive Predictive Value MXScarna(20): 0.710 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.634 Carnac(seed): 0.414 Sensitivity RNAalifold(seed): 0.465 Carnac(seed): 0.192 Positive Predictive Value RNAalifold(seed): 0.867 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	22 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.553 Carnac(seed): 0.110 Sensitivity Murlet(20): 0.404 Carnac(seed): 0.012 Positive Predictive Value Murlet(20): 0.762 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	28 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Carnac(seed): 0.385 Sensitivity CentroidAlifold(seed): 0.513 Carnac(seed): 0.167 Positive Predictive Value CentroidAlifold(seed): 0.909 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	22 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.572 Carnac(seed): 0.110 Sensitivity Carnac(20): 0.355 Carnac(seed): 0.012 Positive Predictive Value Carnac(20): 0.927 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	17 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.592 Carnac(seed): 0.452 Sensitivity IPknot: 0.492 Carnac(seed): 0.229 Positive Predictive Value IPknot: 0.712 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.45076534967e-08	14 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.516 Carnac(seed): 0.220 Sensitivity CentroidHomfold‑LAST: 0.431 Carnac(seed): 0.049 Positive Predictive Value CentroidHomfold‑LAST: 0.625 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	29 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.588 Carnac(seed): 0.392 Sensitivity Contrafold: 0.514 Carnac(seed): 0.172 Positive Predictive Value Contrafold: 0.673 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.02343278931e-08	29 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.554 Carnac(seed): 0.392 Sensitivity Sfold: 0.469 Carnac(seed): 0.172 Positive Predictive Value Sfold: 0.657 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.564 Carnac(seed): 0.179 Sensitivity HotKnots: 0.506 Carnac(seed): 0.032 Positive Predictive Value HotKnots: 0.634 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.574 Carnac(seed): 0.385 Sensitivity CentroidFold: 0.480 Carnac(seed): 0.167 Positive Predictive Value CentroidFold: 0.687 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 Carnac(seed): 0.216 Sensitivity TurboFold(seed): 0.434 Carnac(seed): 0.047 Positive Predictive Value TurboFold(seed): 0.650 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.58287649515e-08	27 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.541 Carnac(seed): 0.390 Sensitivity MaxExpect: 0.468 Carnac(seed): 0.171 Positive Predictive Value MaxExpect: 0.626 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	22 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.473 Carnac(seed): 0.110 Sensitivity RSpredict(20): 0.367 Carnac(seed): 0.012 Positive Predictive Value RSpredict(20): 0.616 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.583 Carnac(seed): 0.179 Sensitivity PknotsRG: 0.519 Carnac(seed): 0.032 Positive Predictive Value PknotsRG: 0.659 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	3 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.333 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.208 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.538 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	29 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.527 Carnac(seed): 0.392 Sensitivity UNAFold: 0.462 Carnac(seed): 0.172 Positive Predictive Value UNAFold: 0.603 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	22 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.529 Carnac(seed): 0.411 Sensitivity ProbKnot: 0.465 Carnac(seed): 0.190 Positive Predictive Value ProbKnot: 0.602 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	13 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.611 Carnac(seed): 0.091 Sensitivity Cylofold: 0.499 Carnac(seed): 0.008 Positive Predictive Value Cylofold: 0.753 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	29 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.529 Carnac(seed): 0.392 Sensitivity RNAfold: 0.466 Carnac(seed): 0.172 Positive Predictive Value RNAfold: 0.603 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 Carnac(seed): 0.265 Sensitivity RNASampler(seed): 0.342 Carnac(seed): 0.071 Positive Predictive Value RNASampler(seed): 0.684 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	28 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.555 Carnac(seed): 0.179 Sensitivity RNAsubopt: 0.497 Carnac(seed): 0.032 Positive Predictive Value RNAsubopt: 0.625 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	10 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.431 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.360 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.523 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.64686604905e-09	16 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.563 Carnac(seed): 0.163 Sensitivity Afold: 0.509 Carnac(seed): 0.027 Positive Predictive Value Afold: 0.628 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.36849473644e-08	28 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.556 Carnac(seed): 0.179 Sensitivity RNAshapes: 0.490 Carnac(seed): 0.032 Positive Predictive Value RNAshapes: 0.636 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	22 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.487 Carnac(seed): 0.411 Sensitivity Fold: 0.433 Carnac(seed): 0.190 Positive Predictive Value Fold: 0.548 Carnac(seed): 0.890 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	29 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.518 Carnac(seed): 0.392 Sensitivity McQFold: 0.446 Carnac(seed): 0.172 Positive Predictive Value McQFold: 0.603 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.472 Carnac(seed): 0.217 Sensitivity RNASLOpt: 0.392 Carnac(seed): 0.047 Positive Predictive Value RNASLOpt: 0.574 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.77512146924e-08	22 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.471 Carnac(seed): 0.110 Sensitivity Mastr(20): 0.293 Carnac(seed): 0.012 Positive Predictive Value Mastr(20): 0.764 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.89920829651e-08	10 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 Carnac(seed): 0.249 Sensitivity Multilign(seed): 0.432 Carnac(seed): 0.063 Positive Predictive Value Multilign(seed): 0.723 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.67657656842e-08	28 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.525 Carnac(seed): 0.179 Sensitivity Pknots: 0.478 Carnac(seed): 0.032 Positive Predictive Value Pknots: 0.583 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.489 Carnac(seed): 0.192 Sensitivity Vsfold4: 0.406 Carnac(seed): 0.037 Positive Predictive Value Vsfold4: 0.594 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	7 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.483 Carnac(seed): 0.132 Sensitivity CRWrnafold: 0.428 Carnac(seed): 0.017 Positive Predictive Value CRWrnafold: 0.554 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	24 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.448 Carnac(seed): 0.197 Sensitivity Murlet(seed): 0.245 Carnac(seed): 0.039 Positive Predictive Value Murlet(seed): 0.825 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.456 Carnac(seed): 0.188 Sensitivity Vsfold5: 0.391 Carnac(seed): 0.036 Positive Predictive Value Vsfold5: 0.539 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.412 Carnac(seed): 0.196 Sensitivity MCFold: 0.430 Carnac(seed): 0.039 Positive Predictive Value MCFold: 0.401 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.651 Carnac(seed): 0.236 Sensitivity Alterna: 0.542 Carnac(seed): 0.056 Positive Predictive Value Alterna: 0.789 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	12 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.495 Carnac(seed): 0.194 Sensitivity RDfolder: 0.379 Carnac(seed): 0.038 Positive Predictive Value RDfolder: 0.657 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.62913390836e-08	17 Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.452 RNAwolf: 0.401 Sensitivity Carnac(seed): 0.229 RNAwolf: 0.373 Positive Predictive Value Carnac(seed): 0.890 RNAwolf: 0.432 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000233863577759	9 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.289 Carnac(seed): 0.273 Sensitivity NanoFolder: 0.308 Carnac(seed): 0.075 Positive Predictive Value NanoFolder: 0.279 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0		- RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.430 Carnac(seed): 0.392 Sensitivity RSpredict(seed): 0.274 Carnac(seed): 0.172 Positive Predictive Value RSpredict(seed): 0.674 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.06544643719e-08	= Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.202 PPfold(seed): 0.194 Sensitivity Carnac(seed): 0.041 PPfold(seed): 0.055 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.00321313388056	? CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Carnac(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 Carnac(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs DAFS(20) Matthews Correlation Coefficient Carnac(seed): N/A DAFS(20): N/A Sensitivity Carnac(seed): N/A DAFS(20): N/A Positive Predictive Value Carnac(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(20): N/A Carnac(seed): N/A Sensitivity PETfold_2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs Carnac(seed) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(seed): N/A Sensitivity DAFS(seed): N/A Carnac(seed): N/A Positive Predictive Value DAFS(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.179 Mastr(seed): 0.033 Sensitivity Carnac(seed): 0.032 Mastr(seed): 0.003 Positive Predictive Value Carnac(seed): 1.000 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08
RSpredict(seed)	35 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.683 RSpredict(seed): 0.163 Sensitivity CentroidAlifold(20): 0.532 RSpredict(seed): 0.063 Positive Predictive Value CentroidAlifold(20): 0.880 RSpredict(seed): 0.429 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.688 RSpredict(seed): 0.416 Sensitivity PETfold_pre2.0(seed): 0.566 RSpredict(seed): 0.264 Positive Predictive Value PETfold_pre2.0(seed): 0.838 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	36 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.655 RSpredict(seed): 0.174 Sensitivity RNAalifold(20): 0.513 RSpredict(seed): 0.068 Positive Predictive Value RNAalifold(20): 0.841 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.647 RSpredict(seed): 0.340 Sensitivity MXScarna(seed): 0.538 RSpredict(seed): 0.191 Positive Predictive Value MXScarna(seed): 0.781 RSpredict(seed): 0.606 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.663 RSpredict(seed): 0.129 Sensitivity PPfold(20): 0.528 RSpredict(seed): 0.048 Positive Predictive Value PPfold(20): 0.836 RSpredict(seed): 0.361 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	25 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.667 RSpredict(seed): 0.397 Sensitivity ContextFold: 0.551 RSpredict(seed): 0.251 Positive Predictive Value ContextFold: 0.809 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.85839946686e-08	36 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.616 RSpredict(seed): 0.174 Sensitivity RNASampler(20): 0.481 RSpredict(seed): 0.068 Positive Predictive Value RNASampler(20): 0.792 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.631 RSpredict(seed): 0.294 Sensitivity PETfold_pre2.0(20): 0.496 RSpredict(seed): 0.144 Positive Predictive Value PETfold_pre2.0(20): 0.804 RSpredict(seed): 0.602 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	20 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 RSpredict(seed): 0.129 Sensitivity TurboFold(20): 0.508 RSpredict(seed): 0.048 Positive Predictive Value TurboFold(20): 0.752 RSpredict(seed): 0.361 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	36 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.609 RSpredict(seed): 0.174 Sensitivity MXScarna(20): 0.509 RSpredict(seed): 0.068 Positive Predictive Value MXScarna(20): 0.732 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.606 RSpredict(seed): 0.428 Sensitivity RNAalifold(seed): 0.427 RSpredict(seed): 0.273 Positive Predictive Value RNAalifold(seed): 0.861 RSpredict(seed): 0.673 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	36 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.589 RSpredict(seed): 0.174 Sensitivity Murlet(20): 0.441 RSpredict(seed): 0.068 Positive Predictive Value Murlet(20): 0.790 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.621 RSpredict(seed): 0.334 Sensitivity CentroidAlifold(seed): 0.428 RSpredict(seed): 0.187 Positive Predictive Value CentroidAlifold(seed): 0.900 RSpredict(seed): 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.594 RSpredict(seed): 0.174 Sensitivity Carnac(20): 0.395 RSpredict(seed): 0.068 Positive Predictive Value Carnac(20): 0.897 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.599 RSpredict(seed): 0.395 Sensitivity IPknot: 0.501 RSpredict(seed): 0.246 Positive Predictive Value IPknot: 0.717 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.592 RSpredict(seed): 0.128 Sensitivity CentroidHomfold‑LAST: 0.503 RSpredict(seed): 0.051 Positive Predictive Value CentroidHomfold‑LAST: 0.703 RSpredict(seed): 0.328 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	51 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.571 RSpredict(seed): 0.337 Sensitivity Contrafold: 0.508 RSpredict(seed): 0.189 Positive Predictive Value Contrafold: 0.643 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.541 RSpredict(seed): 0.337 Sensitivity Sfold: 0.461 RSpredict(seed): 0.189 Positive Predictive Value Sfold: 0.635 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.539 RSpredict(seed): 0.178 Sensitivity HotKnots: 0.489 RSpredict(seed): 0.075 Positive Predictive Value HotKnots: 0.600 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.557 RSpredict(seed): 0.334 Sensitivity CentroidFold: 0.476 RSpredict(seed): 0.187 Positive Predictive Value CentroidFold: 0.654 RSpredict(seed): 0.599 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 RSpredict(seed): 0.213 Sensitivity TurboFold(seed): 0.434 RSpredict(seed): 0.092 Positive Predictive Value TurboFold(seed): 0.650 RSpredict(seed): 0.500 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.00475527001e-08	47 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.544 RSpredict(seed): 0.334 Sensitivity MaxExpect: 0.477 RSpredict(seed): 0.187 Positive Predictive Value MaxExpect: 0.622 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.540 RSpredict(seed): 0.274 Sensitivity RSpredict(20): 0.416 RSpredict(seed): 0.127 Positive Predictive Value RSpredict(20): 0.705 RSpredict(seed): 0.593 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.563 RSpredict(seed): 0.178 Sensitivity PknotsRG: 0.507 RSpredict(seed): 0.075 Positive Predictive Value PknotsRG: 0.630 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.539 RSpredict(seed): 0.015 Sensitivity CMfinder(20): 0.389 RSpredict(seed): 0.005 Positive Predictive Value CMfinder(20): 0.751 RSpredict(seed): 0.053 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.00780879471e-09	51 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.521 RSpredict(seed): 0.337 Sensitivity UNAFold: 0.462 RSpredict(seed): 0.189 Positive Predictive Value UNAFold: 0.590 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.535 RSpredict(seed): 0.338 Sensitivity ProbKnot: 0.477 RSpredict(seed): 0.193 Positive Predictive Value ProbKnot: 0.602 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.618 RSpredict(seed): 0.137 Sensitivity Cylofold: 0.519 RSpredict(seed): 0.056 Positive Predictive Value Cylofold: 0.741 RSpredict(seed): 0.348 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	51 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.530 RSpredict(seed): 0.337 Sensitivity RNAfold: 0.472 RSpredict(seed): 0.189 Positive Predictive Value RNAfold: 0.596 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 RSpredict(seed): 0.297 Sensitivity RNASampler(seed): 0.342 RSpredict(seed): 0.154 Positive Predictive Value RNASampler(seed): 0.684 RSpredict(seed): 0.581 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	50 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.540 RSpredict(seed): 0.178 Sensitivity RNAsubopt: 0.489 RSpredict(seed): 0.075 Positive Predictive Value RNAsubopt: 0.600 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.534 RSpredict(seed): 0.132 Sensitivity Multilign(20): 0.449 RSpredict(seed): 0.048 Positive Predictive Value Multilign(20): 0.642 RSpredict(seed): 0.371 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.59578924681e-08	26 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.500 RSpredict(seed): 0.242 Sensitivity Afold: 0.463 RSpredict(seed): 0.112 Positive Predictive Value Afold: 0.544 RSpredict(seed): 0.526 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	50 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.532 RSpredict(seed): 0.178 Sensitivity RNAshapes: 0.474 RSpredict(seed): 0.075 Positive Predictive Value RNAshapes: 0.603 RSpredict(seed): 0.430 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.520 RSpredict(seed): 0.335 Sensitivity Fold: 0.465 RSpredict(seed): 0.190 Positive Predictive Value Fold: 0.582 RSpredict(seed): 0.591 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.510 RSpredict(seed): 0.337 Sensitivity McQFold: 0.441 RSpredict(seed): 0.189 Positive Predictive Value McQFold: 0.591 RSpredict(seed): 0.603 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.501 RSpredict(seed): 0.115 Sensitivity RNASLOpt: 0.413 RSpredict(seed): 0.046 Positive Predictive Value RNASLOpt: 0.615 RSpredict(seed): 0.294 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	36 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.513 RSpredict(seed): 0.174 Sensitivity Mastr(20): 0.346 RSpredict(seed): 0.068 Positive Predictive Value Mastr(20): 0.765 RSpredict(seed): 0.450 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 RSpredict(seed): 0.272 Sensitivity Multilign(seed): 0.432 RSpredict(seed): 0.133 Positive Predictive Value Multilign(seed): 0.723 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.07842257011e-08	48 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.536 RSpredict(seed): 0.178 Sensitivity Pknots: 0.483 RSpredict(seed): 0.075 Positive Predictive Value Pknots: 0.601 RSpredict(seed): 0.434 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.493 RSpredict(seed): 0.173 Sensitivity Vsfold4: 0.417 RSpredict(seed): 0.073 Positive Predictive Value Vsfold4: 0.587 RSpredict(seed): 0.420 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 RSpredict(seed): 0.108 Sensitivity CRWrnafold: 0.472 RSpredict(seed): 0.042 Positive Predictive Value CRWrnafold: 0.616 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	24 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.448 RSpredict(seed): 0.289 Sensitivity Murlet(seed): 0.245 RSpredict(seed): 0.139 Positive Predictive Value Murlet(seed): 0.825 RSpredict(seed): 0.608 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	48 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.457 RSpredict(seed): 0.171 Sensitivity Vsfold5: 0.391 RSpredict(seed): 0.071 Positive Predictive Value Vsfold5: 0.539 RSpredict(seed): 0.416 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.418 RSpredict(seed): 0.165 Sensitivity MCFold: 0.436 RSpredict(seed): 0.067 Positive Predictive Value MCFold: 0.409 RSpredict(seed): 0.414 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.572 RSpredict(seed): 0.286 Sensitivity Alterna: 0.500 RSpredict(seed): 0.140 Positive Predictive Value Alterna: 0.664 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.512 RSpredict(seed): 0.292 Sensitivity RDfolder: 0.415 RSpredict(seed): 0.146 Positive Predictive Value RDfolder: 0.643 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	28 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.415 RSpredict(seed): 0.395 Sensitivity RNAwolf: 0.385 RSpredict(seed): 0.246 Positive Predictive Value RNAwolf: 0.449 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.59469103578e-08	18 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.293 RSpredict(seed): 0.091 Sensitivity NanoFolder: 0.307 RSpredict(seed): 0.037 Positive Predictive Value NanoFolder: 0.290 RSpredict(seed): 0.235 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.30549897711e-08	29 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.430 Carnac(seed): 0.392 Sensitivity RSpredict(seed): 0.274 Carnac(seed): 0.172 Positive Predictive Value RSpredict(seed): 0.674 Carnac(seed): 0.893 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.06544643719e-08		= PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.148 RSpredict(seed): 0.147 Sensitivity PPfold(seed): 0.032 RSpredict(seed): 0.060 Positive Predictive Value PPfold(seed): 0.689 RSpredict(seed): 0.369 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.837952075429	? RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(seed): N/A Sensitivity RSpredict(seed): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RSpredict(seed): 0.513 Sensitivity PETfold_2.0(seed): 0.684 RSpredict(seed): 0.289 Positive Predictive Value PETfold_2.0(seed): 0.897 RSpredict(seed): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs DAFS(20) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(20): N/A Sensitivity RSpredict(seed): N/A DAFS(20): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(seed): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(seed): N/A Sensitivity RSpredict(seed): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.178 Mastr(seed): 0.024 Sensitivity RSpredict(seed): 0.075 Mastr(seed): 0.002 Positive Predictive Value RSpredict(seed): 0.430 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(seed)	20 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 PPfold(seed): 0.072 Sensitivity CentroidAlifold(20): 0.514 PPfold(seed): 0.012 Positive Predictive Value CentroidAlifold(20): 0.877 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	24 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 PPfold(seed): 0.156 Sensitivity PETfold_pre2.0(seed): 0.594 PPfold(seed): 0.036 Positive Predictive Value PETfold_pre2.0(seed): 0.875 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	20 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.643 PPfold(seed): 0.072 Sensitivity RNAalifold(20): 0.503 PPfold(seed): 0.012 Positive Predictive Value RNAalifold(20): 0.826 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.620 PPfold(seed): 0.150 Sensitivity MXScarna(seed): 0.499 PPfold(seed): 0.033 Positive Predictive Value MXScarna(seed): 0.775 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	20 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.663 PPfold(seed): 0.072 Sensitivity PPfold(20): 0.528 PPfold(seed): 0.012 Positive Predictive Value PPfold(20): 0.836 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	24 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.620 PPfold(seed): 0.156 Sensitivity ContextFold: 0.506 PPfold(seed): 0.036 Positive Predictive Value ContextFold: 0.765 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	20 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.582 PPfold(seed): 0.072 Sensitivity RNASampler(20): 0.450 PPfold(seed): 0.012 Positive Predictive Value RNASampler(20): 0.757 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	17 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 PPfold(seed): 0.077 Sensitivity PETfold_pre2.0(20): 0.532 PPfold(seed): 0.014 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.02510705504e-08	20 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 PPfold(seed): 0.072 Sensitivity TurboFold(20): 0.508 PPfold(seed): 0.012 Positive Predictive Value TurboFold(20): 0.752 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	20 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.578 PPfold(seed): 0.072 Sensitivity MXScarna(20): 0.476 PPfold(seed): 0.012 Positive Predictive Value MXScarna(20): 0.706 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.553 PPfold(seed): 0.204 Sensitivity RNAalifold(seed): 0.343 PPfold(seed): 0.061 Positive Predictive Value RNAalifold(seed): 0.897 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	20 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.580 PPfold(seed): 0.072 Sensitivity Murlet(20): 0.439 PPfold(seed): 0.012 Positive Predictive Value Murlet(20): 0.772 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	27 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.575 PPfold(seed): 0.148 Sensitivity CentroidAlifold(seed): 0.351 PPfold(seed): 0.032 Positive Predictive Value CentroidAlifold(seed): 0.947 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	20 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.565 PPfold(seed): 0.072 Sensitivity Carnac(20): 0.372 PPfold(seed): 0.012 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	27 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.589 PPfold(seed): 0.148 Sensitivity IPknot: 0.488 PPfold(seed): 0.032 Positive Predictive Value IPknot: 0.717 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.592 PPfold(seed): 0.149 Sensitivity CentroidHomfold‑LAST: 0.503 PPfold(seed): 0.031 Positive Predictive Value CentroidHomfold‑LAST: 0.703 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.568 PPfold(seed): 0.148 Sensitivity Contrafold: 0.494 PPfold(seed): 0.032 Positive Predictive Value Contrafold: 0.659 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.544 PPfold(seed): 0.148 Sensitivity Sfold: 0.450 PPfold(seed): 0.032 Positive Predictive Value Sfold: 0.664 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.520 PPfold(seed): 0.148 Sensitivity HotKnots: 0.463 PPfold(seed): 0.032 Positive Predictive Value HotKnots: 0.591 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.511 PPfold(seed): 0.148 Sensitivity CentroidFold: 0.426 PPfold(seed): 0.032 Positive Predictive Value CentroidFold: 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	14 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 PPfold(seed): 0.208 Sensitivity TurboFold(seed): 0.434 PPfold(seed): 0.063 Positive Predictive Value TurboFold(seed): 0.650 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.75835195567e-08	27 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.534 PPfold(seed): 0.148 Sensitivity MaxExpect: 0.455 PPfold(seed): 0.032 Positive Predictive Value MaxExpect: 0.633 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	20 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.520 PPfold(seed): 0.072 Sensitivity RSpredict(20): 0.398 PPfold(seed): 0.012 Positive Predictive Value RSpredict(20): 0.685 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	27 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.568 PPfold(seed): 0.148 Sensitivity PknotsRG: 0.499 PPfold(seed): 0.032 Positive Predictive Value PknotsRG: 0.652 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	10 CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.539 PPfold(seed): 0.071 Sensitivity CMfinder(20): 0.389 PPfold(seed): 0.010 Positive Predictive Value CMfinder(20): 0.751 PPfold(seed): 0.500 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.42300079339e-08	27 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.494 PPfold(seed): 0.148 Sensitivity UNAFold: 0.431 PPfold(seed): 0.032 Positive Predictive Value UNAFold: 0.573 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.534 PPfold(seed): 0.148 Sensitivity ProbKnot: 0.469 PPfold(seed): 0.032 Positive Predictive Value ProbKnot: 0.614 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	17 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.584 PPfold(seed): 0.089 Sensitivity Cylofold: 0.486 PPfold(seed): 0.011 Positive Predictive Value Cylofold: 0.709 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	27 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.539 PPfold(seed): 0.148 Sensitivity RNAfold: 0.470 PPfold(seed): 0.032 Positive Predictive Value RNAfold: 0.623 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.417 PPfold(seed): 0.257 Sensitivity RNASampler(seed): 0.283 PPfold(seed): 0.097 Positive Predictive Value RNASampler(seed): 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	27 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.540 PPfold(seed): 0.148 Sensitivity RNAsubopt: 0.478 PPfold(seed): 0.032 Positive Predictive Value RNAsubopt: 0.616 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	19 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.534 PPfold(seed): 0.052 Sensitivity Multilign(20): 0.449 PPfold(seed): 0.007 Positive Predictive Value Multilign(20): 0.642 PPfold(seed): 0.385 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	7 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.492 PPfold(seed): 0.127 Sensitivity Afold: 0.439 PPfold(seed): 0.031 Positive Predictive Value Afold: 0.559 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	27 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.526 PPfold(seed): 0.148 Sensitivity RNAshapes: 0.460 PPfold(seed): 0.032 Positive Predictive Value RNAshapes: 0.608 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.521 PPfold(seed): 0.148 Sensitivity Fold: 0.459 PPfold(seed): 0.032 Positive Predictive Value Fold: 0.599 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.524 PPfold(seed): 0.148 Sensitivity McQFold: 0.448 PPfold(seed): 0.032 Positive Predictive Value McQFold: 0.619 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.501 PPfold(seed): 0.156 Sensitivity RNASLOpt: 0.413 PPfold(seed): 0.036 Positive Predictive Value RNASLOpt: 0.615 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	20 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.518 PPfold(seed): 0.072 Sensitivity Mastr(20): 0.357 PPfold(seed): 0.012 Positive Predictive Value Mastr(20): 0.757 PPfold(seed): 0.429 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	10 Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 PPfold(seed): 0.238 Sensitivity Multilign(seed): 0.432 PPfold(seed): 0.071 Positive Predictive Value Multilign(seed): 0.723 PPfold(seed): 0.813 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08	27 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.488 PPfold(seed): 0.148 Sensitivity Pknots: 0.434 PPfold(seed): 0.032 Positive Predictive Value Pknots: 0.556 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	24 Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.474 PPfold(seed): 0.152 Sensitivity Vsfold4: 0.392 PPfold(seed): 0.032 Positive Predictive Value Vsfold4: 0.581 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 PPfold(seed): 0.114 Sensitivity CRWrnafold: 0.472 PPfold(seed): 0.024 Positive Predictive Value CRWrnafold: 0.616 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	15 Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.418 PPfold(seed): 0.204 Sensitivity Murlet(seed): 0.227 PPfold(seed): 0.061 Positive Predictive Value Murlet(seed): 0.777 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	25 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.427 PPfold(seed): 0.149 Sensitivity Vsfold5: 0.367 PPfold(seed): 0.031 Positive Predictive Value Vsfold5: 0.505 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	22 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.396 PPfold(seed): 0.164 Sensitivity MCFold: 0.408 PPfold(seed): 0.039 Positive Predictive Value MCFold: 0.393 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	6 Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.566 PPfold(seed): 0.153 Sensitivity Alterna: 0.479 PPfold(seed): 0.032 Positive Predictive Value Alterna: 0.679 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	11 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.403 PPfold(seed): 0.116 Sensitivity RDfolder: 0.308 PPfold(seed): 0.018 Positive Predictive Value RDfolder: 0.540 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	27 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.387 PPfold(seed): 0.148 Sensitivity RNAwolf: 0.363 PPfold(seed): 0.032 Positive Predictive Value RNAwolf: 0.422 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.293 PPfold(seed): 0.172 Sensitivity NanoFolder: 0.307 PPfold(seed): 0.041 Positive Predictive Value NanoFolder: 0.290 PPfold(seed): 0.730 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.54914456376e-08	16 Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.202 PPfold(seed): 0.194 Sensitivity Carnac(seed): 0.041 PPfold(seed): 0.055 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.689 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.00321313388056	27 PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.148 RSpredict(seed): 0.147 Sensitivity PPfold(seed): 0.032 RSpredict(seed): 0.060 Positive Predictive Value PPfold(seed): 0.689 RSpredict(seed): 0.369 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.837952075429		? PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 PPfold(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 PPfold(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs DAFS(20) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(20): N/A Sensitivity PPfold(seed): N/A DAFS(20): N/A Positive Predictive Value PPfold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs DAFS(seed) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(seed): N/A Sensitivity PPfold(seed): N/A DAFS(seed): N/A Positive Predictive Value PPfold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.148 Mastr(seed): 0.034 Sensitivity PPfold(seed): 0.032 Mastr(seed): 0.003 Positive Predictive Value PPfold(seed): 0.689 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.02343278931e-08
CMfinder(seed)	0 CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(seed): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(20): N/A Sensitivity CMfinder(seed): N/A Carnac(20): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CentroidFold Matthews Correlation Coefficient CMfinder(seed): N/A CentroidFold: N/A Sensitivity CMfinder(seed): N/A CentroidFold: N/A Positive Predictive Value CMfinder(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(seed): N/A Sensitivity MaxExpect: N/A CMfinder(seed): N/A Positive Predictive Value MaxExpect: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(seed): N/A Sensitivity PknotsRG: N/A CMfinder(seed): N/A Positive Predictive Value PknotsRG: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: N/A CMfinder(seed): N/A Sensitivity UNAFold: N/A CMfinder(seed): N/A Positive Predictive Value UNAFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): N/A RNAsubopt: N/A Sensitivity CMfinder(seed): N/A RNAsubopt: N/A Positive Predictive Value CMfinder(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): N/A Afold: N/A Sensitivity CMfinder(seed): N/A Afold: N/A Positive Predictive Value CMfinder(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): N/A RNASLOpt: N/A Sensitivity CMfinder(seed): N/A RNASLOpt: N/A Positive Predictive Value CMfinder(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(seed): N/A Sensitivity CRWrnafold: N/A CMfinder(seed): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(seed): N/A Sensitivity Vsfold5: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold5: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(seed): N/A Sensitivity RSpredict(seed): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? CMfinder(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs DAFS(20) Matthews Correlation Coefficient CMfinder(seed): N/A DAFS(20): N/A Sensitivity CMfinder(seed): N/A DAFS(20): N/A Positive Predictive Value CMfinder(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(20): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs CMfinder(seed) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(seed): N/A Sensitivity DAFS(seed): N/A CMfinder(seed): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_2.0(seed)	1 PETfold_2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidAlifold(20): 0.662 Sensitivity PETfold_2.0(seed): 0.614 CentroidAlifold(20): 0.474 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidAlifold(20): 0.931 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.775 PETfold_2.0(seed): 0.769 Sensitivity PETfold_pre2.0(seed): 0.642 PETfold_2.0(seed): 0.642 Positive Predictive Value PETfold_pre2.0(seed): 0.938 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNAalifold(20): 0.654 Sensitivity PETfold_2.0(seed): 0.614 RNAalifold(20): 0.491 Positive Predictive Value PETfold_2.0(seed): 0.946 RNAalifold(20): 0.875 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MXScarna(seed): 0.682 Sensitivity PETfold_2.0(seed): 0.642 MXScarna(seed): 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 MXScarna(seed): 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(seed): N/A Sensitivity PPfold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 ContextFold vs PETfold_2.0(seed) Matthews Correlation Coefficient ContextFold: 0.780 PETfold_2.0(seed): 0.769 Sensitivity ContextFold: 0.632 PETfold_2.0(seed): 0.642 Positive Predictive Value ContextFold: 0.968 PETfold_2.0(seed): 0.924 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 RNASampler(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(seed): 0.946 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_pre2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_pre2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(seed): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 MXScarna(20): 0.741 Sensitivity PETfold_2.0(seed): 0.614 MXScarna(20): 0.614 Positive Predictive Value PETfold_2.0(seed): 0.946 MXScarna(20): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RNAalifold(seed): 0.706 Sensitivity PETfold_2.0(seed): 0.684 RNAalifold(seed): 0.500 Positive Predictive Value PETfold_2.0(seed): 0.897 RNAalifold(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Murlet(20): 0.634 Sensitivity PETfold_2.0(seed): 0.614 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(seed): 0.946 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidAlifold(seed): 0.618 Sensitivity PETfold_2.0(seed): 0.642 CentroidAlifold(seed): 0.432 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidAlifold(seed): 0.891 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Carnac(20): 0.576 Sensitivity PETfold_2.0(seed): 0.614 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(seed): 0.946 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 IPknot: 0.610 Sensitivity PETfold_2.0(seed): 0.642 IPknot: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 IPknot: 0.758 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(seed): 0.614 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(seed): 0.946 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Contrafold: 0.649 Sensitivity PETfold_2.0(seed): 0.642 Contrafold: 0.547 Positive Predictive Value PETfold_2.0(seed): 0.924 Contrafold: 0.776 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Sfold: 0.673 Sensitivity PETfold_2.0(seed): 0.642 Sfold: 0.537 Positive Predictive Value PETfold_2.0(seed): 0.924 Sfold: 0.850 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 HotKnots: 0.682 Sensitivity PETfold_2.0(seed): 0.642 HotKnots: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 HotKnots: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 CentroidFold: 0.506 Sensitivity PETfold_2.0(seed): 0.642 CentroidFold: 0.421 Positive Predictive Value PETfold_2.0(seed): 0.924 CentroidFold: 0.615 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity TurboFold(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value TurboFold(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 MaxExpect: 0.657 Sensitivity PETfold_2.0(seed): 0.642 MaxExpect: 0.558 Positive Predictive Value PETfold_2.0(seed): 0.924 MaxExpect: 0.779 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs PETfold_2.0(seed) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(seed): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(seed): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 PknotsRG: 0.687 Sensitivity PETfold_2.0(seed): 0.642 PknotsRG: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 PknotsRG: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 CMfinder(20): 0.383 Sensitivity PETfold_2.0(seed): 0.614 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.946 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 UNAFold: 0.687 Sensitivity PETfold_2.0(seed): 0.642 UNAFold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 UNAFold: 0.821 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 ProbKnot: 0.675 Sensitivity PETfold_2.0(seed): 0.642 ProbKnot: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 ProbKnot: 0.806 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PETfold_2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAfold: 0.682 Sensitivity PETfold_2.0(seed): 0.642 RNAfold: 0.579 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAfold: 0.809 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAsubopt: 0.685 Sensitivity PETfold_2.0(seed): 0.642 RNAsubopt: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAsubopt: 0.831 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A Multilign(20): N/A Sensitivity PETfold_2.0(seed): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs PETfold_2.0(seed) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(seed): N/A Sensitivity Afold: N/A PETfold_2.0(seed): N/A Positive Predictive Value Afold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAshapes: 0.493 Sensitivity PETfold_2.0(seed): 0.642 RNAshapes: 0.411 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAshapes: 0.600 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Fold: 0.665 Sensitivity PETfold_2.0(seed): 0.642 Fold: 0.568 Positive Predictive Value PETfold_2.0(seed): 0.924 Fold: 0.783 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 McQFold: 0.616 Sensitivity PETfold_2.0(seed): 0.642 McQFold: 0.453 Positive Predictive Value PETfold_2.0(seed): 0.924 McQFold: 0.843 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNASLOpt: 0.625 Sensitivity PETfold_2.0(seed): 0.642 RNASLOpt: 0.495 Positive Predictive Value PETfold_2.0(seed): 0.924 RNASLOpt: 0.797 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Mastr(20): 0.189 Sensitivity PETfold_2.0(seed): 0.614 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 Multilign(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient Multilign(seed): 0.873 PETfold_2.0(seed): 0.782 Sensitivity Multilign(seed): 0.789 PETfold_2.0(seed): 0.684 Positive Predictive Value Multilign(seed): 0.968 PETfold_2.0(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	2 PETfold_2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Pknots: 0.607 Sensitivity PETfold_2.0(seed): 0.642 Pknots: 0.516 Positive Predictive Value PETfold_2.0(seed): 0.924 Pknots: 0.721 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold4: 0.167 Sensitivity PETfold_2.0(seed): 0.614 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 CRWrnafold vs PETfold_2.0(seed) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(seed): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(seed): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Murlet(seed): 0.431 Sensitivity PETfold_2.0(seed): 0.684 Murlet(seed): 0.211 Positive Predictive Value PETfold_2.0(seed): 0.897 Murlet(seed): 0.889 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 Vsfold5: 0.156 Sensitivity PETfold_2.0(seed): 0.614 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(seed): 0.946 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_2.0(seed): N/A MCFold: N/A Sensitivity PETfold_2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs PETfold_2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(seed): N/A Sensitivity Alterna: N/A PETfold_2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PETfold_2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 RNAwolf: 0.549 Sensitivity PETfold_2.0(seed): 0.642 RNAwolf: 0.484 Positive Predictive Value PETfold_2.0(seed): 0.924 RNAwolf: 0.630 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 NanoFolder: 0.243 Sensitivity PETfold_2.0(seed): 0.614 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(seed): 0.946 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 Carnac(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 Carnac(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 RSpredict(seed): 0.513 Sensitivity PETfold_2.0(seed): 0.684 RSpredict(seed): 0.289 Positive Predictive Value PETfold_2.0(seed): 0.897 RSpredict(seed): 0.917 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.782 PPfold(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.684 PPfold(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.897 PPfold(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 CMfinder(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? DAFS(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Mastr(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.642 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.924 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0
DAFS(20)	0 CentroidAlifold(20) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A DAFS(20): N/A Sensitivity CentroidAlifold(20): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(20): N/A Sensitivity RNAalifold(20): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(seed) vs DAFS(20) Matthews Correlation Coefficient MXScarna(seed): N/A DAFS(20): N/A Sensitivity MXScarna(seed): N/A DAFS(20): N/A Positive Predictive Value MXScarna(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs DAFS(20) Matthews Correlation Coefficient PPfold(20): N/A DAFS(20): N/A Sensitivity PPfold(20): N/A DAFS(20): N/A Positive Predictive Value PPfold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs DAFS(20) Matthews Correlation Coefficient ContextFold: N/A DAFS(20): N/A Sensitivity ContextFold: N/A DAFS(20): N/A Positive Predictive Value ContextFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs DAFS(20) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(20): N/A Sensitivity RNASampler(20): N/A DAFS(20): N/A Positive Predictive Value RNASampler(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs DAFS(20) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(20): N/A Sensitivity TurboFold(20): N/A DAFS(20): N/A Positive Predictive Value TurboFold(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs DAFS(20) Matthews Correlation Coefficient MXScarna(20): N/A DAFS(20): N/A Sensitivity MXScarna(20): N/A DAFS(20): N/A Positive Predictive Value MXScarna(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs DAFS(20) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(20): N/A Sensitivity RNAalifold(seed): N/A DAFS(20): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs DAFS(20) Matthews Correlation Coefficient Murlet(20): N/A DAFS(20): N/A Sensitivity Murlet(20): N/A DAFS(20): N/A Positive Predictive Value Murlet(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs DAFS(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(20): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs DAFS(20) Matthews Correlation Coefficient Carnac(20): N/A DAFS(20): N/A Sensitivity Carnac(20): N/A DAFS(20): N/A Positive Predictive Value Carnac(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 IPknot vs DAFS(20) Matthews Correlation Coefficient IPknot: N/A DAFS(20): N/A Sensitivity IPknot: N/A DAFS(20): N/A Positive Predictive Value IPknot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs DAFS(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(20): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs DAFS(20) Matthews Correlation Coefficient Contrafold: N/A DAFS(20): N/A Sensitivity Contrafold: N/A DAFS(20): N/A Positive Predictive Value Contrafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs DAFS(20) Matthews Correlation Coefficient Sfold: N/A DAFS(20): N/A Sensitivity Sfold: N/A DAFS(20): N/A Positive Predictive Value Sfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs DAFS(20) Matthews Correlation Coefficient HotKnots: N/A DAFS(20): N/A Sensitivity HotKnots: N/A DAFS(20): N/A Positive Predictive Value HotKnots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs DAFS(20) Matthews Correlation Coefficient CentroidFold: N/A DAFS(20): N/A Sensitivity CentroidFold: N/A DAFS(20): N/A Positive Predictive Value CentroidFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs DAFS(20) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(20): N/A Sensitivity TurboFold(seed): N/A DAFS(20): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs DAFS(20) Matthews Correlation Coefficient MaxExpect: N/A DAFS(20): N/A Sensitivity MaxExpect: N/A DAFS(20): N/A Positive Predictive Value MaxExpect: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs DAFS(20) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(20): N/A Sensitivity RSpredict(20): N/A DAFS(20): N/A Positive Predictive Value RSpredict(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs DAFS(20) Matthews Correlation Coefficient PknotsRG: N/A DAFS(20): N/A Sensitivity PknotsRG: N/A DAFS(20): N/A Positive Predictive Value PknotsRG: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(20) vs CMfinder(20) Matthews Correlation Coefficient DAFS(20): N/A CMfinder(20): N/A Sensitivity DAFS(20): N/A CMfinder(20): N/A Positive Predictive Value DAFS(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs DAFS(20) Matthews Correlation Coefficient UNAFold: N/A DAFS(20): N/A Sensitivity UNAFold: N/A DAFS(20): N/A Positive Predictive Value UNAFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs DAFS(20) Matthews Correlation Coefficient ProbKnot: N/A DAFS(20): N/A Sensitivity ProbKnot: N/A DAFS(20): N/A Positive Predictive Value ProbKnot: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs DAFS(20) Matthews Correlation Coefficient Cylofold: N/A DAFS(20): N/A Sensitivity Cylofold: N/A DAFS(20): N/A Positive Predictive Value Cylofold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs DAFS(20) Matthews Correlation Coefficient RNAfold: N/A DAFS(20): N/A Sensitivity RNAfold: N/A DAFS(20): N/A Positive Predictive Value RNAfold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs DAFS(20) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(20): N/A Sensitivity RNASampler(seed): N/A DAFS(20): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs DAFS(20) Matthews Correlation Coefficient RNAsubopt: N/A DAFS(20): N/A Sensitivity RNAsubopt: N/A DAFS(20): N/A Positive Predictive Value RNAsubopt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs DAFS(20) Matthews Correlation Coefficient Multilign(20): N/A DAFS(20): N/A Sensitivity Multilign(20): N/A DAFS(20): N/A Positive Predictive Value Multilign(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs DAFS(20) Matthews Correlation Coefficient Afold: N/A DAFS(20): N/A Sensitivity Afold: N/A DAFS(20): N/A Positive Predictive Value Afold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs DAFS(20) Matthews Correlation Coefficient RNAshapes: N/A DAFS(20): N/A Sensitivity RNAshapes: N/A DAFS(20): N/A Positive Predictive Value RNAshapes: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs DAFS(20) Matthews Correlation Coefficient Fold: N/A DAFS(20): N/A Sensitivity Fold: N/A DAFS(20): N/A Positive Predictive Value Fold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs DAFS(20) Matthews Correlation Coefficient McQFold: N/A DAFS(20): N/A Sensitivity McQFold: N/A DAFS(20): N/A Positive Predictive Value McQFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASLOpt vs DAFS(20) Matthews Correlation Coefficient RNASLOpt: N/A DAFS(20): N/A Sensitivity RNASLOpt: N/A DAFS(20): N/A Positive Predictive Value RNASLOpt: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs DAFS(20) Matthews Correlation Coefficient Mastr(20): N/A DAFS(20): N/A Sensitivity Mastr(20): N/A DAFS(20): N/A Positive Predictive Value Mastr(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs DAFS(20) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(20): N/A Sensitivity Multilign(seed): N/A DAFS(20): N/A Positive Predictive Value Multilign(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs DAFS(20) Matthews Correlation Coefficient Pknots: N/A DAFS(20): N/A Sensitivity Pknots: N/A DAFS(20): N/A Positive Predictive Value Pknots: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs DAFS(20) Matthews Correlation Coefficient Vsfold4: N/A DAFS(20): N/A Sensitivity Vsfold4: N/A DAFS(20): N/A Positive Predictive Value Vsfold4: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs DAFS(20) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(20): N/A Sensitivity CRWrnafold: N/A DAFS(20): N/A Positive Predictive Value CRWrnafold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs DAFS(20) Matthews Correlation Coefficient Murlet(seed): N/A DAFS(20): N/A Sensitivity Murlet(seed): N/A DAFS(20): N/A Positive Predictive Value Murlet(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs DAFS(20) Matthews Correlation Coefficient Vsfold5: N/A DAFS(20): N/A Sensitivity Vsfold5: N/A DAFS(20): N/A Positive Predictive Value Vsfold5: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs DAFS(20) Matthews Correlation Coefficient MCFold: N/A DAFS(20): N/A Sensitivity MCFold: N/A DAFS(20): N/A Positive Predictive Value MCFold: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs DAFS(20) Matthews Correlation Coefficient Alterna: N/A DAFS(20): N/A Sensitivity Alterna: N/A DAFS(20): N/A Positive Predictive Value Alterna: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs DAFS(20) Matthews Correlation Coefficient RDfolder: N/A DAFS(20): N/A Sensitivity RDfolder: N/A DAFS(20): N/A Positive Predictive Value RDfolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAwolf vs DAFS(20) Matthews Correlation Coefficient RNAwolf: N/A DAFS(20): N/A Sensitivity RNAwolf: N/A DAFS(20): N/A Positive Predictive Value RNAwolf: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs DAFS(20) Matthews Correlation Coefficient NanoFolder: N/A DAFS(20): N/A Sensitivity NanoFolder: N/A DAFS(20): N/A Positive Predictive Value NanoFolder: N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(seed) vs DAFS(20) Matthews Correlation Coefficient Carnac(seed): N/A DAFS(20): N/A Sensitivity Carnac(seed): N/A DAFS(20): N/A Positive Predictive Value Carnac(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs DAFS(20) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(20): N/A Sensitivity RSpredict(seed): N/A DAFS(20): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs DAFS(20) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(20): N/A Sensitivity PPfold(seed): N/A DAFS(20): N/A Positive Predictive Value PPfold(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs DAFS(20) Matthews Correlation Coefficient CMfinder(seed): N/A DAFS(20): N/A Sensitivity CMfinder(seed): N/A DAFS(20): N/A Positive Predictive Value CMfinder(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_2.0(seed) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(seed): N/A DAFS(20): N/A Sensitivity PETfold_2.0(seed): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? DAFS(seed) vs DAFS(20) Matthews Correlation Coefficient DAFS(seed): N/A DAFS(20): N/A Sensitivity DAFS(seed): N/A DAFS(20): N/A Positive Predictive Value DAFS(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs DAFS(20) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(20): N/A Sensitivity Mastr(seed): N/A DAFS(20): N/A Positive Predictive Value Mastr(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_2.0(20)	1 CentroidAlifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.662 PETfold_2.0(20): 0.647 Sensitivity CentroidAlifold(20): 0.474 PETfold_2.0(20): 0.509 Positive Predictive Value CentroidAlifold(20): 0.931 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_pre2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 RNAalifold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(20): 0.654 PETfold_2.0(20): 0.647 Sensitivity RNAalifold(20): 0.491 PETfold_2.0(20): 0.509 Positive Predictive Value RNAalifold(20): 0.875 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MXScarna(seed): 0.563 Sensitivity PETfold_2.0(20): 0.509 MXScarna(seed): 0.456 Positive Predictive Value PETfold_2.0(20): 0.829 MXScarna(seed): 0.703 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(20): N/A PETfold_2.0(20): N/A Sensitivity PPfold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 ContextFold vs PETfold_2.0(20) Matthews Correlation Coefficient ContextFold: 0.760 PETfold_2.0(20): 0.647 Sensitivity ContextFold: 0.579 PETfold_2.0(20): 0.509 Positive Predictive Value ContextFold: 1.000 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASampler(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 RNASampler(20): 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNASampler(20): 0.960 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_pre2.0(20) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.647 PETfold_2.0(20): 0.647 Sensitivity PETfold_pre2.0(20): 0.509 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_pre2.0(20): 0.829 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(20): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(20): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 MXScarna(20) vs PETfold_2.0(20) Matthews Correlation Coefficient MXScarna(20): 0.741 PETfold_2.0(20): 0.647 Sensitivity MXScarna(20): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value MXScarna(20): 0.897 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNAalifold(seed): N/A PETfold_2.0(20): N/A Sensitivity RNAalifold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNAalifold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Murlet(20): 0.634 Sensitivity PETfold_2.0(20): 0.509 Murlet(20): 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidAlifold(seed): 0.484 Sensitivity PETfold_2.0(20): 0.509 CentroidAlifold(seed): 0.281 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidAlifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Carnac(20): 0.576 Sensitivity PETfold_2.0(20): 0.509 Carnac(20): 0.351 Positive Predictive Value PETfold_2.0(20): 0.829 Carnac(20): 0.952 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 IPknot: 0.401 Sensitivity PETfold_2.0(20): 0.509 IPknot: 0.298 Positive Predictive Value PETfold_2.0(20): 0.829 IPknot: 0.548 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidHomfold‑LAST: 0.514 Sensitivity PETfold_2.0(20): 0.509 CentroidHomfold‑LAST: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidHomfold‑LAST: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Contrafold: 0.482 Sensitivity PETfold_2.0(20): 0.509 Contrafold: 0.386 Positive Predictive Value PETfold_2.0(20): 0.829 Contrafold: 0.611 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Sfold: 0.514 Sensitivity PETfold_2.0(20): 0.509 Sfold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 HotKnots: 0.541 Sensitivity PETfold_2.0(20): 0.509 HotKnots: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 HotKnots: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CentroidFold: 0.467 Sensitivity PETfold_2.0(20): 0.509 CentroidFold: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 CentroidFold: 0.600 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_2.0(20): 0.647 MaxExpect: 0.498 Sensitivity PETfold_2.0(20): 0.509 MaxExpect: 0.404 Positive Predictive Value PETfold_2.0(20): 0.829 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(20): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(20): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(20): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_2.0(20): 0.647 PknotsRG: 0.549 Sensitivity PETfold_2.0(20): 0.509 PknotsRG: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 PknotsRG: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 CMfinder(20): 0.383 Sensitivity PETfold_2.0(20): 0.509 CMfinder(20): 0.211 Positive Predictive Value PETfold_2.0(20): 0.829 CMfinder(20): 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 UNAFold: 0.549 Sensitivity PETfold_2.0(20): 0.509 UNAFold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 UNAFold: 0.694 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_2.0(20): 0.647 ProbKnot: 0.527 Sensitivity PETfold_2.0(20): 0.509 ProbKnot: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 ProbKnot: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PETfold_2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_2.0(20): N/A Sensitivity Cylofold: N/A PETfold_2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAfold: 0.541 Sensitivity PETfold_2.0(20): 0.509 RNAfold: 0.439 Positive Predictive Value PETfold_2.0(20): 0.829 RNAfold: 0.676 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAsubopt: 0.542 Sensitivity PETfold_2.0(20): 0.509 RNAsubopt: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A Multilign(20): N/A Sensitivity PETfold_2.0(20): N/A Multilign(20): N/A Positive Predictive Value PETfold_2.0(20): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs PETfold_2.0(20) Matthews Correlation Coefficient Afold: N/A PETfold_2.0(20): N/A Sensitivity Afold: N/A PETfold_2.0(20): N/A Positive Predictive Value Afold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAshapes: 0.199 Sensitivity PETfold_2.0(20): 0.509 RNAshapes: 0.158 Positive Predictive Value PETfold_2.0(20): 0.829 RNAshapes: 0.265 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Fold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Fold: 0.513 Sensitivity PETfold_2.0(20): 0.509 Fold: 0.421 Positive Predictive Value PETfold_2.0(20): 0.829 Fold: 0.632 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_2.0(20): 0.647 McQFold: 0.491 Sensitivity PETfold_2.0(20): 0.509 McQFold: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 McQFold: 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNASLOpt: 0.456 Sensitivity PETfold_2.0(20): 0.509 RNASLOpt: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 RNASLOpt: 0.633 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(20): 0.189 Sensitivity PETfold_2.0(20): 0.509 Mastr(20): 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(20): 0.304 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_2.0(20): N/A Sensitivity Multilign(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Multilign(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Pknots: 0.410 Sensitivity PETfold_2.0(20): 0.509 Pknots: 0.333 Positive Predictive Value PETfold_2.0(20): 0.829 Pknots: 0.514 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold4: 0.167 Sensitivity PETfold_2.0(20): 0.509 Vsfold4: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold4: 0.241 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 CRWrnafold vs PETfold_2.0(20) Matthews Correlation Coefficient CRWrnafold: N/A PETfold_2.0(20): N/A Sensitivity CRWrnafold: N/A PETfold_2.0(20): N/A Positive Predictive Value CRWrnafold: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_2.0(20): N/A Sensitivity Murlet(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value Murlet(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Vsfold5: 0.156 Sensitivity PETfold_2.0(20): 0.509 Vsfold5: 0.123 Positive Predictive Value PETfold_2.0(20): 0.829 Vsfold5: 0.212 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_2.0(20): N/A MCFold: N/A Sensitivity PETfold_2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs PETfold_2.0(20) Matthews Correlation Coefficient Alterna: N/A PETfold_2.0(20): N/A Sensitivity Alterna: N/A PETfold_2.0(20): N/A Positive Predictive Value Alterna: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PETfold_2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_2.0(20): N/A Sensitivity RDfolder: N/A PETfold_2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_2.0(20): 0.647 RNAwolf: 0.431 Sensitivity PETfold_2.0(20): 0.509 RNAwolf: 0.368 Positive Predictive Value PETfold_2.0(20): 0.829 RNAwolf: 0.512 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PETfold_2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_2.0(20): 0.647 NanoFolder: 0.243 Sensitivity PETfold_2.0(20): 0.509 NanoFolder: 0.228 Positive Predictive Value PETfold_2.0(20): 0.829 NanoFolder: 0.271 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_2.0(20): N/A Carnac(seed): N/A Sensitivity PETfold_2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient RSpredict(seed): N/A PETfold_2.0(20): N/A Sensitivity RSpredict(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value RSpredict(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_2.0(20): N/A Sensitivity CMfinder(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient PETfold_2.0(seed): 0.761 PETfold_2.0(20): 0.647 Sensitivity PETfold_2.0(seed): 0.614 PETfold_2.0(20): 0.509 Positive Predictive Value PETfold_2.0(seed): 0.946 PETfold_2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 PETfold_2.0(20) vs DAFS(20) Matthews Correlation Coefficient PETfold_2.0(20): N/A DAFS(20): N/A Sensitivity PETfold_2.0(20): N/A DAFS(20): N/A Positive Predictive Value PETfold_2.0(20): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? DAFS(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(20): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(seed): 0.000 Sensitivity PETfold_2.0(20): 0.509 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0
DAFS(seed)	0 DAFS(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient DAFS(seed): N/A CentroidAlifold(20): N/A Sensitivity DAFS(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value DAFS(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(20): N/A DAFS(seed): N/A Sensitivity RNAalifold(20): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MXScarna(seed) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(seed): N/A Sensitivity DAFS(seed): N/A MXScarna(seed): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs DAFS(seed) Matthews Correlation Coefficient PPfold(20): N/A DAFS(seed): N/A Sensitivity PPfold(20): N/A DAFS(seed): N/A Positive Predictive Value PPfold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs DAFS(seed) Matthews Correlation Coefficient ContextFold: N/A DAFS(seed): N/A Sensitivity ContextFold: N/A DAFS(seed): N/A Positive Predictive Value ContextFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(20): N/A DAFS(seed): N/A Sensitivity RNASampler(20): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs DAFS(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A DAFS(seed): N/A Sensitivity PETfold_pre2.0(20): N/A DAFS(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(20): N/A DAFS(seed): N/A Sensitivity TurboFold(20): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MXScarna(20) Matthews Correlation Coefficient DAFS(seed): N/A MXScarna(20): N/A Sensitivity DAFS(seed): N/A MXScarna(20): N/A Positive Predictive Value DAFS(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs DAFS(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A DAFS(seed): N/A Sensitivity RNAalifold(seed): N/A DAFS(seed): N/A Positive Predictive Value RNAalifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs DAFS(seed) Matthews Correlation Coefficient Murlet(20): N/A DAFS(seed): N/A Sensitivity Murlet(20): N/A DAFS(seed): N/A Positive Predictive Value Murlet(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs DAFS(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A DAFS(seed): N/A Sensitivity CentroidAlifold(seed): N/A DAFS(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Carnac(20) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(20): N/A Sensitivity DAFS(seed): N/A Carnac(20): N/A Positive Predictive Value DAFS(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs IPknot Matthews Correlation Coefficient DAFS(seed): N/A IPknot: N/A Sensitivity DAFS(seed): N/A IPknot: N/A Positive Predictive Value DAFS(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs DAFS(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A DAFS(seed): N/A Sensitivity CentroidHomfold‑LAST: N/A DAFS(seed): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Contrafold Matthews Correlation Coefficient DAFS(seed): N/A Contrafold: N/A Sensitivity DAFS(seed): N/A Contrafold: N/A Positive Predictive Value DAFS(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Sfold Matthews Correlation Coefficient DAFS(seed): N/A Sfold: N/A Sensitivity DAFS(seed): N/A Sfold: N/A Positive Predictive Value DAFS(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs DAFS(seed) Matthews Correlation Coefficient HotKnots: N/A DAFS(seed): N/A Sensitivity HotKnots: N/A DAFS(seed): N/A Positive Predictive Value HotKnots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CentroidFold Matthews Correlation Coefficient DAFS(seed): N/A CentroidFold: N/A Sensitivity DAFS(seed): N/A CentroidFold: N/A Positive Predictive Value DAFS(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs DAFS(seed) Matthews Correlation Coefficient TurboFold(seed): N/A DAFS(seed): N/A Sensitivity TurboFold(seed): N/A DAFS(seed): N/A Positive Predictive Value TurboFold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs DAFS(seed) Matthews Correlation Coefficient MaxExpect: N/A DAFS(seed): N/A Sensitivity MaxExpect: N/A DAFS(seed): N/A Positive Predictive Value MaxExpect: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(20): N/A DAFS(seed): N/A Sensitivity RSpredict(20): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs DAFS(seed) Matthews Correlation Coefficient PknotsRG: N/A DAFS(seed): N/A Sensitivity PknotsRG: N/A DAFS(seed): N/A Positive Predictive Value PknotsRG: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CMfinder(20) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(20): N/A Sensitivity DAFS(seed): N/A CMfinder(20): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs DAFS(seed) Matthews Correlation Coefficient UNAFold: N/A DAFS(seed): N/A Sensitivity UNAFold: N/A DAFS(seed): N/A Positive Predictive Value UNAFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs DAFS(seed) Matthews Correlation Coefficient ProbKnot: N/A DAFS(seed): N/A Sensitivity ProbKnot: N/A DAFS(seed): N/A Positive Predictive Value ProbKnot: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs DAFS(seed) Matthews Correlation Coefficient Cylofold: N/A DAFS(seed): N/A Sensitivity Cylofold: N/A DAFS(seed): N/A Positive Predictive Value Cylofold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAfold Matthews Correlation Coefficient DAFS(seed): N/A RNAfold: N/A Sensitivity DAFS(seed): N/A RNAfold: N/A Positive Predictive Value DAFS(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs DAFS(seed) Matthews Correlation Coefficient RNASampler(seed): N/A DAFS(seed): N/A Sensitivity RNASampler(seed): N/A DAFS(seed): N/A Positive Predictive Value RNASampler(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAsubopt Matthews Correlation Coefficient DAFS(seed): N/A RNAsubopt: N/A Sensitivity DAFS(seed): N/A RNAsubopt: N/A Positive Predictive Value DAFS(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Multilign(20) Matthews Correlation Coefficient DAFS(seed): N/A Multilign(20): N/A Sensitivity DAFS(seed): N/A Multilign(20): N/A Positive Predictive Value DAFS(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Afold Matthews Correlation Coefficient DAFS(seed): N/A Afold: N/A Sensitivity DAFS(seed): N/A Afold: N/A Positive Predictive Value DAFS(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAshapes Matthews Correlation Coefficient DAFS(seed): N/A RNAshapes: N/A Sensitivity DAFS(seed): N/A RNAshapes: N/A Positive Predictive Value DAFS(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs DAFS(seed) Matthews Correlation Coefficient Fold: N/A DAFS(seed): N/A Sensitivity Fold: N/A DAFS(seed): N/A Positive Predictive Value Fold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs DAFS(seed) Matthews Correlation Coefficient McQFold: N/A DAFS(seed): N/A Sensitivity McQFold: N/A DAFS(seed): N/A Positive Predictive Value McQFold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNASLOpt Matthews Correlation Coefficient DAFS(seed): N/A RNASLOpt: N/A Sensitivity DAFS(seed): N/A RNASLOpt: N/A Positive Predictive Value DAFS(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs DAFS(seed) Matthews Correlation Coefficient Mastr(20): N/A DAFS(seed): N/A Sensitivity Mastr(20): N/A DAFS(seed): N/A Positive Predictive Value Mastr(20): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs DAFS(seed) Matthews Correlation Coefficient Multilign(seed): N/A DAFS(seed): N/A Sensitivity Multilign(seed): N/A DAFS(seed): N/A Positive Predictive Value Multilign(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs DAFS(seed) Matthews Correlation Coefficient Pknots: N/A DAFS(seed): N/A Sensitivity Pknots: N/A DAFS(seed): N/A Positive Predictive Value Pknots: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs DAFS(seed) Matthews Correlation Coefficient Vsfold4: N/A DAFS(seed): N/A Sensitivity Vsfold4: N/A DAFS(seed): N/A Positive Predictive Value Vsfold4: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs DAFS(seed) Matthews Correlation Coefficient CRWrnafold: N/A DAFS(seed): N/A Sensitivity CRWrnafold: N/A DAFS(seed): N/A Positive Predictive Value CRWrnafold: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Murlet(seed) Matthews Correlation Coefficient DAFS(seed): N/A Murlet(seed): N/A Sensitivity DAFS(seed): N/A Murlet(seed): N/A Positive Predictive Value DAFS(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs DAFS(seed) Matthews Correlation Coefficient Vsfold5: N/A DAFS(seed): N/A Sensitivity Vsfold5: N/A DAFS(seed): N/A Positive Predictive Value Vsfold5: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs MCFold Matthews Correlation Coefficient DAFS(seed): N/A MCFold: N/A Sensitivity DAFS(seed): N/A MCFold: N/A Positive Predictive Value DAFS(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Alterna Matthews Correlation Coefficient DAFS(seed): N/A Alterna: N/A Sensitivity DAFS(seed): N/A Alterna: N/A Positive Predictive Value DAFS(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs DAFS(seed) Matthews Correlation Coefficient RDfolder: N/A DAFS(seed): N/A Sensitivity RDfolder: N/A DAFS(seed): N/A Positive Predictive Value RDfolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs RNAwolf Matthews Correlation Coefficient DAFS(seed): N/A RNAwolf: N/A Sensitivity DAFS(seed): N/A RNAwolf: N/A Positive Predictive Value DAFS(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs DAFS(seed) Matthews Correlation Coefficient NanoFolder: N/A DAFS(seed): N/A Sensitivity NanoFolder: N/A DAFS(seed): N/A Positive Predictive Value NanoFolder: N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs Carnac(seed) Matthews Correlation Coefficient DAFS(seed): N/A Carnac(seed): N/A Sensitivity DAFS(seed): N/A Carnac(seed): N/A Positive Predictive Value DAFS(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs DAFS(seed) Matthews Correlation Coefficient RSpredict(seed): N/A DAFS(seed): N/A Sensitivity RSpredict(seed): N/A DAFS(seed): N/A Positive Predictive Value RSpredict(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs DAFS(seed) Matthews Correlation Coefficient PPfold(seed): N/A DAFS(seed): N/A Sensitivity PPfold(seed): N/A DAFS(seed): N/A Positive Predictive Value PPfold(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs CMfinder(seed) Matthews Correlation Coefficient DAFS(seed): N/A CMfinder(seed): N/A Sensitivity DAFS(seed): N/A CMfinder(seed): N/A Positive Predictive Value DAFS(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_2.0(seed) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(seed): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(seed): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs DAFS(20) Matthews Correlation Coefficient DAFS(seed): N/A DAFS(20): N/A Sensitivity DAFS(seed): N/A DAFS(20): N/A Positive Predictive Value DAFS(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 DAFS(seed) vs PETfold_2.0(20) Matthews Correlation Coefficient DAFS(seed): N/A PETfold_2.0(20): N/A Sensitivity DAFS(seed): N/A PETfold_2.0(20): N/A Positive Predictive Value DAFS(seed): N/A PETfold_2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Mastr(seed) vs DAFS(seed) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(seed): N/A Sensitivity Mastr(seed): N/A DAFS(seed): N/A Positive Predictive Value Mastr(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Mastr(seed)	36 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.682 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.529 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.882 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 Mastr(seed): 0.034 Sensitivity PETfold_pre2.0(seed): 0.595 Mastr(seed): 0.003 Positive Predictive Value PETfold_pre2.0(seed): 0.879 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.656 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.511 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.846 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.638 Mastr(seed): 0.024 Sensitivity MXScarna(seed): 0.522 Mastr(seed): 0.002 Positive Predictive Value MXScarna(seed): 0.783 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.663 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.528 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.836 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.628 Mastr(seed): 0.034 Sensitivity ContextFold: 0.510 Mastr(seed): 0.003 Positive Predictive Value ContextFold: 0.778 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.612 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.471 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.799 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.649 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.530 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.798 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08	20 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.616 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.508 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.752 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	38 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.611 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.509 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.737 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.549 Mastr(seed): 0.032 Sensitivity RNAalifold(seed): 0.338 Mastr(seed): 0.003 Positive Predictive Value RNAalifold(seed): 0.895 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	38 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.590 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.438 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.799 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.581 Mastr(seed): 0.024 Sensitivity CentroidAlifold(seed): 0.367 Mastr(seed): 0.002 Positive Predictive Value CentroidAlifold(seed): 0.923 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.590 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.389 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.899 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.580 Mastr(seed): 0.033 Sensitivity IPknot: 0.477 Mastr(seed): 0.003 Positive Predictive Value IPknot: 0.709 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	26 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.588 Mastr(seed): 0.034 Sensitivity CentroidHomfold‑LAST: 0.495 Mastr(seed): 0.003 Positive Predictive Value CentroidHomfold‑LAST: 0.704 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	52 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.559 Mastr(seed): 0.023 Sensitivity Contrafold: 0.498 Mastr(seed): 0.002 Positive Predictive Value Contrafold: 0.632 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.560 Mastr(seed): 0.023 Sensitivity Sfold: 0.472 Mastr(seed): 0.002 Positive Predictive Value Sfold: 0.669 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.538 Mastr(seed): 0.023 Sensitivity HotKnots: 0.485 Mastr(seed): 0.002 Positive Predictive Value HotKnots: 0.603 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	50 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.551 Mastr(seed): 0.024 Sensitivity CentroidFold: 0.472 Mastr(seed): 0.002 Positive Predictive Value CentroidFold: 0.649 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.529 Mastr(seed): 0.047 Sensitivity TurboFold(seed): 0.434 Mastr(seed): 0.006 Positive Predictive Value TurboFold(seed): 0.650 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	47 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.559 Mastr(seed): 0.024 Sensitivity MaxExpect: 0.489 Mastr(seed): 0.002 Positive Predictive Value MaxExpect: 0.644 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.552 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.436 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.703 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.562 Mastr(seed): 0.023 Sensitivity PknotsRG: 0.503 Mastr(seed): 0.002 Positive Predictive Value PknotsRG: 0.633 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.521 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.366 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.52214427071e-09	52 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.537 Mastr(seed): 0.023 Sensitivity UNAFold: 0.475 Mastr(seed): 0.002 Positive Predictive Value UNAFold: 0.611 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.550 Mastr(seed): 0.027 Sensitivity ProbKnot: 0.494 Mastr(seed): 0.002 Positive Predictive Value ProbKnot: 0.615 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.618 Mastr(seed): 0.000 Sensitivity Cylofold: 0.519 Mastr(seed): 0.000 Positive Predictive Value Cylofold: 0.741 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	52 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.548 Mastr(seed): 0.023 Sensitivity RNAfold: 0.489 Mastr(seed): 0.002 Positive Predictive Value RNAfold: 0.619 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.482 Mastr(seed): 0.048 Sensitivity RNASampler(seed): 0.342 Mastr(seed): 0.006 Positive Predictive Value RNASampler(seed): 0.684 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.78993384543e-08	52 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.533 Mastr(seed): 0.023 Sensitivity RNAsubopt: 0.480 Mastr(seed): 0.002 Positive Predictive Value RNAsubopt: 0.596 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.534 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.449 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.642 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.45805449719e-08	27 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.499 Mastr(seed): 0.000 Sensitivity Afold: 0.457 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.548 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	52 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.521 Mastr(seed): 0.023 Sensitivity RNAshapes: 0.461 Mastr(seed): 0.002 Positive Predictive Value RNAshapes: 0.594 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.545 Mastr(seed): 0.026 Sensitivity Fold: 0.487 Mastr(seed): 0.002 Positive Predictive Value Fold: 0.614 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.518 Mastr(seed): 0.023 Sensitivity McQFold: 0.447 Mastr(seed): 0.002 Positive Predictive Value McQFold: 0.604 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.499 Mastr(seed): 0.034 Sensitivity RNASLOpt: 0.408 Mastr(seed): 0.003 Positive Predictive Value RNASLOpt: 0.616 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.500 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.336 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.749 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.556 Mastr(seed): 0.054 Sensitivity Multilign(seed): 0.432 Mastr(seed): 0.008 Positive Predictive Value Multilign(seed): 0.723 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.61358433984e-08	50 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.523 Mastr(seed): 0.025 Sensitivity Pknots: 0.469 Mastr(seed): 0.002 Positive Predictive Value Pknots: 0.590 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.479 Mastr(seed): 0.024 Sensitivity Vsfold4: 0.402 Mastr(seed): 0.002 Positive Predictive Value Vsfold4: 0.575 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.536 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.472 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.616 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	24 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.448 Mastr(seed): 0.036 Sensitivity Murlet(seed): 0.245 Mastr(seed): 0.004 Positive Predictive Value Murlet(seed): 0.825 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	50 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.438 Mastr(seed): 0.024 Sensitivity Vsfold5: 0.374 Mastr(seed): 0.002 Positive Predictive Value Vsfold5: 0.520 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.418 Mastr(seed): 0.028 Sensitivity MCFold: 0.436 Mastr(seed): 0.002 Positive Predictive Value MCFold: 0.409 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.572 Mastr(seed): 0.000 Sensitivity Alterna: 0.500 Mastr(seed): 0.000 Positive Predictive Value Alterna: 0.664 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.512 Mastr(seed): 0.000 Sensitivity RDfolder: 0.415 Mastr(seed): 0.000 Positive Predictive Value RDfolder: 0.643 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.389 Mastr(seed): 0.033 Sensitivity RNAwolf: 0.363 Mastr(seed): 0.003 Positive Predictive Value RNAwolf: 0.426 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	19 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.290 Mastr(seed): 0.039 Sensitivity NanoFolder: 0.301 Mastr(seed): 0.004 Positive Predictive Value NanoFolder: 0.288 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	28 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.179 Mastr(seed): 0.033 Sensitivity Carnac(seed): 0.032 Mastr(seed): 0.003 Positive Predictive Value Carnac(seed): 1.000 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	50 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.178 Mastr(seed): 0.024 Sensitivity RSpredict(seed): 0.075 Mastr(seed): 0.002 Positive Predictive Value RSpredict(seed): 0.430 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.148 Mastr(seed): 0.034 Sensitivity PPfold(seed): 0.032 Mastr(seed): 0.003 Positive Predictive Value PPfold(seed): 0.689 Mastr(seed): 0.375 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.02343278931e-08	0 Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(seed): 0.769 Mastr(seed): 0.000 Sensitivity PETfold_2.0(seed): 0.642 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(seed): 0.924 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Mastr(seed) vs DAFS(20) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(20): N/A Sensitivity Mastr(seed): N/A DAFS(20): N/A Positive Predictive Value Mastr(seed): N/A DAFS(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_2.0(20): 0.647 Mastr(seed): 0.000 Sensitivity PETfold_2.0(20): 0.509 Mastr(seed): 0.000 Positive Predictive Value PETfold_2.0(20): 0.829 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Mastr(seed) vs DAFS(seed) Matthews Correlation Coefficient Mastr(seed): N/A DAFS(seed): N/A Sensitivity Mastr(seed): N/A DAFS(seed): N/A Positive Predictive Value Mastr(seed): N/A DAFS(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A

Matthews Correlation Coefficients (MCC) plotted for all methods in a ranking. MCCs were calculated by taking into account all reference and predicted RNA structures by a given method in the entire ranking. The plot includes only methods for which at least 40% of comparisons with other methods is valid (i.e. at least 40% of the comparisons were based on more than 10 predictions for common targets).

Pseudoknotted RNAsextended base pair definition

Summary of pairwise comparisons

Detailed results of pairwise comparisons between methods

Pseudoknotted RNAs
extended base pair definition