CompaRNA - on-line benchmarks of RNA structure prediction methods

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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: Oct. 2, 2012
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 30000
Number of RNA sequences: 58
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 Oct. 2, 2012.

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: 21) 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

54 methods predicting RNA secondary structure were compared with each other (thus each method has 53 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 32 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Tested since	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	MXScarna(seed)	no	2009-06-15	36	1	2	14	34	34
2	CentroidAlifold(20)	yes	2009-07-01	35	0	0	18	23	23
3	RNAalifold(20)	no	2009-02-18	33	2	0	18	25	25
4	RNASampler(20)	no	2009-02-18	32	3	0	18	25	25
5	CentroidFold	yes	2009-08-01	32	7	3	11	52	52
6	MXScarna(20)	no	2009-02-18	30	5	0	18	25	25
7	CentroidAlifold(seed)	yes	2009-07-01	30	6	3	14	33	33
8	Contrafold	yes	2009-02-18	29	12	1	11	58	58
9	Sfold	no	2009-02-18	28	13	1	11	58	58
10	MaxExpect	yes	2009-10-15	27	14	1	11	49	48
11	IPknot	yes	2011-07-01	26	2	1	24	17	17
12	CentroidHomfold‑LAST	yes	2011-05-11	26	2	2	23	18	18
13	HotKnots	no	2009-02-18	26	14	2	11	58	55
14	Carnac(20)	no	2009-02-18	25	9	1	18	25	25
15	ContextFold	yes	2011-11-15	23	0	0	30	14	14
16	ProbKnot	yes	2010-08-10	23	16	3	11	32	32
17	Murlet(20)	yes	2009-02-18	22	11	2	18	25	25
18	UNAFold	no	2009-02-18	21	14	7	11	58	58
19	Fold	no	2010-03-15	21	19	2	11	34	34
20	RNAfold	no	2009-02-18	21	20	1	11	58	58
21	PknotsRG	no	2009-02-18	20	21	1	11	58	58
22	Cylofold	no	2010-06-08	19	17	3	14	33	28
23	RNAalifold(seed)	no	2009-02-18	18	14	1	20	35	19
24	RNAshapes	no	2009-02-18	17	23	2	11	58	55
25	Afold	no	2009-02-18	15	17	3	18	58	42
26	McQFold	yes	2009-02-18	13	26	3	11	58	58
26	Pknots	no	2009-02-18	13	26	3	11	58	53
28	RNAsubopt	no	2009-02-18	13	27	2	11	58	55
29	RSpredict(20)	no	2009-06-03	11	21	3	18	24	24
30	CRWrnafold	yes	2011-08-23	10	13	1	29	16	15
31	Vsfold4	no	2009-02-18	10	32	0	11	58	55
32	Mastr(20)	yes	2009-02-18	9	24	2	18	25	25
33	RNASLOpt	no	2011-11-01	6	12	5	30	14	14
34	Murlet(seed)	yes	2009-02-18	6	26	1	20	35	16
35	Vsfold5	no	2009-02-18	6	35	1	11	58	55
36	RNAwolf	yes	2011-07-01	5	24	0	24	17	17
37	Alterna	no	2009-02-18	5	27	1	20	58	35
38	RDfolder	no	2009-02-18	5	34	0	14	58	37
39	MCFold	yes	2009-02-18	4	37	0	12	58	46
40	RSpredict(seed)	no	2009-06-03	3	36	0	14	34	34
41	PPfold(seed)	yes	2011-04-18	1	22	0	30	11	11
42	Carnac(seed)	no	2009-02-18	1	33	0	19	35	20
43	Mastr(seed)	yes	2009-02-18	0	39	0	14	35	35
N/A	RNASampler(seed)	no	2009-02-18	0	0	0	53	35	9
N/A	TurboFold(seed)	no	2011-04-20	0	0	0	53	11	8
N/A	Multilign(seed)	no	2011-03-01	0	0	0	53	11	4
N/A	NanoFolder	yes	2011-11-17	0	0	0	53	10	9
N/A	TurboFold(20)	no	2011-04-20	0	0	0	53	8	8
N/A	Multilign(20)	no	2011-03-01	0	0	0	53	8	8
N/A	PETfold_pre2.0(seed)	no	2011-11-03	0	0	0	53	8	8
N/A	PPfold(20)	yes	2011-04-18	0	0	0	53	8	8
N/A	PETfold_pre2.0(20)	no	2011-11-03	0	0	0	53	5	5
N/A	CMfinder(seed)	yes	2012-09-01	0	0	0	53	0	0
N/A	CMfinder(20)	yes	2012-09-01	0	0	0	53	0	0

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.


MXScarna(seed)		- CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 MXScarna(seed): 0.668 Sensitivity CentroidAlifold(20): 0.540 MXScarna(seed): 0.551 Positive Predictive Value CentroidAlifold(20): 0.897 MXScarna(seed): 0.812 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 RNAalifold(20): 0.657 Sensitivity MXScarna(seed): 0.556 RNAalifold(20): 0.511 Positive Predictive Value MXScarna(seed): 0.815 RNAalifold(20): 0.848 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 7.51223576774e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 RNASampler(20): 0.648 Sensitivity MXScarna(seed): 0.556 RNASampler(20): 0.504 Positive Predictive Value MXScarna(seed): 0.815 RNASampler(20): 0.837 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 1.51363754408e-07	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.647 CentroidFold: 0.592 Sensitivity MXScarna(seed): 0.530 CentroidFold: 0.510 Positive Predictive Value MXScarna(seed): 0.793 CentroidFold: 0.690 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 MXScarna(20): 0.627 Sensitivity MXScarna(seed): 0.556 MXScarna(20): 0.525 Positive Predictive Value MXScarna(seed): 0.815 MXScarna(20): 0.752 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.647 CentroidAlifold(seed): 0.590 Sensitivity MXScarna(seed): 0.530 CentroidAlifold(seed): 0.377 Positive Predictive Value MXScarna(seed): 0.793 CentroidAlifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.650 Contrafold: 0.565 Sensitivity MXScarna(seed): 0.533 Contrafold: 0.509 Positive Predictive Value MXScarna(seed): 0.796 Contrafold: 0.632 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.650 Sfold: 0.570 Sensitivity MXScarna(seed): 0.533 Sfold: 0.484 Positive Predictive Value MXScarna(seed): 0.796 Sfold: 0.675 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.640 MaxExpect: 0.569 Sensitivity MXScarna(seed): 0.523 MaxExpect: 0.504 Positive Predictive Value MXScarna(seed): 0.785 MaxExpect: 0.646 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.624 IPknot: 0.590 Sensitivity MXScarna(seed): 0.493 IPknot: 0.471 Positive Predictive Value MXScarna(seed): 0.796 IPknot: 0.747 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.97952969696e-09	= MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.624 CentroidHomfold‑LAST: 0.615 Sensitivity MXScarna(seed): 0.493 CentroidHomfold‑LAST: 0.479 Positive Predictive Value MXScarna(seed): 0.796 CentroidHomfold‑LAST: 0.795 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00145582378587	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.650 HotKnots: 0.560 Sensitivity MXScarna(seed): 0.533 HotKnots: 0.508 Positive Predictive Value MXScarna(seed): 0.796 HotKnots: 0.622 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 Carnac(20): 0.607 Sensitivity MXScarna(seed): 0.556 Carnac(20): 0.405 Positive Predictive Value MXScarna(seed): 0.815 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	? ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.616 MXScarna(seed): 0.586 Sensitivity ContextFold: 0.476 MXScarna(seed): 0.457 Positive Predictive Value ContextFold: 0.801 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.638 ProbKnot: 0.553 Sensitivity MXScarna(seed): 0.519 ProbKnot: 0.511 Positive Predictive Value MXScarna(seed): 0.787 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 Murlet(20): 0.593 Sensitivity MXScarna(seed): 0.556 Murlet(20): 0.440 Positive Predictive Value MXScarna(seed): 0.815 Murlet(20): 0.803 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.650 UNAFold: 0.557 Sensitivity MXScarna(seed): 0.533 UNAFold: 0.498 Positive Predictive Value MXScarna(seed): 0.796 UNAFold: 0.627 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.636 Fold: 0.560 Sensitivity MXScarna(seed): 0.518 Fold: 0.504 Positive Predictive Value MXScarna(seed): 0.783 Fold: 0.627 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.650 RNAfold: 0.562 Sensitivity MXScarna(seed): 0.533 RNAfold: 0.506 Positive Predictive Value MXScarna(seed): 0.796 RNAfold: 0.627 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.650 PknotsRG: 0.569 Sensitivity MXScarna(seed): 0.533 PknotsRG: 0.515 Positive Predictive Value MXScarna(seed): 0.796 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	= Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.659 MXScarna(seed): 0.657 Sensitivity Cylofold: 0.554 MXScarna(seed): 0.535 Positive Predictive Value Cylofold: 0.789 MXScarna(seed): 0.812 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.0467887381528	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.599 RNAalifold(seed): 0.539 Sensitivity MXScarna(seed): 0.476 RNAalifold(seed): 0.336 Positive Predictive Value MXScarna(seed): 0.757 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.650 RNAshapes: 0.538 Sensitivity MXScarna(seed): 0.533 RNAshapes: 0.479 Positive Predictive Value MXScarna(seed): 0.796 RNAshapes: 0.609 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.625 Afold: 0.501 Sensitivity MXScarna(seed): 0.508 Afold: 0.467 Positive Predictive Value MXScarna(seed): 0.771 Afold: 0.541 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.650 McQFold: 0.530 Sensitivity MXScarna(seed): 0.533 McQFold: 0.466 Positive Predictive Value MXScarna(seed): 0.796 McQFold: 0.607 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.662 Pknots: 0.577 Sensitivity MXScarna(seed): 0.545 Pknots: 0.520 Positive Predictive Value MXScarna(seed): 0.810 Pknots: 0.647 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.650 RNAsubopt: 0.529 Sensitivity MXScarna(seed): 0.533 RNAsubopt: 0.481 Positive Predictive Value MXScarna(seed): 0.796 RNAsubopt: 0.586 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 RSpredict(20): 0.559 Sensitivity MXScarna(seed): 0.556 RSpredict(20): 0.446 Positive Predictive Value MXScarna(seed): 0.815 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-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 Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.650 Vsfold4: 0.494 Sensitivity MXScarna(seed): 0.533 Vsfold4: 0.419 Positive Predictive Value MXScarna(seed): 0.796 Vsfold4: 0.586 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 Mastr(20): 0.525 Sensitivity MXScarna(seed): 0.556 Mastr(20): 0.350 Positive Predictive Value MXScarna(seed): 0.815 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	? MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.586 RNASLOpt: 0.474 Sensitivity MXScarna(seed): 0.457 RNASLOpt: 0.374 Positive Predictive Value MXScarna(seed): 0.758 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.615 Murlet(seed): 0.475 Sensitivity MXScarna(seed): 0.491 Murlet(seed): 0.270 Positive Predictive Value MXScarna(seed): 0.775 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.650 Vsfold5: 0.463 Sensitivity MXScarna(seed): 0.533 Vsfold5: 0.395 Positive Predictive Value MXScarna(seed): 0.796 Vsfold5: 0.547 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.624 RNAwolf: 0.414 Sensitivity MXScarna(seed): 0.493 RNAwolf: 0.375 Positive Predictive Value MXScarna(seed): 0.796 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-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: 5.19332990918e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.680 RDfolder: 0.509 Sensitivity MXScarna(seed): 0.549 RDfolder: 0.411 Positive Predictive Value MXScarna(seed): 0.849 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.665 MCFold: 0.448 Sensitivity MXScarna(seed): 0.549 MCFold: 0.472 Positive Predictive Value MXScarna(seed): 0.810 MCFold: 0.433 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.650 RSpredict(seed): 0.204 Sensitivity MXScarna(seed): 0.533 RSpredict(seed): 0.088 Positive Predictive Value MXScarna(seed): 0.796 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.624 PPfold(seed): 0.102 Sensitivity MXScarna(seed): 0.493 PPfold(seed): 0.020 Positive Predictive Value MXScarna(seed): 0.796 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.638 Carnac(seed): 0.139 Sensitivity MXScarna(seed): 0.527 Carnac(seed): 0.019 Positive Predictive Value MXScarna(seed): 0.777 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	? MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.594 NanoFolder: 0.346 Sensitivity MXScarna(seed): 0.468 NanoFolder: 0.353 Positive Predictive Value MXScarna(seed): 0.759 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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	? MXScarna(seed) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(seed): 0.577 Multilign(seed): 0.538 Sensitivity MXScarna(seed): 0.464 Multilign(seed): 0.420 Positive Predictive Value MXScarna(seed): 0.727 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.640 Multilign(20): 0.540 Sensitivity MXScarna(seed): 0.511 Multilign(20): 0.456 Positive Predictive Value MXScarna(seed): 0.807 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MXScarna(seed): 0.586 Sensitivity PETfold_pre2.0(seed): 0.551 MXScarna(seed): 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.640 TurboFold(20): 0.594 Sensitivity MXScarna(seed): 0.511 TurboFold(20): 0.470 Positive Predictive Value MXScarna(seed): 0.807 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): N/A CMfinder(20): N/A Sensitivity MXScarna(seed): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(seed): 0.593 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(seed): 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(seed): 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.574 TurboFold(seed): 0.517 Sensitivity MXScarna(seed): 0.452 TurboFold(seed): 0.422 Positive Predictive Value MXScarna(seed): 0.735 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.552 RNASampler(seed): 0.546 Sensitivity MXScarna(seed): 0.431 RNASampler(seed): 0.409 Positive Predictive Value MXScarna(seed): 0.713 RNASampler(seed): 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.665 MXScarna(seed): 0.640 Sensitivity PPfold(20): 0.519 MXScarna(seed): 0.511 Positive Predictive Value PPfold(20): 0.859 MXScarna(seed): 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.650 Mastr(seed): 0.000 Sensitivity MXScarna(seed): 0.533 Mastr(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.796 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(20)	23 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 MXScarna(seed): 0.668 Sensitivity CentroidAlifold(20): 0.540 MXScarna(seed): 0.551 Positive Predictive Value CentroidAlifold(20): 0.897 MXScarna(seed): 0.812 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08		+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAalifold(20): 0.658 Sensitivity CentroidAlifold(20): 0.540 RNAalifold(20): 0.513 Positive Predictive Value CentroidAlifold(20): 0.897 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNASampler(20): 0.644 Sensitivity CentroidAlifold(20): 0.540 RNASampler(20): 0.499 Positive Predictive Value CentroidAlifold(20): 0.897 RNASampler(20): 0.834 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 CentroidFold: 0.610 Sensitivity CentroidAlifold(20): 0.540 CentroidFold: 0.515 Positive Predictive Value CentroidAlifold(20): 0.897 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 MXScarna(20): 0.623 Sensitivity CentroidAlifold(20): 0.540 MXScarna(20): 0.521 Positive Predictive Value CentroidAlifold(20): 0.897 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 CentroidAlifold(seed): 0.629 Sensitivity CentroidAlifold(20): 0.540 CentroidAlifold(seed): 0.417 Positive Predictive Value CentroidAlifold(20): 0.897 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Contrafold: 0.564 Sensitivity CentroidAlifold(20): 0.540 Contrafold: 0.498 Positive Predictive Value CentroidAlifold(20): 0.897 Contrafold: 0.642 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Sfold: 0.592 Sensitivity CentroidAlifold(20): 0.540 Sfold: 0.493 Positive Predictive Value CentroidAlifold(20): 0.897 Sfold: 0.715 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.695 MaxExpect: 0.598 Sensitivity CentroidAlifold(20): 0.540 MaxExpect: 0.520 Positive Predictive Value CentroidAlifold(20): 0.897 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.691 IPknot: 0.571 Sensitivity CentroidAlifold(20): 0.515 IPknot: 0.463 Positive Predictive Value CentroidAlifold(20): 0.933 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.691 CentroidHomfold‑LAST: 0.631 Sensitivity CentroidAlifold(20): 0.515 CentroidHomfold‑LAST: 0.496 Positive Predictive Value CentroidAlifold(20): 0.933 CentroidHomfold‑LAST: 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.695 HotKnots: 0.580 Sensitivity CentroidAlifold(20): 0.540 HotKnots: 0.517 Positive Predictive Value CentroidAlifold(20): 0.897 HotKnots: 0.654 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Carnac(20): 0.605 Sensitivity CentroidAlifold(20): 0.540 Carnac(20): 0.403 Positive Predictive Value CentroidAlifold(20): 0.897 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.650 ContextFold: 0.579 Sensitivity CentroidAlifold(20): 0.473 ContextFold: 0.443 Positive Predictive Value CentroidAlifold(20): 0.898 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.691 ProbKnot: 0.597 Sensitivity CentroidAlifold(20): 0.525 ProbKnot: 0.536 Positive Predictive Value CentroidAlifold(20): 0.912 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.66062906821e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Murlet(20): 0.592 Sensitivity CentroidAlifold(20): 0.540 Murlet(20): 0.440 Positive Predictive Value CentroidAlifold(20): 0.897 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 UNAFold: 0.589 Sensitivity CentroidAlifold(20): 0.540 UNAFold: 0.516 Positive Predictive Value CentroidAlifold(20): 0.897 UNAFold: 0.677 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Fold: 0.581 Sensitivity CentroidAlifold(20): 0.525 Fold: 0.512 Positive Predictive Value CentroidAlifold(20): 0.912 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAfold: 0.567 Sensitivity CentroidAlifold(20): 0.540 RNAfold: 0.504 Positive Predictive Value CentroidAlifold(20): 0.897 RNAfold: 0.643 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.695 PknotsRG: 0.579 Sensitivity CentroidAlifold(20): 0.540 PknotsRG: 0.517 Positive Predictive Value CentroidAlifold(20): 0.897 PknotsRG: 0.652 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Cylofold: 0.661 Sensitivity CentroidAlifold(20): 0.584 Cylofold: 0.553 Positive Predictive Value CentroidAlifold(20): 0.941 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.657 RNAalifold(seed): 0.579 Sensitivity CentroidAlifold(20): 0.475 RNAalifold(seed): 0.366 Positive Predictive Value CentroidAlifold(20): 0.909 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAshapes: 0.558 Sensitivity CentroidAlifold(20): 0.540 RNAshapes: 0.487 Positive Predictive Value CentroidAlifold(20): 0.897 RNAshapes: 0.643 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.655 Afold: 0.508 Sensitivity CentroidAlifold(20): 0.503 Afold: 0.467 Positive Predictive Value CentroidAlifold(20): 0.856 Afold: 0.557 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 McQFold: 0.538 Sensitivity CentroidAlifold(20): 0.540 McQFold: 0.466 Positive Predictive Value CentroidAlifold(20): 0.897 McQFold: 0.624 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.712 Pknots: 0.554 Sensitivity CentroidAlifold(20): 0.566 Pknots: 0.501 Positive Predictive Value CentroidAlifold(20): 0.899 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAsubopt: 0.555 Sensitivity CentroidAlifold(20): 0.540 RNAsubopt: 0.497 Positive Predictive Value CentroidAlifold(20): 0.897 RNAsubopt: 0.624 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RSpredict(20): 0.555 Sensitivity CentroidAlifold(20): 0.540 RSpredict(20): 0.442 Positive Predictive Value CentroidAlifold(20): 0.897 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-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 Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Vsfold4: 0.477 Sensitivity CentroidAlifold(20): 0.540 Vsfold4: 0.397 Positive Predictive Value CentroidAlifold(20): 0.897 Vsfold4: 0.577 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Mastr(20): 0.518 Sensitivity CentroidAlifold(20): 0.540 Mastr(20): 0.343 Positive Predictive Value CentroidAlifold(20): 0.897 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.650 RNASLOpt: 0.467 Sensitivity CentroidAlifold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.898 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.675 Murlet(seed): 0.496 Sensitivity CentroidAlifold(20): 0.500 Murlet(seed): 0.277 Positive Predictive Value CentroidAlifold(20): 0.916 Murlet(seed): 0.893 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Vsfold5: 0.440 Sensitivity CentroidAlifold(20): 0.540 Vsfold5: 0.370 Positive Predictive Value CentroidAlifold(20): 0.897 Vsfold5: 0.527 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.691 RNAwolf: 0.364 Sensitivity CentroidAlifold(20): 0.515 RNAwolf: 0.333 Positive Predictive Value CentroidAlifold(20): 0.933 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 6.48923495589e-09	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.761 RDfolder: 0.525 Sensitivity CentroidAlifold(20): 0.607 RDfolder: 0.413 Positive Predictive Value CentroidAlifold(20): 0.960 RDfolder: 0.678 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.711 MCFold: 0.417 Sensitivity CentroidAlifold(20): 0.568 MCFold: 0.441 Positive Predictive Value CentroidAlifold(20): 0.894 MCFold: 0.402 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RSpredict(seed): 0.218 Sensitivity CentroidAlifold(20): 0.540 RSpredict(seed): 0.090 Positive Predictive Value CentroidAlifold(20): 0.897 RSpredict(seed): 0.539 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 PPfold(seed): 0.026 Sensitivity CentroidAlifold(20): 0.515 PPfold(seed): 0.004 Positive Predictive Value CentroidAlifold(20): 0.933 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.692 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.538 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.893 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	? CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.646 NanoFolder: 0.316 Sensitivity CentroidAlifold(20): 0.473 NanoFolder: 0.324 Positive Predictive Value CentroidAlifold(20): 0.886 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.729 Multilign(seed): 0.631 Sensitivity CentroidAlifold(20): 0.542 Multilign(seed): 0.492 Positive Predictive Value CentroidAlifold(20): 0.985 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Multilign(20): 0.540 Sensitivity CentroidAlifold(20): 0.515 Multilign(20): 0.456 Positive Predictive Value CentroidAlifold(20): 0.933 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 CentroidAlifold(20): 0.650 Sensitivity PETfold_pre2.0(seed): 0.557 CentroidAlifold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 CentroidAlifold(20): 0.898 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 TurboFold(20): 0.594 Sensitivity CentroidAlifold(20): 0.515 TurboFold(20): 0.470 Positive Predictive Value CentroidAlifold(20): 0.933 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(20): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.650 PETfold_pre2.0(20): 0.625 Sensitivity CentroidAlifold(20): 0.473 PETfold_pre2.0(20): 0.497 Positive Predictive Value CentroidAlifold(20): 0.898 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 TurboFold(seed): 0.564 Sensitivity CentroidAlifold(20): 0.490 TurboFold(seed): 0.457 Positive Predictive Value CentroidAlifold(20): 0.922 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.585 RNASampler(seed): 0.546 Sensitivity CentroidAlifold(20): 0.409 RNASampler(seed): 0.409 Positive Predictive Value CentroidAlifold(20): 0.842 RNASampler(seed): 0.733 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 PPfold(20): 0.665 Sensitivity CentroidAlifold(20): 0.515 PPfold(20): 0.519 Positive Predictive Value CentroidAlifold(20): 0.933 PPfold(20): 0.859 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.540 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.897 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08
RNAalifold(20)	24 MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 RNAalifold(20): 0.657 Sensitivity MXScarna(seed): 0.556 RNAalifold(20): 0.511 Positive Predictive Value MXScarna(seed): 0.815 RNAalifold(20): 0.848 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 7.51223576774e-08	23 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAalifold(20): 0.658 Sensitivity CentroidAlifold(20): 0.540 RNAalifold(20): 0.513 Positive Predictive Value CentroidAlifold(20): 0.897 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08		+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 RNASampler(20): 0.640 Sensitivity RNAalifold(20): 0.510 RNASampler(20): 0.491 Positive Predictive Value RNAalifold(20): 0.854 RNASampler(20): 0.839 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.658 CentroidFold: 0.610 Sensitivity RNAalifold(20): 0.513 CentroidFold: 0.515 Positive Predictive Value RNAalifold(20): 0.847 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 MXScarna(20): 0.621 Sensitivity RNAalifold(20): 0.510 MXScarna(20): 0.518 Positive Predictive Value RNAalifold(20): 0.854 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.658 CentroidAlifold(seed): 0.629 Sensitivity RNAalifold(20): 0.513 CentroidAlifold(seed): 0.417 Positive Predictive Value RNAalifold(20): 0.847 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.659 Contrafold: 0.554 Sensitivity RNAalifold(20): 0.510 Contrafold: 0.488 Positive Predictive Value RNAalifold(20): 0.854 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.659 Sfold: 0.593 Sensitivity RNAalifold(20): 0.510 Sfold: 0.492 Positive Predictive Value RNAalifold(20): 0.854 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.658 MaxExpect: 0.598 Sensitivity RNAalifold(20): 0.513 MaxExpect: 0.520 Positive Predictive Value RNAalifold(20): 0.847 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	? RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.627 IPknot: 0.571 Sensitivity RNAalifold(20): 0.481 IPknot: 0.463 Positive Predictive Value RNAalifold(20): 0.823 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 RNAalifold(20): 0.627 Sensitivity CentroidHomfold‑LAST: 0.496 RNAalifold(20): 0.481 Positive Predictive Value CentroidHomfold‑LAST: 0.807 RNAalifold(20): 0.823 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.659 HotKnots: 0.580 Sensitivity RNAalifold(20): 0.510 HotKnots: 0.514 Positive Predictive Value RNAalifold(20): 0.854 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Carnac(20): 0.601 Sensitivity RNAalifold(20): 0.510 Carnac(20): 0.397 Positive Predictive Value RNAalifold(20): 0.854 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	? ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.579 RNAalifold(20): 0.553 Sensitivity ContextFold: 0.443 RNAalifold(20): 0.407 Positive Predictive Value ContextFold: 0.763 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.646 ProbKnot: 0.597 Sensitivity RNAalifold(20): 0.494 ProbKnot: 0.536 Positive Predictive Value RNAalifold(20): 0.847 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Murlet(20): 0.592 Sensitivity RNAalifold(20): 0.510 Murlet(20): 0.437 Positive Predictive Value RNAalifold(20): 0.854 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.659 UNAFold: 0.589 Sensitivity RNAalifold(20): 0.510 UNAFold: 0.513 Positive Predictive Value RNAalifold(20): 0.854 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.646 Fold: 0.581 Sensitivity RNAalifold(20): 0.494 Fold: 0.512 Positive Predictive Value RNAalifold(20): 0.847 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.659 RNAfold: 0.569 Sensitivity RNAalifold(20): 0.510 RNAfold: 0.502 Positive Predictive Value RNAalifold(20): 0.854 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.659 PknotsRG: 0.581 Sensitivity RNAalifold(20): 0.510 PknotsRG: 0.516 Positive Predictive Value RNAalifold(20): 0.854 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.706 Cylofold: 0.661 Sensitivity RNAalifold(20): 0.560 Cylofold: 0.553 Positive Predictive Value RNAalifold(20): 0.895 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.602 RNAalifold(seed): 0.578 Sensitivity RNAalifold(20): 0.441 RNAalifold(seed): 0.364 Positive Predictive Value RNAalifold(20): 0.823 RNAalifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.659 RNAshapes: 0.554 Sensitivity RNAalifold(20): 0.510 RNAshapes: 0.482 Positive Predictive Value RNAalifold(20): 0.854 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.610 Afold: 0.513 Sensitivity RNAalifold(20): 0.467 Afold: 0.464 Positive Predictive Value RNAalifold(20): 0.798 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.659 McQFold: 0.529 Sensitivity RNAalifold(20): 0.510 McQFold: 0.456 Positive Predictive Value RNAalifold(20): 0.854 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.676 Pknots: 0.540 Sensitivity RNAalifold(20): 0.535 Pknots: 0.487 Positive Predictive Value RNAalifold(20): 0.857 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.659 RNAsubopt: 0.545 Sensitivity RNAalifold(20): 0.510 RNAsubopt: 0.486 Positive Predictive Value RNAalifold(20): 0.854 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.657 RSpredict(20): 0.559 Sensitivity RNAalifold(20): 0.511 RSpredict(20): 0.446 Positive Predictive Value RNAalifold(20): 0.848 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-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 Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.659 Vsfold4: 0.473 Sensitivity RNAalifold(20): 0.510 Vsfold4: 0.393 Positive Predictive Value RNAalifold(20): 0.854 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Mastr(20): 0.523 Sensitivity RNAalifold(20): 0.510 Mastr(20): 0.348 Positive Predictive Value RNAalifold(20): 0.854 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.553 RNASLOpt: 0.467 Sensitivity RNAalifold(20): 0.407 RNASLOpt: 0.383 Positive Predictive Value RNAalifold(20): 0.756 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.618 Murlet(seed): 0.496 Sensitivity RNAalifold(20): 0.466 Murlet(seed): 0.277 Positive Predictive Value RNAalifold(20): 0.824 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.659 Vsfold5: 0.425 Sensitivity RNAalifold(20): 0.510 Vsfold5: 0.358 Positive Predictive Value RNAalifold(20): 0.854 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	? RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.627 RNAwolf: 0.364 Sensitivity RNAalifold(20): 0.481 RNAwolf: 0.333 Positive Predictive Value RNAalifold(20): 0.823 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 1.89649746203e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.733 RDfolder: 0.539 Sensitivity RNAalifold(20): 0.576 RDfolder: 0.427 Positive Predictive Value RNAalifold(20): 0.939 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.673 MCFold: 0.425 Sensitivity RNAalifold(20): 0.543 MCFold: 0.448 Positive Predictive Value RNAalifold(20): 0.838 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.657 RSpredict(seed): 0.232 Sensitivity RNAalifold(20): 0.511 RSpredict(seed): 0.097 Positive Predictive Value RNAalifold(20): 0.848 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.627 PPfold(seed): 0.026 Sensitivity RNAalifold(20): 0.481 PPfold(seed): 0.004 Positive Predictive Value RNAalifold(20): 0.823 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.647 Carnac(seed): 0.122 Sensitivity RNAalifold(20): 0.505 Carnac(seed): 0.015 Positive Predictive Value RNAalifold(20): 0.833 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	? RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.565 NanoFolder: 0.316 Sensitivity RNAalifold(20): 0.432 NanoFolder: 0.324 Positive Predictive Value RNAalifold(20): 0.744 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.702 Multilign(seed): 0.631 Sensitivity RNAalifold(20): 0.542 Multilign(seed): 0.492 Positive Predictive Value RNAalifold(20): 0.914 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.627 Multilign(20): 0.540 Sensitivity RNAalifold(20): 0.481 Multilign(20): 0.456 Positive Predictive Value RNAalifold(20): 0.823 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(seed): 0.557 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.627 TurboFold(20): 0.594 Sensitivity RNAalifold(20): 0.481 TurboFold(20): 0.470 Positive Predictive Value RNAalifold(20): 0.823 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(20): N/A Sensitivity RNAalifold(20): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(20): 0.497 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.599 TurboFold(seed): 0.564 Sensitivity RNAalifold(20): 0.453 TurboFold(seed): 0.457 Positive Predictive Value RNAalifold(20): 0.797 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 RNAalifold(20): 0.512 Sensitivity RNASampler(seed): 0.434 RNAalifold(20): 0.402 Positive Predictive Value RNASampler(seed): 0.754 RNAalifold(20): 0.657 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.665 RNAalifold(20): 0.627 Sensitivity PPfold(20): 0.519 RNAalifold(20): 0.481 Positive Predictive Value PPfold(20): 0.859 RNAalifold(20): 0.823 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.659 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.510 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.854 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(20)	24 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 RNASampler(20): 0.648 Sensitivity MXScarna(seed): 0.556 RNASampler(20): 0.504 Positive Predictive Value MXScarna(seed): 0.815 RNASampler(20): 0.837 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 1.51363754408e-07	23 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNASampler(20): 0.644 Sensitivity CentroidAlifold(20): 0.540 RNASampler(20): 0.499 Positive Predictive Value CentroidAlifold(20): 0.897 RNASampler(20): 0.834 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	25 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 RNASampler(20): 0.640 Sensitivity RNAalifold(20): 0.510 RNASampler(20): 0.491 Positive Predictive Value RNAalifold(20): 0.854 RNASampler(20): 0.839 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08		+ RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.644 CentroidFold: 0.610 Sensitivity RNASampler(20): 0.499 CentroidFold: 0.515 Positive Predictive Value RNASampler(20): 0.834 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.640 MXScarna(20): 0.621 Sensitivity RNASampler(20): 0.491 MXScarna(20): 0.518 Positive Predictive Value RNASampler(20): 0.839 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.644 CentroidAlifold(seed): 0.629 Sensitivity RNASampler(20): 0.499 CentroidAlifold(seed): 0.417 Positive Predictive Value RNASampler(20): 0.834 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 2.82781450476e-07	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.640 Contrafold: 0.554 Sensitivity RNASampler(20): 0.491 Contrafold: 0.488 Positive Predictive Value RNASampler(20): 0.839 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.640 Sfold: 0.593 Sensitivity RNASampler(20): 0.491 Sfold: 0.492 Positive Predictive Value RNASampler(20): 0.839 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.644 MaxExpect: 0.598 Sensitivity RNASampler(20): 0.499 MaxExpect: 0.520 Positive Predictive Value RNASampler(20): 0.834 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.637 IPknot: 0.571 Sensitivity RNASampler(20): 0.478 IPknot: 0.463 Positive Predictive Value RNASampler(20): 0.854 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.637 CentroidHomfold‑LAST: 0.631 Sensitivity RNASampler(20): 0.478 CentroidHomfold‑LAST: 0.496 Positive Predictive Value RNASampler(20): 0.854 CentroidHomfold‑LAST: 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.640 HotKnots: 0.580 Sensitivity RNASampler(20): 0.491 HotKnots: 0.514 Positive Predictive Value RNASampler(20): 0.839 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.640 Carnac(20): 0.601 Sensitivity RNASampler(20): 0.491 Carnac(20): 0.397 Positive Predictive Value RNASampler(20): 0.839 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.579 RNASampler(20): 0.569 Sensitivity ContextFold: 0.443 RNASampler(20): 0.419 Positive Predictive Value ContextFold: 0.763 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.633 ProbKnot: 0.597 Sensitivity RNASampler(20): 0.478 ProbKnot: 0.536 Positive Predictive Value RNASampler(20): 0.843 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.640 Murlet(20): 0.592 Sensitivity RNASampler(20): 0.491 Murlet(20): 0.437 Positive Predictive Value RNASampler(20): 0.839 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.640 UNAFold: 0.589 Sensitivity RNASampler(20): 0.491 UNAFold: 0.513 Positive Predictive Value RNASampler(20): 0.839 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.633 Fold: 0.581 Sensitivity RNASampler(20): 0.478 Fold: 0.512 Positive Predictive Value RNASampler(20): 0.843 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.640 RNAfold: 0.569 Sensitivity RNASampler(20): 0.491 RNAfold: 0.502 Positive Predictive Value RNASampler(20): 0.839 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.640 PknotsRG: 0.581 Sensitivity RNASampler(20): 0.491 PknotsRG: 0.516 Positive Predictive Value RNASampler(20): 0.839 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.702 Cylofold: 0.661 Sensitivity RNASampler(20): 0.545 Cylofold: 0.553 Positive Predictive Value RNASampler(20): 0.907 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.589 RNAalifold(seed): 0.578 Sensitivity RNASampler(20): 0.441 RNAalifold(seed): 0.364 Positive Predictive Value RNASampler(20): 0.790 RNAalifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.640 RNAshapes: 0.554 Sensitivity RNASampler(20): 0.491 RNAshapes: 0.482 Positive Predictive Value RNASampler(20): 0.839 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.600 Afold: 0.513 Sensitivity RNASampler(20): 0.461 Afold: 0.464 Positive Predictive Value RNASampler(20): 0.782 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.640 McQFold: 0.529 Sensitivity RNASampler(20): 0.491 McQFold: 0.456 Positive Predictive Value RNASampler(20): 0.839 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.664 Pknots: 0.540 Sensitivity RNASampler(20): 0.518 Pknots: 0.487 Positive Predictive Value RNASampler(20): 0.856 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.640 RNAsubopt: 0.545 Sensitivity RNASampler(20): 0.491 RNAsubopt: 0.486 Positive Predictive Value RNASampler(20): 0.839 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.648 RSpredict(20): 0.559 Sensitivity RNASampler(20): 0.504 RSpredict(20): 0.446 Positive Predictive Value RNASampler(20): 0.837 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-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 Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.640 Vsfold4: 0.473 Sensitivity RNASampler(20): 0.491 Vsfold4: 0.393 Positive Predictive Value RNASampler(20): 0.839 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.640 Mastr(20): 0.523 Sensitivity RNASampler(20): 0.491 Mastr(20): 0.348 Positive Predictive Value RNASampler(20): 0.839 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.98172311752e-08	? RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.569 RNASLOpt: 0.467 Sensitivity RNASampler(20): 0.419 RNASLOpt: 0.383 Positive Predictive Value RNASampler(20): 0.778 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.619 Murlet(seed): 0.496 Sensitivity RNASampler(20): 0.475 Murlet(seed): 0.277 Positive Predictive Value RNASampler(20): 0.812 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.640 Vsfold5: 0.425 Sensitivity RNASampler(20): 0.491 Vsfold5: 0.358 Positive Predictive Value RNASampler(20): 0.839 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.637 RNAwolf: 0.364 Sensitivity RNASampler(20): 0.478 RNAwolf: 0.333 Positive Predictive Value RNASampler(20): 0.854 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 2.20167918023e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.746 RDfolder: 0.539 Sensitivity RNASampler(20): 0.591 RDfolder: 0.427 Positive Predictive Value RNASampler(20): 0.948 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.680 MCFold: 0.425 Sensitivity RNASampler(20): 0.546 MCFold: 0.448 Positive Predictive Value RNASampler(20): 0.850 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.648 RSpredict(seed): 0.232 Sensitivity RNASampler(20): 0.504 RSpredict(seed): 0.097 Positive Predictive Value RNASampler(20): 0.837 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.637 PPfold(seed): 0.026 Sensitivity RNASampler(20): 0.478 PPfold(seed): 0.004 Positive Predictive Value RNASampler(20): 0.854 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.648 Carnac(seed): 0.122 Sensitivity RNASampler(20): 0.502 Carnac(seed): 0.015 Positive Predictive Value RNASampler(20): 0.841 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-08	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.567 NanoFolder: 0.316 Sensitivity RNASampler(20): 0.426 NanoFolder: 0.324 Positive Predictive Value RNASampler(20): 0.759 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.669 Multilign(seed): 0.631 Sensitivity RNASampler(20): 0.483 Multilign(seed): 0.492 Positive Predictive Value RNASampler(20): 0.934 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.637 Multilign(20): 0.540 Sensitivity RNASampler(20): 0.478 Multilign(20): 0.456 Positive Predictive Value RNASampler(20): 0.854 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(seed): 0.557 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.637 TurboFold(20): 0.594 Sensitivity RNASampler(20): 0.478 TurboFold(20): 0.470 Positive Predictive Value RNASampler(20): 0.854 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(20): N/A Sensitivity RNASampler(20): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(20): 0.497 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.615 TurboFold(seed): 0.564 Sensitivity RNASampler(20): 0.453 TurboFold(seed): 0.457 Positive Predictive Value RNASampler(20): 0.840 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 RNASampler(20): 0.541 Sensitivity RNASampler(seed): 0.434 RNASampler(20): 0.438 Positive Predictive Value RNASampler(seed): 0.754 RNASampler(20): 0.671 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.665 RNASampler(20): 0.637 Sensitivity PPfold(20): 0.519 RNASampler(20): 0.478 Positive Predictive Value PPfold(20): 0.859 RNASampler(20): 0.854 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.491 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.839 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08
CentroidFold	33 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.647 CentroidFold: 0.592 Sensitivity MXScarna(seed): 0.530 CentroidFold: 0.510 Positive Predictive Value MXScarna(seed): 0.793 CentroidFold: 0.690 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 CentroidFold: 0.610 Sensitivity CentroidAlifold(20): 0.540 CentroidFold: 0.515 Positive Predictive Value CentroidAlifold(20): 0.897 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	23 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.658 CentroidFold: 0.610 Sensitivity RNAalifold(20): 0.513 CentroidFold: 0.515 Positive Predictive Value RNAalifold(20): 0.847 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.644 CentroidFold: 0.610 Sensitivity RNASampler(20): 0.499 CentroidFold: 0.515 Positive Predictive Value RNASampler(20): 0.834 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08		- MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.623 CentroidFold: 0.610 Sensitivity MXScarna(20): 0.521 CentroidFold: 0.515 Positive Predictive Value MXScarna(20): 0.748 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.54865340847e-08	= CentroidFold vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidFold: 0.592 CentroidAlifold(seed): 0.590 Sensitivity CentroidFold: 0.510 CentroidAlifold(seed): 0.377 Positive Predictive Value CentroidFold: 0.690 CentroidAlifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.0782705756228	+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.517 Contrafold: 0.516 Sensitivity CentroidFold: 0.434 Contrafold: 0.460 Positive Predictive Value CentroidFold: 0.616 Contrafold: 0.579 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 0.000778510229985	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.517 Sfold: 0.479 Sensitivity CentroidFold: 0.434 Sfold: 0.403 Positive Predictive Value CentroidFold: 0.616 Sfold: 0.570 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.568 MaxExpect: 0.558 Sensitivity CentroidFold: 0.463 MaxExpect: 0.478 Positive Predictive Value CentroidFold: 0.697 MaxExpect: 0.651 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	- IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.567 CentroidFold: 0.551 Sensitivity IPknot: 0.463 CentroidFold: 0.447 Positive Predictive Value IPknot: 0.702 CentroidFold: 0.686 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	= CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 CentroidFold: 0.547 Sensitivity CentroidHomfold‑LAST: 0.397 CentroidFold: 0.441 Positive Predictive Value CentroidHomfold‑LAST: 0.784 CentroidFold: 0.687 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.00194269211386	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.596 HotKnots: 0.573 Sensitivity CentroidFold: 0.507 HotKnots: 0.516 Positive Predictive Value CentroidFold: 0.705 HotKnots: 0.642 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.610 Carnac(20): 0.605 Sensitivity CentroidFold: 0.515 Carnac(20): 0.403 Positive Predictive Value CentroidFold: 0.725 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.0940494622033	- ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.601 CentroidFold: 0.520 Sensitivity ContextFold: 0.483 CentroidFold: 0.423 Positive Predictive Value ContextFold: 0.754 CentroidFold: 0.648 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.591 ProbKnot: 0.561 Sensitivity CentroidFold: 0.503 ProbKnot: 0.514 Positive Predictive Value CentroidFold: 0.697 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.610 Murlet(20): 0.592 Sensitivity CentroidFold: 0.515 Murlet(20): 0.440 Positive Predictive Value CentroidFold: 0.725 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.29540574715e-07	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.517 UNAFold: 0.457 Sensitivity CentroidFold: 0.434 UNAFold: 0.412 Positive Predictive Value CentroidFold: 0.616 UNAFold: 0.508 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.605 Fold: 0.570 Sensitivity CentroidFold: 0.517 Fold: 0.509 Positive Predictive Value CentroidFold: 0.712 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.517 RNAfold: 0.448 Sensitivity CentroidFold: 0.434 RNAfold: 0.408 Positive Predictive Value CentroidFold: 0.616 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.517 PknotsRG: 0.441 Sensitivity CentroidFold: 0.434 PknotsRG: 0.403 Positive Predictive Value CentroidFold: 0.616 PknotsRG: 0.484 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.646 Cylofold: 0.607 Sensitivity CentroidFold: 0.539 Cylofold: 0.512 Positive Predictive Value CentroidFold: 0.780 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.576 RNAalifold(seed): 0.539 Sensitivity CentroidFold: 0.490 RNAalifold(seed): 0.337 Positive Predictive Value CentroidFold: 0.679 RNAalifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.596 RNAshapes: 0.545 Sensitivity CentroidFold: 0.507 RNAshapes: 0.480 Positive Predictive Value CentroidFold: 0.705 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.500 Afold: 0.427 Sensitivity CentroidFold: 0.423 Afold: 0.394 Positive Predictive Value CentroidFold: 0.592 Afold: 0.463 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.517 McQFold: 0.388 Sensitivity CentroidFold: 0.434 McQFold: 0.288 Positive Predictive Value CentroidFold: 0.616 McQFold: 0.521 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.619 Pknots: 0.560 Sensitivity CentroidFold: 0.521 Pknots: 0.503 Positive Predictive Value CentroidFold: 0.742 Pknots: 0.630 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.596 RNAsubopt: 0.540 Sensitivity CentroidFold: 0.507 RNAsubopt: 0.486 Positive Predictive Value CentroidFold: 0.705 RNAsubopt: 0.605 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.610 RSpredict(20): 0.555 Sensitivity CentroidFold: 0.515 RSpredict(20): 0.442 Positive Predictive Value CentroidFold: 0.725 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-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: 1.67657656842e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.596 Vsfold4: 0.480 Sensitivity CentroidFold: 0.507 Vsfold4: 0.404 Positive Predictive Value CentroidFold: 0.705 Vsfold4: 0.576 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.610 Mastr(20): 0.518 Sensitivity CentroidFold: 0.515 Mastr(20): 0.343 Positive Predictive Value CentroidFold: 0.725 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.520 RNASLOpt: 0.443 Sensitivity CentroidFold: 0.423 RNASLOpt: 0.365 Positive Predictive Value CentroidFold: 0.648 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.620 Murlet(seed): 0.474 Sensitivity CentroidFold: 0.508 Murlet(seed): 0.270 Positive Predictive Value CentroidFold: 0.760 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.596 Vsfold5: 0.432 Sensitivity CentroidFold: 0.507 Vsfold5: 0.366 Positive Predictive Value CentroidFold: 0.705 Vsfold5: 0.515 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.551 RNAwolf: 0.399 Sensitivity CentroidFold: 0.447 RNAwolf: 0.368 Positive Predictive Value CentroidFold: 0.686 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-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: 0.627 RDfolder: 0.432 Sensitivity CentroidFold: 0.515 RDfolder: 0.337 Positive Predictive Value CentroidFold: 0.772 RDfolder: 0.566 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.613 MCFold: 0.420 Sensitivity CentroidFold: 0.517 MCFold: 0.441 Positive Predictive Value CentroidFold: 0.733 MCFold: 0.409 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.592 RSpredict(seed): 0.194 Sensitivity CentroidFold: 0.510 RSpredict(seed): 0.083 Positive Predictive Value CentroidFold: 0.690 RSpredict(seed): 0.459 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.578 PPfold(seed): 0.102 Sensitivity CentroidFold: 0.465 PPfold(seed): 0.020 Positive Predictive Value CentroidFold: 0.725 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.11142658008e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.625 Carnac(seed): 0.075 Sensitivity CentroidFold: 0.525 Carnac(seed): 0.006 Positive Predictive Value CentroidFold: 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.63594052159e-08	? CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.569 NanoFolder: 0.366 Sensitivity CentroidFold: 0.466 NanoFolder: 0.376 Positive Predictive Value CentroidFold: 0.700 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.573 Multilign(seed): 0.538 Sensitivity CentroidFold: 0.442 Multilign(seed): 0.420 Positive Predictive Value CentroidFold: 0.753 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.575 Multilign(20): 0.540 Sensitivity CentroidFold: 0.470 Multilign(20): 0.456 Positive Predictive Value CentroidFold: 0.709 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidFold: 0.540 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidFold: 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidFold: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.594 CentroidFold: 0.575 Sensitivity TurboFold(20): 0.470 CentroidFold: 0.470 Positive Predictive Value TurboFold(20): 0.756 CentroidFold: 0.709 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: N/A CMfinder(20): N/A Sensitivity CentroidFold: N/A CMfinder(20): N/A Positive Predictive Value CentroidFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidFold: 0.517 Sensitivity PETfold_pre2.0(20): 0.497 CentroidFold: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.555 TurboFold(seed): 0.517 Sensitivity CentroidFold: 0.449 TurboFold(seed): 0.422 Positive Predictive Value CentroidFold: 0.694 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.526 RNASampler(seed): 0.526 Sensitivity CentroidFold: 0.438 RNASampler(seed): 0.389 Positive Predictive Value CentroidFold: 0.637 RNASampler(seed): 0.715 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.665 CentroidFold: 0.575 Sensitivity PPfold(20): 0.519 CentroidFold: 0.470 Positive Predictive Value PPfold(20): 0.859 CentroidFold: 0.709 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.592 Mastr(seed): 0.000 Sensitivity CentroidFold: 0.510 Mastr(seed): 0.000 Positive Predictive Value CentroidFold: 0.690 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(20)	24 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 MXScarna(20): 0.627 Sensitivity MXScarna(seed): 0.556 MXScarna(20): 0.525 Positive Predictive Value MXScarna(seed): 0.815 MXScarna(20): 0.752 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 MXScarna(20): 0.623 Sensitivity CentroidAlifold(20): 0.540 MXScarna(20): 0.521 Positive Predictive Value CentroidAlifold(20): 0.897 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 MXScarna(20): 0.621 Sensitivity RNAalifold(20): 0.510 MXScarna(20): 0.518 Positive Predictive Value RNAalifold(20): 0.854 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.640 MXScarna(20): 0.621 Sensitivity RNASampler(20): 0.491 MXScarna(20): 0.518 Positive Predictive Value RNASampler(20): 0.839 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.623 CentroidFold: 0.610 Sensitivity MXScarna(20): 0.521 CentroidFold: 0.515 Positive Predictive Value MXScarna(20): 0.748 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.54865340847e-08		- CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 MXScarna(20): 0.623 Sensitivity CentroidAlifold(seed): 0.417 MXScarna(20): 0.521 Positive Predictive Value CentroidAlifold(seed): 0.953 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.000984932616326	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.621 Contrafold: 0.554 Sensitivity MXScarna(20): 0.518 Contrafold: 0.488 Positive Predictive Value MXScarna(20): 0.748 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.621 Sfold: 0.593 Sensitivity MXScarna(20): 0.518 Sfold: 0.492 Positive Predictive Value MXScarna(20): 0.748 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.623 MaxExpect: 0.598 Sensitivity MXScarna(20): 0.521 MaxExpect: 0.520 Positive Predictive Value MXScarna(20): 0.748 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.586 IPknot: 0.571 Sensitivity MXScarna(20): 0.474 IPknot: 0.463 Positive Predictive Value MXScarna(20): 0.731 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 MXScarna(20): 0.586 Sensitivity CentroidHomfold‑LAST: 0.496 MXScarna(20): 0.474 Positive Predictive Value CentroidHomfold‑LAST: 0.807 MXScarna(20): 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.621 HotKnots: 0.580 Sensitivity MXScarna(20): 0.518 HotKnots: 0.514 Positive Predictive Value MXScarna(20): 0.748 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.621 Carnac(20): 0.601 Sensitivity MXScarna(20): 0.518 Carnac(20): 0.397 Positive Predictive Value MXScarna(20): 0.748 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	? ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.579 MXScarna(20): 0.501 Sensitivity ContextFold: 0.443 MXScarna(20): 0.401 Positive Predictive Value ContextFold: 0.763 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.618 ProbKnot: 0.597 Sensitivity MXScarna(20): 0.512 ProbKnot: 0.536 Positive Predictive Value MXScarna(20): 0.748 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.621 Murlet(20): 0.592 Sensitivity MXScarna(20): 0.518 Murlet(20): 0.437 Positive Predictive Value MXScarna(20): 0.748 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.621 UNAFold: 0.589 Sensitivity MXScarna(20): 0.518 UNAFold: 0.513 Positive Predictive Value MXScarna(20): 0.748 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.618 Fold: 0.581 Sensitivity MXScarna(20): 0.512 Fold: 0.512 Positive Predictive Value MXScarna(20): 0.748 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.621 RNAfold: 0.569 Sensitivity MXScarna(20): 0.518 RNAfold: 0.502 Positive Predictive Value MXScarna(20): 0.748 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.621 PknotsRG: 0.581 Sensitivity MXScarna(20): 0.518 PknotsRG: 0.516 Positive Predictive Value MXScarna(20): 0.748 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.676 Cylofold: 0.661 Sensitivity MXScarna(20): 0.560 Cylofold: 0.553 Positive Predictive Value MXScarna(20): 0.821 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59979455159e-06	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.589 RNAalifold(seed): 0.578 Sensitivity MXScarna(20): 0.475 RNAalifold(seed): 0.364 Positive Predictive Value MXScarna(20): 0.733 RNAalifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.59567023119e-07	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.621 RNAshapes: 0.554 Sensitivity MXScarna(20): 0.518 RNAshapes: 0.482 Positive Predictive Value MXScarna(20): 0.748 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.584 Afold: 0.513 Sensitivity MXScarna(20): 0.487 Afold: 0.464 Positive Predictive Value MXScarna(20): 0.703 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.621 McQFold: 0.529 Sensitivity MXScarna(20): 0.518 McQFold: 0.456 Positive Predictive Value MXScarna(20): 0.748 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.637 Pknots: 0.540 Sensitivity MXScarna(20): 0.535 Pknots: 0.487 Positive Predictive Value MXScarna(20): 0.764 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.621 RNAsubopt: 0.545 Sensitivity MXScarna(20): 0.518 RNAsubopt: 0.486 Positive Predictive Value MXScarna(20): 0.748 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.627 RSpredict(20): 0.559 Sensitivity MXScarna(20): 0.525 RSpredict(20): 0.446 Positive Predictive Value MXScarna(20): 0.752 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-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 Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.621 Vsfold4: 0.473 Sensitivity MXScarna(20): 0.518 Vsfold4: 0.393 Positive Predictive Value MXScarna(20): 0.748 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.621 Mastr(20): 0.523 Sensitivity MXScarna(20): 0.518 Mastr(20): 0.348 Positive Predictive Value MXScarna(20): 0.748 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.501 RNASLOpt: 0.467 Sensitivity MXScarna(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value MXScarna(20): 0.632 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.610 Murlet(seed): 0.496 Sensitivity MXScarna(20): 0.493 Murlet(seed): 0.277 Positive Predictive Value MXScarna(20): 0.759 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.621 Vsfold5: 0.425 Sensitivity MXScarna(20): 0.518 Vsfold5: 0.358 Positive Predictive Value MXScarna(20): 0.748 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	? MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.586 RNAwolf: 0.364 Sensitivity MXScarna(20): 0.474 RNAwolf: 0.333 Positive Predictive Value MXScarna(20): 0.731 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 1.50834591464e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.703 RDfolder: 0.539 Sensitivity MXScarna(20): 0.576 RDfolder: 0.427 Positive Predictive Value MXScarna(20): 0.866 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.644 MCFold: 0.425 Sensitivity MXScarna(20): 0.542 MCFold: 0.448 Positive Predictive Value MXScarna(20): 0.769 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.627 RSpredict(seed): 0.232 Sensitivity MXScarna(20): 0.525 RSpredict(seed): 0.097 Positive Predictive Value MXScarna(20): 0.752 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	? MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.586 PPfold(seed): 0.026 Sensitivity MXScarna(20): 0.474 PPfold(seed): 0.004 Positive Predictive Value MXScarna(20): 0.731 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.622 Carnac(seed): 0.122 Sensitivity MXScarna(20): 0.521 Carnac(seed): 0.015 Positive Predictive Value MXScarna(20): 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.52609899389e-08	? MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.524 NanoFolder: 0.316 Sensitivity MXScarna(20): 0.439 NanoFolder: 0.324 Positive Predictive Value MXScarna(20): 0.631 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.652 Multilign(seed): 0.631 Sensitivity MXScarna(20): 0.542 Multilign(seed): 0.492 Positive Predictive Value MXScarna(20): 0.790 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.586 Multilign(20): 0.540 Sensitivity MXScarna(20): 0.474 Multilign(20): 0.456 Positive Predictive Value MXScarna(20): 0.731 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(seed): 0.557 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.594 MXScarna(20): 0.586 Sensitivity TurboFold(20): 0.470 MXScarna(20): 0.474 Positive Predictive Value TurboFold(20): 0.756 MXScarna(20): 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): N/A CMfinder(20): N/A Sensitivity MXScarna(20): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 MXScarna(20): 0.554 Sensitivity TurboFold(seed): 0.457 MXScarna(20): 0.444 Positive Predictive Value TurboFold(seed): 0.703 MXScarna(20): 0.697 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 MXScarna(20): 0.539 Sensitivity RNASampler(seed): 0.434 MXScarna(20): 0.447 Positive Predictive Value RNASampler(seed): 0.754 MXScarna(20): 0.653 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.665 MXScarna(20): 0.586 Sensitivity PPfold(20): 0.519 MXScarna(20): 0.474 Positive Predictive Value PPfold(20): 0.859 MXScarna(20): 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.621 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08
CentroidAlifold(seed)	33 MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.647 CentroidAlifold(seed): 0.590 Sensitivity MXScarna(seed): 0.530 CentroidAlifold(seed): 0.377 Positive Predictive Value MXScarna(seed): 0.793 CentroidAlifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 CentroidAlifold(seed): 0.629 Sensitivity CentroidAlifold(20): 0.540 CentroidAlifold(seed): 0.417 Positive Predictive Value CentroidAlifold(20): 0.897 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.658 CentroidAlifold(seed): 0.629 Sensitivity RNAalifold(20): 0.513 CentroidAlifold(seed): 0.417 Positive Predictive Value RNAalifold(20): 0.847 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.644 CentroidAlifold(seed): 0.629 Sensitivity RNASampler(20): 0.499 CentroidAlifold(seed): 0.417 Positive Predictive Value RNASampler(20): 0.834 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 2.82781450476e-07	33 CentroidFold vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidFold: 0.592 CentroidAlifold(seed): 0.590 Sensitivity CentroidFold: 0.510 CentroidAlifold(seed): 0.377 Positive Predictive Value CentroidFold: 0.690 CentroidAlifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 0.0782705756228	23 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 MXScarna(20): 0.623 Sensitivity CentroidAlifold(seed): 0.417 MXScarna(20): 0.521 Positive Predictive Value CentroidAlifold(seed): 0.953 MXScarna(20): 0.748 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.000984932616326		+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Contrafold: 0.562 Sensitivity CentroidAlifold(seed): 0.377 Contrafold: 0.505 Positive Predictive Value CentroidAlifold(seed): 0.925 Contrafold: 0.629 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Sfold: 0.566 Sensitivity CentroidAlifold(seed): 0.377 Sfold: 0.480 Positive Predictive Value CentroidAlifold(seed): 0.925 Sfold: 0.672 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 7.5939721025e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.591 MaxExpect: 0.569 Sensitivity CentroidAlifold(seed): 0.378 MaxExpect: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.927 MaxExpect: 0.646 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.22032703654e-06	= IPknot vs CentroidAlifold(seed) Matthews Correlation Coefficient IPknot: 0.590 CentroidAlifold(seed): 0.583 Sensitivity IPknot: 0.471 CentroidAlifold(seed): 0.347 Positive Predictive Value IPknot: 0.747 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.017418519964	- CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 CentroidAlifold(seed): 0.583 Sensitivity CentroidHomfold‑LAST: 0.479 CentroidAlifold(seed): 0.347 Positive Predictive Value CentroidHomfold‑LAST: 0.795 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 HotKnots: 0.557 Sensitivity CentroidAlifold(seed): 0.377 HotKnots: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.925 HotKnots: 0.619 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Carnac(20): 0.605 Sensitivity CentroidAlifold(seed): 0.417 Carnac(20): 0.403 Positive Predictive Value CentroidAlifold(seed): 0.953 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	? ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.616 CentroidAlifold(seed): 0.542 Sensitivity ContextFold: 0.476 CentroidAlifold(seed): 0.299 Positive Predictive Value ContextFold: 0.801 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.586 ProbKnot: 0.553 Sensitivity CentroidAlifold(seed): 0.374 ProbKnot: 0.511 Positive Predictive Value CentroidAlifold(seed): 0.921 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 8.55066880689e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Murlet(20): 0.592 Sensitivity CentroidAlifold(seed): 0.417 Murlet(20): 0.440 Positive Predictive Value CentroidAlifold(seed): 0.953 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 UNAFold: 0.553 Sensitivity CentroidAlifold(seed): 0.377 UNAFold: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.925 UNAFold: 0.624 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 Fold: 0.560 Sensitivity CentroidAlifold(seed): 0.369 Fold: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.922 Fold: 0.627 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.05835476236e-07	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RNAfold: 0.558 Sensitivity CentroidAlifold(seed): 0.377 RNAfold: 0.503 Positive Predictive Value CentroidAlifold(seed): 0.925 RNAfold: 0.623 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 PknotsRG: 0.566 Sensitivity CentroidAlifold(seed): 0.377 PknotsRG: 0.511 Positive Predictive Value CentroidAlifold(seed): 0.925 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 4.48494289621e-08	- Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.659 CentroidAlifold(seed): 0.601 Sensitivity Cylofold: 0.554 CentroidAlifold(seed): 0.369 Positive Predictive Value Cylofold: 0.789 CentroidAlifold(seed): 0.985 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.652 RNAalifold(seed): 0.539 Sensitivity CentroidAlifold(seed): 0.462 RNAalifold(seed): 0.337 Positive Predictive Value CentroidAlifold(seed): 0.921 RNAalifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RNAshapes: 0.534 Sensitivity CentroidAlifold(seed): 0.377 RNAshapes: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.925 RNAshapes: 0.605 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.570 Afold: 0.495 Sensitivity CentroidAlifold(seed): 0.365 Afold: 0.462 Positive Predictive Value CentroidAlifold(seed): 0.893 Afold: 0.535 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 McQFold: 0.526 Sensitivity CentroidAlifold(seed): 0.377 McQFold: 0.463 Positive Predictive Value CentroidAlifold(seed): 0.925 McQFold: 0.603 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.598 Pknots: 0.573 Sensitivity CentroidAlifold(seed): 0.375 Pknots: 0.516 Positive Predictive Value CentroidAlifold(seed): 0.961 Pknots: 0.643 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 2.38297003775e-06	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RNAsubopt: 0.525 Sensitivity CentroidAlifold(seed): 0.377 RNAsubopt: 0.478 Positive Predictive Value CentroidAlifold(seed): 0.925 RNAsubopt: 0.582 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 RSpredict(20): 0.555 Sensitivity CentroidAlifold(seed): 0.417 RSpredict(20): 0.442 Positive Predictive Value CentroidAlifold(seed): 0.953 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-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 Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Vsfold4: 0.490 Sensitivity CentroidAlifold(seed): 0.377 Vsfold4: 0.415 Positive Predictive Value CentroidAlifold(seed): 0.925 Vsfold4: 0.582 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Mastr(20): 0.518 Sensitivity CentroidAlifold(seed): 0.417 Mastr(20): 0.343 Positive Predictive Value CentroidAlifold(seed): 0.953 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.542 RNASLOpt: 0.474 Sensitivity CentroidAlifold(seed): 0.299 RNASLOpt: 0.374 Positive Predictive Value CentroidAlifold(seed): 0.987 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.702 Murlet(seed): 0.474 Sensitivity CentroidAlifold(seed): 0.508 Murlet(seed): 0.270 Positive Predictive Value CentroidAlifold(seed): 0.972 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Vsfold5: 0.459 Sensitivity CentroidAlifold(seed): 0.377 Vsfold5: 0.391 Positive Predictive Value CentroidAlifold(seed): 0.925 Vsfold5: 0.543 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 RNAwolf: 0.414 Sensitivity CentroidAlifold(seed): 0.347 RNAwolf: 0.375 Positive Predictive Value CentroidAlifold(seed): 0.984 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.64481516727e-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: 0.591940867349	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.595 RDfolder: 0.499 Sensitivity CentroidAlifold(seed): 0.369 RDfolder: 0.402 Positive Predictive Value CentroidAlifold(seed): 0.966 RDfolder: 0.631 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.81788725234e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.603 MCFold: 0.442 Sensitivity CentroidAlifold(seed): 0.377 MCFold: 0.466 Positive Predictive Value CentroidAlifold(seed): 0.971 MCFold: 0.427 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RSpredict(seed): 0.194 Sensitivity CentroidAlifold(seed): 0.377 RSpredict(seed): 0.083 Positive Predictive Value CentroidAlifold(seed): 0.925 RSpredict(seed): 0.459 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 PPfold(seed): 0.102 Sensitivity CentroidAlifold(seed): 0.347 PPfold(seed): 0.020 Positive Predictive Value CentroidAlifold(seed): 0.984 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.08932646657e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.673 Carnac(seed): 0.075 Sensitivity CentroidAlifold(seed): 0.468 Carnac(seed): 0.006 Positive Predictive Value CentroidAlifold(seed): 0.971 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	? CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.533 NanoFolder: 0.346 Sensitivity CentroidAlifold(seed): 0.289 NanoFolder: 0.353 Positive Predictive Value CentroidAlifold(seed): 0.986 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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	? CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 Multilign(seed): 0.538 Sensitivity CentroidAlifold(seed): 0.478 Multilign(seed): 0.420 Positive Predictive Value CentroidAlifold(seed): 0.985 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.637 Multilign(20): 0.540 Sensitivity CentroidAlifold(seed): 0.415 Multilign(20): 0.456 Positive Predictive Value CentroidAlifold(seed): 0.982 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidAlifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidAlifold(seed): 0.299 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.637 TurboFold(20): 0.594 Sensitivity CentroidAlifold(seed): 0.415 TurboFold(20): 0.470 Positive Predictive Value CentroidAlifold(seed): 0.982 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidAlifold(seed): 0.613 Sensitivity PETfold_pre2.0(20): 0.497 CentroidAlifold(seed): 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidAlifold(seed): 0.985 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.627 TurboFold(seed): 0.517 Sensitivity CentroidAlifold(seed): 0.403 TurboFold(seed): 0.422 Positive Predictive Value CentroidAlifold(seed): 0.981 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.655 RNASampler(seed): 0.526 Sensitivity CentroidAlifold(seed): 0.449 RNASampler(seed): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.960 RNASampler(seed): 0.715 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.665 CentroidAlifold(seed): 0.637 Sensitivity PPfold(20): 0.519 CentroidAlifold(seed): 0.415 Positive Predictive Value PPfold(20): 0.859 CentroidAlifold(seed): 0.982 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Mastr(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.377 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.925 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08
Contrafold	34 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.650 Contrafold: 0.565 Sensitivity MXScarna(seed): 0.533 Contrafold: 0.509 Positive Predictive Value MXScarna(seed): 0.796 Contrafold: 0.632 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Contrafold: 0.564 Sensitivity CentroidAlifold(20): 0.540 Contrafold: 0.498 Positive Predictive Value CentroidAlifold(20): 0.897 Contrafold: 0.642 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.659 Contrafold: 0.554 Sensitivity RNAalifold(20): 0.510 Contrafold: 0.488 Positive Predictive Value RNAalifold(20): 0.854 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.640 Contrafold: 0.554 Sensitivity RNASampler(20): 0.491 Contrafold: 0.488 Positive Predictive Value RNASampler(20): 0.839 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	52 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.517 Contrafold: 0.516 Sensitivity CentroidFold: 0.434 Contrafold: 0.460 Positive Predictive Value CentroidFold: 0.616 Contrafold: 0.579 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 0.000778510229985	25 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.621 Contrafold: 0.554 Sensitivity MXScarna(20): 0.518 Contrafold: 0.488 Positive Predictive Value MXScarna(20): 0.748 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	33 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Contrafold: 0.562 Sensitivity CentroidAlifold(seed): 0.377 Contrafold: 0.505 Positive Predictive Value CentroidAlifold(seed): 0.925 Contrafold: 0.629 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.526 Sfold: 0.464 Sensitivity Contrafold: 0.462 Sfold: 0.387 Positive Predictive Value Contrafold: 0.599 Sfold: 0.557 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.564 MaxExpect: 0.558 Sensitivity Contrafold: 0.487 MaxExpect: 0.478 Positive Predictive Value Contrafold: 0.654 MaxExpect: 0.651 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 0.000142443097854	- IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.567 Contrafold: 0.543 Sensitivity IPknot: 0.463 Contrafold: 0.459 Positive Predictive Value IPknot: 0.702 Contrafold: 0.649 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	- CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Contrafold: 0.538 Sensitivity CentroidHomfold‑LAST: 0.397 Contrafold: 0.452 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Contrafold: 0.648 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 7.39697035932e-08	= HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.569 Contrafold: 0.568 Sensitivity HotKnots: 0.506 Contrafold: 0.498 Positive Predictive Value HotKnots: 0.644 Contrafold: 0.653 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 0.258868738329	- Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.601 Contrafold: 0.554 Sensitivity Carnac(20): 0.397 Contrafold: 0.488 Positive Predictive Value Carnac(20): 0.914 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	- ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.601 Contrafold: 0.517 Sensitivity ContextFold: 0.483 Contrafold: 0.438 Positive Predictive Value ContextFold: 0.754 Contrafold: 0.618 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.574 ProbKnot: 0.561 Sensitivity Contrafold: 0.510 ProbKnot: 0.514 Positive Predictive Value Contrafold: 0.649 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.592 Contrafold: 0.554 Sensitivity Murlet(20): 0.437 Contrafold: 0.488 Positive Predictive Value Murlet(20): 0.807 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.526 UNAFold: 0.445 Sensitivity Contrafold: 0.462 UNAFold: 0.395 Positive Predictive Value Contrafold: 0.599 UNAFold: 0.502 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.588 Fold: 0.570 Sensitivity Contrafold: 0.523 Fold: 0.509 Positive Predictive Value Contrafold: 0.666 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.526 RNAfold: 0.441 Sensitivity Contrafold: 0.462 RNAfold: 0.395 Positive Predictive Value Contrafold: 0.599 RNAfold: 0.492 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.526 PknotsRG: 0.433 Sensitivity Contrafold: 0.462 PknotsRG: 0.389 Positive Predictive Value Contrafold: 0.599 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.629 Cylofold: 0.607 Sensitivity Contrafold: 0.546 Cylofold: 0.512 Positive Predictive Value Contrafold: 0.730 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 7.39132889808e-08	+ Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.556 RNAalifold(seed): 0.539 Sensitivity Contrafold: 0.497 RNAalifold(seed): 0.336 Positive Predictive Value Contrafold: 0.625 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.568 RNAshapes: 0.539 Sensitivity Contrafold: 0.498 RNAshapes: 0.470 Positive Predictive Value Contrafold: 0.653 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.516 Afold: 0.427 Sensitivity Contrafold: 0.456 Afold: 0.386 Positive Predictive Value Contrafold: 0.585 Afold: 0.474 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.526 McQFold: 0.368 Sensitivity Contrafold: 0.462 McQFold: 0.281 Positive Predictive Value Contrafold: 0.599 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.588 Pknots: 0.547 Sensitivity Contrafold: 0.508 Pknots: 0.489 Positive Predictive Value Contrafold: 0.687 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.568 RNAsubopt: 0.531 Sensitivity Contrafold: 0.498 RNAsubopt: 0.473 Positive Predictive Value Contrafold: 0.653 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.569 RSpredict(20): 0.559 Sensitivity Contrafold: 0.503 RSpredict(20): 0.446 Positive Predictive Value Contrafold: 0.647 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 3.54044765699e-05	+ 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: 2.7402423548e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.568 Vsfold4: 0.478 Sensitivity Contrafold: 0.498 Vsfold4: 0.399 Positive Predictive Value Contrafold: 0.653 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.554 Mastr(20): 0.523 Sensitivity Contrafold: 0.488 Mastr(20): 0.348 Positive Predictive Value Contrafold: 0.634 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.517 RNASLOpt: 0.443 Sensitivity Contrafold: 0.438 RNASLOpt: 0.365 Positive Predictive Value Contrafold: 0.618 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.52090997893e-09	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.599 Murlet(seed): 0.475 Sensitivity Contrafold: 0.516 Murlet(seed): 0.270 Positive Predictive Value Contrafold: 0.700 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.568 Vsfold5: 0.426 Sensitivity Contrafold: 0.498 Vsfold5: 0.359 Positive Predictive Value Contrafold: 0.653 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.543 RNAwolf: 0.399 Sensitivity Contrafold: 0.459 RNAwolf: 0.368 Positive Predictive Value Contrafold: 0.649 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.10198558684e-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: 0.443 Sensitivity Contrafold: 0.507 RDfolder: 0.342 Positive Predictive Value Contrafold: 0.725 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.582 MCFold: 0.419 Sensitivity Contrafold: 0.506 MCFold: 0.437 Positive Predictive Value Contrafold: 0.677 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.565 RSpredict(seed): 0.204 Sensitivity Contrafold: 0.509 RSpredict(seed): 0.088 Positive Predictive Value Contrafold: 0.632 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.559 PPfold(seed): 0.102 Sensitivity Contrafold: 0.471 PPfold(seed): 0.020 Positive Predictive Value Contrafold: 0.672 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.3551590886e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.606 Carnac(seed): 0.139 Sensitivity Contrafold: 0.533 Carnac(seed): 0.019 Positive Predictive Value Contrafold: 0.694 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.564 NanoFolder: 0.366 Sensitivity Contrafold: 0.479 NanoFolder: 0.376 Positive Predictive Value Contrafold: 0.671 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.552 Multilign(seed): 0.538 Sensitivity Contrafold: 0.449 Multilign(seed): 0.420 Positive Predictive Value Contrafold: 0.689 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.561 Multilign(20): 0.540 Sensitivity Contrafold: 0.478 Multilign(20): 0.456 Positive Predictive Value Contrafold: 0.665 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Contrafold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.551 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Contrafold: 0.633 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.594 Contrafold: 0.561 Sensitivity TurboFold(20): 0.470 Contrafold: 0.478 Positive Predictive Value TurboFold(20): 0.756 Contrafold: 0.665 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: N/A CMfinder(20): N/A Sensitivity Contrafold: N/A CMfinder(20): N/A Positive Predictive Value Contrafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Contrafold: 0.511 Sensitivity PETfold_pre2.0(20): 0.497 Contrafold: 0.437 Positive Predictive Value PETfold_pre2.0(20): 0.790 Contrafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.543 TurboFold(seed): 0.517 Sensitivity Contrafold: 0.456 TurboFold(seed): 0.422 Positive Predictive Value Contrafold: 0.652 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.546 Contrafold: 0.512 Sensitivity RNASampler(seed): 0.409 Contrafold: 0.453 Positive Predictive Value RNASampler(seed): 0.734 Contrafold: 0.584 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.665 Contrafold: 0.561 Sensitivity PPfold(20): 0.519 Contrafold: 0.478 Positive Predictive Value PPfold(20): 0.859 Contrafold: 0.665 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.555 Mastr(seed): 0.000 Sensitivity Contrafold: 0.497 Mastr(seed): 0.000 Positive Predictive Value Contrafold: 0.623 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
Sfold	34 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.650 Sfold: 0.570 Sensitivity MXScarna(seed): 0.533 Sfold: 0.484 Positive Predictive Value MXScarna(seed): 0.796 Sfold: 0.675 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Sfold: 0.592 Sensitivity CentroidAlifold(20): 0.540 Sfold: 0.493 Positive Predictive Value CentroidAlifold(20): 0.897 Sfold: 0.715 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.659 Sfold: 0.593 Sensitivity RNAalifold(20): 0.510 Sfold: 0.492 Positive Predictive Value RNAalifold(20): 0.854 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.640 Sfold: 0.593 Sensitivity RNASampler(20): 0.491 Sfold: 0.492 Positive Predictive Value RNASampler(20): 0.839 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	52 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.517 Sfold: 0.479 Sensitivity CentroidFold: 0.434 Sfold: 0.403 Positive Predictive Value CentroidFold: 0.616 Sfold: 0.570 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.621 Sfold: 0.593 Sensitivity MXScarna(20): 0.518 Sfold: 0.492 Positive Predictive Value MXScarna(20): 0.748 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	33 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Sfold: 0.566 Sensitivity CentroidAlifold(seed): 0.377 Sfold: 0.480 Positive Predictive Value CentroidAlifold(seed): 0.925 Sfold: 0.672 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 7.5939721025e-08	58 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.526 Sfold: 0.464 Sensitivity Contrafold: 0.462 Sfold: 0.387 Positive Predictive Value Contrafold: 0.599 Sfold: 0.557 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08		- MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.558 Sfold: 0.518 Sensitivity MaxExpect: 0.478 Sfold: 0.424 Positive Predictive Value MaxExpect: 0.651 Sfold: 0.634 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.85233844192e-08	- IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.567 Sfold: 0.524 Sensitivity IPknot: 0.463 Sfold: 0.425 Positive Predictive Value IPknot: 0.702 Sfold: 0.652 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-08	- CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Sfold: 0.520 Sensitivity CentroidHomfold‑LAST: 0.397 Sfold: 0.420 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Sfold: 0.652 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.574 HotKnots: 0.569 Sensitivity Sfold: 0.480 HotKnots: 0.506 Positive Predictive Value Sfold: 0.691 HotKnots: 0.644 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 6.06606238843e-08	- Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.601 Sfold: 0.593 Sensitivity Carnac(20): 0.397 Sfold: 0.492 Positive Predictive Value Carnac(20): 0.914 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.33078868561e-05	- ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.601 Sfold: 0.480 Sensitivity ContextFold: 0.483 Sfold: 0.393 Positive Predictive Value ContextFold: 0.754 Sfold: 0.595 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.574 ProbKnot: 0.561 Sensitivity Sfold: 0.486 ProbKnot: 0.514 Positive Predictive Value Sfold: 0.682 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.593 Murlet(20): 0.592 Sensitivity Sfold: 0.492 Murlet(20): 0.437 Positive Predictive Value Sfold: 0.718 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.105836163587	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.464 UNAFold: 0.445 Sensitivity Sfold: 0.387 UNAFold: 0.395 Positive Predictive Value Sfold: 0.557 UNAFold: 0.502 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.581 Fold: 0.570 Sensitivity Sfold: 0.492 Fold: 0.509 Positive Predictive Value Sfold: 0.689 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.464 RNAfold: 0.441 Sensitivity Sfold: 0.387 RNAfold: 0.395 Positive Predictive Value Sfold: 0.557 RNAfold: 0.492 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.464 PknotsRG: 0.433 Sensitivity Sfold: 0.387 PknotsRG: 0.389 Positive Predictive Value Sfold: 0.557 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.616 Cylofold: 0.607 Sensitivity Sfold: 0.512 Cylofold: 0.512 Positive Predictive Value Sfold: 0.748 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000380952570321	+ Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.573 RNAalifold(seed): 0.539 Sensitivity Sfold: 0.482 RNAalifold(seed): 0.336 Positive Predictive Value Sfold: 0.685 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.574 RNAshapes: 0.539 Sensitivity Sfold: 0.480 RNAshapes: 0.470 Positive Predictive Value Sfold: 0.691 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.449 Afold: 0.427 Sensitivity Sfold: 0.377 Afold: 0.386 Positive Predictive Value Sfold: 0.536 Afold: 0.474 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.464 McQFold: 0.368 Sensitivity Sfold: 0.387 McQFold: 0.281 Positive Predictive Value Sfold: 0.557 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.596 Pknots: 0.547 Sensitivity Sfold: 0.492 Pknots: 0.489 Positive Predictive Value Sfold: 0.727 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.574 RNAsubopt: 0.531 Sensitivity Sfold: 0.480 RNAsubopt: 0.473 Positive Predictive Value Sfold: 0.691 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.597 RSpredict(20): 0.559 Sensitivity Sfold: 0.498 RSpredict(20): 0.446 Positive Predictive Value Sfold: 0.720 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.36778461742e-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: 1.95070920198e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.574 Vsfold4: 0.478 Sensitivity Sfold: 0.480 Vsfold4: 0.399 Positive Predictive Value Sfold: 0.691 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.593 Mastr(20): 0.523 Sensitivity Sfold: 0.492 Mastr(20): 0.348 Positive Predictive Value Sfold: 0.718 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.480 RNASLOpt: 0.443 Sensitivity Sfold: 0.393 RNASLOpt: 0.365 Positive Predictive Value Sfold: 0.595 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.627 Murlet(seed): 0.475 Sensitivity Sfold: 0.507 Murlet(seed): 0.270 Positive Predictive Value Sfold: 0.779 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.574 Vsfold5: 0.426 Sensitivity Sfold: 0.480 Vsfold5: 0.359 Positive Predictive Value Sfold: 0.691 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.524 RNAwolf: 0.399 Sensitivity Sfold: 0.425 RNAwolf: 0.368 Positive Predictive Value Sfold: 0.652 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-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: 0.586 RDfolder: 0.443 Sensitivity Sfold: 0.474 RDfolder: 0.342 Positive Predictive Value Sfold: 0.733 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.603 MCFold: 0.419 Sensitivity Sfold: 0.503 MCFold: 0.437 Positive Predictive Value Sfold: 0.729 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.570 RSpredict(seed): 0.204 Sensitivity Sfold: 0.484 RSpredict(seed): 0.088 Positive Predictive Value Sfold: 0.675 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.539 PPfold(seed): 0.102 Sensitivity Sfold: 0.426 PPfold(seed): 0.020 Positive Predictive Value Sfold: 0.691 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.61680779366e-09	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.643 Carnac(seed): 0.139 Sensitivity Sfold: 0.537 Carnac(seed): 0.019 Positive Predictive Value Sfold: 0.774 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.504 NanoFolder: 0.366 Sensitivity Sfold: 0.408 NanoFolder: 0.376 Positive Predictive Value Sfold: 0.629 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.600 Multilign(seed): 0.538 Sensitivity Sfold: 0.471 Multilign(seed): 0.420 Positive Predictive Value Sfold: 0.774 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.579 Multilign(20): 0.540 Sensitivity Sfold: 0.467 Multilign(20): 0.456 Positive Predictive Value Sfold: 0.724 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Sfold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 Sfold: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Sfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.594 Sfold: 0.579 Sensitivity TurboFold(20): 0.470 Sfold: 0.467 Positive Predictive Value TurboFold(20): 0.756 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: N/A CMfinder(20): N/A Sensitivity Sfold: N/A CMfinder(20): N/A Positive Predictive Value Sfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Sfold: 0.507 Sensitivity PETfold_pre2.0(20): 0.497 Sfold: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 Sfold: 0.627 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.556 TurboFold(seed): 0.517 Sensitivity Sfold: 0.445 TurboFold(seed): 0.422 Positive Predictive Value Sfold: 0.701 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.575 RNASampler(seed): 0.546 Sensitivity Sfold: 0.478 RNASampler(seed): 0.409 Positive Predictive Value Sfold: 0.695 RNASampler(seed): 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.665 Sfold: 0.579 Sensitivity PPfold(20): 0.519 Sfold: 0.467 Positive Predictive Value PPfold(20): 0.859 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.568 Mastr(seed): 0.000 Sensitivity Sfold: 0.479 Mastr(seed): 0.000 Positive Predictive Value Sfold: 0.676 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
MaxExpect	30 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.640 MaxExpect: 0.569 Sensitivity MXScarna(seed): 0.523 MaxExpect: 0.504 Positive Predictive Value MXScarna(seed): 0.785 MaxExpect: 0.646 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.695 MaxExpect: 0.598 Sensitivity CentroidAlifold(20): 0.540 MaxExpect: 0.520 Positive Predictive Value CentroidAlifold(20): 0.897 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.658 MaxExpect: 0.598 Sensitivity RNAalifold(20): 0.513 MaxExpect: 0.520 Positive Predictive Value RNAalifold(20): 0.847 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	23 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.644 MaxExpect: 0.598 Sensitivity RNASampler(20): 0.499 MaxExpect: 0.520 Positive Predictive Value RNASampler(20): 0.834 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	48 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.568 MaxExpect: 0.558 Sensitivity CentroidFold: 0.463 MaxExpect: 0.478 Positive Predictive Value CentroidFold: 0.697 MaxExpect: 0.651 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.623 MaxExpect: 0.598 Sensitivity MXScarna(20): 0.521 MaxExpect: 0.520 Positive Predictive Value MXScarna(20): 0.748 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.591 MaxExpect: 0.569 Sensitivity CentroidAlifold(seed): 0.378 MaxExpect: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.927 MaxExpect: 0.646 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.22032703654e-06	48 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.564 MaxExpect: 0.558 Sensitivity Contrafold: 0.487 MaxExpect: 0.478 Positive Predictive Value Contrafold: 0.654 MaxExpect: 0.651 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 0.000142443097854	48 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.558 Sfold: 0.518 Sensitivity MaxExpect: 0.478 Sfold: 0.424 Positive Predictive Value MaxExpect: 0.651 Sfold: 0.634 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.85233844192e-08		- IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.567 MaxExpect: 0.487 Sensitivity IPknot: 0.463 MaxExpect: 0.417 Positive Predictive Value IPknot: 0.702 MaxExpect: 0.577 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	- CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 MaxExpect: 0.484 Sensitivity CentroidHomfold‑LAST: 0.397 MaxExpect: 0.412 Positive Predictive Value CentroidHomfold‑LAST: 0.784 MaxExpect: 0.578 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.571 HotKnots: 0.570 Sensitivity MaxExpect: 0.502 HotKnots: 0.513 Positive Predictive Value MaxExpect: 0.654 HotKnots: 0.637 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 0.00049899371755	- Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.605 MaxExpect: 0.598 Sensitivity Carnac(20): 0.403 MaxExpect: 0.520 Positive Predictive Value Carnac(20): 0.913 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 1.15003019969e-05	- ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.601 MaxExpect: 0.446 Sensitivity ContextFold: 0.483 MaxExpect: 0.385 Positive Predictive Value ContextFold: 0.754 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.567 ProbKnot: 0.561 Sensitivity MaxExpect: 0.501 ProbKnot: 0.514 Positive Predictive Value MaxExpect: 0.646 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.598 Murlet(20): 0.592 Sensitivity MaxExpect: 0.520 Murlet(20): 0.440 Positive Predictive Value MaxExpect: 0.692 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.000361978838932	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.558 UNAFold: 0.504 Sensitivity MaxExpect: 0.478 UNAFold: 0.437 Positive Predictive Value MaxExpect: 0.651 UNAFold: 0.582 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 1.10039559051e-07	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.578 Fold: 0.570 Sensitivity MaxExpect: 0.511 Fold: 0.509 Positive Predictive Value MaxExpect: 0.658 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.558 RNAfold: 0.491 Sensitivity MaxExpect: 0.478 RNAfold: 0.430 Positive Predictive Value MaxExpect: 0.651 RNAfold: 0.561 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.558 PknotsRG: 0.481 Sensitivity MaxExpect: 0.478 PknotsRG: 0.423 Positive Predictive Value MaxExpect: 0.651 PknotsRG: 0.547 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.623 Cylofold: 0.607 Sensitivity MaxExpect: 0.539 Cylofold: 0.512 Positive Predictive Value MaxExpect: 0.726 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.74095189891e-07	- RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.529 MaxExpect: 0.521 Sensitivity RNAalifold(seed): 0.328 MaxExpect: 0.462 Positive Predictive Value RNAalifold(seed): 0.856 MaxExpect: 0.590 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00023129009914	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.571 RNAshapes: 0.546 Sensitivity MaxExpect: 0.502 RNAshapes: 0.481 Positive Predictive Value MaxExpect: 0.654 RNAshapes: 0.625 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.545 Afold: 0.479 Sensitivity MaxExpect: 0.471 Afold: 0.424 Positive Predictive Value MaxExpect: 0.632 Afold: 0.543 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.558 McQFold: 0.434 Sensitivity MaxExpect: 0.478 McQFold: 0.368 Positive Predictive Value MaxExpect: 0.651 McQFold: 0.514 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.598 Pknots: 0.555 Sensitivity MaxExpect: 0.519 Pknots: 0.499 Positive Predictive Value MaxExpect: 0.695 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.571 RNAsubopt: 0.540 Sensitivity MaxExpect: 0.502 RNAsubopt: 0.486 Positive Predictive Value MaxExpect: 0.654 RNAsubopt: 0.605 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.598 RSpredict(20): 0.555 Sensitivity MaxExpect: 0.520 RSpredict(20): 0.442 Positive Predictive Value MaxExpect: 0.692 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-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: 5.72327175742e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.571 Vsfold4: 0.470 Sensitivity MaxExpect: 0.502 Vsfold4: 0.395 Positive Predictive Value MaxExpect: 0.654 Vsfold4: 0.566 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.598 Mastr(20): 0.518 Sensitivity MaxExpect: 0.520 Mastr(20): 0.343 Positive Predictive Value MaxExpect: 0.692 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	= MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.446 RNASLOpt: 0.443 Sensitivity MaxExpect: 0.385 RNASLOpt: 0.365 Positive Predictive Value MaxExpect: 0.526 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.150312415084	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.556 Murlet(seed): 0.467 Sensitivity MaxExpect: 0.476 Murlet(seed): 0.266 Positive Predictive Value MaxExpect: 0.656 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.44715536483e-09	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.571 Vsfold5: 0.420 Sensitivity MaxExpect: 0.502 Vsfold5: 0.355 Positive Predictive Value MaxExpect: 0.654 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.487 RNAwolf: 0.399 Sensitivity MaxExpect: 0.417 RNAwolf: 0.368 Positive Predictive Value MaxExpect: 0.577 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-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: 5.19332990918e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.586 RDfolder: 0.426 Sensitivity MaxExpect: 0.497 RDfolder: 0.329 Positive Predictive Value MaxExpect: 0.701 RDfolder: 0.565 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.581 MCFold: 0.403 Sensitivity MaxExpect: 0.507 MCFold: 0.424 Positive Predictive Value MaxExpect: 0.672 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.569 RSpredict(seed): 0.180 Sensitivity MaxExpect: 0.504 RSpredict(seed): 0.076 Positive Predictive Value MaxExpect: 0.646 RSpredict(seed): 0.432 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.513 PPfold(seed): 0.102 Sensitivity MaxExpect: 0.434 PPfold(seed): 0.020 Positive Predictive Value MaxExpect: 0.615 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.595 Carnac(seed): 0.077 Sensitivity MaxExpect: 0.517 Carnac(seed): 0.006 Positive Predictive Value MaxExpect: 0.689 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.36130997681e-08	? MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.488 NanoFolder: 0.366 Sensitivity MaxExpect: 0.418 NanoFolder: 0.376 Positive Predictive Value MaxExpect: 0.578 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.538 MaxExpect: 0.507 Sensitivity Multilign(seed): 0.420 MaxExpect: 0.413 Positive Predictive Value Multilign(seed): 0.699 MaxExpect: 0.633 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs Multilign(20) Matthews Correlation Coefficient MaxExpect: 0.543 Multilign(20): 0.540 Sensitivity MaxExpect: 0.463 Multilign(20): 0.456 Positive Predictive Value MaxExpect: 0.644 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MaxExpect: 0.458 Sensitivity PETfold_pre2.0(seed): 0.551 MaxExpect: 0.390 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.594 MaxExpect: 0.543 Sensitivity TurboFold(20): 0.470 MaxExpect: 0.463 Positive Predictive Value TurboFold(20): 0.756 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(20): N/A Sensitivity MaxExpect: N/A CMfinder(20): N/A Positive Predictive Value MaxExpect: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MaxExpect: 0.479 Sensitivity PETfold_pre2.0(20): 0.497 MaxExpect: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 MaxExpect: 0.561 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.517 MaxExpect: 0.490 Sensitivity TurboFold(seed): 0.422 MaxExpect: 0.414 Positive Predictive Value TurboFold(seed): 0.642 MaxExpect: 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.500 MaxExpect: 0.418 Sensitivity RNASampler(seed): 0.373 MaxExpect: 0.377 Positive Predictive Value RNASampler(seed): 0.675 MaxExpect: 0.470 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.665 MaxExpect: 0.543 Sensitivity PPfold(20): 0.519 MaxExpect: 0.463 Positive Predictive Value PPfold(20): 0.859 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.569 Mastr(seed): 0.000 Sensitivity MaxExpect: 0.504 Mastr(seed): 0.000 Positive Predictive Value MaxExpect: 0.646 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
IPknot	11 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.624 IPknot: 0.590 Sensitivity MXScarna(seed): 0.493 IPknot: 0.471 Positive Predictive Value MXScarna(seed): 0.796 IPknot: 0.747 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.97952969696e-09	8 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.691 IPknot: 0.571 Sensitivity CentroidAlifold(20): 0.515 IPknot: 0.463 Positive Predictive Value CentroidAlifold(20): 0.933 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.627 IPknot: 0.571 Sensitivity RNAalifold(20): 0.481 IPknot: 0.463 Positive Predictive Value RNAalifold(20): 0.823 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.637 IPknot: 0.571 Sensitivity RNASampler(20): 0.478 IPknot: 0.463 Positive Predictive Value RNASampler(20): 0.854 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.567 CentroidFold: 0.551 Sensitivity IPknot: 0.463 CentroidFold: 0.447 Positive Predictive Value IPknot: 0.702 CentroidFold: 0.686 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	8 MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.586 IPknot: 0.571 Sensitivity MXScarna(20): 0.474 IPknot: 0.463 Positive Predictive Value MXScarna(20): 0.731 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 IPknot vs CentroidAlifold(seed) Matthews Correlation Coefficient IPknot: 0.590 CentroidAlifold(seed): 0.583 Sensitivity IPknot: 0.471 CentroidAlifold(seed): 0.347 Positive Predictive Value IPknot: 0.747 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.017418519964	17 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.567 Contrafold: 0.543 Sensitivity IPknot: 0.463 Contrafold: 0.459 Positive Predictive Value IPknot: 0.702 Contrafold: 0.649 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	17 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.567 Sfold: 0.524 Sensitivity IPknot: 0.463 Sfold: 0.425 Positive Predictive Value IPknot: 0.702 Sfold: 0.652 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-08	17 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.567 MaxExpect: 0.487 Sensitivity IPknot: 0.463 MaxExpect: 0.417 Positive Predictive Value IPknot: 0.702 MaxExpect: 0.577 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08		+ IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.567 CentroidHomfold‑LAST: 0.558 Sensitivity IPknot: 0.463 CentroidHomfold‑LAST: 0.402 Positive Predictive Value IPknot: 0.702 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000619290629009	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.567 HotKnots: 0.543 Sensitivity IPknot: 0.463 HotKnots: 0.481 Positive Predictive Value IPknot: 0.702 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	? IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.571 Carnac(20): 0.560 Sensitivity IPknot: 0.463 Carnac(20): 0.367 Positive Predictive Value IPknot: 0.710 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.601 IPknot: 0.538 Sensitivity ContextFold: 0.483 IPknot: 0.443 Positive Predictive Value ContextFold: 0.754 IPknot: 0.660 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.567 ProbKnot: 0.495 Sensitivity IPknot: 0.463 ProbKnot: 0.443 Positive Predictive Value IPknot: 0.702 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	? Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.581 IPknot: 0.571 Sensitivity Murlet(20): 0.433 IPknot: 0.463 Positive Predictive Value Murlet(20): 0.785 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.567 UNAFold: 0.497 Sensitivity IPknot: 0.463 UNAFold: 0.433 Positive Predictive Value IPknot: 0.702 UNAFold: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.567 Fold: 0.487 Sensitivity IPknot: 0.463 Fold: 0.423 Positive Predictive Value IPknot: 0.702 Fold: 0.568 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.567 RNAfold: 0.524 Sensitivity IPknot: 0.463 RNAfold: 0.451 Positive Predictive Value IPknot: 0.702 RNAfold: 0.615 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.567 PknotsRG: 0.539 Sensitivity IPknot: 0.463 PknotsRG: 0.473 Positive Predictive Value IPknot: 0.702 PknotsRG: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.586 Cylofold: 0.537 Sensitivity IPknot: 0.474 Cylofold: 0.454 Positive Predictive Value IPknot: 0.732 Cylofold: 0.643 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	? RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.523 IPknot: 0.505 Sensitivity RNAalifold(seed): 0.344 IPknot: 0.402 Positive Predictive Value RNAalifold(seed): 0.800 IPknot: 0.641 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.567 RNAshapes: 0.515 Sensitivity IPknot: 0.463 RNAshapes: 0.443 Positive Predictive Value IPknot: 0.702 RNAshapes: 0.606 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	? IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.567 Afold: 0.516 Sensitivity IPknot: 0.462 Afold: 0.467 Positive Predictive Value IPknot: 0.702 Afold: 0.578 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.567 McQFold: 0.501 Sensitivity IPknot: 0.463 McQFold: 0.427 Positive Predictive Value IPknot: 0.702 McQFold: 0.596 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.567 Pknots: 0.471 Sensitivity IPknot: 0.463 Pknots: 0.421 Positive Predictive Value IPknot: 0.702 Pknots: 0.535 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.567 RNAsubopt: 0.473 Sensitivity IPknot: 0.463 RNAsubopt: 0.414 Positive Predictive Value IPknot: 0.702 RNAsubopt: 0.550 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	? IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.571 RSpredict(20): 0.489 Sensitivity IPknot: 0.463 RSpredict(20): 0.367 Positive Predictive Value IPknot: 0.710 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 2.89169006118e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.567 Vsfold4: 0.425 Sensitivity IPknot: 0.463 Vsfold4: 0.354 Positive Predictive Value IPknot: 0.702 Vsfold4: 0.520 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	? IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.571 Mastr(20): 0.567 Sensitivity IPknot: 0.463 Mastr(20): 0.389 Positive Predictive Value IPknot: 0.710 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.538 RNASLOpt: 0.443 Sensitivity IPknot: 0.443 RNASLOpt: 0.365 Positive Predictive Value IPknot: 0.660 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	? IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.505 Murlet(seed): 0.451 Sensitivity IPknot: 0.402 Murlet(seed): 0.268 Positive Predictive Value IPknot: 0.641 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.567 Vsfold5: 0.369 Sensitivity IPknot: 0.463 Vsfold5: 0.318 Positive Predictive Value IPknot: 0.702 Vsfold5: 0.437 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.567 RNAwolf: 0.399 Sensitivity IPknot: 0.463 RNAwolf: 0.368 Positive Predictive Value IPknot: 0.702 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-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: 0.543 RDfolder: 0.302 Sensitivity IPknot: 0.426 RDfolder: 0.219 Positive Predictive Value IPknot: 0.701 RDfolder: 0.434 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.570 MCFold: 0.449 Sensitivity IPknot: 0.469 MCFold: 0.474 Positive Predictive Value IPknot: 0.698 MCFold: 0.434 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.02533530638e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.590 RSpredict(seed): 0.193 Sensitivity IPknot: 0.471 RSpredict(seed): 0.084 Positive Predictive Value IPknot: 0.747 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.74569091494e-09	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.590 PPfold(seed): 0.102 Sensitivity IPknot: 0.471 PPfold(seed): 0.020 Positive Predictive Value IPknot: 0.747 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-08	? IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.544 Carnac(seed): 0.123 Sensitivity IPknot: 0.437 Carnac(seed): 0.015 Positive Predictive Value IPknot: 0.685 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.594 NanoFolder: 0.366 Sensitivity IPknot: 0.486 NanoFolder: 0.376 Positive Predictive Value IPknot: 0.733 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.560 Multilign(seed): 0.538 Sensitivity IPknot: 0.435 Multilign(seed): 0.420 Positive Predictive Value IPknot: 0.732 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.571 Multilign(20): 0.540 Sensitivity IPknot: 0.463 Multilign(20): 0.456 Positive Predictive Value IPknot: 0.710 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 IPknot: 0.551 Sensitivity PETfold_pre2.0(seed): 0.551 IPknot: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.594 IPknot: 0.571 Sensitivity TurboFold(20): 0.470 IPknot: 0.463 Positive Predictive Value TurboFold(20): 0.756 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: N/A CMfinder(20): N/A Sensitivity IPknot: N/A CMfinder(20): N/A Positive Predictive Value IPknot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 IPknot: 0.502 Sensitivity PETfold_pre2.0(20): 0.497 IPknot: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 IPknot: 0.616 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.544 TurboFold(seed): 0.517 Sensitivity IPknot: 0.437 TurboFold(seed): 0.422 Positive Predictive Value IPknot: 0.685 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.493 RNASampler(seed): 0.471 Sensitivity IPknot: 0.395 RNASampler(seed): 0.341 Positive Predictive Value IPknot: 0.622 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.665 IPknot: 0.571 Sensitivity PPfold(20): 0.519 IPknot: 0.463 Positive Predictive Value PPfold(20): 0.859 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.590 Mastr(seed): 0.000 Sensitivity IPknot: 0.471 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.747 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08
CentroidHomfold‑LAST	11 MXScarna(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient MXScarna(seed): 0.624 CentroidHomfold‑LAST: 0.615 Sensitivity MXScarna(seed): 0.493 CentroidHomfold‑LAST: 0.479 Positive Predictive Value MXScarna(seed): 0.796 CentroidHomfold‑LAST: 0.795 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00145582378587	8 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.691 CentroidHomfold‑LAST: 0.631 Sensitivity CentroidAlifold(20): 0.515 CentroidHomfold‑LAST: 0.496 Positive Predictive Value CentroidAlifold(20): 0.933 CentroidHomfold‑LAST: 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 RNAalifold(20): 0.627 Sensitivity CentroidHomfold‑LAST: 0.496 RNAalifold(20): 0.481 Positive Predictive Value CentroidHomfold‑LAST: 0.807 RNAalifold(20): 0.823 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(20): 0.637 CentroidHomfold‑LAST: 0.631 Sensitivity RNASampler(20): 0.478 CentroidHomfold‑LAST: 0.496 Positive Predictive Value RNASampler(20): 0.854 CentroidHomfold‑LAST: 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	18 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 CentroidFold: 0.547 Sensitivity CentroidHomfold‑LAST: 0.397 CentroidFold: 0.441 Positive Predictive Value CentroidHomfold‑LAST: 0.784 CentroidFold: 0.687 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.00194269211386	8 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 MXScarna(20): 0.586 Sensitivity CentroidHomfold‑LAST: 0.496 MXScarna(20): 0.474 Positive Predictive Value CentroidHomfold‑LAST: 0.807 MXScarna(20): 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 CentroidAlifold(seed): 0.583 Sensitivity CentroidHomfold‑LAST: 0.479 CentroidAlifold(seed): 0.347 Positive Predictive Value CentroidHomfold‑LAST: 0.795 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	18 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Contrafold: 0.538 Sensitivity CentroidHomfold‑LAST: 0.397 Contrafold: 0.452 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Contrafold: 0.648 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 7.39697035932e-08	18 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Sfold: 0.520 Sensitivity CentroidHomfold‑LAST: 0.397 Sfold: 0.420 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Sfold: 0.652 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.96907987703e-08	18 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 MaxExpect: 0.484 Sensitivity CentroidHomfold‑LAST: 0.397 MaxExpect: 0.412 Positive Predictive Value CentroidHomfold‑LAST: 0.784 MaxExpect: 0.578 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	17 IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.567 CentroidHomfold‑LAST: 0.558 Sensitivity IPknot: 0.463 CentroidHomfold‑LAST: 0.402 Positive Predictive Value IPknot: 0.702 CentroidHomfold‑LAST: 0.783 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000619290629009		+ CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 HotKnots: 0.539 Sensitivity CentroidHomfold‑LAST: 0.397 HotKnots: 0.473 Positive Predictive Value CentroidHomfold‑LAST: 0.784 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64536816295e-07	? CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Carnac(20): 0.560 Sensitivity CentroidHomfold‑LAST: 0.496 Carnac(20): 0.367 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.601 CentroidHomfold‑LAST: 0.515 Sensitivity ContextFold: 0.483 CentroidHomfold‑LAST: 0.365 Positive Predictive Value ContextFold: 0.754 CentroidHomfold‑LAST: 0.734 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 ProbKnot: 0.493 Sensitivity CentroidHomfold‑LAST: 0.397 ProbKnot: 0.439 Positive Predictive Value CentroidHomfold‑LAST: 0.784 ProbKnot: 0.563 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	? CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Murlet(20): 0.581 Sensitivity CentroidHomfold‑LAST: 0.496 Murlet(20): 0.433 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Murlet(20): 0.785 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 UNAFold: 0.494 Sensitivity CentroidHomfold‑LAST: 0.397 UNAFold: 0.427 Positive Predictive Value CentroidHomfold‑LAST: 0.784 UNAFold: 0.579 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Fold: 0.484 Sensitivity CentroidHomfold‑LAST: 0.397 Fold: 0.418 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Fold: 0.569 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 RNAfold: 0.520 Sensitivity CentroidHomfold‑LAST: 0.397 RNAfold: 0.444 Positive Predictive Value CentroidHomfold‑LAST: 0.784 RNAfold: 0.615 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 PknotsRG: 0.535 Sensitivity CentroidHomfold‑LAST: 0.397 PknotsRG: 0.466 Positive Predictive Value CentroidHomfold‑LAST: 0.784 PknotsRG: 0.621 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.581 Cylofold: 0.533 Sensitivity CentroidHomfold‑LAST: 0.395 Cylofold: 0.446 Positive Predictive Value CentroidHomfold‑LAST: 0.860 Cylofold: 0.647 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.55268413083e-08	? CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.532 RNAalifold(seed): 0.523 Sensitivity CentroidHomfold‑LAST: 0.407 RNAalifold(seed): 0.344 Positive Predictive Value CentroidHomfold‑LAST: 0.702 RNAalifold(seed): 0.800 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 RNAshapes: 0.511 Sensitivity CentroidHomfold‑LAST: 0.397 RNAshapes: 0.437 Positive Predictive Value CentroidHomfold‑LAST: 0.784 RNAshapes: 0.606 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.52609899389e-08	? Afold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Afold: 0.516 CentroidHomfold‑LAST: 0.401 Sensitivity Afold: 0.467 CentroidHomfold‑LAST: 0.286 Positive Predictive Value Afold: 0.578 CentroidHomfold‑LAST: 0.570 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 McQFold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.397 McQFold: 0.421 Positive Predictive Value CentroidHomfold‑LAST: 0.784 McQFold: 0.599 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Pknots: 0.470 Sensitivity CentroidHomfold‑LAST: 0.397 Pknots: 0.416 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Pknots: 0.540 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 RNAsubopt: 0.471 Sensitivity CentroidHomfold‑LAST: 0.397 RNAsubopt: 0.408 Positive Predictive Value CentroidHomfold‑LAST: 0.784 RNAsubopt: 0.552 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.69956606048e-08	? CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 RSpredict(20): 0.489 Sensitivity CentroidHomfold‑LAST: 0.496 RSpredict(20): 0.367 Positive Predictive Value CentroidHomfold‑LAST: 0.807 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 2.69132796717e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Vsfold4: 0.425 Sensitivity CentroidHomfold‑LAST: 0.397 Vsfold4: 0.351 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Vsfold4: 0.526 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	? CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Mastr(20): 0.567 Sensitivity CentroidHomfold‑LAST: 0.496 Mastr(20): 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.515 RNASLOpt: 0.443 Sensitivity CentroidHomfold‑LAST: 0.365 RNASLOpt: 0.365 Positive Predictive Value CentroidHomfold‑LAST: 0.734 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	? CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.532 Murlet(seed): 0.451 Sensitivity CentroidHomfold‑LAST: 0.407 Murlet(seed): 0.268 Positive Predictive Value CentroidHomfold‑LAST: 0.702 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Vsfold5: 0.358 Sensitivity CentroidHomfold‑LAST: 0.397 Vsfold5: 0.307 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Vsfold5: 0.429 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.558 RNAwolf: 0.399 Sensitivity CentroidHomfold‑LAST: 0.402 RNAwolf: 0.368 Positive Predictive Value CentroidHomfold‑LAST: 0.783 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.87872347734e-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: 7.68522644707e-09	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.618 RDfolder: 0.310 Sensitivity CentroidHomfold‑LAST: 0.443 RDfolder: 0.221 Positive Predictive Value CentroidHomfold‑LAST: 0.871 RDfolder: 0.451 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 8.61680779366e-09	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.527 MCFold: 0.432 Sensitivity CentroidHomfold‑LAST: 0.375 MCFold: 0.454 Positive Predictive Value CentroidHomfold‑LAST: 0.748 MCFold: 0.421 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 RSpredict(seed): 0.193 Sensitivity CentroidHomfold‑LAST: 0.479 RSpredict(seed): 0.084 Positive Predictive Value CentroidHomfold‑LAST: 0.795 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.26497248087e-08	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 PPfold(seed): 0.102 Sensitivity CentroidHomfold‑LAST: 0.479 PPfold(seed): 0.020 Positive Predictive Value CentroidHomfold‑LAST: 0.795 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	? CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.563 Carnac(seed): 0.123 Sensitivity CentroidHomfold‑LAST: 0.437 Carnac(seed): 0.015 Positive Predictive Value CentroidHomfold‑LAST: 0.732 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.521 NanoFolder: 0.366 Sensitivity CentroidHomfold‑LAST: 0.386 NanoFolder: 0.376 Positive Predictive Value CentroidHomfold‑LAST: 0.710 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Multilign(seed): 0.538 Sensitivity CentroidHomfold‑LAST: 0.420 Multilign(seed): 0.420 Positive Predictive Value CentroidHomfold‑LAST: 0.817 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Multilign(20): 0.540 Sensitivity CentroidHomfold‑LAST: 0.496 Multilign(20): 0.456 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidHomfold‑LAST: 0.575 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidHomfold‑LAST: 0.453 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidHomfold‑LAST: 0.737 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 TurboFold(20): 0.594 Sensitivity CentroidHomfold‑LAST: 0.496 TurboFold(20): 0.470 Positive Predictive Value CentroidHomfold‑LAST: 0.807 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(20): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidHomfold‑LAST: 0.581 Sensitivity PETfold_pre2.0(20): 0.497 CentroidHomfold‑LAST: 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidHomfold‑LAST: 0.729 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.563 TurboFold(seed): 0.517 Sensitivity CentroidHomfold‑LAST: 0.437 TurboFold(seed): 0.422 Positive Predictive Value CentroidHomfold‑LAST: 0.732 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.471 CentroidHomfold‑LAST: 0.416 Sensitivity RNASampler(seed): 0.341 CentroidHomfold‑LAST: 0.326 Positive Predictive Value RNASampler(seed): 0.657 CentroidHomfold‑LAST: 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.665 CentroidHomfold‑LAST: 0.631 Sensitivity PPfold(20): 0.519 CentroidHomfold‑LAST: 0.496 Positive Predictive Value PPfold(20): 0.859 CentroidHomfold‑LAST: 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.479 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.795 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.9460272886e-09
HotKnots	34 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.650 HotKnots: 0.560 Sensitivity MXScarna(seed): 0.533 HotKnots: 0.508 Positive Predictive Value MXScarna(seed): 0.796 HotKnots: 0.622 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.695 HotKnots: 0.580 Sensitivity CentroidAlifold(20): 0.540 HotKnots: 0.517 Positive Predictive Value CentroidAlifold(20): 0.897 HotKnots: 0.654 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	25 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.659 HotKnots: 0.580 Sensitivity RNAalifold(20): 0.510 HotKnots: 0.514 Positive Predictive Value RNAalifold(20): 0.854 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.640 HotKnots: 0.580 Sensitivity RNASampler(20): 0.491 HotKnots: 0.514 Positive Predictive Value RNASampler(20): 0.839 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	50 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.596 HotKnots: 0.573 Sensitivity CentroidFold: 0.507 HotKnots: 0.516 Positive Predictive Value CentroidFold: 0.705 HotKnots: 0.642 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.621 HotKnots: 0.580 Sensitivity MXScarna(20): 0.518 HotKnots: 0.514 Positive Predictive Value MXScarna(20): 0.748 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	33 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 HotKnots: 0.557 Sensitivity CentroidAlifold(seed): 0.377 HotKnots: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.925 HotKnots: 0.619 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.569 Contrafold: 0.568 Sensitivity HotKnots: 0.506 Contrafold: 0.498 Positive Predictive Value HotKnots: 0.644 Contrafold: 0.653 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 0.258868738329	55 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.574 HotKnots: 0.569 Sensitivity Sfold: 0.480 HotKnots: 0.506 Positive Predictive Value Sfold: 0.691 HotKnots: 0.644 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 6.06606238843e-08	47 MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.571 HotKnots: 0.570 Sensitivity MaxExpect: 0.502 HotKnots: 0.513 Positive Predictive Value MaxExpect: 0.654 HotKnots: 0.637 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 0.00049899371755	17 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.567 HotKnots: 0.543 Sensitivity IPknot: 0.463 HotKnots: 0.481 Positive Predictive Value IPknot: 0.702 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	18 CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 HotKnots: 0.539 Sensitivity CentroidHomfold‑LAST: 0.397 HotKnots: 0.473 Positive Predictive Value CentroidHomfold‑LAST: 0.784 HotKnots: 0.621 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.64536816295e-07		- Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.601 HotKnots: 0.580 Sensitivity Carnac(20): 0.397 HotKnots: 0.514 Positive Predictive Value Carnac(20): 0.914 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.24386558293e-07	- ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.601 HotKnots: 0.509 Sensitivity ContextFold: 0.483 HotKnots: 0.460 Positive Predictive Value ContextFold: 0.754 HotKnots: 0.570 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.571 ProbKnot: 0.561 Sensitivity HotKnots: 0.518 ProbKnot: 0.514 Positive Predictive Value HotKnots: 0.633 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.16758253407e-07	- Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.592 HotKnots: 0.580 Sensitivity Murlet(20): 0.437 HotKnots: 0.514 Positive Predictive Value Murlet(20): 0.807 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 2.16681265449e-06	= UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.571 HotKnots: 0.569 Sensitivity UNAFold: 0.500 HotKnots: 0.506 Positive Predictive Value UNAFold: 0.655 HotKnots: 0.644 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 0.00662473470579	+ HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.581 Fold: 0.570 Sensitivity HotKnots: 0.528 Fold: 0.509 Positive Predictive Value HotKnots: 0.644 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.6410608252e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.569 RNAfold: 0.551 Sensitivity HotKnots: 0.506 RNAfold: 0.487 Positive Predictive Value HotKnots: 0.644 RNAfold: 0.628 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.569 PknotsRG: 0.552 Sensitivity HotKnots: 0.506 PknotsRG: 0.492 Positive Predictive Value HotKnots: 0.644 PknotsRG: 0.625 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.625 Cylofold: 0.607 Sensitivity HotKnots: 0.555 Cylofold: 0.512 Positive Predictive Value HotKnots: 0.709 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.43288893557e-07	+ HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.560 RNAalifold(seed): 0.539 Sensitivity HotKnots: 0.510 RNAalifold(seed): 0.336 Positive Predictive Value HotKnots: 0.618 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.569 RNAshapes: 0.539 Sensitivity HotKnots: 0.506 RNAshapes: 0.470 Positive Predictive Value HotKnots: 0.644 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.556 Afold: 0.528 Sensitivity HotKnots: 0.504 Afold: 0.478 Positive Predictive Value HotKnots: 0.618 Afold: 0.587 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.569 McQFold: 0.523 Sensitivity HotKnots: 0.506 McQFold: 0.449 Positive Predictive Value HotKnots: 0.644 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.592 Pknots: 0.547 Sensitivity HotKnots: 0.518 Pknots: 0.489 Positive Predictive Value HotKnots: 0.683 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.569 RNAsubopt: 0.531 Sensitivity HotKnots: 0.506 RNAsubopt: 0.473 Positive Predictive Value HotKnots: 0.644 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.585 RSpredict(20): 0.559 Sensitivity HotKnots: 0.522 RSpredict(20): 0.446 Positive Predictive Value HotKnots: 0.659 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-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: 2.30549897711e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.569 Vsfold4: 0.478 Sensitivity HotKnots: 0.506 Vsfold4: 0.399 Positive Predictive Value HotKnots: 0.644 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.580 Mastr(20): 0.523 Sensitivity HotKnots: 0.514 Mastr(20): 0.348 Positive Predictive Value HotKnots: 0.658 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.509 RNASLOpt: 0.443 Sensitivity HotKnots: 0.460 RNASLOpt: 0.365 Positive Predictive Value HotKnots: 0.570 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.614 Murlet(seed): 0.475 Sensitivity HotKnots: 0.536 Murlet(seed): 0.270 Positive Predictive Value HotKnots: 0.707 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.569 Vsfold5: 0.426 Sensitivity HotKnots: 0.506 Vsfold5: 0.359 Positive Predictive Value HotKnots: 0.644 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.543 RNAwolf: 0.399 Sensitivity HotKnots: 0.481 RNAwolf: 0.368 Positive Predictive Value HotKnots: 0.621 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-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: 3.56938820447e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.600 RDfolder: 0.443 Sensitivity HotKnots: 0.516 RDfolder: 0.342 Positive Predictive Value HotKnots: 0.707 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.594 MCFold: 0.419 Sensitivity HotKnots: 0.526 MCFold: 0.437 Positive Predictive Value HotKnots: 0.677 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.560 RSpredict(seed): 0.204 Sensitivity HotKnots: 0.508 RSpredict(seed): 0.088 Positive Predictive Value HotKnots: 0.622 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.566 PPfold(seed): 0.102 Sensitivity HotKnots: 0.487 PPfold(seed): 0.020 Positive Predictive Value HotKnots: 0.664 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.10032755566e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.631 Carnac(seed): 0.139 Sensitivity HotKnots: 0.559 Carnac(seed): 0.019 Positive Predictive Value HotKnots: 0.717 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	? HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.535 NanoFolder: 0.366 Sensitivity HotKnots: 0.473 NanoFolder: 0.376 Positive Predictive Value HotKnots: 0.613 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.621 Multilign(seed): 0.538 Sensitivity HotKnots: 0.507 Multilign(seed): 0.420 Positive Predictive Value HotKnots: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.609 Multilign(20): 0.540 Sensitivity HotKnots: 0.526 Multilign(20): 0.456 Positive Predictive Value HotKnots: 0.710 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 HotKnots: 0.518 Sensitivity PETfold_pre2.0(seed): 0.551 HotKnots: 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 HotKnots: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.609 TurboFold(20): 0.594 Sensitivity HotKnots: 0.526 TurboFold(20): 0.470 Positive Predictive Value HotKnots: 0.710 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 HotKnots: 0.561 Sensitivity PETfold_pre2.0(20): 0.497 HotKnots: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 HotKnots: 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.599 TurboFold(seed): 0.517 Sensitivity HotKnots: 0.521 TurboFold(seed): 0.422 Positive Predictive Value HotKnots: 0.695 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.546 HotKnots: 0.530 Sensitivity RNASampler(seed): 0.409 HotKnots: 0.486 Positive Predictive Value RNASampler(seed): 0.734 HotKnots: 0.583 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.665 HotKnots: 0.609 Sensitivity PPfold(20): 0.519 HotKnots: 0.526 Positive Predictive Value PPfold(20): 0.859 HotKnots: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.558 Mastr(seed): 0.000 Sensitivity HotKnots: 0.503 Mastr(seed): 0.000 Positive Predictive Value HotKnots: 0.623 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(20)	24 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 Carnac(20): 0.607 Sensitivity MXScarna(seed): 0.556 Carnac(20): 0.405 Positive Predictive Value MXScarna(seed): 0.815 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Carnac(20): 0.605 Sensitivity CentroidAlifold(20): 0.540 Carnac(20): 0.403 Positive Predictive Value CentroidAlifold(20): 0.897 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Carnac(20): 0.601 Sensitivity RNAalifold(20): 0.510 Carnac(20): 0.397 Positive Predictive Value RNAalifold(20): 0.854 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.640 Carnac(20): 0.601 Sensitivity RNASampler(20): 0.491 Carnac(20): 0.397 Positive Predictive Value RNASampler(20): 0.839 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.610 Carnac(20): 0.605 Sensitivity CentroidFold: 0.515 Carnac(20): 0.403 Positive Predictive Value CentroidFold: 0.725 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.0940494622033	25 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.621 Carnac(20): 0.601 Sensitivity MXScarna(20): 0.518 Carnac(20): 0.397 Positive Predictive Value MXScarna(20): 0.748 Carnac(20): 0.914 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	23 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Carnac(20): 0.605 Sensitivity CentroidAlifold(seed): 0.417 Carnac(20): 0.403 Positive Predictive Value CentroidAlifold(seed): 0.953 Carnac(20): 0.913 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.601 Contrafold: 0.554 Sensitivity Carnac(20): 0.397 Contrafold: 0.488 Positive Predictive Value Carnac(20): 0.914 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.601 Sfold: 0.593 Sensitivity Carnac(20): 0.397 Sfold: 0.492 Positive Predictive Value Carnac(20): 0.914 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.33078868561e-05	23 Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.605 MaxExpect: 0.598 Sensitivity Carnac(20): 0.403 MaxExpect: 0.520 Positive Predictive Value Carnac(20): 0.913 MaxExpect: 0.692 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 1.15003019969e-05	8 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.571 Carnac(20): 0.560 Sensitivity IPknot: 0.463 Carnac(20): 0.367 Positive Predictive Value IPknot: 0.710 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Carnac(20): 0.560 Sensitivity CentroidHomfold‑LAST: 0.496 Carnac(20): 0.367 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	25 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.601 HotKnots: 0.580 Sensitivity Carnac(20): 0.397 HotKnots: 0.514 Positive Predictive Value Carnac(20): 0.914 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.24386558293e-07		? ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.579 Carnac(20): 0.476 Sensitivity ContextFold: 0.443 Carnac(20): 0.281 Positive Predictive Value ContextFold: 0.763 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.597 Carnac(20): 0.585 Sensitivity ProbKnot: 0.536 Carnac(20): 0.372 Positive Predictive Value ProbKnot: 0.669 Carnac(20): 0.923 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.96021798202e-08	+ Carnac(20) vs Murlet(20) Matthews Correlation Coefficient Carnac(20): 0.601 Murlet(20): 0.592 Sensitivity Carnac(20): 0.397 Murlet(20): 0.437 Positive Predictive Value Carnac(20): 0.914 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.26649320034e-05	+ Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.601 UNAFold: 0.589 Sensitivity Carnac(20): 0.397 UNAFold: 0.513 Positive Predictive Value Carnac(20): 0.914 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 7.27211512036e-08	+ Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.585 Fold: 0.581 Sensitivity Carnac(20): 0.372 Fold: 0.512 Positive Predictive Value Carnac(20): 0.923 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000701583593059	+ Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.601 RNAfold: 0.569 Sensitivity Carnac(20): 0.397 RNAfold: 0.502 Positive Predictive Value Carnac(20): 0.914 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.601 PknotsRG: 0.581 Sensitivity Carnac(20): 0.397 PknotsRG: 0.516 Positive Predictive Value Carnac(20): 0.914 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 8.68922211961e-08	- Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.661 Carnac(20): 0.635 Sensitivity Cylofold: 0.553 Carnac(20): 0.435 Positive Predictive Value Cylofold: 0.796 Carnac(20): 0.932 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.95743112377e-06	- RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 Carnac(20): 0.549 Sensitivity RNAalifold(seed): 0.364 Carnac(20): 0.319 Positive Predictive Value RNAalifold(seed): 0.919 Carnac(20): 0.948 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.601 RNAshapes: 0.554 Sensitivity Carnac(20): 0.397 RNAshapes: 0.482 Positive Predictive Value Carnac(20): 0.914 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.599 Afold: 0.513 Sensitivity Carnac(20): 0.390 Afold: 0.464 Positive Predictive Value Carnac(20): 0.921 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.601 McQFold: 0.529 Sensitivity Carnac(20): 0.397 McQFold: 0.456 Positive Predictive Value Carnac(20): 0.914 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.619 Pknots: 0.540 Sensitivity Carnac(20): 0.423 Pknots: 0.487 Positive Predictive Value Carnac(20): 0.911 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.601 RNAsubopt: 0.545 Sensitivity Carnac(20): 0.397 RNAsubopt: 0.486 Positive Predictive Value Carnac(20): 0.914 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.607 RSpredict(20): 0.559 Sensitivity Carnac(20): 0.405 RSpredict(20): 0.446 Positive Predictive Value Carnac(20): 0.915 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-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 Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.601 Vsfold4: 0.473 Sensitivity Carnac(20): 0.397 Vsfold4: 0.393 Positive Predictive Value Carnac(20): 0.914 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.601 Mastr(20): 0.523 Sensitivity Carnac(20): 0.397 Mastr(20): 0.348 Positive Predictive Value Carnac(20): 0.914 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.476 RNASLOpt: 0.467 Sensitivity Carnac(20): 0.281 RNASLOpt: 0.383 Positive Predictive Value Carnac(20): 0.810 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.569 Murlet(seed): 0.496 Sensitivity Carnac(20): 0.342 Murlet(seed): 0.277 Positive Predictive Value Carnac(20): 0.949 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.601 Vsfold5: 0.425 Sensitivity Carnac(20): 0.397 Vsfold5: 0.358 Positive Predictive Value Carnac(20): 0.914 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.560 RNAwolf: 0.364 Sensitivity Carnac(20): 0.367 RNAwolf: 0.333 Positive Predictive Value Carnac(20): 0.861 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 8.35333035499e-09	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.643 RDfolder: 0.539 Sensitivity Carnac(20): 0.459 RDfolder: 0.427 Positive Predictive Value Carnac(20): 0.907 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.645 MCFold: 0.425 Sensitivity Carnac(20): 0.454 MCFold: 0.448 Positive Predictive Value Carnac(20): 0.920 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.607 RSpredict(seed): 0.232 Sensitivity Carnac(20): 0.405 RSpredict(seed): 0.097 Positive Predictive Value Carnac(20): 0.915 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.560 PPfold(seed): 0.026 Sensitivity Carnac(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.611 Carnac(seed): 0.122 Sensitivity Carnac(20): 0.404 Carnac(seed): 0.015 Positive Predictive Value Carnac(20): 0.931 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	? Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.506 NanoFolder: 0.316 Sensitivity Carnac(20): 0.318 NanoFolder: 0.324 Positive Predictive Value Carnac(20): 0.810 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.631 Carnac(20): 0.612 Sensitivity Multilign(seed): 0.492 Carnac(20): 0.424 Positive Predictive Value Multilign(seed): 0.817 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Multilign(20) Matthews Correlation Coefficient Carnac(20): 0.560 Multilign(20): 0.540 Sensitivity Carnac(20): 0.367 Multilign(20): 0.456 Positive Predictive Value Carnac(20): 0.861 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(seed): 0.557 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Carnac(20): 0.560 Sensitivity TurboFold(20): 0.470 Carnac(20): 0.367 Positive Predictive Value TurboFold(20): 0.756 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): N/A CMfinder(20): N/A Sensitivity Carnac(20): N/A CMfinder(20): N/A Positive Predictive Value Carnac(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Carnac(20): 0.544 Sensitivity TurboFold(seed): 0.457 Carnac(20): 0.342 Positive Predictive Value TurboFold(seed): 0.703 Carnac(20): 0.874 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNASampler(seed) Matthews Correlation Coefficient Carnac(20): 0.600 RNASampler(seed): 0.570 Sensitivity Carnac(20): 0.374 RNASampler(seed): 0.434 Positive Predictive Value Carnac(20): 0.965 RNASampler(seed): 0.754 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.665 Carnac(20): 0.560 Sensitivity PPfold(20): 0.519 Carnac(20): 0.367 Positive Predictive Value PPfold(20): 0.859 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.601 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.397 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.914 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08
ContextFold	8 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.616 MXScarna(seed): 0.586 Sensitivity ContextFold: 0.476 MXScarna(seed): 0.457 Positive Predictive Value ContextFold: 0.801 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.650 ContextFold: 0.579 Sensitivity CentroidAlifold(20): 0.473 ContextFold: 0.443 Positive Predictive Value CentroidAlifold(20): 0.898 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.579 RNAalifold(20): 0.553 Sensitivity ContextFold: 0.443 RNAalifold(20): 0.407 Positive Predictive Value ContextFold: 0.763 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.579 RNASampler(20): 0.569 Sensitivity ContextFold: 0.443 RNASampler(20): 0.419 Positive Predictive Value ContextFold: 0.763 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	14 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.601 CentroidFold: 0.520 Sensitivity ContextFold: 0.483 CentroidFold: 0.423 Positive Predictive Value ContextFold: 0.754 CentroidFold: 0.648 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	5 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.579 MXScarna(20): 0.501 Sensitivity ContextFold: 0.443 MXScarna(20): 0.401 Positive Predictive Value ContextFold: 0.763 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.616 CentroidAlifold(seed): 0.542 Sensitivity ContextFold: 0.476 CentroidAlifold(seed): 0.299 Positive Predictive Value ContextFold: 0.801 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.601 Contrafold: 0.517 Sensitivity ContextFold: 0.483 Contrafold: 0.438 Positive Predictive Value ContextFold: 0.754 Contrafold: 0.618 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	14 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.601 Sfold: 0.480 Sensitivity ContextFold: 0.483 Sfold: 0.393 Positive Predictive Value ContextFold: 0.754 Sfold: 0.595 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	14 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.601 MaxExpect: 0.446 Sensitivity ContextFold: 0.483 MaxExpect: 0.385 Positive Predictive Value ContextFold: 0.754 MaxExpect: 0.526 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	14 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.601 IPknot: 0.538 Sensitivity ContextFold: 0.483 IPknot: 0.443 Positive Predictive Value ContextFold: 0.754 IPknot: 0.660 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	14 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.601 CentroidHomfold‑LAST: 0.515 Sensitivity ContextFold: 0.483 CentroidHomfold‑LAST: 0.365 Positive Predictive Value ContextFold: 0.754 CentroidHomfold‑LAST: 0.734 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	14 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.601 HotKnots: 0.509 Sensitivity ContextFold: 0.483 HotKnots: 0.460 Positive Predictive Value ContextFold: 0.754 HotKnots: 0.570 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	5 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.579 Carnac(20): 0.476 Sensitivity ContextFold: 0.443 Carnac(20): 0.281 Positive Predictive Value ContextFold: 0.763 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.601 ProbKnot: 0.461 Sensitivity ContextFold: 0.483 ProbKnot: 0.418 Positive Predictive Value ContextFold: 0.754 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.13392142882e-08	? ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.579 Murlet(20): 0.496 Sensitivity ContextFold: 0.443 Murlet(20): 0.353 Positive Predictive Value ContextFold: 0.763 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.601 UNAFold: 0.451 Sensitivity ContextFold: 0.483 UNAFold: 0.400 Positive Predictive Value ContextFold: 0.754 UNAFold: 0.516 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.601 Fold: 0.447 Sensitivity ContextFold: 0.483 Fold: 0.393 Positive Predictive Value ContextFold: 0.754 Fold: 0.518 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.47941000302e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.601 RNAfold: 0.483 Sensitivity ContextFold: 0.483 RNAfold: 0.423 Positive Predictive Value ContextFold: 0.754 RNAfold: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.66062906821e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.601 PknotsRG: 0.506 Sensitivity ContextFold: 0.483 PknotsRG: 0.453 Positive Predictive Value ContextFold: 0.754 PknotsRG: 0.573 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.608 Cylofold: 0.492 Sensitivity ContextFold: 0.492 Cylofold: 0.422 Positive Predictive Value ContextFold: 0.759 Cylofold: 0.584 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08	? ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.488 RNAalifold(seed): 0.472 Sensitivity ContextFold: 0.376 RNAalifold(seed): 0.293 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.601 RNAshapes: 0.472 Sensitivity ContextFold: 0.483 RNAshapes: 0.413 Positive Predictive Value ContextFold: 0.754 RNAshapes: 0.548 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	? ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.504 Afold: 0.475 Sensitivity ContextFold: 0.406 Afold: 0.442 Positive Predictive Value ContextFold: 0.632 Afold: 0.518 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.601 McQFold: 0.445 Sensitivity ContextFold: 0.483 McQFold: 0.385 Positive Predictive Value ContextFold: 0.754 McQFold: 0.522 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.601 Pknots: 0.408 Sensitivity ContextFold: 0.483 Pknots: 0.373 Positive Predictive Value ContextFold: 0.754 Pknots: 0.456 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.601 RNAsubopt: 0.424 Sensitivity ContextFold: 0.483 RNAsubopt: 0.378 Positive Predictive Value ContextFold: 0.754 RNAsubopt: 0.486 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	? ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.579 RSpredict(20): 0.352 Sensitivity ContextFold: 0.443 RSpredict(20): 0.251 Positive Predictive Value ContextFold: 0.763 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ 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: 2.76499031155e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.601 Vsfold4: 0.408 Sensitivity ContextFold: 0.483 Vsfold4: 0.340 Positive Predictive Value ContextFold: 0.754 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.34821445183e-08	? ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.579 Mastr(20): 0.488 Sensitivity ContextFold: 0.443 Mastr(20): 0.305 Positive Predictive Value ContextFold: 0.763 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.601 RNASLOpt: 0.443 Sensitivity ContextFold: 0.483 RNASLOpt: 0.365 Positive Predictive Value ContextFold: 0.754 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	? ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.488 Murlet(seed): 0.425 Sensitivity ContextFold: 0.376 Murlet(seed): 0.248 Positive Predictive Value ContextFold: 0.641 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.601 Vsfold5: 0.340 Sensitivity ContextFold: 0.483 Vsfold5: 0.295 Positive Predictive Value ContextFold: 0.754 Vsfold5: 0.401 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.601 RNAwolf: 0.349 Sensitivity ContextFold: 0.483 RNAwolf: 0.323 Positive Predictive Value ContextFold: 0.754 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-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: 0.537 RDfolder: 0.229 Sensitivity ContextFold: 0.425 RDfolder: 0.168 Positive Predictive Value ContextFold: 0.689 RDfolder: 0.329 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.599 MCFold: 0.441 Sensitivity ContextFold: 0.486 MCFold: 0.474 Positive Predictive Value ContextFold: 0.743 MCFold: 0.419 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	? ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.616 RSpredict(seed): 0.110 Sensitivity ContextFold: 0.476 RSpredict(seed): 0.047 Positive Predictive Value ContextFold: 0.801 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.616 PPfold(seed): 0.121 Sensitivity ContextFold: 0.476 PPfold(seed): 0.028 Positive Predictive Value ContextFold: 0.801 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.576 Carnac(seed): 0.146 Sensitivity ContextFold: 0.449 Carnac(seed): 0.021 Positive Predictive Value ContextFold: 0.743 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.632 NanoFolder: 0.366 Sensitivity ContextFold: 0.498 NanoFolder: 0.376 Positive Predictive Value ContextFold: 0.807 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.532 Multilign(seed): 0.403 Sensitivity ContextFold: 0.435 Multilign(seed): 0.306 Positive Predictive Value ContextFold: 0.659 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.579 Multilign(20): 0.474 Sensitivity ContextFold: 0.443 Multilign(20): 0.401 Positive Predictive Value ContextFold: 0.763 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ContextFold: 0.616 Sensitivity PETfold_pre2.0(seed): 0.551 ContextFold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ContextFold: 0.801 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.579 TurboFold(20): 0.542 Sensitivity ContextFold: 0.443 TurboFold(20): 0.425 Positive Predictive Value ContextFold: 0.763 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: N/A CMfinder(20): N/A Sensitivity ContextFold: N/A CMfinder(20): N/A Positive Predictive Value ContextFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ContextFold: 0.579 Sensitivity PETfold_pre2.0(20): 0.497 ContextFold: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.576 TurboFold(seed): 0.460 Sensitivity ContextFold: 0.449 TurboFold(seed): 0.380 Positive Predictive Value ContextFold: 0.743 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.351 RNASampler(seed): 0.198 Sensitivity ContextFold: 0.283 RNASampler(seed): 0.151 Positive Predictive Value ContextFold: 0.441 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.616 ContextFold: 0.579 Sensitivity PPfold(20): 0.473 ContextFold: 0.443 Positive Predictive Value PPfold(20): 0.806 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.616 Mastr(seed): 0.000 Sensitivity ContextFold: 0.476 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.801 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
ProbKnot	21 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.638 ProbKnot: 0.553 Sensitivity MXScarna(seed): 0.519 ProbKnot: 0.511 Positive Predictive Value MXScarna(seed): 0.787 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.89920829651e-08	15 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.691 ProbKnot: 0.597 Sensitivity CentroidAlifold(20): 0.525 ProbKnot: 0.536 Positive Predictive Value CentroidAlifold(20): 0.912 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.66062906821e-08	15 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.646 ProbKnot: 0.597 Sensitivity RNAalifold(20): 0.494 ProbKnot: 0.536 Positive Predictive Value RNAalifold(20): 0.847 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.633 ProbKnot: 0.597 Sensitivity RNASampler(20): 0.478 ProbKnot: 0.536 Positive Predictive Value RNASampler(20): 0.843 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	32 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.591 ProbKnot: 0.561 Sensitivity CentroidFold: 0.503 ProbKnot: 0.514 Positive Predictive Value CentroidFold: 0.697 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.618 ProbKnot: 0.597 Sensitivity MXScarna(20): 0.512 ProbKnot: 0.536 Positive Predictive Value MXScarna(20): 0.748 ProbKnot: 0.669 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.64481516727e-08	21 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.586 ProbKnot: 0.553 Sensitivity CentroidAlifold(seed): 0.374 ProbKnot: 0.511 Positive Predictive Value CentroidAlifold(seed): 0.921 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 8.55066880689e-08	32 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.574 ProbKnot: 0.561 Sensitivity Contrafold: 0.510 ProbKnot: 0.514 Positive Predictive Value Contrafold: 0.649 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.574 ProbKnot: 0.561 Sensitivity Sfold: 0.486 ProbKnot: 0.514 Positive Predictive Value Sfold: 0.682 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.567 ProbKnot: 0.561 Sensitivity MaxExpect: 0.501 ProbKnot: 0.514 Positive Predictive Value MaxExpect: 0.646 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.567 ProbKnot: 0.495 Sensitivity IPknot: 0.463 ProbKnot: 0.443 Positive Predictive Value IPknot: 0.702 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	18 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 ProbKnot: 0.493 Sensitivity CentroidHomfold‑LAST: 0.397 ProbKnot: 0.439 Positive Predictive Value CentroidHomfold‑LAST: 0.784 ProbKnot: 0.563 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	32 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.571 ProbKnot: 0.561 Sensitivity HotKnots: 0.518 ProbKnot: 0.514 Positive Predictive Value HotKnots: 0.633 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.16758253407e-07	15 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.597 Carnac(20): 0.585 Sensitivity ProbKnot: 0.536 Carnac(20): 0.372 Positive Predictive Value ProbKnot: 0.669 Carnac(20): 0.923 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.96021798202e-08	14 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.601 ProbKnot: 0.461 Sensitivity ContextFold: 0.483 ProbKnot: 0.418 Positive Predictive Value ContextFold: 0.754 ProbKnot: 0.517 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.13392142882e-08		+ ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.597 Murlet(20): 0.590 Sensitivity ProbKnot: 0.536 Murlet(20): 0.432 Positive Predictive Value ProbKnot: 0.669 Murlet(20): 0.808 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.920170871e-06	= ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.561 UNAFold: 0.560 Sensitivity ProbKnot: 0.514 UNAFold: 0.501 Positive Predictive Value ProbKnot: 0.617 UNAFold: 0.631 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.0173545140323	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.561 Fold: 0.559 Sensitivity ProbKnot: 0.514 Fold: 0.498 Positive Predictive Value ProbKnot: 0.617 Fold: 0.630 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.000230581642477	= ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.561 RNAfold: 0.559 Sensitivity ProbKnot: 0.514 RNAfold: 0.502 Positive Predictive Value ProbKnot: 0.617 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.10675413758	= PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.563 ProbKnot: 0.561 Sensitivity PknotsRG: 0.511 ProbKnot: 0.514 Positive Predictive Value PknotsRG: 0.625 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.0853441262641	+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.608 Cylofold: 0.599 Sensitivity ProbKnot: 0.547 Cylofold: 0.503 Positive Predictive Value ProbKnot: 0.682 Cylofold: 0.720 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.10701214729e-05	- RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.505 ProbKnot: 0.484 Sensitivity RNAalifold(seed): 0.304 ProbKnot: 0.450 Positive Predictive Value RNAalifold(seed): 0.844 ProbKnot: 0.523 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.06286140723e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.561 RNAshapes: 0.548 Sensitivity ProbKnot: 0.514 RNAshapes: 0.485 Positive Predictive Value ProbKnot: 0.617 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.542 Afold: 0.533 Sensitivity ProbKnot: 0.508 Afold: 0.499 Positive Predictive Value ProbKnot: 0.582 Afold: 0.574 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.40179680388e-07	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.561 McQFold: 0.546 Sensitivity ProbKnot: 0.514 McQFold: 0.478 Positive Predictive Value ProbKnot: 0.617 McQFold: 0.628 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.09925167801e-06	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.598 Pknots: 0.578 Sensitivity ProbKnot: 0.540 Pknots: 0.516 Positive Predictive Value ProbKnot: 0.668 Pknots: 0.654 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.34568509467e-07	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.561 RNAsubopt: 0.543 Sensitivity ProbKnot: 0.514 RNAsubopt: 0.489 Positive Predictive Value ProbKnot: 0.617 RNAsubopt: 0.606 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.597 RSpredict(20): 0.538 Sensitivity ProbKnot: 0.536 RSpredict(20): 0.424 Positive Predictive Value ProbKnot: 0.669 RSpredict(20): 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-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: 3.69948253166e-05	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.561 Vsfold4: 0.462 Sensitivity ProbKnot: 0.514 Vsfold4: 0.392 Positive Predictive Value ProbKnot: 0.617 Vsfold4: 0.551 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.597 Mastr(20): 0.483 Sensitivity ProbKnot: 0.536 Mastr(20): 0.297 Positive Predictive Value ProbKnot: 0.669 Mastr(20): 0.791 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.461 RNASLOpt: 0.443 Sensitivity ProbKnot: 0.418 RNASLOpt: 0.365 Positive Predictive Value ProbKnot: 0.517 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 6.46512660639e-07	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.509 Murlet(seed): 0.452 Sensitivity ProbKnot: 0.461 Murlet(seed): 0.249 Positive Predictive Value ProbKnot: 0.568 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.53972656358e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.561 Vsfold5: 0.428 Sensitivity ProbKnot: 0.514 Vsfold5: 0.366 Positive Predictive Value ProbKnot: 0.617 Vsfold5: 0.506 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.495 RNAwolf: 0.399 Sensitivity ProbKnot: 0.443 RNAwolf: 0.368 Positive Predictive Value ProbKnot: 0.560 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-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: 1.70887622364e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.566 RDfolder: 0.412 Sensitivity ProbKnot: 0.506 RDfolder: 0.317 Positive Predictive Value ProbKnot: 0.643 RDfolder: 0.549 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.587 MCFold: 0.458 Sensitivity ProbKnot: 0.536 MCFold: 0.476 Positive Predictive Value ProbKnot: 0.648 MCFold: 0.449 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.553 RSpredict(seed): 0.139 Sensitivity ProbKnot: 0.511 RSpredict(seed): 0.055 Positive Predictive Value ProbKnot: 0.603 RSpredict(seed): 0.355 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.513 PPfold(seed): 0.102 Sensitivity ProbKnot: 0.457 PPfold(seed): 0.020 Positive Predictive Value ProbKnot: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.572 Carnac(seed): 0.088 Sensitivity ProbKnot: 0.516 Carnac(seed): 0.008 Positive Predictive Value ProbKnot: 0.641 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.16131455263e-08	? ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.499 NanoFolder: 0.366 Sensitivity ProbKnot: 0.447 NanoFolder: 0.376 Positive Predictive Value ProbKnot: 0.565 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.538 ProbKnot: 0.493 Sensitivity Multilign(seed): 0.420 ProbKnot: 0.413 Positive Predictive Value Multilign(seed): 0.699 ProbKnot: 0.600 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs Multilign(20) Matthews Correlation Coefficient ProbKnot: 0.542 Multilign(20): 0.540 Sensitivity ProbKnot: 0.481 Multilign(20): 0.456 Positive Predictive Value ProbKnot: 0.616 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ProbKnot: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 ProbKnot: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.594 ProbKnot: 0.542 Sensitivity TurboFold(20): 0.470 ProbKnot: 0.481 Positive Predictive Value TurboFold(20): 0.756 ProbKnot: 0.616 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(20): N/A Sensitivity ProbKnot: N/A CMfinder(20): N/A Positive Predictive Value ProbKnot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ProbKnot: 0.488 Sensitivity PETfold_pre2.0(20): 0.497 ProbKnot: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ProbKnot: 0.544 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.517 ProbKnot: 0.489 Sensitivity TurboFold(seed): 0.422 ProbKnot: 0.433 Positive Predictive Value TurboFold(seed): 0.642 ProbKnot: 0.559 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.467 ProbKnot: 0.358 Sensitivity RNASampler(seed): 0.341 ProbKnot: 0.348 Positive Predictive Value RNASampler(seed): 0.644 ProbKnot: 0.375 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.665 ProbKnot: 0.542 Sensitivity PPfold(20): 0.519 ProbKnot: 0.481 Positive Predictive Value PPfold(20): 0.859 ProbKnot: 0.616 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.553 Mastr(seed): 0.000 Sensitivity ProbKnot: 0.511 Mastr(seed): 0.000 Positive Predictive Value ProbKnot: 0.603 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08
Murlet(20)	24 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 Murlet(20): 0.593 Sensitivity MXScarna(seed): 0.556 Murlet(20): 0.440 Positive Predictive Value MXScarna(seed): 0.815 Murlet(20): 0.803 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	23 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Murlet(20): 0.592 Sensitivity CentroidAlifold(20): 0.540 Murlet(20): 0.440 Positive Predictive Value CentroidAlifold(20): 0.897 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Murlet(20): 0.592 Sensitivity RNAalifold(20): 0.510 Murlet(20): 0.437 Positive Predictive Value RNAalifold(20): 0.854 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.640 Murlet(20): 0.592 Sensitivity RNASampler(20): 0.491 Murlet(20): 0.437 Positive Predictive Value RNASampler(20): 0.839 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.94031556815e-08	23 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.610 Murlet(20): 0.592 Sensitivity CentroidFold: 0.515 Murlet(20): 0.440 Positive Predictive Value CentroidFold: 0.725 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.29540574715e-07	25 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.621 Murlet(20): 0.592 Sensitivity MXScarna(20): 0.518 Murlet(20): 0.437 Positive Predictive Value MXScarna(20): 0.748 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	23 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Murlet(20): 0.592 Sensitivity CentroidAlifold(seed): 0.417 Murlet(20): 0.440 Positive Predictive Value CentroidAlifold(seed): 0.953 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.592 Contrafold: 0.554 Sensitivity Murlet(20): 0.437 Contrafold: 0.488 Positive Predictive Value Murlet(20): 0.807 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.593 Murlet(20): 0.592 Sensitivity Sfold: 0.492 Murlet(20): 0.437 Positive Predictive Value Sfold: 0.718 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.105836163587	23 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.598 Murlet(20): 0.592 Sensitivity MaxExpect: 0.520 Murlet(20): 0.440 Positive Predictive Value MaxExpect: 0.692 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.000361978838932	8 Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.581 IPknot: 0.571 Sensitivity Murlet(20): 0.433 IPknot: 0.463 Positive Predictive Value Murlet(20): 0.785 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Murlet(20): 0.581 Sensitivity CentroidHomfold‑LAST: 0.496 Murlet(20): 0.433 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Murlet(20): 0.785 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	25 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.592 HotKnots: 0.580 Sensitivity Murlet(20): 0.437 HotKnots: 0.514 Positive Predictive Value Murlet(20): 0.807 HotKnots: 0.658 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 2.16681265449e-06	25 Carnac(20) vs Murlet(20) Matthews Correlation Coefficient Carnac(20): 0.601 Murlet(20): 0.592 Sensitivity Carnac(20): 0.397 Murlet(20): 0.437 Positive Predictive Value Carnac(20): 0.914 Murlet(20): 0.807 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.26649320034e-05	5 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.579 Murlet(20): 0.496 Sensitivity ContextFold: 0.443 Murlet(20): 0.353 Positive Predictive Value ContextFold: 0.763 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	15 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.597 Murlet(20): 0.590 Sensitivity ProbKnot: 0.536 Murlet(20): 0.432 Positive Predictive Value ProbKnot: 0.669 Murlet(20): 0.808 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.920170871e-06		= Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.592 UNAFold: 0.589 Sensitivity Murlet(20): 0.437 UNAFold: 0.513 Positive Predictive Value Murlet(20): 0.807 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.00572131440621	+ Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.590 Fold: 0.581 Sensitivity Murlet(20): 0.432 Fold: 0.512 Positive Predictive Value Murlet(20): 0.808 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000569606146608	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.592 RNAfold: 0.569 Sensitivity Murlet(20): 0.437 RNAfold: 0.502 Positive Predictive Value Murlet(20): 0.807 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 6.32937386918e-08	+ Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.592 PknotsRG: 0.581 Sensitivity Murlet(20): 0.437 PknotsRG: 0.516 Positive Predictive Value Murlet(20): 0.807 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.94602596382e-06	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.685 Cylofold: 0.661 Sensitivity Murlet(20): 0.528 Cylofold: 0.553 Positive Predictive Value Murlet(20): 0.893 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.35850794473e-08	- RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 Murlet(20): 0.535 Sensitivity RNAalifold(seed): 0.364 Murlet(20): 0.371 Positive Predictive Value RNAalifold(seed): 0.919 Murlet(20): 0.775 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.592 RNAshapes: 0.554 Sensitivity Murlet(20): 0.437 RNAshapes: 0.482 Positive Predictive Value Murlet(20): 0.807 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.550 Afold: 0.513 Sensitivity Murlet(20): 0.402 Afold: 0.464 Positive Predictive Value Murlet(20): 0.756 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.592 McQFold: 0.529 Sensitivity Murlet(20): 0.437 McQFold: 0.456 Positive Predictive Value Murlet(20): 0.807 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.618 Pknots: 0.540 Sensitivity Murlet(20): 0.467 Pknots: 0.487 Positive Predictive Value Murlet(20): 0.822 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.592 RNAsubopt: 0.545 Sensitivity Murlet(20): 0.437 RNAsubopt: 0.486 Positive Predictive Value Murlet(20): 0.807 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.593 RSpredict(20): 0.559 Sensitivity Murlet(20): 0.440 RSpredict(20): 0.446 Positive Predictive Value Murlet(20): 0.803 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-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 Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.592 Vsfold4: 0.473 Sensitivity Murlet(20): 0.437 Vsfold4: 0.393 Positive Predictive Value Murlet(20): 0.807 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.592 Mastr(20): 0.523 Sensitivity Murlet(20): 0.437 Mastr(20): 0.348 Positive Predictive Value Murlet(20): 0.807 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.496 RNASLOpt: 0.467 Sensitivity Murlet(20): 0.353 RNASLOpt: 0.383 Positive Predictive Value Murlet(20): 0.702 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.567 Murlet(seed): 0.496 Sensitivity Murlet(20): 0.405 Murlet(seed): 0.277 Positive Predictive Value Murlet(20): 0.799 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.592 Vsfold5: 0.425 Sensitivity Murlet(20): 0.437 Vsfold5: 0.358 Positive Predictive Value Murlet(20): 0.807 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	? Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.581 RNAwolf: 0.364 Sensitivity Murlet(20): 0.433 RNAwolf: 0.333 Positive Predictive Value Murlet(20): 0.785 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 1.52299983238e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.667 RDfolder: 0.539 Sensitivity Murlet(20): 0.504 RDfolder: 0.427 Positive Predictive Value Murlet(20): 0.890 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.619 MCFold: 0.425 Sensitivity Murlet(20): 0.477 MCFold: 0.448 Positive Predictive Value Murlet(20): 0.808 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.593 RSpredict(seed): 0.232 Sensitivity Murlet(20): 0.440 RSpredict(seed): 0.097 Positive Predictive Value Murlet(20): 0.803 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.581 PPfold(seed): 0.026 Sensitivity Murlet(20): 0.433 PPfold(seed): 0.004 Positive Predictive Value Murlet(20): 0.785 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.604 Carnac(seed): 0.122 Sensitivity Murlet(20): 0.446 Carnac(seed): 0.015 Positive Predictive Value Murlet(20): 0.822 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.74172190343e-08	? Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.503 NanoFolder: 0.316 Sensitivity Murlet(20): 0.372 NanoFolder: 0.324 Positive Predictive Value Murlet(20): 0.688 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.696 Multilign(seed): 0.631 Sensitivity Murlet(20): 0.534 Multilign(seed): 0.492 Positive Predictive Value Murlet(20): 0.913 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.581 Multilign(20): 0.540 Sensitivity Murlet(20): 0.433 Multilign(20): 0.456 Positive Predictive Value Murlet(20): 0.785 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.557 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Murlet(20): 0.581 Sensitivity TurboFold(20): 0.470 Murlet(20): 0.433 Positive Predictive Value TurboFold(20): 0.756 Murlet(20): 0.785 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(20): N/A Sensitivity Murlet(20): N/A CMfinder(20): N/A Positive Predictive Value Murlet(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.497 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(20): 0.790 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Murlet(20): 0.557 Sensitivity TurboFold(seed): 0.457 Murlet(20): 0.407 Positive Predictive Value TurboFold(seed): 0.703 Murlet(20): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 Murlet(20): 0.492 Sensitivity RNASampler(seed): 0.434 Murlet(20): 0.374 Positive Predictive Value RNASampler(seed): 0.754 Murlet(20): 0.651 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.665 Murlet(20): 0.581 Sensitivity PPfold(20): 0.519 Murlet(20): 0.433 Positive Predictive Value PPfold(20): 0.859 Murlet(20): 0.785 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.592 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.437 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.807 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.98172311752e-08
UNAFold	34 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.650 UNAFold: 0.557 Sensitivity MXScarna(seed): 0.533 UNAFold: 0.498 Positive Predictive Value MXScarna(seed): 0.796 UNAFold: 0.627 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 UNAFold: 0.589 Sensitivity CentroidAlifold(20): 0.540 UNAFold: 0.516 Positive Predictive Value CentroidAlifold(20): 0.897 UNAFold: 0.677 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	25 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.659 UNAFold: 0.589 Sensitivity RNAalifold(20): 0.510 UNAFold: 0.513 Positive Predictive Value RNAalifold(20): 0.854 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	25 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.640 UNAFold: 0.589 Sensitivity RNASampler(20): 0.491 UNAFold: 0.513 Positive Predictive Value RNASampler(20): 0.839 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	52 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.517 UNAFold: 0.457 Sensitivity CentroidFold: 0.434 UNAFold: 0.412 Positive Predictive Value CentroidFold: 0.616 UNAFold: 0.508 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.621 UNAFold: 0.589 Sensitivity MXScarna(20): 0.518 UNAFold: 0.513 Positive Predictive Value MXScarna(20): 0.748 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 UNAFold: 0.553 Sensitivity CentroidAlifold(seed): 0.377 UNAFold: 0.494 Positive Predictive Value CentroidAlifold(seed): 0.925 UNAFold: 0.624 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.526 UNAFold: 0.445 Sensitivity Contrafold: 0.462 UNAFold: 0.395 Positive Predictive Value Contrafold: 0.599 UNAFold: 0.502 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.464 UNAFold: 0.445 Sensitivity Sfold: 0.387 UNAFold: 0.395 Positive Predictive Value Sfold: 0.557 UNAFold: 0.502 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.558 UNAFold: 0.504 Sensitivity MaxExpect: 0.478 UNAFold: 0.437 Positive Predictive Value MaxExpect: 0.651 UNAFold: 0.582 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 1.10039559051e-07	17 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.567 UNAFold: 0.497 Sensitivity IPknot: 0.463 UNAFold: 0.433 Positive Predictive Value IPknot: 0.702 UNAFold: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	18 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 UNAFold: 0.494 Sensitivity CentroidHomfold‑LAST: 0.397 UNAFold: 0.427 Positive Predictive Value CentroidHomfold‑LAST: 0.784 UNAFold: 0.579 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.86109605532e-08	55 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.571 HotKnots: 0.569 Sensitivity UNAFold: 0.500 HotKnots: 0.506 Positive Predictive Value UNAFold: 0.655 HotKnots: 0.644 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 0.00662473470579	25 Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.601 UNAFold: 0.589 Sensitivity Carnac(20): 0.397 UNAFold: 0.513 Positive Predictive Value Carnac(20): 0.914 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 7.27211512036e-08	14 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.601 UNAFold: 0.451 Sensitivity ContextFold: 0.483 UNAFold: 0.400 Positive Predictive Value ContextFold: 0.754 UNAFold: 0.516 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	32 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.561 UNAFold: 0.560 Sensitivity ProbKnot: 0.514 UNAFold: 0.501 Positive Predictive Value ProbKnot: 0.617 UNAFold: 0.631 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.0173545140323	25 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.592 UNAFold: 0.589 Sensitivity Murlet(20): 0.437 UNAFold: 0.513 Positive Predictive Value Murlet(20): 0.807 UNAFold: 0.681 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.00572131440621		= UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.572 Fold: 0.570 Sensitivity UNAFold: 0.512 Fold: 0.509 Positive Predictive Value UNAFold: 0.644 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.014979478926	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.445 RNAfold: 0.441 Sensitivity UNAFold: 0.395 RNAfold: 0.395 Positive Predictive Value UNAFold: 0.502 RNAfold: 0.492 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.445 PknotsRG: 0.433 Sensitivity UNAFold: 0.395 PknotsRG: 0.389 Positive Predictive Value UNAFold: 0.502 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	= UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.612 Cylofold: 0.607 Sensitivity UNAFold: 0.535 Cylofold: 0.512 Positive Predictive Value UNAFold: 0.706 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00868735948554	+ UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.544 RNAalifold(seed): 0.539 Sensitivity UNAFold: 0.486 RNAalifold(seed): 0.336 Positive Predictive Value UNAFold: 0.613 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.00666128245e-05	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.571 RNAshapes: 0.539 Sensitivity UNAFold: 0.500 RNAshapes: 0.470 Positive Predictive Value UNAFold: 0.655 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	= UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.429 Afold: 0.427 Sensitivity UNAFold: 0.383 Afold: 0.386 Positive Predictive Value UNAFold: 0.481 Afold: 0.474 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 0.0336931477392	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.445 McQFold: 0.368 Sensitivity UNAFold: 0.395 McQFold: 0.281 Positive Predictive Value UNAFold: 0.502 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.595 Pknots: 0.547 Sensitivity UNAFold: 0.514 Pknots: 0.489 Positive Predictive Value UNAFold: 0.695 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.571 RNAsubopt: 0.531 Sensitivity UNAFold: 0.500 RNAsubopt: 0.473 Positive Predictive Value UNAFold: 0.655 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.594 RSpredict(20): 0.559 Sensitivity UNAFold: 0.521 RSpredict(20): 0.446 Positive Predictive Value UNAFold: 0.681 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-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: 4.11681652902e-07	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.571 Vsfold4: 0.478 Sensitivity UNAFold: 0.500 Vsfold4: 0.399 Positive Predictive Value UNAFold: 0.655 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.589 Mastr(20): 0.523 Sensitivity UNAFold: 0.513 Mastr(20): 0.348 Positive Predictive Value UNAFold: 0.681 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	= UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.451 RNASLOpt: 0.443 Sensitivity UNAFold: 0.400 RNASLOpt: 0.365 Positive Predictive Value UNAFold: 0.516 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.013974662571	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.592 Murlet(seed): 0.475 Sensitivity UNAFold: 0.507 Murlet(seed): 0.270 Positive Predictive Value UNAFold: 0.697 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.571 Vsfold5: 0.426 Sensitivity UNAFold: 0.500 Vsfold5: 0.359 Positive Predictive Value UNAFold: 0.655 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.497 RNAwolf: 0.399 Sensitivity UNAFold: 0.433 RNAwolf: 0.368 Positive Predictive Value UNAFold: 0.578 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-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: 0.591 RDfolder: 0.443 Sensitivity UNAFold: 0.499 RDfolder: 0.342 Positive Predictive Value UNAFold: 0.707 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.597 MCFold: 0.419 Sensitivity UNAFold: 0.520 MCFold: 0.437 Positive Predictive Value UNAFold: 0.691 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.557 RSpredict(seed): 0.204 Sensitivity UNAFold: 0.498 RSpredict(seed): 0.088 Positive Predictive Value UNAFold: 0.627 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.490 PPfold(seed): 0.102 Sensitivity UNAFold: 0.417 PPfold(seed): 0.020 Positive Predictive Value UNAFold: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.615 Carnac(seed): 0.139 Sensitivity UNAFold: 0.537 Carnac(seed): 0.019 Positive Predictive Value UNAFold: 0.710 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	? UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.463 NanoFolder: 0.366 Sensitivity UNAFold: 0.405 NanoFolder: 0.376 Positive Predictive Value UNAFold: 0.536 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.538 UNAFold: 0.525 Sensitivity Multilign(seed): 0.420 UNAFold: 0.428 Positive Predictive Value Multilign(seed): 0.699 UNAFold: 0.656 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.556 Multilign(20): 0.540 Sensitivity UNAFold: 0.474 Multilign(20): 0.456 Positive Predictive Value UNAFold: 0.660 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 UNAFold: 0.413 Sensitivity PETfold_pre2.0(seed): 0.551 UNAFold: 0.358 Positive Predictive Value PETfold_pre2.0(seed): 0.843 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.594 UNAFold: 0.556 Sensitivity TurboFold(20): 0.470 UNAFold: 0.474 Positive Predictive Value TurboFold(20): 0.756 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: N/A CMfinder(20): N/A Sensitivity UNAFold: N/A CMfinder(20): N/A Positive Predictive Value UNAFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 UNAFold: 0.478 Sensitivity PETfold_pre2.0(20): 0.497 UNAFold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 UNAFold: 0.551 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.517 UNAFold: 0.498 Sensitivity TurboFold(seed): 0.422 UNAFold: 0.426 Positive Predictive Value TurboFold(seed): 0.642 UNAFold: 0.589 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.546 UNAFold: 0.510 Sensitivity RNASampler(seed): 0.409 UNAFold: 0.457 Positive Predictive Value RNASampler(seed): 0.734 UNAFold: 0.575 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.665 UNAFold: 0.556 Sensitivity PPfold(20): 0.519 UNAFold: 0.474 Positive Predictive Value PPfold(20): 0.859 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.555 Mastr(seed): 0.000 Sensitivity UNAFold: 0.493 Mastr(seed): 0.000 Positive Predictive Value UNAFold: 0.628 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	22 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.636 Fold: 0.560 Sensitivity MXScarna(seed): 0.518 Fold: 0.504 Positive Predictive Value MXScarna(seed): 0.783 Fold: 0.627 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	15 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Fold: 0.581 Sensitivity CentroidAlifold(20): 0.525 Fold: 0.512 Positive Predictive Value CentroidAlifold(20): 0.912 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	15 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.646 Fold: 0.581 Sensitivity RNAalifold(20): 0.494 Fold: 0.512 Positive Predictive Value RNAalifold(20): 0.847 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.82627677697e-08	15 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.633 Fold: 0.581 Sensitivity RNASampler(20): 0.478 Fold: 0.512 Positive Predictive Value RNASampler(20): 0.843 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	34 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.605 Fold: 0.570 Sensitivity CentroidFold: 0.517 Fold: 0.509 Positive Predictive Value CentroidFold: 0.712 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.618 Fold: 0.581 Sensitivity MXScarna(20): 0.512 Fold: 0.512 Positive Predictive Value MXScarna(20): 0.748 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	22 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 Fold: 0.560 Sensitivity CentroidAlifold(seed): 0.369 Fold: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.922 Fold: 0.627 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.05835476236e-07	34 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.588 Fold: 0.570 Sensitivity Contrafold: 0.523 Fold: 0.509 Positive Predictive Value Contrafold: 0.666 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.581 Fold: 0.570 Sensitivity Sfold: 0.492 Fold: 0.509 Positive Predictive Value Sfold: 0.689 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08	34 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.578 Fold: 0.570 Sensitivity MaxExpect: 0.511 Fold: 0.509 Positive Predictive Value MaxExpect: 0.658 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.567 Fold: 0.487 Sensitivity IPknot: 0.463 Fold: 0.423 Positive Predictive Value IPknot: 0.702 Fold: 0.568 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	18 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Fold: 0.484 Sensitivity CentroidHomfold‑LAST: 0.397 Fold: 0.418 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Fold: 0.569 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	34 HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.581 Fold: 0.570 Sensitivity HotKnots: 0.528 Fold: 0.509 Positive Predictive Value HotKnots: 0.644 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.6410608252e-08	15 Carnac(20) vs Fold Matthews Correlation Coefficient Carnac(20): 0.585 Fold: 0.581 Sensitivity Carnac(20): 0.372 Fold: 0.512 Positive Predictive Value Carnac(20): 0.923 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000701583593059	14 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.601 Fold: 0.447 Sensitivity ContextFold: 0.483 Fold: 0.393 Positive Predictive Value ContextFold: 0.754 Fold: 0.518 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.47941000302e-08	32 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.561 Fold: 0.559 Sensitivity ProbKnot: 0.514 Fold: 0.498 Positive Predictive Value ProbKnot: 0.617 Fold: 0.630 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.000230581642477	15 Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.590 Fold: 0.581 Sensitivity Murlet(20): 0.432 Fold: 0.512 Positive Predictive Value Murlet(20): 0.808 Fold: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000569606146608	34 UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.572 Fold: 0.570 Sensitivity UNAFold: 0.512 Fold: 0.509 Positive Predictive Value UNAFold: 0.644 Fold: 0.643 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 0.014979478926		+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.570 RNAfold: 0.556 Sensitivity Fold: 0.509 RNAfold: 0.501 Positive Predictive Value Fold: 0.643 RNAfold: 0.622 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.70738736246e-07	+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.570 PknotsRG: 0.560 Sensitivity Fold: 0.509 PknotsRG: 0.509 Positive Predictive Value Fold: 0.643 PknotsRG: 0.621 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.83595875043e-07	+ Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.614 Cylofold: 0.607 Sensitivity Fold: 0.536 Cylofold: 0.512 Positive Predictive Value Fold: 0.709 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000778510229985	- RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.505 Fold: 0.476 Sensitivity RNAalifold(seed): 0.304 Fold: 0.434 Positive Predictive Value RNAalifold(seed): 0.844 Fold: 0.525 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.570 RNAshapes: 0.556 Sensitivity Fold: 0.509 RNAshapes: 0.493 Positive Predictive Value Fold: 0.643 RNAshapes: 0.631 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.547 Afold: 0.545 Sensitivity Fold: 0.504 Afold: 0.510 Positive Predictive Value Fold: 0.598 Afold: 0.586 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 8.01634185435e-05	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.570 McQFold: 0.552 Sensitivity Fold: 0.509 McQFold: 0.478 Positive Predictive Value Fold: 0.643 McQFold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.75828119249e-07	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.606 Pknots: 0.582 Sensitivity Fold: 0.532 Pknots: 0.520 Positive Predictive Value Fold: 0.697 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.570 RNAsubopt: 0.559 Sensitivity Fold: 0.509 RNAsubopt: 0.504 Positive Predictive Value Fold: 0.643 RNAsubopt: 0.623 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.581 RSpredict(20): 0.538 Sensitivity Fold: 0.512 RSpredict(20): 0.424 Positive Predictive Value Fold: 0.662 RSpredict(20): 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.9966815982e-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: 2.7402423548e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.570 Vsfold4: 0.479 Sensitivity Fold: 0.509 Vsfold4: 0.406 Positive Predictive Value Fold: 0.643 Vsfold4: 0.571 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.581 Mastr(20): 0.483 Sensitivity Fold: 0.512 Mastr(20): 0.297 Positive Predictive Value Fold: 0.662 Mastr(20): 0.791 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	= Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.447 RNASLOpt: 0.443 Sensitivity Fold: 0.393 RNASLOpt: 0.365 Positive Predictive Value Fold: 0.518 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.976227115967	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.493 Murlet(seed): 0.452 Sensitivity Fold: 0.434 Murlet(seed): 0.249 Positive Predictive Value Fold: 0.567 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.98343147122e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.570 Vsfold5: 0.439 Sensitivity Fold: 0.509 Vsfold5: 0.374 Positive Predictive Value Fold: 0.643 Vsfold5: 0.521 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.487 RNAwolf: 0.399 Sensitivity Fold: 0.423 RNAwolf: 0.368 Positive Predictive Value Fold: 0.568 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-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: 3.16042554876e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.581 RDfolder: 0.429 Sensitivity Fold: 0.499 RDfolder: 0.333 Positive Predictive Value Fold: 0.685 RDfolder: 0.564 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.585 MCFold: 0.448 Sensitivity Fold: 0.518 MCFold: 0.466 Positive Predictive Value Fold: 0.667 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.560 RSpredict(seed): 0.134 Sensitivity Fold: 0.504 RSpredict(seed): 0.054 Positive Predictive Value Fold: 0.627 RSpredict(seed): 0.340 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.516 PPfold(seed): 0.102 Sensitivity Fold: 0.443 PPfold(seed): 0.020 Positive Predictive Value Fold: 0.610 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.551 Carnac(seed): 0.088 Sensitivity Fold: 0.486 Carnac(seed): 0.008 Positive Predictive Value Fold: 0.630 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	? Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.523 NanoFolder: 0.366 Sensitivity Fold: 0.453 NanoFolder: 0.376 Positive Predictive Value Fold: 0.610 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.538 Fold: 0.504 Sensitivity Multilign(seed): 0.420 Fold: 0.413 Positive Predictive Value Multilign(seed): 0.699 Fold: 0.626 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.540 Fold: 0.510 Sensitivity Multilign(20): 0.456 Fold: 0.441 Positive Predictive Value Multilign(20): 0.647 Fold: 0.598 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Fold: 0.465 Sensitivity PETfold_pre2.0(seed): 0.551 Fold: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Fold: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.594 Fold: 0.510 Sensitivity TurboFold(20): 0.470 Fold: 0.441 Positive Predictive Value TurboFold(20): 0.756 Fold: 0.598 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: N/A CMfinder(20): N/A Sensitivity Fold: N/A CMfinder(20): N/A Positive Predictive Value Fold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Fold: 0.429 Sensitivity PETfold_pre2.0(20): 0.497 Fold: 0.377 Positive Predictive Value PETfold_pre2.0(20): 0.790 Fold: 0.496 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.517 Fold: 0.456 Sensitivity TurboFold(seed): 0.422 Fold: 0.392 Positive Predictive Value TurboFold(seed): 0.642 Fold: 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.467 Fold: 0.365 Sensitivity RNASampler(seed): 0.341 Fold: 0.341 Positive Predictive Value RNASampler(seed): 0.644 Fold: 0.397 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.665 Fold: 0.510 Sensitivity PPfold(20): 0.519 Fold: 0.441 Positive Predictive Value PPfold(20): 0.859 Fold: 0.598 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.560 Mastr(seed): 0.000 Sensitivity Fold: 0.504 Mastr(seed): 0.000 Positive Predictive Value Fold: 0.627 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08
RNAfold	34 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.650 RNAfold: 0.562 Sensitivity MXScarna(seed): 0.533 RNAfold: 0.506 Positive Predictive Value MXScarna(seed): 0.796 RNAfold: 0.627 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAfold: 0.567 Sensitivity CentroidAlifold(20): 0.540 RNAfold: 0.504 Positive Predictive Value CentroidAlifold(20): 0.897 RNAfold: 0.643 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.659 RNAfold: 0.569 Sensitivity RNAalifold(20): 0.510 RNAfold: 0.502 Positive Predictive Value RNAalifold(20): 0.854 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.640 RNAfold: 0.569 Sensitivity RNASampler(20): 0.491 RNAfold: 0.502 Positive Predictive Value RNASampler(20): 0.839 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	52 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.517 RNAfold: 0.448 Sensitivity CentroidFold: 0.434 RNAfold: 0.408 Positive Predictive Value CentroidFold: 0.616 RNAfold: 0.493 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.621 RNAfold: 0.569 Sensitivity MXScarna(20): 0.518 RNAfold: 0.502 Positive Predictive Value MXScarna(20): 0.748 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	33 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RNAfold: 0.558 Sensitivity CentroidAlifold(seed): 0.377 RNAfold: 0.503 Positive Predictive Value CentroidAlifold(seed): 0.925 RNAfold: 0.623 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.526 RNAfold: 0.441 Sensitivity Contrafold: 0.462 RNAfold: 0.395 Positive Predictive Value Contrafold: 0.599 RNAfold: 0.492 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.464 RNAfold: 0.441 Sensitivity Sfold: 0.387 RNAfold: 0.395 Positive Predictive Value Sfold: 0.557 RNAfold: 0.492 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.558 RNAfold: 0.491 Sensitivity MaxExpect: 0.478 RNAfold: 0.430 Positive Predictive Value MaxExpect: 0.651 RNAfold: 0.561 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.567 RNAfold: 0.524 Sensitivity IPknot: 0.463 RNAfold: 0.451 Positive Predictive Value IPknot: 0.702 RNAfold: 0.615 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	18 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 RNAfold: 0.520 Sensitivity CentroidHomfold‑LAST: 0.397 RNAfold: 0.444 Positive Predictive Value CentroidHomfold‑LAST: 0.784 RNAfold: 0.615 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	55 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.569 RNAfold: 0.551 Sensitivity HotKnots: 0.506 RNAfold: 0.487 Positive Predictive Value HotKnots: 0.644 RNAfold: 0.628 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.601 RNAfold: 0.569 Sensitivity Carnac(20): 0.397 RNAfold: 0.502 Positive Predictive Value Carnac(20): 0.914 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	14 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.601 RNAfold: 0.483 Sensitivity ContextFold: 0.483 RNAfold: 0.423 Positive Predictive Value ContextFold: 0.754 RNAfold: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.66062906821e-08	32 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.561 RNAfold: 0.559 Sensitivity ProbKnot: 0.514 RNAfold: 0.502 Positive Predictive Value ProbKnot: 0.617 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.10675413758	25 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.592 RNAfold: 0.569 Sensitivity Murlet(20): 0.437 RNAfold: 0.502 Positive Predictive Value Murlet(20): 0.807 RNAfold: 0.649 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 6.32937386918e-08	58 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.445 RNAfold: 0.441 Sensitivity UNAFold: 0.395 RNAfold: 0.395 Positive Predictive Value UNAFold: 0.502 RNAfold: 0.492 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.570 RNAfold: 0.556 Sensitivity Fold: 0.509 RNAfold: 0.501 Positive Predictive Value Fold: 0.643 RNAfold: 0.622 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.70738736246e-07		+ RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.441 PknotsRG: 0.433 Sensitivity RNAfold: 0.395 PknotsRG: 0.389 Positive Predictive Value RNAfold: 0.492 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.607 RNAfold: 0.586 Sensitivity Cylofold: 0.512 RNAfold: 0.513 Positive Predictive Value Cylofold: 0.727 RNAfold: 0.677 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.559 RNAalifold(seed): 0.539 Sensitivity RNAfold: 0.506 RNAalifold(seed): 0.336 Positive Predictive Value RNAfold: 0.621 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.66763272401e-08	+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.551 RNAshapes: 0.539 Sensitivity RNAfold: 0.487 RNAshapes: 0.470 Positive Predictive Value RNAfold: 0.628 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.427 RNAfold: 0.423 Sensitivity Afold: 0.386 RNAfold: 0.382 Positive Predictive Value Afold: 0.474 RNAfold: 0.468 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 2.29562105844e-05	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.441 McQFold: 0.368 Sensitivity RNAfold: 0.395 McQFold: 0.281 Positive Predictive Value RNAfold: 0.492 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.572 Pknots: 0.547 Sensitivity RNAfold: 0.497 Pknots: 0.489 Positive Predictive Value RNAfold: 0.666 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 2.28033735003e-07	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.551 RNAsubopt: 0.531 Sensitivity RNAfold: 0.487 RNAsubopt: 0.473 Positive Predictive Value RNAfold: 0.628 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.572 RSpredict(20): 0.559 Sensitivity RNAfold: 0.509 RSpredict(20): 0.446 Positive Predictive Value RNAfold: 0.647 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.000176748592514	+ 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: 2.84041289224e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.551 Vsfold4: 0.478 Sensitivity RNAfold: 0.487 Vsfold4: 0.399 Positive Predictive Value RNAfold: 0.628 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.569 Mastr(20): 0.523 Sensitivity RNAfold: 0.502 Mastr(20): 0.348 Positive Predictive Value RNAfold: 0.649 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.483 RNASLOpt: 0.443 Sensitivity RNAfold: 0.423 RNASLOpt: 0.365 Positive Predictive Value RNAfold: 0.560 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.614 Murlet(seed): 0.475 Sensitivity RNAfold: 0.531 Murlet(seed): 0.270 Positive Predictive Value RNAfold: 0.715 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.551 Vsfold5: 0.426 Sensitivity RNAfold: 0.487 Vsfold5: 0.359 Positive Predictive Value RNAfold: 0.628 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.524 RNAwolf: 0.399 Sensitivity RNAfold: 0.451 RNAwolf: 0.368 Positive Predictive Value RNAfold: 0.615 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-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: 0.568 RDfolder: 0.443 Sensitivity RNAfold: 0.482 RDfolder: 0.342 Positive Predictive Value RNAfold: 0.679 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.582 MCFold: 0.419 Sensitivity RNAfold: 0.510 MCFold: 0.437 Positive Predictive Value RNAfold: 0.670 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.562 RSpredict(seed): 0.204 Sensitivity RNAfold: 0.506 RSpredict(seed): 0.088 Positive Predictive Value RNAfold: 0.627 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.565 PPfold(seed): 0.102 Sensitivity RNAfold: 0.476 PPfold(seed): 0.020 Positive Predictive Value RNAfold: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.61680779366e-09	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.615 Carnac(seed): 0.139 Sensitivity RNAfold: 0.542 Carnac(seed): 0.019 Positive Predictive Value RNAfold: 0.703 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.546 NanoFolder: 0.366 Sensitivity RNAfold: 0.473 NanoFolder: 0.376 Positive Predictive Value RNAfold: 0.636 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? RNAfold vs Multilign(seed) Matthews Correlation Coefficient RNAfold: 0.621 Multilign(seed): 0.538 Sensitivity RNAfold: 0.507 Multilign(seed): 0.420 Positive Predictive Value RNAfold: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.555 Multilign(20): 0.540 Sensitivity RNAfold: 0.474 Multilign(20): 0.456 Positive Predictive Value RNAfold: 0.656 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAfold: 0.515 Sensitivity PETfold_pre2.0(seed): 0.551 RNAfold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.594 RNAfold: 0.555 Sensitivity TurboFold(20): 0.470 RNAfold: 0.474 Positive Predictive Value TurboFold(20): 0.756 RNAfold: 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: N/A CMfinder(20): N/A Sensitivity RNAfold: N/A CMfinder(20): N/A Positive Predictive Value RNAfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAfold: 0.476 Sensitivity PETfold_pre2.0(20): 0.497 RNAfold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.544 TurboFold(seed): 0.517 Sensitivity RNAfold: 0.468 TurboFold(seed): 0.422 Positive Predictive Value RNAfold: 0.641 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.549 RNASampler(seed): 0.546 Sensitivity RNAfold: 0.496 RNASampler(seed): 0.409 Positive Predictive Value RNAfold: 0.612 RNASampler(seed): 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.665 RNAfold: 0.555 Sensitivity PPfold(20): 0.519 RNAfold: 0.474 Positive Predictive Value PPfold(20): 0.859 RNAfold: 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.559 Mastr(seed): 0.000 Sensitivity RNAfold: 0.501 Mastr(seed): 0.000 Positive Predictive Value RNAfold: 0.629 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	34 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.650 PknotsRG: 0.569 Sensitivity MXScarna(seed): 0.533 PknotsRG: 0.515 Positive Predictive Value MXScarna(seed): 0.796 PknotsRG: 0.633 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	23 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.695 PknotsRG: 0.579 Sensitivity CentroidAlifold(20): 0.540 PknotsRG: 0.517 Positive Predictive Value CentroidAlifold(20): 0.897 PknotsRG: 0.652 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.659 PknotsRG: 0.581 Sensitivity RNAalifold(20): 0.510 PknotsRG: 0.516 Positive Predictive Value RNAalifold(20): 0.854 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.640 PknotsRG: 0.581 Sensitivity RNASampler(20): 0.491 PknotsRG: 0.516 Positive Predictive Value RNASampler(20): 0.839 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	52 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.517 PknotsRG: 0.441 Sensitivity CentroidFold: 0.434 PknotsRG: 0.403 Positive Predictive Value CentroidFold: 0.616 PknotsRG: 0.484 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.621 PknotsRG: 0.581 Sensitivity MXScarna(20): 0.518 PknotsRG: 0.516 Positive Predictive Value MXScarna(20): 0.748 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	33 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 PknotsRG: 0.566 Sensitivity CentroidAlifold(seed): 0.377 PknotsRG: 0.511 Positive Predictive Value CentroidAlifold(seed): 0.925 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 4.48494289621e-08	58 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.526 PknotsRG: 0.433 Sensitivity Contrafold: 0.462 PknotsRG: 0.389 Positive Predictive Value Contrafold: 0.599 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.464 PknotsRG: 0.433 Sensitivity Sfold: 0.387 PknotsRG: 0.389 Positive Predictive Value Sfold: 0.557 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.558 PknotsRG: 0.481 Sensitivity MaxExpect: 0.478 PknotsRG: 0.423 Positive Predictive Value MaxExpect: 0.651 PknotsRG: 0.547 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.567 PknotsRG: 0.539 Sensitivity IPknot: 0.463 PknotsRG: 0.473 Positive Predictive Value IPknot: 0.702 PknotsRG: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	18 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 PknotsRG: 0.535 Sensitivity CentroidHomfold‑LAST: 0.397 PknotsRG: 0.466 Positive Predictive Value CentroidHomfold‑LAST: 0.784 PknotsRG: 0.621 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	55 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.569 PknotsRG: 0.552 Sensitivity HotKnots: 0.506 PknotsRG: 0.492 Positive Predictive Value HotKnots: 0.644 PknotsRG: 0.625 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.601 PknotsRG: 0.581 Sensitivity Carnac(20): 0.397 PknotsRG: 0.516 Positive Predictive Value Carnac(20): 0.914 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 8.68922211961e-08	14 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.601 PknotsRG: 0.506 Sensitivity ContextFold: 0.483 PknotsRG: 0.453 Positive Predictive Value ContextFold: 0.754 PknotsRG: 0.573 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	32 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.563 ProbKnot: 0.561 Sensitivity PknotsRG: 0.511 ProbKnot: 0.514 Positive Predictive Value PknotsRG: 0.625 ProbKnot: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.0853441262641	25 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.592 PknotsRG: 0.581 Sensitivity Murlet(20): 0.437 PknotsRG: 0.516 Positive Predictive Value Murlet(20): 0.807 PknotsRG: 0.659 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.94602596382e-06	58 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.445 PknotsRG: 0.433 Sensitivity UNAFold: 0.395 PknotsRG: 0.389 Positive Predictive Value UNAFold: 0.502 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.570 PknotsRG: 0.560 Sensitivity Fold: 0.509 PknotsRG: 0.509 Positive Predictive Value Fold: 0.643 PknotsRG: 0.621 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 1.83595875043e-07	58 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.441 PknotsRG: 0.433 Sensitivity RNAfold: 0.395 PknotsRG: 0.389 Positive Predictive Value RNAfold: 0.492 PknotsRG: 0.482 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.607 PknotsRG: 0.593 Sensitivity Cylofold: 0.512 PknotsRG: 0.525 Positive Predictive Value Cylofold: 0.727 PknotsRG: 0.677 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.33522642e-07	+ PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.573 RNAalifold(seed): 0.539 Sensitivity PknotsRG: 0.521 RNAalifold(seed): 0.336 Positive Predictive Value PknotsRG: 0.632 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.552 RNAshapes: 0.539 Sensitivity PknotsRG: 0.492 RNAshapes: 0.470 Positive Predictive Value PknotsRG: 0.625 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.85233844192e-08	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.427 PknotsRG: 0.413 Sensitivity Afold: 0.386 PknotsRG: 0.374 Positive Predictive Value Afold: 0.474 PknotsRG: 0.456 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.433 McQFold: 0.368 Sensitivity PknotsRG: 0.389 McQFold: 0.281 Positive Predictive Value PknotsRG: 0.482 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.574 Pknots: 0.547 Sensitivity PknotsRG: 0.503 Pknots: 0.489 Positive Predictive Value PknotsRG: 0.661 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.552 RNAsubopt: 0.531 Sensitivity PknotsRG: 0.492 RNAsubopt: 0.473 Positive Predictive Value PknotsRG: 0.625 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.584 RSpredict(20): 0.559 Sensitivity PknotsRG: 0.522 RSpredict(20): 0.446 Positive Predictive Value PknotsRG: 0.657 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 7.95107997107e-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: 2.36983135185e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.552 Vsfold4: 0.478 Sensitivity PknotsRG: 0.492 Vsfold4: 0.399 Positive Predictive Value PknotsRG: 0.625 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.581 Mastr(20): 0.523 Sensitivity PknotsRG: 0.516 Mastr(20): 0.348 Positive Predictive Value PknotsRG: 0.659 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.506 RNASLOpt: 0.443 Sensitivity PknotsRG: 0.453 RNASLOpt: 0.365 Positive Predictive Value PknotsRG: 0.573 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.635 Murlet(seed): 0.475 Sensitivity PknotsRG: 0.555 Murlet(seed): 0.270 Positive Predictive Value PknotsRG: 0.733 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.552 Vsfold5: 0.426 Sensitivity PknotsRG: 0.492 Vsfold5: 0.359 Positive Predictive Value PknotsRG: 0.625 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.539 RNAwolf: 0.399 Sensitivity PknotsRG: 0.473 RNAwolf: 0.368 Positive Predictive Value PknotsRG: 0.621 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-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: 0.581 RDfolder: 0.443 Sensitivity PknotsRG: 0.497 RDfolder: 0.342 Positive Predictive Value PknotsRG: 0.688 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.583 MCFold: 0.419 Sensitivity PknotsRG: 0.516 MCFold: 0.437 Positive Predictive Value PknotsRG: 0.665 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.569 RSpredict(seed): 0.204 Sensitivity PknotsRG: 0.515 RSpredict(seed): 0.088 Positive Predictive Value PknotsRG: 0.633 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.600 PPfold(seed): 0.102 Sensitivity PknotsRG: 0.513 PPfold(seed): 0.020 Positive Predictive Value PknotsRG: 0.709 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.631 Carnac(seed): 0.139 Sensitivity PknotsRG: 0.560 Carnac(seed): 0.019 Positive Predictive Value PknotsRG: 0.716 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	? PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.550 NanoFolder: 0.366 Sensitivity PknotsRG: 0.482 NanoFolder: 0.376 Positive Predictive Value PknotsRG: 0.633 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.616 Multilign(seed): 0.538 Sensitivity PknotsRG: 0.500 Multilign(seed): 0.420 Positive Predictive Value PknotsRG: 0.767 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.600 Multilign(20): 0.540 Sensitivity PknotsRG: 0.522 Multilign(20): 0.456 Positive Predictive Value PknotsRG: 0.695 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PknotsRG: 0.569 Sensitivity PETfold_pre2.0(seed): 0.551 PknotsRG: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PknotsRG: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.600 TurboFold(20): 0.594 Sensitivity PknotsRG: 0.522 TurboFold(20): 0.470 Positive Predictive Value PknotsRG: 0.695 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(20): N/A Sensitivity PknotsRG: N/A CMfinder(20): N/A Positive Predictive Value PknotsRG: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(20): 0.497 PknotsRG: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 PknotsRG: 0.618 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.592 TurboFold(seed): 0.517 Sensitivity PknotsRG: 0.517 TurboFold(seed): 0.422 Positive Predictive Value PknotsRG: 0.683 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PknotsRG Matthews Correlation Coefficient RNASampler(seed): 0.546 PknotsRG: 0.544 Sensitivity RNASampler(seed): 0.409 PknotsRG: 0.493 Positive Predictive Value RNASampler(seed): 0.734 PknotsRG: 0.604 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.665 PknotsRG: 0.600 Sensitivity PPfold(20): 0.519 PknotsRG: 0.522 Positive Predictive Value PPfold(20): 0.859 PknotsRG: 0.695 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.568 Mastr(seed): 0.000 Sensitivity PknotsRG: 0.511 Mastr(seed): 0.000 Positive Predictive Value PknotsRG: 0.636 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08
Cylofold	16 Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.659 MXScarna(seed): 0.657 Sensitivity Cylofold: 0.554 MXScarna(seed): 0.535 Positive Predictive Value Cylofold: 0.789 MXScarna(seed): 0.812 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.0467887381528	11 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.740 Cylofold: 0.661 Sensitivity CentroidAlifold(20): 0.584 Cylofold: 0.553 Positive Predictive Value CentroidAlifold(20): 0.941 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.87872347734e-08	11 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.706 Cylofold: 0.661 Sensitivity RNAalifold(20): 0.560 Cylofold: 0.553 Positive Predictive Value RNAalifold(20): 0.895 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	11 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.702 Cylofold: 0.661 Sensitivity RNASampler(20): 0.545 Cylofold: 0.553 Positive Predictive Value RNASampler(20): 0.907 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	28 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.646 Cylofold: 0.607 Sensitivity CentroidFold: 0.539 Cylofold: 0.512 Positive Predictive Value CentroidFold: 0.780 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	11 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.676 Cylofold: 0.661 Sensitivity MXScarna(20): 0.560 Cylofold: 0.553 Positive Predictive Value MXScarna(20): 0.821 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59979455159e-06	16 Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.659 CentroidAlifold(seed): 0.601 Sensitivity Cylofold: 0.554 CentroidAlifold(seed): 0.369 Positive Predictive Value Cylofold: 0.789 CentroidAlifold(seed): 0.985 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.69132796717e-08	28 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.629 Cylofold: 0.607 Sensitivity Contrafold: 0.546 Cylofold: 0.512 Positive Predictive Value Contrafold: 0.730 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 7.39132889808e-08	28 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.616 Cylofold: 0.607 Sensitivity Sfold: 0.512 Cylofold: 0.512 Positive Predictive Value Sfold: 0.748 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000380952570321	28 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.623 Cylofold: 0.607 Sensitivity MaxExpect: 0.539 Cylofold: 0.512 Positive Predictive Value MaxExpect: 0.726 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.74095189891e-07	15 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.586 Cylofold: 0.537 Sensitivity IPknot: 0.474 Cylofold: 0.454 Positive Predictive Value IPknot: 0.732 Cylofold: 0.643 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	16 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.581 Cylofold: 0.533 Sensitivity CentroidHomfold‑LAST: 0.395 Cylofold: 0.446 Positive Predictive Value CentroidHomfold‑LAST: 0.860 Cylofold: 0.647 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.55268413083e-08	28 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.625 Cylofold: 0.607 Sensitivity HotKnots: 0.555 Cylofold: 0.512 Positive Predictive Value HotKnots: 0.709 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.43288893557e-07	11 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.661 Carnac(20): 0.635 Sensitivity Cylofold: 0.553 Carnac(20): 0.435 Positive Predictive Value Cylofold: 0.796 Carnac(20): 0.932 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.95743112377e-06	12 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.608 Cylofold: 0.492 Sensitivity ContextFold: 0.492 Cylofold: 0.422 Positive Predictive Value ContextFold: 0.759 Cylofold: 0.584 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08	27 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.608 Cylofold: 0.599 Sensitivity ProbKnot: 0.547 Cylofold: 0.503 Positive Predictive Value ProbKnot: 0.682 Cylofold: 0.720 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.10701214729e-05	11 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.685 Cylofold: 0.661 Sensitivity Murlet(20): 0.528 Cylofold: 0.553 Positive Predictive Value Murlet(20): 0.893 Cylofold: 0.796 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.35850794473e-08	28 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.612 Cylofold: 0.607 Sensitivity UNAFold: 0.535 Cylofold: 0.512 Positive Predictive Value UNAFold: 0.706 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00868735948554	28 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.614 Cylofold: 0.607 Sensitivity Fold: 0.536 Cylofold: 0.512 Positive Predictive Value Fold: 0.709 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000778510229985	28 Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.607 RNAfold: 0.586 Sensitivity Cylofold: 0.512 RNAfold: 0.513 Positive Predictive Value Cylofold: 0.727 RNAfold: 0.677 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.607 PknotsRG: 0.593 Sensitivity Cylofold: 0.512 PknotsRG: 0.525 Positive Predictive Value Cylofold: 0.727 PknotsRG: 0.677 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.33522642e-07		? Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.640 RNAalifold(seed): 0.556 Sensitivity Cylofold: 0.532 RNAalifold(seed): 0.362 Positive Predictive Value Cylofold: 0.777 RNAalifold(seed): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.607 RNAshapes: 0.594 Sensitivity Cylofold: 0.512 RNAshapes: 0.516 Positive Predictive Value Cylofold: 0.727 RNAshapes: 0.690 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 9.34100095224e-08	= Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.632 Cylofold: 0.621 Sensitivity Afold: 0.573 Cylofold: 0.533 Positive Predictive Value Afold: 0.703 Cylofold: 0.729 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00238442710916	- McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.641 Cylofold: 0.607 Sensitivity McQFold: 0.546 Cylofold: 0.512 Positive Predictive Value McQFold: 0.758 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	- Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.617 Cylofold: 0.607 Sensitivity Pknots: 0.549 Cylofold: 0.512 Positive Predictive Value Pknots: 0.698 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.27663599501e-06	+ Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.607 RNAsubopt: 0.592 Sensitivity Cylofold: 0.512 RNAsubopt: 0.518 Positive Predictive Value Cylofold: 0.727 RNAsubopt: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.24386558293e-07	+ Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.661 RSpredict(20): 0.618 Sensitivity Cylofold: 0.553 RSpredict(20): 0.501 Positive Predictive Value Cylofold: 0.796 RSpredict(20): 0.768 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-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: 2.12160100812e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.607 Vsfold4: 0.529 Sensitivity Cylofold: 0.512 Vsfold4: 0.441 Positive Predictive Value Cylofold: 0.727 Vsfold4: 0.642 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.69811216434e-08	+ Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.661 Mastr(20): 0.566 Sensitivity Cylofold: 0.553 Mastr(20): 0.384 Positive Predictive Value Cylofold: 0.796 Mastr(20): 0.840 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.05690340753e-08	+ Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.492 RNASLOpt: 0.438 Sensitivity Cylofold: 0.422 RNASLOpt: 0.351 Positive Predictive Value Cylofold: 0.584 RNASLOpt: 0.556 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.61358433984e-08	? Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.619 Murlet(seed): 0.444 Sensitivity Cylofold: 0.509 Murlet(seed): 0.247 Positive Predictive Value Cylofold: 0.758 Murlet(seed): 0.805 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.607 Vsfold5: 0.480 Sensitivity Cylofold: 0.512 Vsfold5: 0.406 Positive Predictive Value Cylofold: 0.727 Vsfold5: 0.575 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.537 RNAwolf: 0.451 Sensitivity Cylofold: 0.454 RNAwolf: 0.411 Positive Predictive Value Cylofold: 0.643 RNAwolf: 0.506 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-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: 2.59578924681e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.642 RDfolder: 0.416 Sensitivity Cylofold: 0.540 RDfolder: 0.323 Positive Predictive Value Cylofold: 0.771 RDfolder: 0.548 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.613 MCFold: 0.460 Sensitivity Cylofold: 0.517 MCFold: 0.476 Positive Predictive Value Cylofold: 0.732 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.659 RSpredict(seed): 0.150 Sensitivity Cylofold: 0.554 RSpredict(seed): 0.061 Positive Predictive Value Cylofold: 0.789 RSpredict(seed): 0.379 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.630 PPfold(seed): 0.128 Sensitivity Cylofold: 0.519 PPfold(seed): 0.022 Positive Predictive Value Cylofold: 0.773 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.646 Carnac(seed): 0.103 Sensitivity Cylofold: 0.533 Carnac(seed): 0.011 Positive Predictive Value Cylofold: 0.787 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	? Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.520 NanoFolder: 0.410 Sensitivity Cylofold: 0.433 NanoFolder: 0.411 Positive Predictive Value Cylofold: 0.634 NanoFolder: 0.420 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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	? Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.575 Multilign(seed): 0.538 Sensitivity Cylofold: 0.457 Multilign(seed): 0.420 Positive Predictive Value Cylofold: 0.733 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.653 Multilign(20): 0.582 Sensitivity Cylofold: 0.536 Multilign(20): 0.470 Positive Predictive Value Cylofold: 0.803 Multilign(20): 0.729 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Cylofold: 0.601 Sensitivity PETfold_pre2.0(seed): 0.521 Cylofold: 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.821 Cylofold: 0.735 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.653 TurboFold(20): 0.647 Sensitivity Cylofold: 0.536 TurboFold(20): 0.497 Positive Predictive Value Cylofold: 0.803 TurboFold(20): 0.850 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.666 Cylofold: 0.620 Sensitivity PETfold_pre2.0(20): 0.513 Cylofold: 0.513 Positive Predictive Value PETfold_pre2.0(20): 0.872 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.645 TurboFold(seed): 0.553 Sensitivity Cylofold: 0.528 TurboFold(seed): 0.426 Positive Predictive Value Cylofold: 0.795 TurboFold(seed): 0.728 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.571 RNASampler(seed): 0.510 Sensitivity Cylofold: 0.489 RNASampler(seed): 0.366 Positive Predictive Value Cylofold: 0.674 RNASampler(seed): 0.716 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.710 Cylofold: 0.653 Sensitivity PPfold(20): 0.552 Cylofold: 0.536 Positive Predictive Value PPfold(20): 0.918 Cylofold: 0.803 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.659 Mastr(seed): 0.000 Sensitivity Cylofold: 0.554 Mastr(seed): 0.000 Positive Predictive Value Cylofold: 0.789 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.41358941668e-08
RNAalifold(seed)	19 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.599 RNAalifold(seed): 0.539 Sensitivity MXScarna(seed): 0.476 RNAalifold(seed): 0.336 Positive Predictive Value MXScarna(seed): 0.757 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	14 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.657 RNAalifold(seed): 0.579 Sensitivity CentroidAlifold(20): 0.475 RNAalifold(seed): 0.366 Positive Predictive Value CentroidAlifold(20): 0.909 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	15 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.602 RNAalifold(seed): 0.578 Sensitivity RNAalifold(20): 0.441 RNAalifold(seed): 0.364 Positive Predictive Value RNAalifold(20): 0.823 RNAalifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	15 RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.589 RNAalifold(seed): 0.578 Sensitivity RNASampler(20): 0.441 RNAalifold(seed): 0.364 Positive Predictive Value RNASampler(20): 0.790 RNAalifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	18 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.576 RNAalifold(seed): 0.539 Sensitivity CentroidFold: 0.490 RNAalifold(seed): 0.337 Positive Predictive Value CentroidFold: 0.679 RNAalifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	15 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.589 RNAalifold(seed): 0.578 Sensitivity MXScarna(20): 0.475 RNAalifold(seed): 0.364 Positive Predictive Value MXScarna(20): 0.733 RNAalifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.59567023119e-07	18 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.652 RNAalifold(seed): 0.539 Sensitivity CentroidAlifold(seed): 0.462 RNAalifold(seed): 0.337 Positive Predictive Value CentroidAlifold(seed): 0.921 RNAalifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	19 Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.556 RNAalifold(seed): 0.539 Sensitivity Contrafold: 0.497 RNAalifold(seed): 0.336 Positive Predictive Value Contrafold: 0.625 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	19 Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.573 RNAalifold(seed): 0.539 Sensitivity Sfold: 0.482 RNAalifold(seed): 0.336 Positive Predictive Value Sfold: 0.685 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.71568867205e-08	17 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.529 MaxExpect: 0.521 Sensitivity RNAalifold(seed): 0.328 MaxExpect: 0.462 Positive Predictive Value RNAalifold(seed): 0.856 MaxExpect: 0.590 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00023129009914	7 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.523 IPknot: 0.505 Sensitivity RNAalifold(seed): 0.344 IPknot: 0.402 Positive Predictive Value RNAalifold(seed): 0.800 IPknot: 0.641 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.532 RNAalifold(seed): 0.523 Sensitivity CentroidHomfold‑LAST: 0.407 RNAalifold(seed): 0.344 Positive Predictive Value CentroidHomfold‑LAST: 0.702 RNAalifold(seed): 0.800 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	19 HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.560 RNAalifold(seed): 0.539 Sensitivity HotKnots: 0.510 RNAalifold(seed): 0.336 Positive Predictive Value HotKnots: 0.618 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.18141491686e-08	15 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 Carnac(20): 0.549 Sensitivity RNAalifold(seed): 0.364 Carnac(20): 0.319 Positive Predictive Value RNAalifold(seed): 0.919 Carnac(20): 0.948 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.06323189071e-08	5 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.488 RNAalifold(seed): 0.472 Sensitivity ContextFold: 0.376 RNAalifold(seed): 0.293 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	13 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.505 ProbKnot: 0.484 Sensitivity RNAalifold(seed): 0.304 ProbKnot: 0.450 Positive Predictive Value RNAalifold(seed): 0.844 ProbKnot: 0.523 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.06286140723e-08	15 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 Murlet(20): 0.535 Sensitivity RNAalifold(seed): 0.364 Murlet(20): 0.371 Positive Predictive Value RNAalifold(seed): 0.919 Murlet(20): 0.775 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	19 UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.544 RNAalifold(seed): 0.539 Sensitivity UNAFold: 0.486 RNAalifold(seed): 0.336 Positive Predictive Value UNAFold: 0.613 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.00666128245e-05	13 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.505 Fold: 0.476 Sensitivity RNAalifold(seed): 0.304 Fold: 0.434 Positive Predictive Value RNAalifold(seed): 0.844 Fold: 0.525 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	19 RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.559 RNAalifold(seed): 0.539 Sensitivity RNAfold: 0.506 RNAalifold(seed): 0.336 Positive Predictive Value RNAfold: 0.621 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.66763272401e-08	19 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.573 RNAalifold(seed): 0.539 Sensitivity PknotsRG: 0.521 RNAalifold(seed): 0.336 Positive Predictive Value PknotsRG: 0.632 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	9 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.640 RNAalifold(seed): 0.556 Sensitivity Cylofold: 0.532 RNAalifold(seed): 0.362 Positive Predictive Value Cylofold: 0.777 RNAalifold(seed): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0		= RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.540 RNAalifold(seed): 0.539 Sensitivity RNAshapes: 0.481 RNAalifold(seed): 0.336 Positive Predictive Value RNAshapes: 0.611 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.15263054993	- Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.519 RNAalifold(seed): 0.483 Sensitivity Afold: 0.485 RNAalifold(seed): 0.288 Positive Predictive Value Afold: 0.558 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.539 McQFold: 0.531 Sensitivity RNAalifold(seed): 0.336 McQFold: 0.476 Positive Predictive Value RNAalifold(seed): 0.866 McQFold: 0.595 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.03725476497e-05	+ RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.584 Pknots: 0.576 Sensitivity RNAalifold(seed): 0.385 Pknots: 0.521 Positive Predictive Value RNAalifold(seed): 0.890 Pknots: 0.641 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00048756164258	+ RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.539 RNAsubopt: 0.520 Sensitivity RNAalifold(seed): 0.336 RNAsubopt: 0.476 Positive Predictive Value RNAalifold(seed): 0.866 RNAsubopt: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 RSpredict(20): 0.491 Sensitivity RNAalifold(seed): 0.364 RSpredict(20): 0.380 Positive Predictive Value RNAalifold(seed): 0.919 RSpredict(20): 0.639 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-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 Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.539 Vsfold4: 0.456 Sensitivity RNAalifold(seed): 0.336 Vsfold4: 0.388 Positive Predictive Value RNAalifold(seed): 0.866 Vsfold4: 0.540 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 Mastr(20): 0.394 Sensitivity RNAalifold(seed): 0.364 Mastr(20): 0.207 Positive Predictive Value RNAalifold(seed): 0.919 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	? RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.472 RNASLOpt: 0.390 Sensitivity RNAalifold(seed): 0.293 RNASLOpt: 0.323 Positive Predictive Value RNAalifold(seed): 0.765 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 Murlet(seed): 0.475 Sensitivity RNAalifold(seed): 0.398 Murlet(seed): 0.270 Positive Predictive Value RNAalifold(seed): 0.890 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.539 Vsfold5: 0.433 Sensitivity RNAalifold(seed): 0.336 Vsfold5: 0.369 Positive Predictive Value RNAalifold(seed): 0.866 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	? RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.523 RNAwolf: 0.370 Sensitivity RNAalifold(seed): 0.344 RNAwolf: 0.344 Positive Predictive Value RNAalifold(seed): 0.800 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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): 0.587 RDfolder: 0.546 Sensitivity RNAalifold(seed): 0.409 RDfolder: 0.418 Positive Predictive Value RNAalifold(seed): 0.850 RDfolder: 0.725 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.37408564874e-07	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.563 MCFold: 0.465 Sensitivity RNAalifold(seed): 0.364 MCFold: 0.479 Positive Predictive Value RNAalifold(seed): 0.874 MCFold: 0.458 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.539 RSpredict(seed): 0.284 Sensitivity RNAalifold(seed): 0.336 RSpredict(seed): 0.136 Positive Predictive Value RNAalifold(seed): 0.866 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	? RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.523 PPfold(seed): 0.133 Sensitivity RNAalifold(seed): 0.344 PPfold(seed): 0.033 Positive Predictive Value RNAalifold(seed): 0.800 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 Carnac(seed): 0.159 Sensitivity RNAalifold(seed): 0.398 Carnac(seed): 0.026 Positive Predictive Value RNAalifold(seed): 0.890 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.459 NanoFolder: 0.280 Sensitivity RNAalifold(seed): 0.289 NanoFolder: 0.298 Positive Predictive Value RNAalifold(seed): 0.733 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.544 Multilign(seed): 0.538 Sensitivity RNAalifold(seed): 0.399 Multilign(seed): 0.420 Positive Predictive Value RNAalifold(seed): 0.753 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 Multilign(20): 0.480 Sensitivity RNAalifold(seed): 0.381 Multilign(20): 0.402 Positive Predictive Value RNAalifold(seed): 0.923 Multilign(20): 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 RNAalifold(seed): 0.472 Sensitivity PETfold_pre2.0(seed): 0.459 RNAalifold(seed): 0.293 Positive Predictive Value PETfold_pre2.0(seed): 0.726 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 TurboFold(20): 0.547 Sensitivity RNAalifold(seed): 0.381 TurboFold(20): 0.423 Positive Predictive Value RNAalifold(seed): 0.923 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(20): N/A Sensitivity RNAalifold(seed): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.586 PETfold_pre2.0(20): 0.527 Sensitivity RNAalifold(seed): 0.345 PETfold_pre2.0(20): 0.407 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.523 TurboFold(seed): 0.471 Sensitivity RNAalifold(seed): 0.344 TurboFold(seed): 0.383 Positive Predictive Value RNAalifold(seed): 0.800 TurboFold(seed): 0.588 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 RNAalifold(seed): 0.514 Sensitivity RNASampler(seed): 0.409 RNAalifold(seed): 0.330 Positive Predictive Value RNASampler(seed): 0.734 RNAalifold(seed): 0.805 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.603 RNAalifold(seed): 0.591 Sensitivity PPfold(20): 0.455 RNAalifold(seed): 0.381 Positive Predictive Value PPfold(20): 0.804 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.539 Mastr(seed): 0.000 Sensitivity RNAalifold(seed): 0.336 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.866 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08
RNAshapes	34 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.650 RNAshapes: 0.538 Sensitivity MXScarna(seed): 0.533 RNAshapes: 0.479 Positive Predictive Value MXScarna(seed): 0.796 RNAshapes: 0.609 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAshapes: 0.558 Sensitivity CentroidAlifold(20): 0.540 RNAshapes: 0.487 Positive Predictive Value CentroidAlifold(20): 0.897 RNAshapes: 0.643 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.659 RNAshapes: 0.554 Sensitivity RNAalifold(20): 0.510 RNAshapes: 0.482 Positive Predictive Value RNAalifold(20): 0.854 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.640 RNAshapes: 0.554 Sensitivity RNASampler(20): 0.491 RNAshapes: 0.482 Positive Predictive Value RNASampler(20): 0.839 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	50 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.596 RNAshapes: 0.545 Sensitivity CentroidFold: 0.507 RNAshapes: 0.480 Positive Predictive Value CentroidFold: 0.705 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.621 RNAshapes: 0.554 Sensitivity MXScarna(20): 0.518 RNAshapes: 0.482 Positive Predictive Value MXScarna(20): 0.748 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RNAshapes: 0.534 Sensitivity CentroidAlifold(seed): 0.377 RNAshapes: 0.475 Positive Predictive Value CentroidAlifold(seed): 0.925 RNAshapes: 0.605 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	55 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.568 RNAshapes: 0.539 Sensitivity Contrafold: 0.498 RNAshapes: 0.470 Positive Predictive Value Contrafold: 0.653 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.574 RNAshapes: 0.539 Sensitivity Sfold: 0.480 RNAshapes: 0.470 Positive Predictive Value Sfold: 0.691 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.571 RNAshapes: 0.546 Sensitivity MaxExpect: 0.502 RNAshapes: 0.481 Positive Predictive Value MaxExpect: 0.654 RNAshapes: 0.625 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.567 RNAshapes: 0.515 Sensitivity IPknot: 0.463 RNAshapes: 0.443 Positive Predictive Value IPknot: 0.702 RNAshapes: 0.606 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	18 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 RNAshapes: 0.511 Sensitivity CentroidHomfold‑LAST: 0.397 RNAshapes: 0.437 Positive Predictive Value CentroidHomfold‑LAST: 0.784 RNAshapes: 0.606 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.52609899389e-08	55 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.569 RNAshapes: 0.539 Sensitivity HotKnots: 0.506 RNAshapes: 0.470 Positive Predictive Value HotKnots: 0.644 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.601 RNAshapes: 0.554 Sensitivity Carnac(20): 0.397 RNAshapes: 0.482 Positive Predictive Value Carnac(20): 0.914 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	14 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.601 RNAshapes: 0.472 Sensitivity ContextFold: 0.483 RNAshapes: 0.413 Positive Predictive Value ContextFold: 0.754 RNAshapes: 0.548 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	32 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.561 RNAshapes: 0.548 Sensitivity ProbKnot: 0.514 RNAshapes: 0.485 Positive Predictive Value ProbKnot: 0.617 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.592 RNAshapes: 0.554 Sensitivity Murlet(20): 0.437 RNAshapes: 0.482 Positive Predictive Value Murlet(20): 0.807 RNAshapes: 0.642 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	55 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.571 RNAshapes: 0.539 Sensitivity UNAFold: 0.500 RNAshapes: 0.470 Positive Predictive Value UNAFold: 0.655 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.570 RNAshapes: 0.556 Sensitivity Fold: 0.509 RNAshapes: 0.493 Positive Predictive Value Fold: 0.643 RNAshapes: 0.631 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 4.1569883686e-08	55 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.551 RNAshapes: 0.539 Sensitivity RNAfold: 0.487 RNAshapes: 0.470 Positive Predictive Value RNAfold: 0.628 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.552 RNAshapes: 0.539 Sensitivity PknotsRG: 0.492 RNAshapes: 0.470 Positive Predictive Value PknotsRG: 0.625 RNAshapes: 0.622 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.85233844192e-08	28 Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.607 RNAshapes: 0.594 Sensitivity Cylofold: 0.512 RNAshapes: 0.516 Positive Predictive Value Cylofold: 0.727 RNAshapes: 0.690 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 9.34100095224e-08	19 RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.540 RNAalifold(seed): 0.539 Sensitivity RNAshapes: 0.481 RNAalifold(seed): 0.336 Positive Predictive Value RNAshapes: 0.611 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.15263054993		- Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.528 RNAshapes: 0.522 Sensitivity Afold: 0.478 RNAshapes: 0.464 Positive Predictive Value Afold: 0.587 RNAshapes: 0.593 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 2.03613300529e-05	+ RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.539 McQFold: 0.523 Sensitivity RNAshapes: 0.470 McQFold: 0.449 Positive Predictive Value RNAshapes: 0.622 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.561 Pknots: 0.547 Sensitivity RNAshapes: 0.483 Pknots: 0.489 Positive Predictive Value RNAshapes: 0.658 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 9.17559933998e-05	+ RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.539 RNAsubopt: 0.531 Sensitivity RNAshapes: 0.470 RNAsubopt: 0.473 Positive Predictive Value RNAshapes: 0.622 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 2.12176083234e-07	= RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.563 RSpredict(20): 0.559 Sensitivity RNAshapes: 0.492 RSpredict(20): 0.446 Positive Predictive Value RNAshapes: 0.648 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.00701036536754	+ 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: 2.00627773251e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.539 Vsfold4: 0.478 Sensitivity RNAshapes: 0.470 Vsfold4: 0.399 Positive Predictive Value RNAshapes: 0.622 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.554 Mastr(20): 0.523 Sensitivity RNAshapes: 0.482 Mastr(20): 0.348 Positive Predictive Value RNAshapes: 0.642 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.11890491782e-07	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.472 RNASLOpt: 0.443 Sensitivity RNAshapes: 0.413 RNASLOpt: 0.365 Positive Predictive Value RNAshapes: 0.548 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.594 Murlet(seed): 0.475 Sensitivity RNAshapes: 0.511 Murlet(seed): 0.270 Positive Predictive Value RNAshapes: 0.697 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.539 Vsfold5: 0.426 Sensitivity RNAshapes: 0.470 Vsfold5: 0.359 Positive Predictive Value RNAshapes: 0.622 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.515 RNAwolf: 0.399 Sensitivity RNAshapes: 0.443 RNAwolf: 0.368 Positive Predictive Value RNAshapes: 0.606 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.50323628132e-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: 3.56938820447e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.557 RDfolder: 0.443 Sensitivity RNAshapes: 0.467 RDfolder: 0.342 Positive Predictive Value RNAshapes: 0.673 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.569 MCFold: 0.419 Sensitivity RNAshapes: 0.494 MCFold: 0.437 Positive Predictive Value RNAshapes: 0.663 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.538 RSpredict(seed): 0.204 Sensitivity RNAshapes: 0.479 RSpredict(seed): 0.088 Positive Predictive Value RNAshapes: 0.609 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.537 PPfold(seed): 0.102 Sensitivity RNAshapes: 0.454 PPfold(seed): 0.020 Positive Predictive Value RNAshapes: 0.643 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.601 Carnac(seed): 0.139 Sensitivity RNAshapes: 0.526 Carnac(seed): 0.019 Positive Predictive Value RNAshapes: 0.693 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.514 NanoFolder: 0.366 Sensitivity RNAshapes: 0.447 NanoFolder: 0.376 Positive Predictive Value RNAshapes: 0.599 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? RNAshapes vs Multilign(seed) Matthews Correlation Coefficient RNAshapes: 0.621 Multilign(seed): 0.538 Sensitivity RNAshapes: 0.507 Multilign(seed): 0.420 Positive Predictive Value RNAshapes: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.555 Multilign(20): 0.540 Sensitivity RNAshapes: 0.470 Multilign(20): 0.456 Positive Predictive Value RNAshapes: 0.661 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAshapes: 0.476 Sensitivity PETfold_pre2.0(seed): 0.551 RNAshapes: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAshapes: 0.562 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.594 RNAshapes: 0.555 Sensitivity TurboFold(20): 0.470 RNAshapes: 0.470 Positive Predictive Value TurboFold(20): 0.756 RNAshapes: 0.661 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: N/A CMfinder(20): N/A Sensitivity RNAshapes: N/A CMfinder(20): N/A Positive Predictive Value RNAshapes: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAshapes: 0.475 Sensitivity PETfold_pre2.0(20): 0.497 RNAshapes: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAshapes: 0.552 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.544 TurboFold(seed): 0.517 Sensitivity RNAshapes: 0.464 TurboFold(seed): 0.422 Positive Predictive Value RNAshapes: 0.646 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.546 RNAshapes: 0.535 Sensitivity RNASampler(seed): 0.409 RNAshapes: 0.482 Positive Predictive Value RNASampler(seed): 0.734 RNAshapes: 0.599 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.665 RNAshapes: 0.555 Sensitivity PPfold(20): 0.519 RNAshapes: 0.470 Positive Predictive Value PPfold(20): 0.859 RNAshapes: 0.661 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.533 Mastr(seed): 0.000 Sensitivity RNAshapes: 0.472 Mastr(seed): 0.000 Positive Predictive Value RNAshapes: 0.606 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
Afold	23 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.625 Afold: 0.501 Sensitivity MXScarna(seed): 0.508 Afold: 0.467 Positive Predictive Value MXScarna(seed): 0.771 Afold: 0.541 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.655 Afold: 0.508 Sensitivity CentroidAlifold(20): 0.503 Afold: 0.467 Positive Predictive Value CentroidAlifold(20): 0.856 Afold: 0.557 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.39551335374e-08	17 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.610 Afold: 0.513 Sensitivity RNAalifold(20): 0.467 Afold: 0.464 Positive Predictive Value RNAalifold(20): 0.798 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	17 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.600 Afold: 0.513 Sensitivity RNASampler(20): 0.461 Afold: 0.464 Positive Predictive Value RNASampler(20): 0.782 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	36 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.500 Afold: 0.427 Sensitivity CentroidFold: 0.423 Afold: 0.394 Positive Predictive Value CentroidFold: 0.592 Afold: 0.463 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.584 Afold: 0.513 Sensitivity MXScarna(20): 0.487 Afold: 0.464 Positive Predictive Value MXScarna(20): 0.703 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	22 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.570 Afold: 0.495 Sensitivity CentroidAlifold(seed): 0.365 Afold: 0.462 Positive Predictive Value CentroidAlifold(seed): 0.893 Afold: 0.535 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	42 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.516 Afold: 0.427 Sensitivity Contrafold: 0.456 Afold: 0.386 Positive Predictive Value Contrafold: 0.585 Afold: 0.474 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.449 Afold: 0.427 Sensitivity Sfold: 0.377 Afold: 0.386 Positive Predictive Value Sfold: 0.536 Afold: 0.474 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.545 Afold: 0.479 Sensitivity MaxExpect: 0.471 Afold: 0.424 Positive Predictive Value MaxExpect: 0.632 Afold: 0.543 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.567 Afold: 0.516 Sensitivity IPknot: 0.462 Afold: 0.467 Positive Predictive Value IPknot: 0.702 Afold: 0.578 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Afold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Afold: 0.516 CentroidHomfold‑LAST: 0.401 Sensitivity Afold: 0.467 CentroidHomfold‑LAST: 0.286 Positive Predictive Value Afold: 0.578 CentroidHomfold‑LAST: 0.570 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	39 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.556 Afold: 0.528 Sensitivity HotKnots: 0.504 Afold: 0.478 Positive Predictive Value HotKnots: 0.618 Afold: 0.587 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.599 Afold: 0.513 Sensitivity Carnac(20): 0.390 Afold: 0.464 Positive Predictive Value Carnac(20): 0.921 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	6 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.504 Afold: 0.475 Sensitivity ContextFold: 0.406 Afold: 0.442 Positive Predictive Value ContextFold: 0.632 Afold: 0.518 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	18 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.542 Afold: 0.533 Sensitivity ProbKnot: 0.508 Afold: 0.499 Positive Predictive Value ProbKnot: 0.582 Afold: 0.574 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.40179680388e-07	17 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.550 Afold: 0.513 Sensitivity Murlet(20): 0.402 Afold: 0.464 Positive Predictive Value Murlet(20): 0.756 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	42 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.429 Afold: 0.427 Sensitivity UNAFold: 0.383 Afold: 0.386 Positive Predictive Value UNAFold: 0.481 Afold: 0.474 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 0.0336931477392	19 Fold vs Afold Matthews Correlation Coefficient Fold: 0.547 Afold: 0.545 Sensitivity Fold: 0.504 Afold: 0.510 Positive Predictive Value Fold: 0.598 Afold: 0.586 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 8.01634185435e-05	42 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.427 RNAfold: 0.423 Sensitivity Afold: 0.386 RNAfold: 0.382 Positive Predictive Value Afold: 0.474 RNAfold: 0.468 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 2.29562105844e-05	42 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.427 PknotsRG: 0.413 Sensitivity Afold: 0.386 PknotsRG: 0.374 Positive Predictive Value Afold: 0.474 PknotsRG: 0.456 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.632 Cylofold: 0.621 Sensitivity Afold: 0.573 Cylofold: 0.533 Positive Predictive Value Afold: 0.703 Cylofold: 0.729 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00238442710916	14 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.519 RNAalifold(seed): 0.483 Sensitivity Afold: 0.485 RNAalifold(seed): 0.288 Positive Predictive Value Afold: 0.558 RNAalifold(seed): 0.814 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.61358433984e-08	39 Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.528 RNAshapes: 0.522 Sensitivity Afold: 0.478 RNAshapes: 0.464 Positive Predictive Value Afold: 0.587 RNAshapes: 0.593 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 2.03613300529e-05		+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.427 McQFold: 0.348 Sensitivity Afold: 0.386 McQFold: 0.265 Positive Predictive Value Afold: 0.474 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.569 Afold: 0.557 Sensitivity Pknots: 0.518 Afold: 0.493 Positive Predictive Value Pknots: 0.631 Afold: 0.635 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 2.23046259944e-06	+ Afold vs RNAsubopt Matthews Correlation Coefficient Afold: 0.528 RNAsubopt: 0.522 Sensitivity Afold: 0.478 RNAsubopt: 0.474 Positive Predictive Value Afold: 0.587 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.53079410487e-06	- RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.558 Afold: 0.517 Sensitivity RSpredict(20): 0.472 Afold: 0.475 Positive Predictive Value RSpredict(20): 0.664 Afold: 0.566 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.42300079339e-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 Vsfold4 Matthews Correlation Coefficient Afold: 0.528 Vsfold4: 0.468 Sensitivity Afold: 0.478 Vsfold4: 0.395 Positive Predictive Value Afold: 0.587 Vsfold4: 0.560 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.516 Afold: 0.513 Sensitivity Mastr(20): 0.340 Afold: 0.464 Positive Predictive Value Mastr(20): 0.787 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0978527593275	? Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.475 RNASLOpt: 0.420 Sensitivity Afold: 0.442 RNASLOpt: 0.376 Positive Predictive Value Afold: 0.518 RNASLOpt: 0.477 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.586 Murlet(seed): 0.453 Sensitivity Afold: 0.520 Murlet(seed): 0.267 Positive Predictive Value Afold: 0.665 Murlet(seed): 0.774 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.528 Vsfold5: 0.418 Sensitivity Afold: 0.478 Vsfold5: 0.355 Positive Predictive Value Afold: 0.587 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.516 RNAwolf: 0.449 Sensitivity Afold: 0.467 RNAwolf: 0.417 Positive Predictive Value Afold: 0.578 RNAwolf: 0.491 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ 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: 5.50294594097e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.549 RDfolder: 0.456 Sensitivity Afold: 0.478 RDfolder: 0.360 Positive Predictive Value Afold: 0.642 RDfolder: 0.591 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.555 MCFold: 0.424 Sensitivity Afold: 0.497 MCFold: 0.444 Positive Predictive Value Afold: 0.627 MCFold: 0.414 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.501 RSpredict(seed): 0.244 Sensitivity Afold: 0.467 RSpredict(seed): 0.114 Positive Predictive Value Afold: 0.541 RSpredict(seed): 0.527 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.489 PPfold(seed): 0.187 Sensitivity Afold: 0.443 PPfold(seed): 0.066 Positive Predictive Value Afold: 0.547 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.597 Carnac(seed): 0.175 Sensitivity Afold: 0.540 Carnac(seed): 0.031 Positive Predictive Value Afold: 0.665 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	? Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.513 NanoFolder: 0.311 Sensitivity Afold: 0.481 NanoFolder: 0.349 Positive Predictive Value Afold: 0.554 NanoFolder: 0.285 Number of pairs reference - predicted secondary structure: 4 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 Multilign(seed) Matthews Correlation Coefficient Afold: 0.700 Multilign(seed): 0.476 Sensitivity Afold: 0.574 Multilign(seed): 0.370 Positive Predictive Value Afold: 0.861 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.461 Multilign(20): 0.405 Sensitivity Afold: 0.419 Multilign(20): 0.360 Positive Predictive Value Afold: 0.514 Multilign(20): 0.463 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 Afold: 0.389 Sensitivity PETfold_pre2.0(seed): 0.403 Afold: 0.375 Positive Predictive Value PETfold_pre2.0(seed): 0.644 Afold: 0.409 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.501 Afold: 0.461 Sensitivity TurboFold(20): 0.395 Afold: 0.419 Positive Predictive Value TurboFold(20): 0.642 Afold: 0.514 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: N/A CMfinder(20): N/A Sensitivity Afold: N/A CMfinder(20): N/A Positive Predictive Value Afold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.333 Afold: 0.311 Sensitivity PETfold_pre2.0(20): 0.250 Afold: 0.308 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.320 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.489 TurboFold(seed): 0.373 Sensitivity Afold: 0.443 TurboFold(seed): 0.321 Positive Predictive Value Afold: 0.547 TurboFold(seed): 0.442 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.540 Afold: 0.528 Sensitivity RNASampler(seed): 0.415 Afold: 0.483 Positive Predictive Value RNASampler(seed): 0.708 Afold: 0.582 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.496 Afold: 0.461 Sensitivity PPfold(20): 0.360 Afold: 0.419 Positive Predictive Value PPfold(20): 0.689 Afold: 0.514 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.499 Mastr(seed): 0.000 Sensitivity Afold: 0.460 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.546 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08
McQFold	34 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.650 McQFold: 0.530 Sensitivity MXScarna(seed): 0.533 McQFold: 0.466 Positive Predictive Value MXScarna(seed): 0.796 McQFold: 0.607 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.695 McQFold: 0.538 Sensitivity CentroidAlifold(20): 0.540 McQFold: 0.466 Positive Predictive Value CentroidAlifold(20): 0.897 McQFold: 0.624 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	25 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.659 McQFold: 0.529 Sensitivity RNAalifold(20): 0.510 McQFold: 0.456 Positive Predictive Value RNAalifold(20): 0.854 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.640 McQFold: 0.529 Sensitivity RNASampler(20): 0.491 McQFold: 0.456 Positive Predictive Value RNASampler(20): 0.839 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	52 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.517 McQFold: 0.388 Sensitivity CentroidFold: 0.434 McQFold: 0.288 Positive Predictive Value CentroidFold: 0.616 McQFold: 0.521 Number of pairs reference - predicted secondary structure: 52 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.621 McQFold: 0.529 Sensitivity MXScarna(20): 0.518 McQFold: 0.456 Positive Predictive Value MXScarna(20): 0.748 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	33 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 McQFold: 0.526 Sensitivity CentroidAlifold(seed): 0.377 McQFold: 0.463 Positive Predictive Value CentroidAlifold(seed): 0.925 McQFold: 0.603 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.526 McQFold: 0.368 Sensitivity Contrafold: 0.462 McQFold: 0.281 Positive Predictive Value Contrafold: 0.599 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.464 McQFold: 0.368 Sensitivity Sfold: 0.387 McQFold: 0.281 Positive Predictive Value Sfold: 0.557 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.558 McQFold: 0.434 Sensitivity MaxExpect: 0.478 McQFold: 0.368 Positive Predictive Value MaxExpect: 0.651 McQFold: 0.514 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.567 McQFold: 0.501 Sensitivity IPknot: 0.463 McQFold: 0.427 Positive Predictive Value IPknot: 0.702 McQFold: 0.596 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.61358433984e-08	18 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 McQFold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.397 McQFold: 0.421 Positive Predictive Value CentroidHomfold‑LAST: 0.784 McQFold: 0.599 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78993384543e-08	55 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.569 McQFold: 0.523 Sensitivity HotKnots: 0.506 McQFold: 0.449 Positive Predictive Value HotKnots: 0.644 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.601 McQFold: 0.529 Sensitivity Carnac(20): 0.397 McQFold: 0.456 Positive Predictive Value Carnac(20): 0.914 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	14 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.601 McQFold: 0.445 Sensitivity ContextFold: 0.483 McQFold: 0.385 Positive Predictive Value ContextFold: 0.754 McQFold: 0.522 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.43692248862e-08	32 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.561 McQFold: 0.546 Sensitivity ProbKnot: 0.514 McQFold: 0.478 Positive Predictive Value ProbKnot: 0.617 McQFold: 0.628 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.09925167801e-06	25 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.592 McQFold: 0.529 Sensitivity Murlet(20): 0.437 McQFold: 0.456 Positive Predictive Value Murlet(20): 0.807 McQFold: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	58 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.445 McQFold: 0.368 Sensitivity UNAFold: 0.395 McQFold: 0.281 Positive Predictive Value UNAFold: 0.502 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.570 McQFold: 0.552 Sensitivity Fold: 0.509 McQFold: 0.478 Positive Predictive Value Fold: 0.643 McQFold: 0.640 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.75828119249e-07	58 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.441 McQFold: 0.368 Sensitivity RNAfold: 0.395 McQFold: 0.281 Positive Predictive Value RNAfold: 0.492 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.433 McQFold: 0.368 Sensitivity PknotsRG: 0.389 McQFold: 0.281 Positive Predictive Value PknotsRG: 0.482 McQFold: 0.481 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.641 Cylofold: 0.607 Sensitivity McQFold: 0.546 Cylofold: 0.512 Positive Predictive Value McQFold: 0.758 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	19 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.539 McQFold: 0.531 Sensitivity RNAalifold(seed): 0.336 McQFold: 0.476 Positive Predictive Value RNAalifold(seed): 0.866 McQFold: 0.595 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.03725476497e-05	55 RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.539 McQFold: 0.523 Sensitivity RNAshapes: 0.470 McQFold: 0.449 Positive Predictive Value RNAshapes: 0.622 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.427 McQFold: 0.348 Sensitivity Afold: 0.386 McQFold: 0.265 Positive Predictive Value Afold: 0.474 McQFold: 0.459 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08		= McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.550 Pknots: 0.547 Sensitivity McQFold: 0.465 Pknots: 0.489 Positive Predictive Value McQFold: 0.658 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0193465255264	- RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.531 McQFold: 0.523 Sensitivity RNAsubopt: 0.473 McQFold: 0.449 Positive Predictive Value RNAsubopt: 0.601 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 1.22032703654e-06	- RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.559 McQFold: 0.543 Sensitivity RSpredict(20): 0.446 McQFold: 0.471 Positive Predictive Value RSpredict(20): 0.705 McQFold: 0.630 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.000123289528193	+ 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: 1.20718263679e-07	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.523 Vsfold4: 0.478 Sensitivity McQFold: 0.449 Vsfold4: 0.399 Positive Predictive Value McQFold: 0.613 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	= McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.529 Mastr(20): 0.523 Sensitivity McQFold: 0.456 Mastr(20): 0.348 Positive Predictive Value McQFold: 0.618 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.294741380356	= McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.445 RNASLOpt: 0.443 Sensitivity McQFold: 0.385 RNASLOpt: 0.365 Positive Predictive Value McQFold: 0.522 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0739904251478	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.601 Murlet(seed): 0.475 Sensitivity McQFold: 0.522 Murlet(seed): 0.270 Positive Predictive Value McQFold: 0.698 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.523 Vsfold5: 0.426 Sensitivity McQFold: 0.449 Vsfold5: 0.359 Positive Predictive Value McQFold: 0.613 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.501 RNAwolf: 0.399 Sensitivity McQFold: 0.427 RNAwolf: 0.368 Positive Predictive Value McQFold: 0.596 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-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: 0.592 RDfolder: 0.443 Sensitivity McQFold: 0.484 RDfolder: 0.342 Positive Predictive Value McQFold: 0.733 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.554 MCFold: 0.419 Sensitivity McQFold: 0.468 MCFold: 0.437 Positive Predictive Value McQFold: 0.664 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.530 RSpredict(seed): 0.204 Sensitivity McQFold: 0.466 RSpredict(seed): 0.088 Positive Predictive Value McQFold: 0.607 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.539 PPfold(seed): 0.102 Sensitivity McQFold: 0.462 PPfold(seed): 0.020 Positive Predictive Value McQFold: 0.637 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.574 Carnac(seed): 0.139 Sensitivity McQFold: 0.501 Carnac(seed): 0.019 Positive Predictive Value McQFold: 0.662 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	? McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.474 NanoFolder: 0.366 Sensitivity McQFold: 0.412 NanoFolder: 0.376 Positive Predictive Value McQFold: 0.554 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.621 Multilign(seed): 0.538 Sensitivity McQFold: 0.507 Multilign(seed): 0.420 Positive Predictive Value McQFold: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.540 McQFold: 0.526 Sensitivity Multilign(20): 0.456 McQFold: 0.452 Positive Predictive Value Multilign(20): 0.647 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 McQFold: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 McQFold: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 McQFold: 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.594 McQFold: 0.526 Sensitivity TurboFold(20): 0.470 McQFold: 0.452 Positive Predictive Value TurboFold(20): 0.756 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: N/A CMfinder(20): N/A Sensitivity McQFold: N/A CMfinder(20): N/A Positive Predictive Value McQFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 McQFold: 0.409 Sensitivity PETfold_pre2.0(20): 0.497 McQFold: 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.790 McQFold: 0.466 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.517 McQFold: 0.512 Sensitivity TurboFold(seed): 0.422 McQFold: 0.445 Positive Predictive Value TurboFold(seed): 0.642 McQFold: 0.597 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.546 McQFold: 0.534 Sensitivity RNASampler(seed): 0.409 McQFold: 0.486 Positive Predictive Value RNASampler(seed): 0.734 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.665 McQFold: 0.526 Sensitivity PPfold(20): 0.519 McQFold: 0.452 Positive Predictive Value PPfold(20): 0.859 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.520 Mastr(seed): 0.000 Sensitivity McQFold: 0.455 Mastr(seed): 0.000 Positive Predictive Value McQFold: 0.599 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
Pknots	32 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.662 Pknots: 0.577 Sensitivity MXScarna(seed): 0.545 Pknots: 0.520 Positive Predictive Value MXScarna(seed): 0.810 Pknots: 0.647 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.712 Pknots: 0.554 Sensitivity CentroidAlifold(20): 0.566 Pknots: 0.501 Positive Predictive Value CentroidAlifold(20): 0.899 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.676 Pknots: 0.540 Sensitivity RNAalifold(20): 0.535 Pknots: 0.487 Positive Predictive Value RNAalifold(20): 0.857 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.664 Pknots: 0.540 Sensitivity RNASampler(20): 0.518 Pknots: 0.487 Positive Predictive Value RNASampler(20): 0.856 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	48 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.619 Pknots: 0.560 Sensitivity CentroidFold: 0.521 Pknots: 0.503 Positive Predictive Value CentroidFold: 0.742 Pknots: 0.630 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.637 Pknots: 0.540 Sensitivity MXScarna(20): 0.535 Pknots: 0.487 Positive Predictive Value MXScarna(20): 0.764 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	31 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.598 Pknots: 0.573 Sensitivity CentroidAlifold(seed): 0.375 Pknots: 0.516 Positive Predictive Value CentroidAlifold(seed): 0.961 Pknots: 0.643 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 2.38297003775e-06	53 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.588 Pknots: 0.547 Sensitivity Contrafold: 0.508 Pknots: 0.489 Positive Predictive Value Contrafold: 0.687 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.596 Pknots: 0.547 Sensitivity Sfold: 0.492 Pknots: 0.489 Positive Predictive Value Sfold: 0.727 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.598 Pknots: 0.555 Sensitivity MaxExpect: 0.519 Pknots: 0.499 Positive Predictive Value MaxExpect: 0.695 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.567 Pknots: 0.471 Sensitivity IPknot: 0.463 Pknots: 0.421 Positive Predictive Value IPknot: 0.702 Pknots: 0.535 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.20167918023e-08	18 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Pknots: 0.470 Sensitivity CentroidHomfold‑LAST: 0.397 Pknots: 0.416 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Pknots: 0.540 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.61358433984e-08	53 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.592 Pknots: 0.547 Sensitivity HotKnots: 0.518 Pknots: 0.489 Positive Predictive Value HotKnots: 0.683 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.619 Pknots: 0.540 Sensitivity Carnac(20): 0.423 Pknots: 0.487 Positive Predictive Value Carnac(20): 0.911 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.601 Pknots: 0.408 Sensitivity ContextFold: 0.483 Pknots: 0.373 Positive Predictive Value ContextFold: 0.754 Pknots: 0.456 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.26346675981e-08	30 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.598 Pknots: 0.578 Sensitivity ProbKnot: 0.540 Pknots: 0.516 Positive Predictive Value ProbKnot: 0.668 Pknots: 0.654 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.34568509467e-07	24 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.618 Pknots: 0.540 Sensitivity Murlet(20): 0.467 Pknots: 0.487 Positive Predictive Value Murlet(20): 0.822 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	53 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.595 Pknots: 0.547 Sensitivity UNAFold: 0.514 Pknots: 0.489 Positive Predictive Value UNAFold: 0.695 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.606 Pknots: 0.582 Sensitivity Fold: 0.532 Pknots: 0.520 Positive Predictive Value Fold: 0.697 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	53 RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.572 Pknots: 0.547 Sensitivity RNAfold: 0.497 Pknots: 0.489 Positive Predictive Value RNAfold: 0.666 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 2.28033735003e-07	53 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.574 Pknots: 0.547 Sensitivity PknotsRG: 0.503 Pknots: 0.489 Positive Predictive Value PknotsRG: 0.661 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.48494289621e-08	28 Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.617 Cylofold: 0.607 Sensitivity Pknots: 0.549 Cylofold: 0.512 Positive Predictive Value Pknots: 0.698 Cylofold: 0.727 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.27663599501e-06	17 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.584 Pknots: 0.576 Sensitivity RNAalifold(seed): 0.385 Pknots: 0.521 Positive Predictive Value RNAalifold(seed): 0.890 Pknots: 0.641 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00048756164258	53 RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.561 Pknots: 0.547 Sensitivity RNAshapes: 0.483 Pknots: 0.489 Positive Predictive Value RNAshapes: 0.658 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 9.17559933998e-05	37 Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.569 Afold: 0.557 Sensitivity Pknots: 0.518 Afold: 0.493 Positive Predictive Value Pknots: 0.631 Afold: 0.635 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 2.23046259944e-06	53 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.550 Pknots: 0.547 Sensitivity McQFold: 0.465 Pknots: 0.489 Positive Predictive Value McQFold: 0.658 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0193465255264		= RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.547 Pknots: 0.547 Sensitivity RNAsubopt: 0.480 Pknots: 0.489 Positive Predictive Value RNAsubopt: 0.631 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.967834906263	= RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.564 Pknots: 0.559 Sensitivity RSpredict(20): 0.448 Pknots: 0.507 Positive Predictive Value RSpredict(20): 0.715 Pknots: 0.623 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.0209117840203	- 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: 2.01323596851e-07	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.547 Vsfold4: 0.501 Sensitivity Pknots: 0.489 Vsfold4: 0.412 Positive Predictive Value Pknots: 0.620 Vsfold4: 0.617 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.561 Pknots: 0.540 Sensitivity Mastr(20): 0.401 Pknots: 0.487 Positive Predictive Value Mastr(20): 0.790 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 1.19178247576e-06	- RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.443 Pknots: 0.408 Sensitivity RNASLOpt: 0.365 Pknots: 0.373 Positive Predictive Value RNASLOpt: 0.547 Pknots: 0.456 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.4308705233e-08	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.563 Murlet(seed): 0.475 Sensitivity Pknots: 0.509 Murlet(seed): 0.270 Positive Predictive Value Pknots: 0.628 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.547 Vsfold5: 0.443 Sensitivity Pknots: 0.489 Vsfold5: 0.372 Positive Predictive Value Pknots: 0.620 Vsfold5: 0.536 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.471 RNAwolf: 0.399 Sensitivity Pknots: 0.421 RNAwolf: 0.368 Positive Predictive Value Pknots: 0.535 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-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: 0.599 RDfolder: 0.443 Sensitivity Pknots: 0.523 RDfolder: 0.342 Positive Predictive Value Pknots: 0.696 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.552 MCFold: 0.419 Sensitivity Pknots: 0.497 MCFold: 0.437 Positive Predictive Value Pknots: 0.619 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.577 RSpredict(seed): 0.210 Sensitivity Pknots: 0.520 RSpredict(seed): 0.091 Positive Predictive Value Pknots: 0.647 RSpredict(seed): 0.492 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.532 PPfold(seed): 0.102 Sensitivity Pknots: 0.462 PPfold(seed): 0.020 Positive Predictive Value Pknots: 0.620 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.08519761914e-09	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.553 Carnac(seed): 0.139 Sensitivity Pknots: 0.502 Carnac(seed): 0.019 Positive Predictive Value Pknots: 0.616 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.404 NanoFolder: 0.366 Sensitivity Pknots: 0.360 NanoFolder: 0.376 Positive Predictive Value Pknots: 0.461 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.555 Multilign(seed): 0.538 Sensitivity Pknots: 0.464 Multilign(seed): 0.420 Positive Predictive Value Pknots: 0.674 Multilign(seed): 0.699 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): 0.540 Pknots: 0.505 Sensitivity Multilign(20): 0.456 Pknots: 0.441 Positive Predictive Value Multilign(20): 0.647 Pknots: 0.586 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): 0.680 Pknots: 0.452 Sensitivity PETfold_pre2.0(seed): 0.551 Pknots: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Pknots: 0.518 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.594 Pknots: 0.505 Sensitivity TurboFold(20): 0.470 Pknots: 0.441 Positive Predictive Value TurboFold(20): 0.756 Pknots: 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Pknots: 0.371 Sensitivity PETfold_pre2.0(20): 0.497 Pknots: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Pknots: 0.418 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.517 Pknots: 0.492 Sensitivity TurboFold(seed): 0.422 Pknots: 0.433 Positive Predictive Value TurboFold(seed): 0.642 Pknots: 0.567 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.546 Pknots: 0.541 Sensitivity RNASampler(seed): 0.409 Pknots: 0.514 Positive Predictive Value RNASampler(seed): 0.734 Pknots: 0.575 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.665 Pknots: 0.505 Sensitivity PPfold(20): 0.519 Pknots: 0.441 Positive Predictive Value PPfold(20): 0.859 Pknots: 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.562 Mastr(seed): 0.000 Sensitivity Pknots: 0.504 Mastr(seed): 0.000 Positive Predictive Value Pknots: 0.632 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08
RNAsubopt	34 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.650 RNAsubopt: 0.529 Sensitivity MXScarna(seed): 0.533 RNAsubopt: 0.481 Positive Predictive Value MXScarna(seed): 0.796 RNAsubopt: 0.586 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RNAsubopt: 0.555 Sensitivity CentroidAlifold(20): 0.540 RNAsubopt: 0.497 Positive Predictive Value CentroidAlifold(20): 0.897 RNAsubopt: 0.624 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.659 RNAsubopt: 0.545 Sensitivity RNAalifold(20): 0.510 RNAsubopt: 0.486 Positive Predictive Value RNAalifold(20): 0.854 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.640 RNAsubopt: 0.545 Sensitivity RNASampler(20): 0.491 RNAsubopt: 0.486 Positive Predictive Value RNASampler(20): 0.839 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	50 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.596 RNAsubopt: 0.540 Sensitivity CentroidFold: 0.507 RNAsubopt: 0.486 Positive Predictive Value CentroidFold: 0.705 RNAsubopt: 0.605 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.621 RNAsubopt: 0.545 Sensitivity MXScarna(20): 0.518 RNAsubopt: 0.486 Positive Predictive Value MXScarna(20): 0.748 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RNAsubopt: 0.525 Sensitivity CentroidAlifold(seed): 0.377 RNAsubopt: 0.478 Positive Predictive Value CentroidAlifold(seed): 0.925 RNAsubopt: 0.582 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.568 RNAsubopt: 0.531 Sensitivity Contrafold: 0.498 RNAsubopt: 0.473 Positive Predictive Value Contrafold: 0.653 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.574 RNAsubopt: 0.531 Sensitivity Sfold: 0.480 RNAsubopt: 0.473 Positive Predictive Value Sfold: 0.691 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.571 RNAsubopt: 0.540 Sensitivity MaxExpect: 0.502 RNAsubopt: 0.486 Positive Predictive Value MaxExpect: 0.654 RNAsubopt: 0.605 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.567 RNAsubopt: 0.473 Sensitivity IPknot: 0.463 RNAsubopt: 0.414 Positive Predictive Value IPknot: 0.702 RNAsubopt: 0.550 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	18 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 RNAsubopt: 0.471 Sensitivity CentroidHomfold‑LAST: 0.397 RNAsubopt: 0.408 Positive Predictive Value CentroidHomfold‑LAST: 0.784 RNAsubopt: 0.552 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.69956606048e-08	55 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.569 RNAsubopt: 0.531 Sensitivity HotKnots: 0.506 RNAsubopt: 0.473 Positive Predictive Value HotKnots: 0.644 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.601 RNAsubopt: 0.545 Sensitivity Carnac(20): 0.397 RNAsubopt: 0.486 Positive Predictive Value Carnac(20): 0.914 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	14 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.601 RNAsubopt: 0.424 Sensitivity ContextFold: 0.483 RNAsubopt: 0.378 Positive Predictive Value ContextFold: 0.754 RNAsubopt: 0.486 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	32 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.561 RNAsubopt: 0.543 Sensitivity ProbKnot: 0.514 RNAsubopt: 0.489 Positive Predictive Value ProbKnot: 0.617 RNAsubopt: 0.606 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.592 RNAsubopt: 0.545 Sensitivity Murlet(20): 0.437 RNAsubopt: 0.486 Positive Predictive Value Murlet(20): 0.807 RNAsubopt: 0.616 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	55 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.571 RNAsubopt: 0.531 Sensitivity UNAFold: 0.500 RNAsubopt: 0.473 Positive Predictive Value UNAFold: 0.655 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.570 RNAsubopt: 0.559 Sensitivity Fold: 0.509 RNAsubopt: 0.504 Positive Predictive Value Fold: 0.643 RNAsubopt: 0.623 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.551 RNAsubopt: 0.531 Sensitivity RNAfold: 0.487 RNAsubopt: 0.473 Positive Predictive Value RNAfold: 0.628 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.552 RNAsubopt: 0.531 Sensitivity PknotsRG: 0.492 RNAsubopt: 0.473 Positive Predictive Value PknotsRG: 0.625 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.607 RNAsubopt: 0.592 Sensitivity Cylofold: 0.512 RNAsubopt: 0.518 Positive Predictive Value Cylofold: 0.727 RNAsubopt: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.24386558293e-07	19 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.539 RNAsubopt: 0.520 Sensitivity RNAalifold(seed): 0.336 RNAsubopt: 0.476 Positive Predictive Value RNAalifold(seed): 0.866 RNAsubopt: 0.572 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.59578924681e-08	55 RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.539 RNAsubopt: 0.531 Sensitivity RNAshapes: 0.470 RNAsubopt: 0.473 Positive Predictive Value RNAshapes: 0.622 RNAsubopt: 0.601 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 2.12176083234e-07	39 Afold vs RNAsubopt Matthews Correlation Coefficient Afold: 0.528 RNAsubopt: 0.522 Sensitivity Afold: 0.478 RNAsubopt: 0.474 Positive Predictive Value Afold: 0.587 RNAsubopt: 0.579 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.53079410487e-06	55 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.531 McQFold: 0.523 Sensitivity RNAsubopt: 0.473 McQFold: 0.449 Positive Predictive Value RNAsubopt: 0.601 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 1.22032703654e-06	53 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.547 Pknots: 0.547 Sensitivity RNAsubopt: 0.480 Pknots: 0.489 Positive Predictive Value RNAsubopt: 0.631 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.967834906263		= RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.560 RSpredict(20): 0.559 Sensitivity RNAsubopt: 0.502 RSpredict(20): 0.446 Positive Predictive Value RNAsubopt: 0.629 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.590817397584	- 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: 0.000108465172428	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.531 Vsfold4: 0.478 Sensitivity RNAsubopt: 0.473 Vsfold4: 0.399 Positive Predictive Value RNAsubopt: 0.601 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.545 Mastr(20): 0.523 Sensitivity RNAsubopt: 0.486 Mastr(20): 0.348 Positive Predictive Value RNAsubopt: 0.616 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.13709158556e-05	- RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.443 RNAsubopt: 0.424 Sensitivity RNASLOpt: 0.365 RNAsubopt: 0.378 Positive Predictive Value RNASLOpt: 0.547 RNAsubopt: 0.486 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.551 Murlet(seed): 0.475 Sensitivity RNAsubopt: 0.485 Murlet(seed): 0.270 Positive Predictive Value RNAsubopt: 0.630 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.531 Vsfold5: 0.426 Sensitivity RNAsubopt: 0.473 Vsfold5: 0.359 Positive Predictive Value RNAsubopt: 0.601 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.473 RNAwolf: 0.399 Sensitivity RNAsubopt: 0.414 RNAwolf: 0.368 Positive Predictive Value RNAsubopt: 0.550 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-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: 3.56938820447e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.550 RDfolder: 0.443 Sensitivity RNAsubopt: 0.468 RDfolder: 0.342 Positive Predictive Value RNAsubopt: 0.656 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.551 MCFold: 0.419 Sensitivity RNAsubopt: 0.486 MCFold: 0.437 Positive Predictive Value RNAsubopt: 0.632 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.529 RSpredict(seed): 0.204 Sensitivity RNAsubopt: 0.481 RSpredict(seed): 0.088 Positive Predictive Value RNAsubopt: 0.586 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.500 PPfold(seed): 0.102 Sensitivity RNAsubopt: 0.429 PPfold(seed): 0.020 Positive Predictive Value RNAsubopt: 0.591 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.585 Carnac(seed): 0.139 Sensitivity RNAsubopt: 0.521 Carnac(seed): 0.019 Positive Predictive Value RNAsubopt: 0.661 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.89920829651e-08	? RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.461 NanoFolder: 0.366 Sensitivity RNAsubopt: 0.408 NanoFolder: 0.376 Positive Predictive Value RNAsubopt: 0.529 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.538 RNAsubopt: 0.522 Sensitivity Multilign(seed): 0.420 RNAsubopt: 0.428 Positive Predictive Value Multilign(seed): 0.699 RNAsubopt: 0.648 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.551 Multilign(20): 0.540 Sensitivity RNAsubopt: 0.474 Multilign(20): 0.456 Positive Predictive Value RNAsubopt: 0.646 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAsubopt: 0.431 Sensitivity PETfold_pre2.0(seed): 0.551 RNAsubopt: 0.378 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAsubopt: 0.500 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.594 RNAsubopt: 0.551 Sensitivity TurboFold(20): 0.470 RNAsubopt: 0.474 Positive Predictive Value TurboFold(20): 0.756 RNAsubopt: 0.646 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: N/A CMfinder(20): N/A Sensitivity RNAsubopt: N/A CMfinder(20): N/A Positive Predictive Value RNAsubopt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAsubopt: 0.477 Sensitivity PETfold_pre2.0(20): 0.497 RNAsubopt: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAsubopt: 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.517 RNAsubopt: 0.492 Sensitivity TurboFold(seed): 0.422 RNAsubopt: 0.426 Positive Predictive Value TurboFold(seed): 0.642 RNAsubopt: 0.577 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.546 RNAsubopt: 0.472 Sensitivity RNASampler(seed): 0.409 RNAsubopt: 0.438 Positive Predictive Value RNASampler(seed): 0.734 RNAsubopt: 0.515 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.665 RNAsubopt: 0.551 Sensitivity PPfold(20): 0.519 RNAsubopt: 0.474 Positive Predictive Value PPfold(20): 0.859 RNAsubopt: 0.646 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.519 Mastr(seed): 0.000 Sensitivity RNAsubopt: 0.470 Mastr(seed): 0.000 Positive Predictive Value RNAsubopt: 0.578 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(20)	24 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 RSpredict(20): 0.559 Sensitivity MXScarna(seed): 0.556 RSpredict(20): 0.446 Positive Predictive Value MXScarna(seed): 0.815 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RSpredict(20): 0.555 Sensitivity CentroidAlifold(20): 0.540 RSpredict(20): 0.442 Positive Predictive Value CentroidAlifold(20): 0.897 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.657 RSpredict(20): 0.559 Sensitivity RNAalifold(20): 0.511 RSpredict(20): 0.446 Positive Predictive Value RNAalifold(20): 0.848 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.648 RSpredict(20): 0.559 Sensitivity RNASampler(20): 0.504 RSpredict(20): 0.446 Positive Predictive Value RNASampler(20): 0.837 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.610 RSpredict(20): 0.555 Sensitivity CentroidFold: 0.515 RSpredict(20): 0.442 Positive Predictive Value CentroidFold: 0.725 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.627 RSpredict(20): 0.559 Sensitivity MXScarna(20): 0.525 RSpredict(20): 0.446 Positive Predictive Value MXScarna(20): 0.752 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	23 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 RSpredict(20): 0.555 Sensitivity CentroidAlifold(seed): 0.417 RSpredict(20): 0.442 Positive Predictive Value CentroidAlifold(seed): 0.953 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.569 RSpredict(20): 0.559 Sensitivity Contrafold: 0.503 RSpredict(20): 0.446 Positive Predictive Value Contrafold: 0.647 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 3.54044765699e-05	24 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.597 RSpredict(20): 0.559 Sensitivity Sfold: 0.498 RSpredict(20): 0.446 Positive Predictive Value Sfold: 0.720 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.36778461742e-08	23 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.598 RSpredict(20): 0.555 Sensitivity MaxExpect: 0.520 RSpredict(20): 0.442 Positive Predictive Value MaxExpect: 0.692 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	8 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.571 RSpredict(20): 0.489 Sensitivity IPknot: 0.463 RSpredict(20): 0.367 Positive Predictive Value IPknot: 0.710 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 RSpredict(20): 0.489 Sensitivity CentroidHomfold‑LAST: 0.496 RSpredict(20): 0.367 Positive Predictive Value CentroidHomfold‑LAST: 0.807 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	24 HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.585 RSpredict(20): 0.559 Sensitivity HotKnots: 0.522 RSpredict(20): 0.446 Positive Predictive Value HotKnots: 0.659 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.607 RSpredict(20): 0.559 Sensitivity Carnac(20): 0.405 RSpredict(20): 0.446 Positive Predictive Value Carnac(20): 0.915 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	5 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.579 RSpredict(20): 0.352 Sensitivity ContextFold: 0.443 RSpredict(20): 0.251 Positive Predictive Value ContextFold: 0.763 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	15 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.597 RSpredict(20): 0.538 Sensitivity ProbKnot: 0.536 RSpredict(20): 0.424 Positive Predictive Value ProbKnot: 0.669 RSpredict(20): 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-08	24 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.593 RSpredict(20): 0.559 Sensitivity Murlet(20): 0.440 RSpredict(20): 0.446 Positive Predictive Value Murlet(20): 0.803 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	24 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.594 RSpredict(20): 0.559 Sensitivity UNAFold: 0.521 RSpredict(20): 0.446 Positive Predictive Value UNAFold: 0.681 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.581 RSpredict(20): 0.538 Sensitivity Fold: 0.512 RSpredict(20): 0.424 Positive Predictive Value Fold: 0.662 RSpredict(20): 0.686 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.9966815982e-08	24 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.572 RSpredict(20): 0.559 Sensitivity RNAfold: 0.509 RSpredict(20): 0.446 Positive Predictive Value RNAfold: 0.647 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.000176748592514	24 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.584 RSpredict(20): 0.559 Sensitivity PknotsRG: 0.522 RSpredict(20): 0.446 Positive Predictive Value PknotsRG: 0.657 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 7.95107997107e-08	11 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.661 RSpredict(20): 0.618 Sensitivity Cylofold: 0.553 RSpredict(20): 0.501 Positive Predictive Value Cylofold: 0.796 RSpredict(20): 0.768 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-08	15 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 RSpredict(20): 0.491 Sensitivity RNAalifold(seed): 0.364 RSpredict(20): 0.380 Positive Predictive Value RNAalifold(seed): 0.919 RSpredict(20): 0.639 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-08	24 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.563 RSpredict(20): 0.559 Sensitivity RNAshapes: 0.492 RSpredict(20): 0.446 Positive Predictive Value RNAshapes: 0.648 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.00701036536754	16 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.558 Afold: 0.517 Sensitivity RSpredict(20): 0.472 Afold: 0.475 Positive Predictive Value RSpredict(20): 0.664 Afold: 0.566 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.42300079339e-08	24 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.559 McQFold: 0.543 Sensitivity RSpredict(20): 0.446 McQFold: 0.471 Positive Predictive Value RSpredict(20): 0.705 McQFold: 0.630 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.000123289528193	23 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.564 Pknots: 0.559 Sensitivity RSpredict(20): 0.448 Pknots: 0.507 Positive Predictive Value RSpredict(20): 0.715 Pknots: 0.623 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.0209117840203	24 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.560 RSpredict(20): 0.559 Sensitivity RNAsubopt: 0.502 RSpredict(20): 0.446 Positive Predictive Value RNAsubopt: 0.629 RSpredict(20): 0.705 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 0.590817397584		? 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	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.559 Vsfold4: 0.483 Sensitivity RSpredict(20): 0.446 Vsfold4: 0.403 Positive Predictive Value RSpredict(20): 0.705 Vsfold4: 0.583 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.559 Mastr(20): 0.525 Sensitivity RSpredict(20): 0.446 Mastr(20): 0.350 Positive Predictive Value RSpredict(20): 0.705 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 9.19274550403e-08	? RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.467 RSpredict(20): 0.352 Sensitivity RNASLOpt: 0.383 RSpredict(20): 0.251 Positive Predictive Value RNASLOpt: 0.577 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.496 RSpredict(20): 0.481 Sensitivity Murlet(seed): 0.277 RSpredict(20): 0.367 Positive Predictive Value Murlet(seed): 0.895 RSpredict(20): 0.636 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.92154683637e-05	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.559 Vsfold5: 0.445 Sensitivity RSpredict(20): 0.446 Vsfold5: 0.375 Positive Predictive Value RSpredict(20): 0.705 Vsfold5: 0.534 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.489 RNAwolf: 0.364 Sensitivity RSpredict(20): 0.367 RNAwolf: 0.333 Positive Predictive Value RSpredict(20): 0.660 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 1.4651262096e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.648 RDfolder: 0.539 Sensitivity RSpredict(20): 0.494 RDfolder: 0.427 Positive Predictive Value RSpredict(20): 0.858 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.598 MCFold: 0.425 Sensitivity RSpredict(20): 0.495 MCFold: 0.448 Positive Predictive Value RSpredict(20): 0.728 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.559 RSpredict(seed): 0.232 Sensitivity RSpredict(20): 0.446 RSpredict(seed): 0.097 Positive Predictive Value RSpredict(20): 0.705 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	? RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.489 PPfold(seed): 0.026 Sensitivity RSpredict(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value RSpredict(20): 0.660 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.528 Carnac(seed): 0.122 Sensitivity RSpredict(20): 0.414 Carnac(seed): 0.015 Positive Predictive Value RSpredict(20): 0.679 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-08	? RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.337 NanoFolder: 0.316 Sensitivity RSpredict(20): 0.243 NanoFolder: 0.324 Positive Predictive Value RSpredict(20): 0.474 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.631 RSpredict(20): 0.591 Sensitivity Multilign(seed): 0.492 RSpredict(20): 0.441 Positive Predictive Value Multilign(seed): 0.817 RSpredict(20): 0.800 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.540 RSpredict(20): 0.489 Sensitivity Multilign(20): 0.456 RSpredict(20): 0.367 Positive Predictive Value Multilign(20): 0.647 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(seed): 0.557 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.594 RSpredict(20): 0.489 Sensitivity TurboFold(20): 0.470 RSpredict(20): 0.367 Positive Predictive Value TurboFold(20): 0.756 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(20): N/A Sensitivity RSpredict(20): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 RSpredict(20): 0.478 Sensitivity TurboFold(seed): 0.457 RSpredict(20): 0.362 Positive Predictive Value TurboFold(seed): 0.703 RSpredict(20): 0.638 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 RSpredict(20): 0.502 Sensitivity RNASampler(seed): 0.434 RSpredict(20): 0.461 Positive Predictive Value RNASampler(seed): 0.754 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.665 RSpredict(20): 0.489 Sensitivity PPfold(20): 0.519 RSpredict(20): 0.367 Positive Predictive Value PPfold(20): 0.859 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.559 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.446 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.705 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08
CRWrnafold	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 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 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	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	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: 1.67657656842e-08	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	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	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: 2.7402423548e-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: 1.95070920198e-08	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: 5.72327175742e-08	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: 2.89169006118e-08	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: 2.69132796717e-08	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: 2.30549897711e-08	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	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: 2.76499031155e-08	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: 3.69948253166e-05	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	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: 4.11681652902e-07	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: 2.7402423548e-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: 2.84041289224e-08	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: 2.36983135185e-08	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: 2.12160100812e-08	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	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: 2.00627773251e-08	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 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: 1.20718263679e-07	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: 2.01323596851e-07	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: 0.000108465172428	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		+ 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: 2.66715895098e-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	= 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: 0.00388586748353	? 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: 9.64686604905e-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: 1.86109605532e-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: 1.31583660336e-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: 2.35965341511e-08	? 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 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 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 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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
Vsfold4	34 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.650 Vsfold4: 0.494 Sensitivity MXScarna(seed): 0.533 Vsfold4: 0.419 Positive Predictive Value MXScarna(seed): 0.796 Vsfold4: 0.586 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Vsfold4: 0.477 Sensitivity CentroidAlifold(20): 0.540 Vsfold4: 0.397 Positive Predictive Value CentroidAlifold(20): 0.897 Vsfold4: 0.577 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	25 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.659 Vsfold4: 0.473 Sensitivity RNAalifold(20): 0.510 Vsfold4: 0.393 Positive Predictive Value RNAalifold(20): 0.854 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	25 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.640 Vsfold4: 0.473 Sensitivity RNASampler(20): 0.491 Vsfold4: 0.393 Positive Predictive Value RNASampler(20): 0.839 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	50 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.596 Vsfold4: 0.480 Sensitivity CentroidFold: 0.507 Vsfold4: 0.404 Positive Predictive Value CentroidFold: 0.705 Vsfold4: 0.576 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.621 Vsfold4: 0.473 Sensitivity MXScarna(20): 0.518 Vsfold4: 0.393 Positive Predictive Value MXScarna(20): 0.748 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Vsfold4: 0.490 Sensitivity CentroidAlifold(seed): 0.377 Vsfold4: 0.415 Positive Predictive Value CentroidAlifold(seed): 0.925 Vsfold4: 0.582 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	55 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.568 Vsfold4: 0.478 Sensitivity Contrafold: 0.498 Vsfold4: 0.399 Positive Predictive Value Contrafold: 0.653 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.574 Vsfold4: 0.478 Sensitivity Sfold: 0.480 Vsfold4: 0.399 Positive Predictive Value Sfold: 0.691 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.571 Vsfold4: 0.470 Sensitivity MaxExpect: 0.502 Vsfold4: 0.395 Positive Predictive Value MaxExpect: 0.654 Vsfold4: 0.566 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.567 Vsfold4: 0.425 Sensitivity IPknot: 0.463 Vsfold4: 0.354 Positive Predictive Value IPknot: 0.702 Vsfold4: 0.520 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	18 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Vsfold4: 0.425 Sensitivity CentroidHomfold‑LAST: 0.397 Vsfold4: 0.351 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Vsfold4: 0.526 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	55 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.569 Vsfold4: 0.478 Sensitivity HotKnots: 0.506 Vsfold4: 0.399 Positive Predictive Value HotKnots: 0.644 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.601 Vsfold4: 0.473 Sensitivity Carnac(20): 0.397 Vsfold4: 0.393 Positive Predictive Value Carnac(20): 0.914 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	14 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.601 Vsfold4: 0.408 Sensitivity ContextFold: 0.483 Vsfold4: 0.340 Positive Predictive Value ContextFold: 0.754 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.34821445183e-08	32 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.561 Vsfold4: 0.462 Sensitivity ProbKnot: 0.514 Vsfold4: 0.392 Positive Predictive Value ProbKnot: 0.617 Vsfold4: 0.551 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.592 Vsfold4: 0.473 Sensitivity Murlet(20): 0.437 Vsfold4: 0.393 Positive Predictive Value Murlet(20): 0.807 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	55 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.571 Vsfold4: 0.478 Sensitivity UNAFold: 0.500 Vsfold4: 0.399 Positive Predictive Value UNAFold: 0.655 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.570 Vsfold4: 0.479 Sensitivity Fold: 0.509 Vsfold4: 0.406 Positive Predictive Value Fold: 0.643 Vsfold4: 0.571 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.551 Vsfold4: 0.478 Sensitivity RNAfold: 0.487 Vsfold4: 0.399 Positive Predictive Value RNAfold: 0.628 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.552 Vsfold4: 0.478 Sensitivity PknotsRG: 0.492 Vsfold4: 0.399 Positive Predictive Value PknotsRG: 0.625 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.607 Vsfold4: 0.529 Sensitivity Cylofold: 0.512 Vsfold4: 0.441 Positive Predictive Value Cylofold: 0.727 Vsfold4: 0.642 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.69811216434e-08	19 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.539 Vsfold4: 0.456 Sensitivity RNAalifold(seed): 0.336 Vsfold4: 0.388 Positive Predictive Value RNAalifold(seed): 0.866 Vsfold4: 0.540 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	55 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.539 Vsfold4: 0.478 Sensitivity RNAshapes: 0.470 Vsfold4: 0.399 Positive Predictive Value RNAshapes: 0.622 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.528 Vsfold4: 0.468 Sensitivity Afold: 0.478 Vsfold4: 0.395 Positive Predictive Value Afold: 0.587 Vsfold4: 0.560 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.523 Vsfold4: 0.478 Sensitivity McQFold: 0.449 Vsfold4: 0.399 Positive Predictive Value McQFold: 0.613 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.547 Vsfold4: 0.501 Sensitivity Pknots: 0.489 Vsfold4: 0.412 Positive Predictive Value Pknots: 0.620 Vsfold4: 0.617 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.531 Vsfold4: 0.478 Sensitivity RNAsubopt: 0.473 Vsfold4: 0.399 Positive Predictive Value RNAsubopt: 0.601 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.559 Vsfold4: 0.483 Sensitivity RSpredict(20): 0.446 Vsfold4: 0.403 Positive Predictive Value RSpredict(20): 0.705 Vsfold4: 0.583 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	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: 2.66715895098e-08		- Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.523 Vsfold4: 0.473 Sensitivity Mastr(20): 0.348 Vsfold4: 0.393 Positive Predictive Value Mastr(20): 0.790 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	- RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.443 Vsfold4: 0.408 Sensitivity RNASLOpt: 0.365 Vsfold4: 0.340 Positive Predictive Value RNASLOpt: 0.547 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.7488605325e-07	+ Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.497 Murlet(seed): 0.475 Sensitivity Vsfold4: 0.407 Murlet(seed): 0.270 Positive Predictive Value Vsfold4: 0.613 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.478 Vsfold5: 0.426 Sensitivity Vsfold4: 0.399 Vsfold5: 0.359 Positive Predictive Value Vsfold4: 0.579 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.425 RNAwolf: 0.399 Sensitivity Vsfold4: 0.354 RNAwolf: 0.368 Positive Predictive Value Vsfold4: 0.520 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-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: 0.443 Sensitivity Vsfold4: 0.462 RDfolder: 0.342 Positive Predictive Value Vsfold4: 0.713 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.499 MCFold: 0.419 Sensitivity Vsfold4: 0.411 MCFold: 0.437 Positive Predictive Value Vsfold4: 0.613 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.494 RSpredict(seed): 0.204 Sensitivity Vsfold4: 0.419 RSpredict(seed): 0.088 Positive Predictive Value Vsfold4: 0.586 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.454 PPfold(seed): 0.102 Sensitivity Vsfold4: 0.367 PPfold(seed): 0.020 Positive Predictive Value Vsfold4: 0.570 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.10032755566e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.496 Carnac(seed): 0.139 Sensitivity Vsfold4: 0.411 Carnac(seed): 0.019 Positive Predictive Value Vsfold4: 0.605 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	? Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.393 NanoFolder: 0.366 Sensitivity Vsfold4: 0.325 NanoFolder: 0.376 Positive Predictive Value Vsfold4: 0.486 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.538 Vsfold4: 0.366 Sensitivity Multilign(seed): 0.420 Vsfold4: 0.297 Positive Predictive Value Multilign(seed): 0.699 Vsfold4: 0.466 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.540 Vsfold4: 0.437 Sensitivity Multilign(20): 0.456 Vsfold4: 0.356 Positive Predictive Value Multilign(20): 0.647 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold4: 0.437 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold4: 0.350 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold4: 0.553 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.594 Vsfold4: 0.437 Sensitivity TurboFold(20): 0.470 Vsfold4: 0.356 Positive Predictive Value TurboFold(20): 0.756 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(20): N/A Sensitivity Vsfold4: N/A CMfinder(20): N/A Positive Predictive Value Vsfold4: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold4: 0.401 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold4: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold4: 0.505 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.517 Vsfold4: 0.380 Sensitivity TurboFold(seed): 0.422 Vsfold4: 0.308 Positive Predictive Value TurboFold(seed): 0.642 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.546 Vsfold4: 0.412 Sensitivity RNASampler(seed): 0.409 Vsfold4: 0.351 Positive Predictive Value RNASampler(seed): 0.734 Vsfold4: 0.490 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.665 Vsfold4: 0.437 Sensitivity PPfold(20): 0.519 Vsfold4: 0.356 Positive Predictive Value PPfold(20): 0.859 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.486 Mastr(seed): 0.000 Sensitivity Vsfold4: 0.411 Mastr(seed): 0.000 Positive Predictive Value Vsfold4: 0.580 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
Mastr(20)	24 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.672 Mastr(20): 0.525 Sensitivity MXScarna(seed): 0.556 Mastr(20): 0.350 Positive Predictive Value MXScarna(seed): 0.815 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	23 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Mastr(20): 0.518 Sensitivity CentroidAlifold(20): 0.540 Mastr(20): 0.343 Positive Predictive Value CentroidAlifold(20): 0.897 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Mastr(20): 0.523 Sensitivity RNAalifold(20): 0.510 Mastr(20): 0.348 Positive Predictive Value RNAalifold(20): 0.854 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.640 Mastr(20): 0.523 Sensitivity RNASampler(20): 0.491 Mastr(20): 0.348 Positive Predictive Value RNASampler(20): 0.839 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.98172311752e-08	23 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.610 Mastr(20): 0.518 Sensitivity CentroidFold: 0.515 Mastr(20): 0.343 Positive Predictive Value CentroidFold: 0.725 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.621 Mastr(20): 0.523 Sensitivity MXScarna(20): 0.518 Mastr(20): 0.348 Positive Predictive Value MXScarna(20): 0.748 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.629 Mastr(20): 0.518 Sensitivity CentroidAlifold(seed): 0.417 Mastr(20): 0.343 Positive Predictive Value CentroidAlifold(seed): 0.953 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.554 Mastr(20): 0.523 Sensitivity Contrafold: 0.488 Mastr(20): 0.348 Positive Predictive Value Contrafold: 0.634 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.59469103578e-08	25 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.593 Mastr(20): 0.523 Sensitivity Sfold: 0.492 Mastr(20): 0.348 Positive Predictive Value Sfold: 0.718 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	23 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.598 Mastr(20): 0.518 Sensitivity MaxExpect: 0.520 Mastr(20): 0.343 Positive Predictive Value MaxExpect: 0.692 Mastr(20): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	8 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.571 Mastr(20): 0.567 Sensitivity IPknot: 0.463 Mastr(20): 0.389 Positive Predictive Value IPknot: 0.710 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Mastr(20): 0.567 Sensitivity CentroidHomfold‑LAST: 0.496 Mastr(20): 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	25 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.580 Mastr(20): 0.523 Sensitivity HotKnots: 0.514 Mastr(20): 0.348 Positive Predictive Value HotKnots: 0.658 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	25 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.601 Mastr(20): 0.523 Sensitivity Carnac(20): 0.397 Mastr(20): 0.348 Positive Predictive Value Carnac(20): 0.914 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	5 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.579 Mastr(20): 0.488 Sensitivity ContextFold: 0.443 Mastr(20): 0.305 Positive Predictive Value ContextFold: 0.763 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	15 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.597 Mastr(20): 0.483 Sensitivity ProbKnot: 0.536 Mastr(20): 0.297 Positive Predictive Value ProbKnot: 0.669 Mastr(20): 0.791 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.06323189071e-08	25 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.592 Mastr(20): 0.523 Sensitivity Murlet(20): 0.437 Mastr(20): 0.348 Positive Predictive Value Murlet(20): 0.807 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.589 Mastr(20): 0.523 Sensitivity UNAFold: 0.513 Mastr(20): 0.348 Positive Predictive Value UNAFold: 0.681 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.581 Mastr(20): 0.483 Sensitivity Fold: 0.512 Mastr(20): 0.297 Positive Predictive Value Fold: 0.662 Mastr(20): 0.791 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	25 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.569 Mastr(20): 0.523 Sensitivity RNAfold: 0.502 Mastr(20): 0.348 Positive Predictive Value RNAfold: 0.649 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.581 Mastr(20): 0.523 Sensitivity PknotsRG: 0.516 Mastr(20): 0.348 Positive Predictive Value PknotsRG: 0.659 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.59469103578e-08	11 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.661 Mastr(20): 0.566 Sensitivity Cylofold: 0.553 Mastr(20): 0.384 Positive Predictive Value Cylofold: 0.796 Mastr(20): 0.840 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.05690340753e-08	15 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.578 Mastr(20): 0.394 Sensitivity RNAalifold(seed): 0.364 Mastr(20): 0.207 Positive Predictive Value RNAalifold(seed): 0.919 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	25 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.554 Mastr(20): 0.523 Sensitivity RNAshapes: 0.482 Mastr(20): 0.348 Positive Predictive Value RNAshapes: 0.642 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.11890491782e-07	17 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.516 Afold: 0.513 Sensitivity Mastr(20): 0.340 Afold: 0.464 Positive Predictive Value Mastr(20): 0.787 Afold: 0.572 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0978527593275	25 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.529 Mastr(20): 0.523 Sensitivity McQFold: 0.456 Mastr(20): 0.348 Positive Predictive Value McQFold: 0.618 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 0.294741380356	24 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.561 Pknots: 0.540 Sensitivity Mastr(20): 0.401 Pknots: 0.487 Positive Predictive Value Mastr(20): 0.790 Pknots: 0.605 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 1.19178247576e-06	25 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.545 Mastr(20): 0.523 Sensitivity RNAsubopt: 0.486 Mastr(20): 0.348 Positive Predictive Value RNAsubopt: 0.616 Mastr(20): 0.790 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 1.13709158556e-05	24 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.559 Mastr(20): 0.525 Sensitivity RSpredict(20): 0.446 Mastr(20): 0.350 Positive Predictive Value RSpredict(20): 0.705 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 9.19274550403e-08	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	25 Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.523 Vsfold4: 0.473 Sensitivity Mastr(20): 0.348 Vsfold4: 0.393 Positive Predictive Value Mastr(20): 0.790 Vsfold4: 0.574 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08		? Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.488 RNASLOpt: 0.467 Sensitivity Mastr(20): 0.305 RNASLOpt: 0.383 Positive Predictive Value Mastr(20): 0.785 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.496 Mastr(20): 0.443 Sensitivity Murlet(seed): 0.277 Mastr(20): 0.263 Positive Predictive Value Murlet(seed): 0.895 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.523 Vsfold5: 0.425 Sensitivity Mastr(20): 0.348 Vsfold5: 0.358 Positive Predictive Value Mastr(20): 0.790 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.567 RNAwolf: 0.364 Sensitivity Mastr(20): 0.389 RNAwolf: 0.333 Positive Predictive Value Mastr(20): 0.833 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ 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: 1.43692248862e-08	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.651 RDfolder: 0.539 Sensitivity Mastr(20): 0.504 RDfolder: 0.427 Positive Predictive Value Mastr(20): 0.849 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.595 MCFold: 0.425 Sensitivity Mastr(20): 0.427 MCFold: 0.448 Positive Predictive Value Mastr(20): 0.834 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.525 RSpredict(seed): 0.232 Sensitivity Mastr(20): 0.350 RSpredict(seed): 0.097 Positive Predictive Value Mastr(20): 0.792 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	? Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.567 PPfold(seed): 0.026 Sensitivity Mastr(20): 0.389 PPfold(seed): 0.004 Positive Predictive Value Mastr(20): 0.833 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.522 Carnac(seed): 0.122 Sensitivity Mastr(20): 0.360 Carnac(seed): 0.015 Positive Predictive Value Mastr(20): 0.764 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	? Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.499 NanoFolder: 0.316 Sensitivity Mastr(20): 0.324 NanoFolder: 0.324 Positive Predictive Value Mastr(20): 0.774 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.631 Mastr(20): 0.560 Sensitivity Multilign(seed): 0.492 Mastr(20): 0.415 Positive Predictive Value Multilign(seed): 0.817 Mastr(20): 0.766 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.567 Multilign(20): 0.540 Sensitivity Mastr(20): 0.389 Multilign(20): 0.456 Positive Predictive Value Mastr(20): 0.833 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(seed): 0.557 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Mastr(20): 0.567 Sensitivity TurboFold(20): 0.470 Mastr(20): 0.389 Positive Predictive Value TurboFold(20): 0.756 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(20): N/A Sensitivity Mastr(20): N/A CMfinder(20): N/A Positive Predictive Value Mastr(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Mastr(20): 0.542 Sensitivity TurboFold(seed): 0.457 Mastr(20): 0.366 Positive Predictive Value TurboFold(seed): 0.703 Mastr(20): 0.809 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): 0.570 Mastr(20): 0.526 Sensitivity RNASampler(seed): 0.434 Mastr(20): 0.311 Positive Predictive Value RNASampler(seed): 0.754 Mastr(20): 0.895 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.665 Mastr(20): 0.567 Sensitivity PPfold(20): 0.519 Mastr(20): 0.389 Positive Predictive Value PPfold(20): 0.859 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.523 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.348 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.790 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08
RNASLOpt	8 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.586 RNASLOpt: 0.474 Sensitivity MXScarna(seed): 0.457 RNASLOpt: 0.374 Positive Predictive Value MXScarna(seed): 0.758 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.650 RNASLOpt: 0.467 Sensitivity CentroidAlifold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value CentroidAlifold(20): 0.898 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.553 RNASLOpt: 0.467 Sensitivity RNAalifold(20): 0.407 RNASLOpt: 0.383 Positive Predictive Value RNAalifold(20): 0.756 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.569 RNASLOpt: 0.467 Sensitivity RNASampler(20): 0.419 RNASLOpt: 0.383 Positive Predictive Value RNASampler(20): 0.778 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	14 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.520 RNASLOpt: 0.443 Sensitivity CentroidFold: 0.423 RNASLOpt: 0.365 Positive Predictive Value CentroidFold: 0.648 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	5 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.501 RNASLOpt: 0.467 Sensitivity MXScarna(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value MXScarna(20): 0.632 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.542 RNASLOpt: 0.474 Sensitivity CentroidAlifold(seed): 0.299 RNASLOpt: 0.374 Positive Predictive Value CentroidAlifold(seed): 0.987 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.517 RNASLOpt: 0.443 Sensitivity Contrafold: 0.438 RNASLOpt: 0.365 Positive Predictive Value Contrafold: 0.618 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 5.52090997893e-09	14 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.480 RNASLOpt: 0.443 Sensitivity Sfold: 0.393 RNASLOpt: 0.365 Positive Predictive Value Sfold: 0.595 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	14 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.446 RNASLOpt: 0.443 Sensitivity MaxExpect: 0.385 RNASLOpt: 0.365 Positive Predictive Value MaxExpect: 0.526 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.150312415084	14 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.538 RNASLOpt: 0.443 Sensitivity IPknot: 0.443 RNASLOpt: 0.365 Positive Predictive Value IPknot: 0.660 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	14 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.515 RNASLOpt: 0.443 Sensitivity CentroidHomfold‑LAST: 0.365 RNASLOpt: 0.365 Positive Predictive Value CentroidHomfold‑LAST: 0.734 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	14 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.509 RNASLOpt: 0.443 Sensitivity HotKnots: 0.460 RNASLOpt: 0.365 Positive Predictive Value HotKnots: 0.570 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.36983135185e-08	5 Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.476 RNASLOpt: 0.467 Sensitivity Carnac(20): 0.281 RNASLOpt: 0.383 Positive Predictive Value Carnac(20): 0.810 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	14 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.601 RNASLOpt: 0.443 Sensitivity ContextFold: 0.483 RNASLOpt: 0.365 Positive Predictive Value ContextFold: 0.754 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	14 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.461 RNASLOpt: 0.443 Sensitivity ProbKnot: 0.418 RNASLOpt: 0.365 Positive Predictive Value ProbKnot: 0.517 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 6.46512660639e-07	5 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.496 RNASLOpt: 0.467 Sensitivity Murlet(20): 0.353 RNASLOpt: 0.383 Positive Predictive Value Murlet(20): 0.702 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	14 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.451 RNASLOpt: 0.443 Sensitivity UNAFold: 0.400 RNASLOpt: 0.365 Positive Predictive Value UNAFold: 0.516 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.013974662571	14 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.447 RNASLOpt: 0.443 Sensitivity Fold: 0.393 RNASLOpt: 0.365 Positive Predictive Value Fold: 0.518 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.976227115967	14 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.483 RNASLOpt: 0.443 Sensitivity RNAfold: 0.423 RNASLOpt: 0.365 Positive Predictive Value RNAfold: 0.560 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.93248927742e-08	14 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.506 RNASLOpt: 0.443 Sensitivity PknotsRG: 0.453 RNASLOpt: 0.365 Positive Predictive Value PknotsRG: 0.573 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.91763127434e-08	12 Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.492 RNASLOpt: 0.438 Sensitivity Cylofold: 0.422 RNASLOpt: 0.351 Positive Predictive Value Cylofold: 0.584 RNASLOpt: 0.556 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.61358433984e-08	5 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.472 RNASLOpt: 0.390 Sensitivity RNAalifold(seed): 0.293 RNASLOpt: 0.323 Positive Predictive Value RNAalifold(seed): 0.765 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	14 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.472 RNASLOpt: 0.443 Sensitivity RNAshapes: 0.413 RNASLOpt: 0.365 Positive Predictive Value RNAshapes: 0.548 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.34193807955e-08	6 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.475 RNASLOpt: 0.420 Sensitivity Afold: 0.442 RNASLOpt: 0.376 Positive Predictive Value Afold: 0.518 RNASLOpt: 0.477 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	14 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.445 RNASLOpt: 0.443 Sensitivity McQFold: 0.385 RNASLOpt: 0.365 Positive Predictive Value McQFold: 0.522 RNASLOpt: 0.547 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0739904251478	14 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.443 Pknots: 0.408 Sensitivity RNASLOpt: 0.365 Pknots: 0.373 Positive Predictive Value RNASLOpt: 0.547 Pknots: 0.456 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.4308705233e-08	14 RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.443 RNAsubopt: 0.424 Sensitivity RNASLOpt: 0.365 RNAsubopt: 0.378 Positive Predictive Value RNASLOpt: 0.547 RNAsubopt: 0.486 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	5 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.467 RSpredict(20): 0.352 Sensitivity RNASLOpt: 0.383 RSpredict(20): 0.251 Positive Predictive Value RNASLOpt: 0.577 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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: 0.00388586748353	14 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.443 Vsfold4: 0.408 Sensitivity RNASLOpt: 0.365 Vsfold4: 0.340 Positive Predictive Value RNASLOpt: 0.547 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 4.7488605325e-07	5 Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.488 RNASLOpt: 0.467 Sensitivity Mastr(20): 0.305 RNASLOpt: 0.383 Positive Predictive Value Mastr(20): 0.785 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.425 RNASLOpt: 0.390 Sensitivity Murlet(seed): 0.248 RNASLOpt: 0.323 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.443 Vsfold5: 0.340 Sensitivity RNASLOpt: 0.365 Vsfold5: 0.295 Positive Predictive Value RNASLOpt: 0.547 Vsfold5: 0.401 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.443 RNAwolf: 0.349 Sensitivity RNASLOpt: 0.365 RNAwolf: 0.323 Positive Predictive Value RNASLOpt: 0.547 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.40919803867e-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: 0.392 RDfolder: 0.229 Sensitivity RNASLOpt: 0.299 RDfolder: 0.168 Positive Predictive Value RNASLOpt: 0.526 RDfolder: 0.329 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.461 MCFold: 0.441 Sensitivity RNASLOpt: 0.393 MCFold: 0.474 Positive Predictive Value RNASLOpt: 0.550 MCFold: 0.419 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.14792285362e-08	? RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 RSpredict(seed): 0.110 Sensitivity RNASLOpt: 0.374 RSpredict(seed): 0.047 Positive Predictive Value RNASLOpt: 0.609 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 PPfold(seed): 0.121 Sensitivity RNASLOpt: 0.374 PPfold(seed): 0.028 Positive Predictive Value RNASLOpt: 0.609 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 Carnac(seed): 0.146 Sensitivity RNASLOpt: 0.380 Carnac(seed): 0.021 Positive Predictive Value RNASLOpt: 0.582 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.475 NanoFolder: 0.366 Sensitivity RNASLOpt: 0.386 NanoFolder: 0.376 Positive Predictive Value RNASLOpt: 0.591 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.403 RNASLOpt: 0.332 Sensitivity Multilign(seed): 0.306 RNASLOpt: 0.242 Positive Predictive Value Multilign(seed): 0.543 RNASLOpt: 0.469 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.474 RNASLOpt: 0.467 Sensitivity Multilign(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value Multilign(20): 0.568 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNASLOpt: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 RNASLOpt: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.542 RNASLOpt: 0.467 Sensitivity TurboFold(20): 0.425 RNASLOpt: 0.383 Positive Predictive Value TurboFold(20): 0.696 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: N/A CMfinder(20): N/A Sensitivity RNASLOpt: N/A CMfinder(20): N/A Positive Predictive Value RNASLOpt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASLOpt: 0.467 Sensitivity PETfold_pre2.0(20): 0.497 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs TurboFold(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 TurboFold(seed): 0.460 Sensitivity RNASLOpt: 0.380 TurboFold(seed): 0.380 Positive Predictive Value RNASLOpt: 0.582 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.295 RNASampler(seed): 0.198 Sensitivity RNASLOpt: 0.283 RNASampler(seed): 0.151 Positive Predictive Value RNASLOpt: 0.313 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.616 RNASLOpt: 0.467 Sensitivity PPfold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value PPfold(20): 0.806 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.374 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.609 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Murlet(seed)	16 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.615 Murlet(seed): 0.475 Sensitivity MXScarna(seed): 0.491 Murlet(seed): 0.270 Positive Predictive Value MXScarna(seed): 0.775 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.16042554876e-08	13 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.675 Murlet(seed): 0.496 Sensitivity CentroidAlifold(20): 0.500 Murlet(seed): 0.277 Positive Predictive Value CentroidAlifold(20): 0.916 Murlet(seed): 0.893 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	14 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.618 Murlet(seed): 0.496 Sensitivity RNAalifold(20): 0.466 Murlet(seed): 0.277 Positive Predictive Value RNAalifold(20): 0.824 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.42300079339e-08	14 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.619 Murlet(seed): 0.496 Sensitivity RNASampler(20): 0.475 Murlet(seed): 0.277 Positive Predictive Value RNASampler(20): 0.812 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.08252958266e-08	15 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.620 Murlet(seed): 0.474 Sensitivity CentroidFold: 0.508 Murlet(seed): 0.270 Positive Predictive Value CentroidFold: 0.760 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	14 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.610 Murlet(seed): 0.496 Sensitivity MXScarna(20): 0.493 Murlet(seed): 0.277 Positive Predictive Value MXScarna(20): 0.759 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	15 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.702 Murlet(seed): 0.474 Sensitivity CentroidAlifold(seed): 0.508 Murlet(seed): 0.270 Positive Predictive Value CentroidAlifold(seed): 0.972 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	16 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.599 Murlet(seed): 0.475 Sensitivity Contrafold: 0.516 Murlet(seed): 0.270 Positive Predictive Value Contrafold: 0.700 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.02344513449e-08	16 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.627 Murlet(seed): 0.475 Sensitivity Sfold: 0.507 Murlet(seed): 0.270 Positive Predictive Value Sfold: 0.779 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	14 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.556 Murlet(seed): 0.467 Sensitivity MaxExpect: 0.476 Murlet(seed): 0.266 Positive Predictive Value MaxExpect: 0.656 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.44715536483e-09	7 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.505 Murlet(seed): 0.451 Sensitivity IPknot: 0.402 Murlet(seed): 0.268 Positive Predictive Value IPknot: 0.641 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.532 Murlet(seed): 0.451 Sensitivity CentroidHomfold‑LAST: 0.407 Murlet(seed): 0.268 Positive Predictive Value CentroidHomfold‑LAST: 0.702 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	16 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.614 Murlet(seed): 0.475 Sensitivity HotKnots: 0.536 Murlet(seed): 0.270 Positive Predictive Value HotKnots: 0.707 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	14 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.569 Murlet(seed): 0.496 Sensitivity Carnac(20): 0.342 Murlet(seed): 0.277 Positive Predictive Value Carnac(20): 0.949 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.5677163434e-08	5 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.488 Murlet(seed): 0.425 Sensitivity ContextFold: 0.376 Murlet(seed): 0.248 Positive Predictive Value ContextFold: 0.641 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.509 Murlet(seed): 0.452 Sensitivity ProbKnot: 0.461 Murlet(seed): 0.249 Positive Predictive Value ProbKnot: 0.568 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.53972656358e-08	14 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.567 Murlet(seed): 0.496 Sensitivity Murlet(20): 0.405 Murlet(seed): 0.277 Positive Predictive Value Murlet(20): 0.799 Murlet(seed): 0.895 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.86595104665e-08	16 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.592 Murlet(seed): 0.475 Sensitivity UNAFold: 0.507 Murlet(seed): 0.270 Positive Predictive Value UNAFold: 0.697 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.97012568641e-08	10 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.493 Murlet(seed): 0.452 Sensitivity Fold: 0.434 Murlet(seed): 0.249 Positive Predictive Value Fold: 0.567 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.98343147122e-08	16 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.614 Murlet(seed): 0.475 Sensitivity RNAfold: 0.531 Murlet(seed): 0.270 Positive Predictive Value RNAfold: 0.715 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.22210847902e-08	16 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.635 Murlet(seed): 0.475 Sensitivity PknotsRG: 0.555 Murlet(seed): 0.270 Positive Predictive Value PknotsRG: 0.733 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.78993384543e-08	8 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.619 Murlet(seed): 0.444 Sensitivity Cylofold: 0.509 Murlet(seed): 0.247 Positive Predictive Value Cylofold: 0.758 Murlet(seed): 0.805 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	16 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 Murlet(seed): 0.475 Sensitivity RNAalifold(seed): 0.398 Murlet(seed): 0.270 Positive Predictive Value RNAalifold(seed): 0.890 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	16 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.594 Murlet(seed): 0.475 Sensitivity RNAshapes: 0.511 Murlet(seed): 0.270 Positive Predictive Value RNAshapes: 0.697 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.97012568641e-08	11 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.586 Murlet(seed): 0.453 Sensitivity Afold: 0.520 Murlet(seed): 0.267 Positive Predictive Value Afold: 0.665 Murlet(seed): 0.774 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.41358941668e-08	16 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.601 Murlet(seed): 0.475 Sensitivity McQFold: 0.522 Murlet(seed): 0.270 Positive Predictive Value McQFold: 0.698 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	16 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.563 Murlet(seed): 0.475 Sensitivity Pknots: 0.509 Murlet(seed): 0.270 Positive Predictive Value Pknots: 0.628 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	16 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.551 Murlet(seed): 0.475 Sensitivity RNAsubopt: 0.485 Murlet(seed): 0.270 Positive Predictive Value RNAsubopt: 0.630 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	14 Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.496 RSpredict(20): 0.481 Sensitivity Murlet(seed): 0.277 RSpredict(20): 0.367 Positive Predictive Value Murlet(seed): 0.895 RSpredict(20): 0.636 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.92154683637e-05	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	16 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.497 Murlet(seed): 0.475 Sensitivity Vsfold4: 0.407 Murlet(seed): 0.270 Positive Predictive Value Vsfold4: 0.613 Murlet(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	14 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.496 Mastr(20): 0.443 Sensitivity Murlet(seed): 0.277 Mastr(20): 0.263 Positive Predictive Value Murlet(seed): 0.895 Mastr(20): 0.754 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.66715895098e-08	5 Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.425 RNASLOpt: 0.390 Sensitivity Murlet(seed): 0.248 RNASLOpt: 0.323 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		= Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.475 Vsfold5: 0.469 Sensitivity Murlet(seed): 0.270 Vsfold5: 0.394 Positive Predictive Value Murlet(seed): 0.841 Vsfold5: 0.565 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.00964022676679	? Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.451 RNAwolf: 0.370 Sensitivity Murlet(seed): 0.268 RNAwolf: 0.344 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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: 0.526 Murlet(seed): 0.504 Sensitivity RDfolder: 0.398 Murlet(seed): 0.316 Positive Predictive Value RDfolder: 0.704 Murlet(seed): 0.813 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.42440948549e-06	+ Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.464 MCFold: 0.448 Sensitivity Murlet(seed): 0.263 MCFold: 0.463 Positive Predictive Value Murlet(seed): 0.823 MCFold: 0.441 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79079429174e-05	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.475 RSpredict(seed): 0.329 Sensitivity Murlet(seed): 0.270 RSpredict(seed): 0.166 Positive Predictive Value Murlet(seed): 0.841 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	? Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.451 PPfold(seed): 0.133 Sensitivity Murlet(seed): 0.268 PPfold(seed): 0.033 Positive Predictive Value Murlet(seed): 0.767 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.475 Carnac(seed): 0.159 Sensitivity Murlet(seed): 0.270 Carnac(seed): 0.026 Positive Predictive Value Murlet(seed): 0.841 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.403 NanoFolder: 0.280 Sensitivity Murlet(seed): 0.237 NanoFolder: 0.298 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 Murlet(seed): 0.425 Sensitivity Multilign(seed): 0.420 Murlet(seed): 0.268 Positive Predictive Value Multilign(seed): 0.699 Murlet(seed): 0.685 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.520 Multilign(20): 0.480 Sensitivity Murlet(seed): 0.296 Multilign(20): 0.402 Positive Predictive Value Murlet(seed): 0.918 Multilign(20): 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 Murlet(seed): 0.425 Sensitivity PETfold_pre2.0(seed): 0.459 Murlet(seed): 0.248 Positive Predictive Value PETfold_pre2.0(seed): 0.726 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.547 Murlet(seed): 0.520 Sensitivity TurboFold(20): 0.423 Murlet(seed): 0.296 Positive Predictive Value TurboFold(20): 0.714 Murlet(seed): 0.918 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Murlet(seed): 0.539 PETfold_pre2.0(20): 0.527 Sensitivity Murlet(seed): 0.292 PETfold_pre2.0(20): 0.407 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.471 Murlet(seed): 0.451 Sensitivity TurboFold(seed): 0.383 Murlet(seed): 0.268 Positive Predictive Value TurboFold(seed): 0.588 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 Murlet(seed): 0.424 Sensitivity RNASampler(seed): 0.409 Murlet(seed): 0.243 Positive Predictive Value RNASampler(seed): 0.734 Murlet(seed): 0.744 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.603 Murlet(seed): 0.520 Sensitivity PPfold(20): 0.455 Murlet(seed): 0.296 Positive Predictive Value PPfold(20): 0.804 Murlet(seed): 0.918 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.475 Mastr(seed): 0.000 Sensitivity Murlet(seed): 0.270 Mastr(seed): 0.000 Positive Predictive Value Murlet(seed): 0.841 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.50323628132e-08
Vsfold5	34 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.650 Vsfold5: 0.463 Sensitivity MXScarna(seed): 0.533 Vsfold5: 0.395 Positive Predictive Value MXScarna(seed): 0.796 Vsfold5: 0.547 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Vsfold5: 0.440 Sensitivity CentroidAlifold(20): 0.540 Vsfold5: 0.370 Positive Predictive Value CentroidAlifold(20): 0.897 Vsfold5: 0.527 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	25 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.659 Vsfold5: 0.425 Sensitivity RNAalifold(20): 0.510 Vsfold5: 0.358 Positive Predictive Value RNAalifold(20): 0.854 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	25 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.640 Vsfold5: 0.425 Sensitivity RNASampler(20): 0.491 Vsfold5: 0.358 Positive Predictive Value RNASampler(20): 0.839 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	50 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.596 Vsfold5: 0.432 Sensitivity CentroidFold: 0.507 Vsfold5: 0.366 Positive Predictive Value CentroidFold: 0.705 Vsfold5: 0.515 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.621 Vsfold5: 0.425 Sensitivity MXScarna(20): 0.518 Vsfold5: 0.358 Positive Predictive Value MXScarna(20): 0.748 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.02343278931e-08	33 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Vsfold5: 0.459 Sensitivity CentroidAlifold(seed): 0.377 Vsfold5: 0.391 Positive Predictive Value CentroidAlifold(seed): 0.925 Vsfold5: 0.543 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	55 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.568 Vsfold5: 0.426 Sensitivity Contrafold: 0.498 Vsfold5: 0.359 Positive Predictive Value Contrafold: 0.653 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.574 Vsfold5: 0.426 Sensitivity Sfold: 0.480 Vsfold5: 0.359 Positive Predictive Value Sfold: 0.691 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.571 Vsfold5: 0.420 Sensitivity MaxExpect: 0.502 Vsfold5: 0.355 Positive Predictive Value MaxExpect: 0.654 Vsfold5: 0.503 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.567 Vsfold5: 0.369 Sensitivity IPknot: 0.463 Vsfold5: 0.318 Positive Predictive Value IPknot: 0.702 Vsfold5: 0.437 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.24270395587e-08	18 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.555 Vsfold5: 0.358 Sensitivity CentroidHomfold‑LAST: 0.397 Vsfold5: 0.307 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Vsfold5: 0.429 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	55 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.569 Vsfold5: 0.426 Sensitivity HotKnots: 0.506 Vsfold5: 0.359 Positive Predictive Value HotKnots: 0.644 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.601 Vsfold5: 0.425 Sensitivity Carnac(20): 0.397 Vsfold5: 0.358 Positive Predictive Value Carnac(20): 0.914 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	14 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.601 Vsfold5: 0.340 Sensitivity ContextFold: 0.483 Vsfold5: 0.295 Positive Predictive Value ContextFold: 0.754 Vsfold5: 0.401 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	32 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.561 Vsfold5: 0.428 Sensitivity ProbKnot: 0.514 Vsfold5: 0.366 Positive Predictive Value ProbKnot: 0.617 Vsfold5: 0.506 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.592 Vsfold5: 0.425 Sensitivity Murlet(20): 0.437 Vsfold5: 0.358 Positive Predictive Value Murlet(20): 0.807 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	55 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.571 Vsfold5: 0.426 Sensitivity UNAFold: 0.500 Vsfold5: 0.359 Positive Predictive Value UNAFold: 0.655 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.570 Vsfold5: 0.439 Sensitivity Fold: 0.509 Vsfold5: 0.374 Positive Predictive Value Fold: 0.643 Vsfold5: 0.521 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	55 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.551 Vsfold5: 0.426 Sensitivity RNAfold: 0.487 Vsfold5: 0.359 Positive Predictive Value RNAfold: 0.628 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.552 Vsfold5: 0.426 Sensitivity PknotsRG: 0.492 Vsfold5: 0.359 Positive Predictive Value PknotsRG: 0.625 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.607 Vsfold5: 0.480 Sensitivity Cylofold: 0.512 Vsfold5: 0.406 Positive Predictive Value Cylofold: 0.727 Vsfold5: 0.575 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	19 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.539 Vsfold5: 0.433 Sensitivity RNAalifold(seed): 0.336 Vsfold5: 0.369 Positive Predictive Value RNAalifold(seed): 0.866 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	55 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.539 Vsfold5: 0.426 Sensitivity RNAshapes: 0.470 Vsfold5: 0.359 Positive Predictive Value RNAshapes: 0.622 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.528 Vsfold5: 0.418 Sensitivity Afold: 0.478 Vsfold5: 0.355 Positive Predictive Value Afold: 0.587 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.523 Vsfold5: 0.426 Sensitivity McQFold: 0.449 Vsfold5: 0.359 Positive Predictive Value McQFold: 0.613 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.547 Vsfold5: 0.443 Sensitivity Pknots: 0.489 Vsfold5: 0.372 Positive Predictive Value Pknots: 0.620 Vsfold5: 0.536 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.531 Vsfold5: 0.426 Sensitivity RNAsubopt: 0.473 Vsfold5: 0.359 Positive Predictive Value RNAsubopt: 0.601 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.559 Vsfold5: 0.445 Sensitivity RSpredict(20): 0.446 Vsfold5: 0.375 Positive Predictive Value RSpredict(20): 0.705 Vsfold5: 0.534 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-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: 9.64686604905e-09	55 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.478 Vsfold5: 0.426 Sensitivity Vsfold4: 0.399 Vsfold5: 0.359 Positive Predictive Value Vsfold4: 0.579 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.523 Vsfold5: 0.425 Sensitivity Mastr(20): 0.348 Vsfold5: 0.358 Positive Predictive Value Mastr(20): 0.790 Vsfold5: 0.511 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.443 Vsfold5: 0.340 Sensitivity RNASLOpt: 0.365 Vsfold5: 0.295 Positive Predictive Value RNASLOpt: 0.547 Vsfold5: 0.401 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	16 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.475 Vsfold5: 0.469 Sensitivity Murlet(seed): 0.270 Vsfold5: 0.394 Positive Predictive Value Murlet(seed): 0.841 Vsfold5: 0.565 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.00964022676679		- RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.399 Vsfold5: 0.369 Sensitivity RNAwolf: 0.368 Vsfold5: 0.318 Positive Predictive Value RNAwolf: 0.444 Vsfold5: 0.437 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.06782861462e-06	- 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: 5.19332990918e-08	+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.513 RDfolder: 0.443 Sensitivity Vsfold5: 0.423 RDfolder: 0.342 Positive Predictive Value Vsfold5: 0.633 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.465 MCFold: 0.419 Sensitivity Vsfold5: 0.391 MCFold: 0.437 Positive Predictive Value Vsfold5: 0.561 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.463 RSpredict(seed): 0.204 Sensitivity Vsfold5: 0.395 RSpredict(seed): 0.088 Positive Predictive Value Vsfold5: 0.547 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.404 PPfold(seed): 0.102 Sensitivity Vsfold5: 0.345 PPfold(seed): 0.020 Positive Predictive Value Vsfold5: 0.482 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.52577670387e-09	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.457 Carnac(seed): 0.139 Sensitivity Vsfold5: 0.386 Carnac(seed): 0.019 Positive Predictive Value Vsfold5: 0.549 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	? NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.366 Vsfold5: 0.327 Sensitivity NanoFolder: 0.376 Vsfold5: 0.280 Positive Predictive Value NanoFolder: 0.364 Vsfold5: 0.392 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.538 Vsfold5: 0.284 Sensitivity Multilign(seed): 0.420 Vsfold5: 0.232 Positive Predictive Value Multilign(seed): 0.699 Vsfold5: 0.364 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.540 Vsfold5: 0.421 Sensitivity Multilign(20): 0.456 Vsfold5: 0.363 Positive Predictive Value Multilign(20): 0.647 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold5: 0.372 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold5: 0.319 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold5: 0.443 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.594 Vsfold5: 0.421 Sensitivity TurboFold(20): 0.470 Vsfold5: 0.363 Positive Predictive Value TurboFold(20): 0.756 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs CMfinder(20) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(20): N/A Sensitivity Vsfold5: N/A CMfinder(20): N/A Positive Predictive Value Vsfold5: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold5: 0.384 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold5: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold5: 0.448 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.517 Vsfold5: 0.364 Sensitivity TurboFold(seed): 0.422 Vsfold5: 0.312 Positive Predictive Value TurboFold(seed): 0.642 Vsfold5: 0.434 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.546 Vsfold5: 0.453 Sensitivity RNASampler(seed): 0.409 Vsfold5: 0.402 Positive Predictive Value RNASampler(seed): 0.734 Vsfold5: 0.516 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.665 Vsfold5: 0.421 Sensitivity PPfold(20): 0.519 Vsfold5: 0.363 Positive Predictive Value PPfold(20): 0.859 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.447 Mastr(seed): 0.000 Sensitivity Vsfold5: 0.381 Mastr(seed): 0.000 Positive Predictive Value Vsfold5: 0.530 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAwolf	11 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.624 RNAwolf: 0.414 Sensitivity MXScarna(seed): 0.493 RNAwolf: 0.375 Positive Predictive Value MXScarna(seed): 0.796 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	8 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.691 RNAwolf: 0.364 Sensitivity CentroidAlifold(20): 0.515 RNAwolf: 0.333 Positive Predictive Value CentroidAlifold(20): 0.933 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.627 RNAwolf: 0.364 Sensitivity RNAalifold(20): 0.481 RNAwolf: 0.333 Positive Predictive Value RNAalifold(20): 0.823 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.637 RNAwolf: 0.364 Sensitivity RNASampler(20): 0.478 RNAwolf: 0.333 Positive Predictive Value RNASampler(20): 0.854 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.551 RNAwolf: 0.399 Sensitivity CentroidFold: 0.447 RNAwolf: 0.368 Positive Predictive Value CentroidFold: 0.686 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-08	8 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.586 RNAwolf: 0.364 Sensitivity MXScarna(20): 0.474 RNAwolf: 0.333 Positive Predictive Value MXScarna(20): 0.731 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 RNAwolf: 0.414 Sensitivity CentroidAlifold(seed): 0.347 RNAwolf: 0.375 Positive Predictive Value CentroidAlifold(seed): 0.984 RNAwolf: 0.467 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.64481516727e-08	17 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.543 RNAwolf: 0.399 Sensitivity Contrafold: 0.459 RNAwolf: 0.368 Positive Predictive Value Contrafold: 0.649 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.10198558684e-08	17 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.524 RNAwolf: 0.399 Sensitivity Sfold: 0.425 RNAwolf: 0.368 Positive Predictive Value Sfold: 0.652 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	17 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.487 RNAwolf: 0.399 Sensitivity MaxExpect: 0.417 RNAwolf: 0.368 Positive Predictive Value MaxExpect: 0.577 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-08	17 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.567 RNAwolf: 0.399 Sensitivity IPknot: 0.463 RNAwolf: 0.368 Positive Predictive Value IPknot: 0.702 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	17 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.558 RNAwolf: 0.399 Sensitivity CentroidHomfold‑LAST: 0.402 RNAwolf: 0.368 Positive Predictive Value CentroidHomfold‑LAST: 0.783 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.87872347734e-08	17 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.543 RNAwolf: 0.399 Sensitivity HotKnots: 0.481 RNAwolf: 0.368 Positive Predictive Value HotKnots: 0.621 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	8 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.560 RNAwolf: 0.364 Sensitivity Carnac(20): 0.367 RNAwolf: 0.333 Positive Predictive Value Carnac(20): 0.861 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.601 RNAwolf: 0.349 Sensitivity ContextFold: 0.483 RNAwolf: 0.323 Positive Predictive Value ContextFold: 0.754 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	17 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.495 RNAwolf: 0.399 Sensitivity ProbKnot: 0.443 RNAwolf: 0.368 Positive Predictive Value ProbKnot: 0.560 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	8 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.581 RNAwolf: 0.364 Sensitivity Murlet(20): 0.433 RNAwolf: 0.333 Positive Predictive Value Murlet(20): 0.785 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.497 RNAwolf: 0.399 Sensitivity UNAFold: 0.433 RNAwolf: 0.368 Positive Predictive Value UNAFold: 0.578 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.94377603181e-08	17 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.487 RNAwolf: 0.399 Sensitivity Fold: 0.423 RNAwolf: 0.368 Positive Predictive Value Fold: 0.568 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	17 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.524 RNAwolf: 0.399 Sensitivity RNAfold: 0.451 RNAwolf: 0.368 Positive Predictive Value RNAfold: 0.615 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	17 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.539 RNAwolf: 0.399 Sensitivity PknotsRG: 0.473 RNAwolf: 0.368 Positive Predictive Value PknotsRG: 0.621 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	15 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.537 RNAwolf: 0.451 Sensitivity Cylofold: 0.454 RNAwolf: 0.411 Positive Predictive Value Cylofold: 0.643 RNAwolf: 0.506 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	7 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.523 RNAwolf: 0.370 Sensitivity RNAalifold(seed): 0.344 RNAwolf: 0.344 Positive Predictive Value RNAalifold(seed): 0.800 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.515 RNAwolf: 0.399 Sensitivity RNAshapes: 0.443 RNAwolf: 0.368 Positive Predictive Value RNAshapes: 0.606 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.50323628132e-08	7 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.516 RNAwolf: 0.449 Sensitivity Afold: 0.467 RNAwolf: 0.417 Positive Predictive Value Afold: 0.578 RNAwolf: 0.491 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.501 RNAwolf: 0.399 Sensitivity McQFold: 0.427 RNAwolf: 0.368 Positive Predictive Value McQFold: 0.596 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	17 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.471 RNAwolf: 0.399 Sensitivity Pknots: 0.421 RNAwolf: 0.368 Positive Predictive Value Pknots: 0.535 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	17 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.473 RNAwolf: 0.399 Sensitivity RNAsubopt: 0.414 RNAwolf: 0.368 Positive Predictive Value RNAsubopt: 0.550 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	8 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.489 RNAwolf: 0.364 Sensitivity RSpredict(20): 0.367 RNAwolf: 0.333 Positive Predictive Value RSpredict(20): 0.660 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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: 1.86109605532e-08	17 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.425 RNAwolf: 0.399 Sensitivity Vsfold4: 0.354 RNAwolf: 0.368 Positive Predictive Value Vsfold4: 0.520 RNAwolf: 0.444 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	8 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.567 RNAwolf: 0.364 Sensitivity Mastr(20): 0.389 RNAwolf: 0.333 Positive Predictive Value Mastr(20): 0.833 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.443 RNAwolf: 0.349 Sensitivity RNASLOpt: 0.365 RNAwolf: 0.323 Positive Predictive Value RNASLOpt: 0.547 RNAwolf: 0.387 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.40919803867e-08	7 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.451 RNAwolf: 0.370 Sensitivity Murlet(seed): 0.268 RNAwolf: 0.344 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.399 Vsfold5: 0.369 Sensitivity RNAwolf: 0.368 Vsfold5: 0.318 Positive Predictive Value RNAwolf: 0.444 Vsfold5: 0.437 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.06782861462e-06		? 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	+ RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.414 RDfolder: 0.302 Sensitivity RNAwolf: 0.378 RDfolder: 0.219 Positive Predictive Value RNAwolf: 0.468 RDfolder: 0.434 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-08	- MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.449 RNAwolf: 0.390 Sensitivity MCFold: 0.474 RNAwolf: 0.366 Positive Predictive Value MCFold: 0.434 RNAwolf: 0.425 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.414 RSpredict(seed): 0.193 Sensitivity RNAwolf: 0.375 RSpredict(seed): 0.084 Positive Predictive Value RNAwolf: 0.467 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.414 PPfold(seed): 0.102 Sensitivity RNAwolf: 0.375 PPfold(seed): 0.020 Positive Predictive Value RNAwolf: 0.467 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.32883086441e-08	? RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.344 Carnac(seed): 0.123 Sensitivity RNAwolf: 0.316 Carnac(seed): 0.015 Positive Predictive Value RNAwolf: 0.384 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.410 NanoFolder: 0.366 Sensitivity RNAwolf: 0.370 NanoFolder: 0.376 Positive Predictive Value RNAwolf: 0.464 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.538 RNAwolf: 0.466 Sensitivity Multilign(seed): 0.420 RNAwolf: 0.413 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.540 RNAwolf: 0.364 Sensitivity Multilign(20): 0.456 RNAwolf: 0.333 Positive Predictive Value Multilign(20): 0.647 RNAwolf: 0.407 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): 0.680 RNAwolf: 0.339 Sensitivity PETfold_pre2.0(seed): 0.551 RNAwolf: 0.307 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAwolf: 0.384 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): 0.594 RNAwolf: 0.364 Sensitivity TurboFold(20): 0.470 RNAwolf: 0.333 Positive Predictive Value TurboFold(20): 0.756 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs CMfinder(20) Matthews Correlation Coefficient RNAwolf: N/A CMfinder(20): N/A Sensitivity RNAwolf: N/A CMfinder(20): N/A Positive Predictive Value RNAwolf: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAwolf: 0.220 Sensitivity PETfold_pre2.0(20): 0.497 RNAwolf: 0.204 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAwolf: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.517 RNAwolf: 0.344 Sensitivity TurboFold(seed): 0.422 RNAwolf: 0.316 Positive Predictive Value TurboFold(seed): 0.642 RNAwolf: 0.384 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.471 RNAwolf: 0.416 Sensitivity RNASampler(seed): 0.341 RNAwolf: 0.403 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.665 RNAwolf: 0.364 Sensitivity PPfold(20): 0.519 RNAwolf: 0.333 Positive Predictive Value PPfold(20): 0.859 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.414 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.375 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.467 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08
Alterna	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: 5.19332990918e-08	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: 6.48923495589e-09	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: 1.89649746203e-08	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: 2.20167918023e-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	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: 1.50834591464e-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: 0.591940867349	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	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: 5.19332990918e-08	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: 7.68522644707e-09	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: 3.56938820447e-08	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: 8.35333035499e-09	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	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: 1.70887622364e-08	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: 1.52299983238e-08	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	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: 3.16042554876e-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	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	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: 2.59578924681e-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	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: 3.56938820447e-08	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: 5.50294594097e-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	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 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: 3.56938820447e-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: 1.4651262096e-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	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	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: 1.43692248862e-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	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: 5.19332990918e-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		+ 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	+ 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 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: 5.1503931209e-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	? 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 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	? 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 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(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	? 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	? 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	? 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	? 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	? 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	? 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	? 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	+ 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: 5.1503931209e-08
RDfolder	22 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.680 RDfolder: 0.509 Sensitivity MXScarna(seed): 0.549 RDfolder: 0.411 Positive Predictive Value MXScarna(seed): 0.849 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	13 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.761 RDfolder: 0.525 Sensitivity CentroidAlifold(20): 0.607 RDfolder: 0.413 Positive Predictive Value CentroidAlifold(20): 0.960 RDfolder: 0.678 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	14 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.733 RDfolder: 0.539 Sensitivity RNAalifold(20): 0.576 RDfolder: 0.427 Positive Predictive Value RNAalifold(20): 0.939 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.58287649515e-08	14 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.746 RDfolder: 0.539 Sensitivity RNASampler(20): 0.591 RDfolder: 0.427 Positive Predictive Value RNASampler(20): 0.948 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.61939086268e-08	33 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.627 RDfolder: 0.432 Sensitivity CentroidFold: 0.515 RDfolder: 0.337 Positive Predictive Value CentroidFold: 0.772 RDfolder: 0.566 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.703 RDfolder: 0.539 Sensitivity MXScarna(20): 0.576 RDfolder: 0.427 Positive Predictive Value MXScarna(20): 0.866 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.05041766982e-08	21 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.595 RDfolder: 0.499 Sensitivity CentroidAlifold(seed): 0.369 RDfolder: 0.402 Positive Predictive Value CentroidAlifold(seed): 0.966 RDfolder: 0.631 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.81788725234e-08	37 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.603 RDfolder: 0.443 Sensitivity Contrafold: 0.507 RDfolder: 0.342 Positive Predictive Value Contrafold: 0.725 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 5.23657817852e-08	37 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.586 RDfolder: 0.443 Sensitivity Sfold: 0.474 RDfolder: 0.342 Positive Predictive Value Sfold: 0.733 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.586 RDfolder: 0.426 Sensitivity MaxExpect: 0.497 RDfolder: 0.329 Positive Predictive Value MaxExpect: 0.701 RDfolder: 0.565 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.543 RDfolder: 0.302 Sensitivity IPknot: 0.426 RDfolder: 0.219 Positive Predictive Value IPknot: 0.701 RDfolder: 0.434 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	12 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.618 RDfolder: 0.310 Sensitivity CentroidHomfold‑LAST: 0.443 RDfolder: 0.221 Positive Predictive Value CentroidHomfold‑LAST: 0.871 RDfolder: 0.451 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 8.61680779366e-09	37 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.600 RDfolder: 0.443 Sensitivity HotKnots: 0.516 RDfolder: 0.342 Positive Predictive Value HotKnots: 0.707 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.643 RDfolder: 0.539 Sensitivity Carnac(20): 0.459 RDfolder: 0.427 Positive Predictive Value Carnac(20): 0.907 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	8 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.537 RDfolder: 0.229 Sensitivity ContextFold: 0.425 RDfolder: 0.168 Positive Predictive Value ContextFold: 0.689 RDfolder: 0.329 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.566 RDfolder: 0.412 Sensitivity ProbKnot: 0.506 RDfolder: 0.317 Positive Predictive Value ProbKnot: 0.643 RDfolder: 0.549 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.33194562506e-08	14 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.667 RDfolder: 0.539 Sensitivity Murlet(20): 0.504 RDfolder: 0.427 Positive Predictive Value Murlet(20): 0.890 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	37 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.591 RDfolder: 0.443 Sensitivity UNAFold: 0.499 RDfolder: 0.342 Positive Predictive Value UNAFold: 0.707 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.581 RDfolder: 0.429 Sensitivity Fold: 0.499 RDfolder: 0.333 Positive Predictive Value Fold: 0.685 RDfolder: 0.564 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.21671975982e-08	37 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.568 RDfolder: 0.443 Sensitivity RNAfold: 0.482 RDfolder: 0.342 Positive Predictive Value RNAfold: 0.679 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.581 RDfolder: 0.443 Sensitivity PknotsRG: 0.497 RDfolder: 0.342 Positive Predictive Value PknotsRG: 0.688 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.642 RDfolder: 0.416 Sensitivity Cylofold: 0.540 RDfolder: 0.323 Positive Predictive Value Cylofold: 0.771 RDfolder: 0.548 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.36130997681e-08	12 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.587 RDfolder: 0.546 Sensitivity RNAalifold(seed): 0.409 RDfolder: 0.418 Positive Predictive Value RNAalifold(seed): 0.850 RDfolder: 0.725 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.37408564874e-07	37 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.557 RDfolder: 0.443 Sensitivity RNAshapes: 0.467 RDfolder: 0.342 Positive Predictive Value RNAshapes: 0.673 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.549 RDfolder: 0.456 Sensitivity Afold: 0.478 RDfolder: 0.360 Positive Predictive Value Afold: 0.642 RDfolder: 0.591 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	37 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.592 RDfolder: 0.443 Sensitivity McQFold: 0.484 RDfolder: 0.342 Positive Predictive Value McQFold: 0.733 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.599 RDfolder: 0.443 Sensitivity Pknots: 0.523 RDfolder: 0.342 Positive Predictive Value Pknots: 0.696 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.550 RDfolder: 0.443 Sensitivity RNAsubopt: 0.468 RDfolder: 0.342 Positive Predictive Value RNAsubopt: 0.656 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.648 RDfolder: 0.539 Sensitivity RSpredict(20): 0.494 RDfolder: 0.427 Positive Predictive Value RSpredict(20): 0.858 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-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: 1.31583660336e-08	37 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.570 RDfolder: 0.443 Sensitivity Vsfold4: 0.462 RDfolder: 0.342 Positive Predictive Value Vsfold4: 0.713 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.651 RDfolder: 0.539 Sensitivity Mastr(20): 0.504 RDfolder: 0.427 Positive Predictive Value Mastr(20): 0.849 RDfolder: 0.691 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.48055519165e-08	8 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.392 RDfolder: 0.229 Sensitivity RNASLOpt: 0.299 RDfolder: 0.168 Positive Predictive Value RNASLOpt: 0.526 RDfolder: 0.329 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.526 Murlet(seed): 0.504 Sensitivity RDfolder: 0.398 Murlet(seed): 0.316 Positive Predictive Value RDfolder: 0.704 Murlet(seed): 0.813 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.42440948549e-06	37 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.513 RDfolder: 0.443 Sensitivity Vsfold5: 0.423 RDfolder: 0.342 Positive Predictive Value Vsfold5: 0.633 RDfolder: 0.585 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.414 RDfolder: 0.302 Sensitivity RNAwolf: 0.378 RDfolder: 0.219 Positive Predictive Value RNAwolf: 0.468 RDfolder: 0.434 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.42300079339e-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		+ RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.462 MCFold: 0.403 Sensitivity RDfolder: 0.353 MCFold: 0.417 Positive Predictive Value RDfolder: 0.616 MCFold: 0.403 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.509 RSpredict(seed): 0.305 Sensitivity RDfolder: 0.411 RSpredict(seed): 0.149 Positive Predictive Value RDfolder: 0.640 RSpredict(seed): 0.637 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.342 PPfold(seed): 0.138 Sensitivity RDfolder: 0.253 PPfold(seed): 0.026 Positive Predictive Value RDfolder: 0.476 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.526 Carnac(seed): 0.205 Sensitivity RDfolder: 0.398 Carnac(seed): 0.043 Positive Predictive Value RDfolder: 0.704 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	? NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.417 RDfolder: 0.257 Sensitivity NanoFolder: 0.405 RDfolder: 0.198 Positive Predictive Value NanoFolder: 0.441 RDfolder: 0.349 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.538 RDfolder: 0.382 Sensitivity Multilign(seed): 0.420 RDfolder: 0.275 Positive Predictive Value Multilign(seed): 0.699 RDfolder: 0.543 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.582 RDfolder: 0.407 Sensitivity Multilign(20): 0.470 RDfolder: 0.295 Positive Predictive Value Multilign(20): 0.729 RDfolder: 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.634 RDfolder: 0.281 Sensitivity PETfold_pre2.0(seed): 0.515 RDfolder: 0.215 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RDfolder: 0.384 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.647 RDfolder: 0.407 Sensitivity TurboFold(20): 0.497 RDfolder: 0.295 Positive Predictive Value TurboFold(20): 0.850 RDfolder: 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): 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): 0.666 RDfolder: 0.387 Sensitivity PETfold_pre2.0(20): 0.513 RDfolder: 0.288 Positive Predictive Value PETfold_pre2.0(20): 0.872 RDfolder: 0.535 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	? RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.644 RDfolder: 0.541 Sensitivity RNASampler(seed): 0.474 RDfolder: 0.406 Positive Predictive Value RNASampler(seed): 0.883 RDfolder: 0.732 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.710 RDfolder: 0.407 Sensitivity PPfold(20): 0.552 RDfolder: 0.295 Positive Predictive Value PPfold(20): 0.918 RDfolder: 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.509 Mastr(seed): 0.000 Sensitivity RDfolder: 0.411 Mastr(seed): 0.000 Positive Predictive Value RDfolder: 0.640 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08
MCFold	28 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.665 MCFold: 0.448 Sensitivity MXScarna(seed): 0.549 MCFold: 0.472 Positive Predictive Value MXScarna(seed): 0.810 MCFold: 0.433 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	20 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.711 MCFold: 0.417 Sensitivity CentroidAlifold(20): 0.568 MCFold: 0.441 Positive Predictive Value CentroidAlifold(20): 0.894 MCFold: 0.402 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	21 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.673 MCFold: 0.425 Sensitivity RNAalifold(20): 0.543 MCFold: 0.448 Positive Predictive Value RNAalifold(20): 0.838 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.680 MCFold: 0.425 Sensitivity RNASampler(20): 0.546 MCFold: 0.448 Positive Predictive Value RNASampler(20): 0.850 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	42 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.613 MCFold: 0.420 Sensitivity CentroidFold: 0.517 MCFold: 0.441 Positive Predictive Value CentroidFold: 0.733 MCFold: 0.409 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.644 MCFold: 0.425 Sensitivity MXScarna(20): 0.542 MCFold: 0.448 Positive Predictive Value MXScarna(20): 0.769 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	27 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.603 MCFold: 0.442 Sensitivity CentroidAlifold(seed): 0.377 MCFold: 0.466 Positive Predictive Value CentroidAlifold(seed): 0.971 MCFold: 0.427 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	46 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.582 MCFold: 0.419 Sensitivity Contrafold: 0.506 MCFold: 0.437 Positive Predictive Value Contrafold: 0.677 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.603 MCFold: 0.419 Sensitivity Sfold: 0.503 MCFold: 0.437 Positive Predictive Value Sfold: 0.729 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.581 MCFold: 0.403 Sensitivity MaxExpect: 0.507 MCFold: 0.424 Positive Predictive Value MaxExpect: 0.672 MCFold: 0.392 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.570 MCFold: 0.449 Sensitivity IPknot: 0.469 MCFold: 0.474 Positive Predictive Value IPknot: 0.698 MCFold: 0.434 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.02533530638e-08	16 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.527 MCFold: 0.432 Sensitivity CentroidHomfold‑LAST: 0.375 MCFold: 0.454 Positive Predictive Value CentroidHomfold‑LAST: 0.748 MCFold: 0.421 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.22797000563e-08	46 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.594 MCFold: 0.419 Sensitivity HotKnots: 0.526 MCFold: 0.437 Positive Predictive Value HotKnots: 0.677 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.645 MCFold: 0.425 Sensitivity Carnac(20): 0.454 MCFold: 0.448 Positive Predictive Value Carnac(20): 0.920 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.94031556815e-08	12 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.599 MCFold: 0.441 Sensitivity ContextFold: 0.486 MCFold: 0.474 Positive Predictive Value ContextFold: 0.743 MCFold: 0.419 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	26 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.587 MCFold: 0.458 Sensitivity ProbKnot: 0.536 MCFold: 0.476 Positive Predictive Value ProbKnot: 0.648 MCFold: 0.449 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.619 MCFold: 0.425 Sensitivity Murlet(20): 0.477 MCFold: 0.448 Positive Predictive Value Murlet(20): 0.808 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	46 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.597 MCFold: 0.419 Sensitivity UNAFold: 0.520 MCFold: 0.437 Positive Predictive Value UNAFold: 0.691 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.585 MCFold: 0.448 Sensitivity Fold: 0.518 MCFold: 0.466 Positive Predictive Value Fold: 0.667 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	46 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.582 MCFold: 0.419 Sensitivity RNAfold: 0.510 MCFold: 0.437 Positive Predictive Value RNAfold: 0.670 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.583 MCFold: 0.419 Sensitivity PknotsRG: 0.516 MCFold: 0.437 Positive Predictive Value PknotsRG: 0.665 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.613 MCFold: 0.460 Sensitivity Cylofold: 0.517 MCFold: 0.476 Positive Predictive Value Cylofold: 0.732 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.563 MCFold: 0.465 Sensitivity RNAalifold(seed): 0.364 MCFold: 0.479 Positive Predictive Value RNAalifold(seed): 0.874 MCFold: 0.458 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	46 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.569 MCFold: 0.419 Sensitivity RNAshapes: 0.494 MCFold: 0.437 Positive Predictive Value RNAshapes: 0.663 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.555 MCFold: 0.424 Sensitivity Afold: 0.497 MCFold: 0.444 Positive Predictive Value Afold: 0.627 MCFold: 0.414 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.554 MCFold: 0.419 Sensitivity McQFold: 0.468 MCFold: 0.437 Positive Predictive Value McQFold: 0.664 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.552 MCFold: 0.419 Sensitivity Pknots: 0.497 MCFold: 0.437 Positive Predictive Value Pknots: 0.619 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.551 MCFold: 0.419 Sensitivity RNAsubopt: 0.486 MCFold: 0.437 Positive Predictive Value RNAsubopt: 0.632 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.598 MCFold: 0.425 Sensitivity RSpredict(20): 0.495 MCFold: 0.448 Positive Predictive Value RSpredict(20): 0.728 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-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: 2.35965341511e-08	46 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.499 MCFold: 0.419 Sensitivity Vsfold4: 0.411 MCFold: 0.437 Positive Predictive Value Vsfold4: 0.613 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.595 MCFold: 0.425 Sensitivity Mastr(20): 0.427 MCFold: 0.448 Positive Predictive Value Mastr(20): 0.834 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 4.98172311752e-08	12 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.461 MCFold: 0.441 Sensitivity RNASLOpt: 0.393 MCFold: 0.474 Positive Predictive Value RNASLOpt: 0.550 MCFold: 0.419 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.14792285362e-08	14 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.464 MCFold: 0.448 Sensitivity Murlet(seed): 0.263 MCFold: 0.463 Positive Predictive Value Murlet(seed): 0.823 MCFold: 0.441 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79079429174e-05	46 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.465 MCFold: 0.419 Sensitivity Vsfold5: 0.391 MCFold: 0.437 Positive Predictive Value Vsfold5: 0.561 MCFold: 0.410 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.449 RNAwolf: 0.390 Sensitivity MCFold: 0.474 RNAwolf: 0.366 Positive Predictive Value MCFold: 0.434 RNAwolf: 0.425 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	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	34 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.462 MCFold: 0.403 Sensitivity RDfolder: 0.353 MCFold: 0.417 Positive Predictive Value RDfolder: 0.616 MCFold: 0.403 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.448 RSpredict(seed): 0.226 Sensitivity MCFold: 0.472 RSpredict(seed): 0.101 Positive Predictive Value MCFold: 0.433 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.454 PPfold(seed): 0.115 Sensitivity MCFold: 0.471 PPfold(seed): 0.025 Positive Predictive Value MCFold: 0.446 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.468 Carnac(seed): 0.148 Sensitivity MCFold: 0.488 Carnac(seed): 0.022 Positive Predictive Value MCFold: 0.455 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	? MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.529 NanoFolder: 0.373 Sensitivity MCFold: 0.552 NanoFolder: 0.397 Positive Predictive Value MCFold: 0.514 NanoFolder: 0.359 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.509 MCFold: 0.472 Sensitivity Multilign(seed): 0.406 MCFold: 0.469 Positive Predictive Value Multilign(seed): 0.650 MCFold: 0.489 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.549 MCFold: 0.459 Sensitivity Multilign(20): 0.469 MCFold: 0.474 Positive Predictive Value Multilign(20): 0.648 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.663 MCFold: 0.441 Sensitivity PETfold_pre2.0(seed): 0.549 MCFold: 0.469 Positive Predictive Value PETfold_pre2.0(seed): 0.807 MCFold: 0.423 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.601 MCFold: 0.459 Sensitivity TurboFold(20): 0.482 MCFold: 0.474 Positive Predictive Value TurboFold(20): 0.753 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.586 MCFold: 0.444 Sensitivity PETfold_pre2.0(20): 0.464 MCFold: 0.472 Positive Predictive Value PETfold_pre2.0(20): 0.744 MCFold: 0.424 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.512 MCFold: 0.456 Sensitivity TurboFold(seed): 0.425 MCFold: 0.471 Positive Predictive Value TurboFold(seed): 0.623 MCFold: 0.450 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.546 MCFold: 0.412 Sensitivity RNASampler(seed): 0.409 MCFold: 0.438 Positive Predictive Value RNASampler(seed): 0.734 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.651 MCFold: 0.459 Sensitivity PPfold(20): 0.504 MCFold: 0.474 Positive Predictive Value PPfold(20): 0.846 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.448 Mastr(seed): 0.000 Sensitivity MCFold: 0.472 Mastr(seed): 0.000 Positive Predictive Value MCFold: 0.433 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08
RSpredict(seed)	34 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.650 RSpredict(seed): 0.204 Sensitivity MXScarna(seed): 0.533 RSpredict(seed): 0.088 Positive Predictive Value MXScarna(seed): 0.796 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 RSpredict(seed): 0.218 Sensitivity CentroidAlifold(20): 0.540 RSpredict(seed): 0.090 Positive Predictive Value CentroidAlifold(20): 0.897 RSpredict(seed): 0.539 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.657 RSpredict(seed): 0.232 Sensitivity RNAalifold(20): 0.511 RSpredict(seed): 0.097 Positive Predictive Value RNAalifold(20): 0.848 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.648 RSpredict(seed): 0.232 Sensitivity RNASampler(20): 0.504 RSpredict(seed): 0.097 Positive Predictive Value RNASampler(20): 0.837 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	33 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.592 RSpredict(seed): 0.194 Sensitivity CentroidFold: 0.510 RSpredict(seed): 0.083 Positive Predictive Value CentroidFold: 0.690 RSpredict(seed): 0.459 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.627 RSpredict(seed): 0.232 Sensitivity MXScarna(20): 0.525 RSpredict(seed): 0.097 Positive Predictive Value MXScarna(20): 0.752 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 RSpredict(seed): 0.194 Sensitivity CentroidAlifold(seed): 0.377 RSpredict(seed): 0.083 Positive Predictive Value CentroidAlifold(seed): 0.925 RSpredict(seed): 0.459 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.565 RSpredict(seed): 0.204 Sensitivity Contrafold: 0.509 RSpredict(seed): 0.088 Positive Predictive Value Contrafold: 0.632 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.570 RSpredict(seed): 0.204 Sensitivity Sfold: 0.484 RSpredict(seed): 0.088 Positive Predictive Value Sfold: 0.675 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.569 RSpredict(seed): 0.180 Sensitivity MaxExpect: 0.504 RSpredict(seed): 0.076 Positive Predictive Value MaxExpect: 0.646 RSpredict(seed): 0.432 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.590 RSpredict(seed): 0.193 Sensitivity IPknot: 0.471 RSpredict(seed): 0.084 Positive Predictive Value IPknot: 0.747 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.74569091494e-09	11 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 RSpredict(seed): 0.193 Sensitivity CentroidHomfold‑LAST: 0.479 RSpredict(seed): 0.084 Positive Predictive Value CentroidHomfold‑LAST: 0.795 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.26497248087e-08	34 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.560 RSpredict(seed): 0.204 Sensitivity HotKnots: 0.508 RSpredict(seed): 0.088 Positive Predictive Value HotKnots: 0.622 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.607 RSpredict(seed): 0.232 Sensitivity Carnac(20): 0.405 RSpredict(seed): 0.097 Positive Predictive Value Carnac(20): 0.915 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.616 RSpredict(seed): 0.110 Sensitivity ContextFold: 0.476 RSpredict(seed): 0.047 Positive Predictive Value ContextFold: 0.801 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	21 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.553 RSpredict(seed): 0.139 Sensitivity ProbKnot: 0.511 RSpredict(seed): 0.055 Positive Predictive Value ProbKnot: 0.603 RSpredict(seed): 0.355 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.593 RSpredict(seed): 0.232 Sensitivity Murlet(20): 0.440 RSpredict(seed): 0.097 Positive Predictive Value Murlet(20): 0.803 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	34 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.557 RSpredict(seed): 0.204 Sensitivity UNAFold: 0.498 RSpredict(seed): 0.088 Positive Predictive Value UNAFold: 0.627 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.560 RSpredict(seed): 0.134 Sensitivity Fold: 0.504 RSpredict(seed): 0.054 Positive Predictive Value Fold: 0.627 RSpredict(seed): 0.340 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.562 RSpredict(seed): 0.204 Sensitivity RNAfold: 0.506 RSpredict(seed): 0.088 Positive Predictive Value RNAfold: 0.627 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.569 RSpredict(seed): 0.204 Sensitivity PknotsRG: 0.515 RSpredict(seed): 0.088 Positive Predictive Value PknotsRG: 0.633 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.659 RSpredict(seed): 0.150 Sensitivity Cylofold: 0.554 RSpredict(seed): 0.061 Positive Predictive Value Cylofold: 0.789 RSpredict(seed): 0.379 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	19 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.539 RSpredict(seed): 0.284 Sensitivity RNAalifold(seed): 0.336 RSpredict(seed): 0.136 Positive Predictive Value RNAalifold(seed): 0.866 RSpredict(seed): 0.597 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	34 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.538 RSpredict(seed): 0.204 Sensitivity RNAshapes: 0.479 RSpredict(seed): 0.088 Positive Predictive Value RNAshapes: 0.609 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.501 RSpredict(seed): 0.244 Sensitivity Afold: 0.467 RSpredict(seed): 0.114 Positive Predictive Value Afold: 0.541 RSpredict(seed): 0.527 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	34 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.530 RSpredict(seed): 0.204 Sensitivity McQFold: 0.466 RSpredict(seed): 0.088 Positive Predictive Value McQFold: 0.607 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.577 RSpredict(seed): 0.210 Sensitivity Pknots: 0.520 RSpredict(seed): 0.091 Positive Predictive Value Pknots: 0.647 RSpredict(seed): 0.492 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.529 RSpredict(seed): 0.204 Sensitivity RNAsubopt: 0.481 RSpredict(seed): 0.088 Positive Predictive Value RNAsubopt: 0.586 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.559 RSpredict(seed): 0.232 Sensitivity RSpredict(20): 0.446 RSpredict(seed): 0.097 Positive Predictive Value RSpredict(20): 0.705 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-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	34 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.494 RSpredict(seed): 0.204 Sensitivity Vsfold4: 0.419 RSpredict(seed): 0.088 Positive Predictive Value Vsfold4: 0.586 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.525 RSpredict(seed): 0.232 Sensitivity Mastr(20): 0.350 RSpredict(seed): 0.097 Positive Predictive Value Mastr(20): 0.792 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	8 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 RSpredict(seed): 0.110 Sensitivity RNASLOpt: 0.374 RSpredict(seed): 0.047 Positive Predictive Value RNASLOpt: 0.609 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	16 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.475 RSpredict(seed): 0.329 Sensitivity Murlet(seed): 0.270 RSpredict(seed): 0.166 Positive Predictive Value Murlet(seed): 0.841 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	34 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.463 RSpredict(seed): 0.204 Sensitivity Vsfold5: 0.395 RSpredict(seed): 0.088 Positive Predictive Value Vsfold5: 0.547 RSpredict(seed): 0.477 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.414 RSpredict(seed): 0.193 Sensitivity RNAwolf: 0.375 RSpredict(seed): 0.084 Positive Predictive Value RNAwolf: 0.467 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.18141491686e-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: 5.1503931209e-08	22 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.509 RSpredict(seed): 0.305 Sensitivity RDfolder: 0.411 RSpredict(seed): 0.149 Positive Predictive Value RDfolder: 0.640 RSpredict(seed): 0.637 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.448 RSpredict(seed): 0.226 Sensitivity MCFold: 0.472 RSpredict(seed): 0.101 Positive Predictive Value MCFold: 0.433 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08		+ RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.193 PPfold(seed): 0.102 Sensitivity RSpredict(seed): 0.084 PPfold(seed): 0.020 Positive Predictive Value RSpredict(seed): 0.455 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.72492216724e-08	+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.270 Carnac(seed): 0.139 Sensitivity RSpredict(seed): 0.126 Carnac(seed): 0.019 Positive Predictive Value RSpredict(seed): 0.587 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	? NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.346 RSpredict(seed): 0.090 Sensitivity NanoFolder: 0.353 RSpredict(seed): 0.038 Positive Predictive Value NanoFolder: 0.349 RSpredict(seed): 0.225 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 RSpredict(seed): 0.323 Sensitivity Multilign(seed): 0.420 RSpredict(seed): 0.174 Positive Predictive Value Multilign(seed): 0.699 RSpredict(seed): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.540 RSpredict(seed): 0.267 Sensitivity Multilign(20): 0.456 RSpredict(seed): 0.111 Positive Predictive Value Multilign(20): 0.647 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RSpredict(seed): 0.110 Sensitivity PETfold_pre2.0(seed): 0.551 RSpredict(seed): 0.047 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 RSpredict(seed): 0.267 Sensitivity TurboFold(20): 0.470 RSpredict(seed): 0.111 Positive Predictive Value TurboFold(20): 0.756 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(20): N/A Sensitivity RSpredict(seed): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(seed): 0.184 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(seed): 0.072 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(seed): 0.480 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 RSpredict(seed): 0.243 Sensitivity TurboFold(seed): 0.422 RSpredict(seed): 0.114 Positive Predictive Value TurboFold(seed): 0.642 RSpredict(seed): 0.526 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 RSpredict(seed): 0.364 Sensitivity RNASampler(seed): 0.409 RSpredict(seed): 0.203 Positive Predictive Value RNASampler(seed): 0.734 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.665 RSpredict(seed): 0.267 Sensitivity PPfold(20): 0.519 RSpredict(seed): 0.111 Positive Predictive Value PPfold(20): 0.859 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.204 Mastr(seed): 0.000 Sensitivity RSpredict(seed): 0.088 Mastr(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.477 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(seed)	11 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.624 PPfold(seed): 0.102 Sensitivity MXScarna(seed): 0.493 PPfold(seed): 0.020 Positive Predictive Value MXScarna(seed): 0.796 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	8 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 PPfold(seed): 0.026 Sensitivity CentroidAlifold(20): 0.515 PPfold(seed): 0.004 Positive Predictive Value CentroidAlifold(20): 0.933 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.627 PPfold(seed): 0.026 Sensitivity RNAalifold(20): 0.481 PPfold(seed): 0.004 Positive Predictive Value RNAalifold(20): 0.823 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.637 PPfold(seed): 0.026 Sensitivity RNASampler(20): 0.478 PPfold(seed): 0.004 Positive Predictive Value RNASampler(20): 0.854 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.578 PPfold(seed): 0.102 Sensitivity CentroidFold: 0.465 PPfold(seed): 0.020 Positive Predictive Value CentroidFold: 0.725 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.11142658008e-08	8 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.586 PPfold(seed): 0.026 Sensitivity MXScarna(20): 0.474 PPfold(seed): 0.004 Positive Predictive Value MXScarna(20): 0.731 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.583 PPfold(seed): 0.102 Sensitivity CentroidAlifold(seed): 0.347 PPfold(seed): 0.020 Positive Predictive Value CentroidAlifold(seed): 0.984 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.08932646657e-08	11 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.559 PPfold(seed): 0.102 Sensitivity Contrafold: 0.471 PPfold(seed): 0.020 Positive Predictive Value Contrafold: 0.672 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.3551590886e-08	11 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.539 PPfold(seed): 0.102 Sensitivity Sfold: 0.426 PPfold(seed): 0.020 Positive Predictive Value Sfold: 0.691 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.61680779366e-09	11 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.513 PPfold(seed): 0.102 Sensitivity MaxExpect: 0.434 PPfold(seed): 0.020 Positive Predictive Value MaxExpect: 0.615 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	11 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.590 PPfold(seed): 0.102 Sensitivity IPknot: 0.471 PPfold(seed): 0.020 Positive Predictive Value IPknot: 0.747 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.00475527001e-08	11 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 PPfold(seed): 0.102 Sensitivity CentroidHomfold‑LAST: 0.479 PPfold(seed): 0.020 Positive Predictive Value CentroidHomfold‑LAST: 0.795 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.21584974784e-08	11 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.566 PPfold(seed): 0.102 Sensitivity HotKnots: 0.487 PPfold(seed): 0.020 Positive Predictive Value HotKnots: 0.664 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.10032755566e-08	8 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.560 PPfold(seed): 0.026 Sensitivity Carnac(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value Carnac(20): 0.861 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.616 PPfold(seed): 0.121 Sensitivity ContextFold: 0.476 PPfold(seed): 0.028 Positive Predictive Value ContextFold: 0.801 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.513 PPfold(seed): 0.102 Sensitivity ProbKnot: 0.457 PPfold(seed): 0.020 Positive Predictive Value ProbKnot: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	8 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.581 PPfold(seed): 0.026 Sensitivity Murlet(20): 0.433 PPfold(seed): 0.004 Positive Predictive Value Murlet(20): 0.785 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.490 PPfold(seed): 0.102 Sensitivity UNAFold: 0.417 PPfold(seed): 0.020 Positive Predictive Value UNAFold: 0.584 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	11 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.516 PPfold(seed): 0.102 Sensitivity Fold: 0.443 PPfold(seed): 0.020 Positive Predictive Value Fold: 0.610 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.80908287419e-08	11 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.565 PPfold(seed): 0.102 Sensitivity RNAfold: 0.476 PPfold(seed): 0.020 Positive Predictive Value RNAfold: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.61680779366e-09	11 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.600 PPfold(seed): 0.102 Sensitivity PknotsRG: 0.513 PPfold(seed): 0.020 Positive Predictive Value PknotsRG: 0.709 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	9 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.630 PPfold(seed): 0.128 Sensitivity Cylofold: 0.519 PPfold(seed): 0.022 Positive Predictive Value Cylofold: 0.773 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.523 PPfold(seed): 0.133 Sensitivity RNAalifold(seed): 0.344 PPfold(seed): 0.033 Positive Predictive Value RNAalifold(seed): 0.800 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	11 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.537 PPfold(seed): 0.102 Sensitivity RNAshapes: 0.454 PPfold(seed): 0.020 Positive Predictive Value RNAshapes: 0.643 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31583660336e-08	4 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.489 PPfold(seed): 0.187 Sensitivity Afold: 0.443 PPfold(seed): 0.066 Positive Predictive Value Afold: 0.547 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.539 PPfold(seed): 0.102 Sensitivity McQFold: 0.462 PPfold(seed): 0.020 Positive Predictive Value McQFold: 0.637 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.26346675981e-08	11 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.532 PPfold(seed): 0.102 Sensitivity Pknots: 0.462 PPfold(seed): 0.020 Positive Predictive Value Pknots: 0.620 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.08519761914e-09	11 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.500 PPfold(seed): 0.102 Sensitivity RNAsubopt: 0.429 PPfold(seed): 0.020 Positive Predictive Value RNAsubopt: 0.591 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	8 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.489 PPfold(seed): 0.026 Sensitivity RSpredict(20): 0.367 PPfold(seed): 0.004 Positive Predictive Value RSpredict(20): 0.660 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	11 Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.454 PPfold(seed): 0.102 Sensitivity Vsfold4: 0.367 PPfold(seed): 0.020 Positive Predictive Value Vsfold4: 0.570 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.10032755566e-08	8 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.567 PPfold(seed): 0.026 Sensitivity Mastr(20): 0.389 PPfold(seed): 0.004 Positive Predictive Value Mastr(20): 0.833 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 PPfold(seed): 0.121 Sensitivity RNASLOpt: 0.374 PPfold(seed): 0.028 Positive Predictive Value RNASLOpt: 0.609 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.451 PPfold(seed): 0.133 Sensitivity Murlet(seed): 0.268 PPfold(seed): 0.033 Positive Predictive Value Murlet(seed): 0.767 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	11 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.404 PPfold(seed): 0.102 Sensitivity Vsfold5: 0.345 PPfold(seed): 0.020 Positive Predictive Value Vsfold5: 0.482 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.52577670387e-09	11 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.414 PPfold(seed): 0.102 Sensitivity RNAwolf: 0.375 PPfold(seed): 0.020 Positive Predictive Value RNAwolf: 0.467 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.32883086441e-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	8 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.342 PPfold(seed): 0.138 Sensitivity RDfolder: 0.253 PPfold(seed): 0.026 Positive Predictive Value RDfolder: 0.476 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.454 PPfold(seed): 0.115 Sensitivity MCFold: 0.471 PPfold(seed): 0.025 Positive Predictive Value MCFold: 0.446 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.193 PPfold(seed): 0.102 Sensitivity RSpredict(seed): 0.084 PPfold(seed): 0.020 Positive Predictive Value RSpredict(seed): 0.455 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.72492216724e-08		? Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.123 PPfold(seed): 0.118 Sensitivity Carnac(seed): 0.015 PPfold(seed): 0.027 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.346 PPfold(seed): 0.125 Sensitivity NanoFolder: 0.353 PPfold(seed): 0.030 Positive Predictive Value NanoFolder: 0.349 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 PPfold(seed): 0.179 Sensitivity Multilign(seed): 0.420 PPfold(seed): 0.043 Positive Predictive Value Multilign(seed): 0.699 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.540 PPfold(seed): 0.026 Sensitivity Multilign(20): 0.456 PPfold(seed): 0.004 Positive Predictive Value Multilign(20): 0.647 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PPfold(seed): 0.121 Sensitivity PETfold_pre2.0(seed): 0.551 PPfold(seed): 0.028 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 PPfold(seed): 0.026 Sensitivity TurboFold(20): 0.470 PPfold(seed): 0.004 Positive Predictive Value TurboFold(20): 0.756 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(seed): 0.034 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(seed): 0.006 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 PPfold(seed): 0.118 Sensitivity TurboFold(seed): 0.422 PPfold(seed): 0.027 Positive Predictive Value TurboFold(seed): 0.642 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.471 PPfold(seed): 0.169 Sensitivity RNASampler(seed): 0.341 PPfold(seed): 0.054 Positive Predictive Value RNASampler(seed): 0.657 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.665 PPfold(seed): 0.026 Sensitivity PPfold(20): 0.519 PPfold(seed): 0.004 Positive Predictive Value PPfold(20): 0.859 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.102 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.020 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08
Carnac(seed)	20 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.638 Carnac(seed): 0.139 Sensitivity MXScarna(seed): 0.527 Carnac(seed): 0.019 Positive Predictive Value MXScarna(seed): 0.777 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.692 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.538 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.893 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	18 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.647 Carnac(seed): 0.122 Sensitivity RNAalifold(20): 0.505 Carnac(seed): 0.015 Positive Predictive Value RNAalifold(20): 0.833 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	18 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.648 Carnac(seed): 0.122 Sensitivity RNASampler(20): 0.502 Carnac(seed): 0.015 Positive Predictive Value RNASampler(20): 0.841 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-08	19 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.625 Carnac(seed): 0.075 Sensitivity CentroidFold: 0.525 Carnac(seed): 0.006 Positive Predictive Value CentroidFold: 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.63594052159e-08	18 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.622 Carnac(seed): 0.122 Sensitivity MXScarna(20): 0.521 Carnac(seed): 0.015 Positive Predictive Value MXScarna(20): 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.52609899389e-08	19 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.673 Carnac(seed): 0.075 Sensitivity CentroidAlifold(seed): 0.468 Carnac(seed): 0.006 Positive Predictive Value CentroidAlifold(seed): 0.971 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	20 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.606 Carnac(seed): 0.139 Sensitivity Contrafold: 0.533 Carnac(seed): 0.019 Positive Predictive Value Contrafold: 0.694 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	20 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.643 Carnac(seed): 0.139 Sensitivity Sfold: 0.537 Carnac(seed): 0.019 Positive Predictive Value Sfold: 0.774 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.595 Carnac(seed): 0.077 Sensitivity MaxExpect: 0.517 Carnac(seed): 0.006 Positive Predictive Value MaxExpect: 0.689 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.36130997681e-08	8 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.544 Carnac(seed): 0.123 Sensitivity IPknot: 0.437 Carnac(seed): 0.015 Positive Predictive Value IPknot: 0.685 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.563 Carnac(seed): 0.123 Sensitivity CentroidHomfold‑LAST: 0.437 Carnac(seed): 0.015 Positive Predictive Value CentroidHomfold‑LAST: 0.732 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	20 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.631 Carnac(seed): 0.139 Sensitivity HotKnots: 0.559 Carnac(seed): 0.019 Positive Predictive Value HotKnots: 0.717 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	18 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.611 Carnac(seed): 0.122 Sensitivity Carnac(20): 0.404 Carnac(seed): 0.015 Positive Predictive Value Carnac(20): 0.931 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.89169006118e-08	6 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.576 Carnac(seed): 0.146 Sensitivity ContextFold: 0.449 Carnac(seed): 0.021 Positive Predictive Value ContextFold: 0.743 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	13 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.572 Carnac(seed): 0.088 Sensitivity ProbKnot: 0.516 Carnac(seed): 0.008 Positive Predictive Value ProbKnot: 0.641 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.16131455263e-08	18 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.604 Carnac(seed): 0.122 Sensitivity Murlet(20): 0.446 Carnac(seed): 0.015 Positive Predictive Value Murlet(20): 0.822 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.74172190343e-08	20 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.615 Carnac(seed): 0.139 Sensitivity UNAFold: 0.537 Carnac(seed): 0.019 Positive Predictive Value UNAFold: 0.710 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	13 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.551 Carnac(seed): 0.088 Sensitivity Fold: 0.486 Carnac(seed): 0.008 Positive Predictive Value Fold: 0.630 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	20 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.615 Carnac(seed): 0.139 Sensitivity RNAfold: 0.542 Carnac(seed): 0.019 Positive Predictive Value RNAfold: 0.703 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	20 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.631 Carnac(seed): 0.139 Sensitivity PknotsRG: 0.560 Carnac(seed): 0.019 Positive Predictive Value PknotsRG: 0.716 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	10 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.646 Carnac(seed): 0.103 Sensitivity Cylofold: 0.533 Carnac(seed): 0.011 Positive Predictive Value Cylofold: 0.787 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	16 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.593 Carnac(seed): 0.159 Sensitivity RNAalifold(seed): 0.398 Carnac(seed): 0.026 Positive Predictive Value RNAalifold(seed): 0.890 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	20 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.601 Carnac(seed): 0.139 Sensitivity RNAshapes: 0.526 Carnac(seed): 0.019 Positive Predictive Value RNAshapes: 0.693 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	14 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.597 Carnac(seed): 0.175 Sensitivity Afold: 0.540 Carnac(seed): 0.031 Positive Predictive Value Afold: 0.665 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.32677072069e-08	20 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.574 Carnac(seed): 0.139 Sensitivity McQFold: 0.501 Carnac(seed): 0.019 Positive Predictive Value McQFold: 0.662 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	20 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.553 Carnac(seed): 0.139 Sensitivity Pknots: 0.502 Carnac(seed): 0.019 Positive Predictive Value Pknots: 0.616 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	20 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.585 Carnac(seed): 0.139 Sensitivity RNAsubopt: 0.521 Carnac(seed): 0.019 Positive Predictive Value RNAsubopt: 0.661 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.89920829651e-08	18 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.528 Carnac(seed): 0.122 Sensitivity RSpredict(20): 0.414 Carnac(seed): 0.015 Positive Predictive Value RSpredict(20): 0.679 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.71568867205e-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	20 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.496 Carnac(seed): 0.139 Sensitivity Vsfold4: 0.411 Carnac(seed): 0.019 Positive Predictive Value Vsfold4: 0.605 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	18 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.522 Carnac(seed): 0.122 Sensitivity Mastr(20): 0.360 Carnac(seed): 0.015 Positive Predictive Value Mastr(20): 0.764 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	6 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 Carnac(seed): 0.146 Sensitivity RNASLOpt: 0.380 Carnac(seed): 0.021 Positive Predictive Value RNASLOpt: 0.582 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	16 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.475 Carnac(seed): 0.159 Sensitivity Murlet(seed): 0.270 Carnac(seed): 0.026 Positive Predictive Value Murlet(seed): 0.841 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	20 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.457 Carnac(seed): 0.139 Sensitivity Vsfold5: 0.386 Carnac(seed): 0.019 Positive Predictive Value Vsfold5: 0.549 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	8 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.344 Carnac(seed): 0.123 Sensitivity RNAwolf: 0.316 Carnac(seed): 0.015 Positive Predictive Value RNAwolf: 0.384 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	11 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.526 Carnac(seed): 0.205 Sensitivity RDfolder: 0.398 Carnac(seed): 0.043 Positive Predictive Value RDfolder: 0.704 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	18 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.468 Carnac(seed): 0.148 Sensitivity MCFold: 0.488 Carnac(seed): 0.022 Positive Predictive Value MCFold: 0.455 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	20 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.270 Carnac(seed): 0.139 Sensitivity RSpredict(seed): 0.126 Carnac(seed): 0.019 Positive Predictive Value RSpredict(seed): 0.587 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	8 Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.123 PPfold(seed): 0.118 Sensitivity Carnac(seed): 0.015 PPfold(seed): 0.027 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.341 Carnac(seed): 0.154 Sensitivity NanoFolder: 0.351 Carnac(seed): 0.024 Positive Predictive Value NanoFolder: 0.339 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? 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	? Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 Carnac(seed): 0.169 Sensitivity Multilign(seed): 0.420 Carnac(seed): 0.029 Positive Predictive Value Multilign(seed): 0.699 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.530 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.444 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.639 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Carnac(seed): 0.146 Sensitivity PETfold_pre2.0(seed): 0.529 Carnac(seed): 0.021 Positive Predictive Value PETfold_pre2.0(seed): 0.805 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.581 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.457 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.745 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs CMfinder(20) Matthews Correlation Coefficient Carnac(seed): N/A CMfinder(20): N/A Sensitivity Carnac(seed): N/A CMfinder(20): N/A Positive Predictive Value Carnac(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 Carnac(seed): 0.123 Sensitivity TurboFold(seed): 0.422 Carnac(seed): 0.015 Positive Predictive Value TurboFold(seed): 0.642 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 Carnac(seed): 0.225 Sensitivity RNASampler(seed): 0.409 Carnac(seed): 0.051 Positive Predictive Value RNASampler(seed): 0.734 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.642 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.494 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.839 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.139 Mastr(seed): 0.000 Sensitivity Carnac(seed): 0.019 Mastr(seed): 0.000 Positive Predictive Value Carnac(seed): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08
NanoFolder	7 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.594 NanoFolder: 0.346 Sensitivity MXScarna(seed): 0.468 NanoFolder: 0.353 Positive Predictive Value MXScarna(seed): 0.759 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.646 NanoFolder: 0.316 Sensitivity CentroidAlifold(20): 0.473 NanoFolder: 0.324 Positive Predictive Value CentroidAlifold(20): 0.886 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.565 NanoFolder: 0.316 Sensitivity RNAalifold(20): 0.432 NanoFolder: 0.324 Positive Predictive Value RNAalifold(20): 0.744 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.567 NanoFolder: 0.316 Sensitivity RNASampler(20): 0.426 NanoFolder: 0.324 Positive Predictive Value RNASampler(20): 0.759 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.569 NanoFolder: 0.366 Sensitivity CentroidFold: 0.466 NanoFolder: 0.376 Positive Predictive Value CentroidFold: 0.700 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.524 NanoFolder: 0.316 Sensitivity MXScarna(20): 0.439 NanoFolder: 0.324 Positive Predictive Value MXScarna(20): 0.631 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.533 NanoFolder: 0.346 Sensitivity CentroidAlifold(seed): 0.289 NanoFolder: 0.353 Positive Predictive Value CentroidAlifold(seed): 0.986 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.564 NanoFolder: 0.366 Sensitivity Contrafold: 0.479 NanoFolder: 0.376 Positive Predictive Value Contrafold: 0.671 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.504 NanoFolder: 0.366 Sensitivity Sfold: 0.408 NanoFolder: 0.376 Positive Predictive Value Sfold: 0.629 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.488 NanoFolder: 0.366 Sensitivity MaxExpect: 0.418 NanoFolder: 0.376 Positive Predictive Value MaxExpect: 0.578 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.594 NanoFolder: 0.366 Sensitivity IPknot: 0.486 NanoFolder: 0.376 Positive Predictive Value IPknot: 0.733 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.521 NanoFolder: 0.366 Sensitivity CentroidHomfold‑LAST: 0.386 NanoFolder: 0.376 Positive Predictive Value CentroidHomfold‑LAST: 0.710 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.535 NanoFolder: 0.366 Sensitivity HotKnots: 0.473 NanoFolder: 0.376 Positive Predictive Value HotKnots: 0.613 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.506 NanoFolder: 0.316 Sensitivity Carnac(20): 0.318 NanoFolder: 0.324 Positive Predictive Value Carnac(20): 0.810 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.632 NanoFolder: 0.366 Sensitivity ContextFold: 0.498 NanoFolder: 0.376 Positive Predictive Value ContextFold: 0.807 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.499 NanoFolder: 0.366 Sensitivity ProbKnot: 0.447 NanoFolder: 0.376 Positive Predictive Value ProbKnot: 0.565 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.503 NanoFolder: 0.316 Sensitivity Murlet(20): 0.372 NanoFolder: 0.324 Positive Predictive Value Murlet(20): 0.688 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.463 NanoFolder: 0.366 Sensitivity UNAFold: 0.405 NanoFolder: 0.376 Positive Predictive Value UNAFold: 0.536 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.523 NanoFolder: 0.366 Sensitivity Fold: 0.453 NanoFolder: 0.376 Positive Predictive Value Fold: 0.610 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.546 NanoFolder: 0.366 Sensitivity RNAfold: 0.473 NanoFolder: 0.376 Positive Predictive Value RNAfold: 0.636 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.550 NanoFolder: 0.366 Sensitivity PknotsRG: 0.482 NanoFolder: 0.376 Positive Predictive Value PknotsRG: 0.633 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.520 NanoFolder: 0.410 Sensitivity Cylofold: 0.433 NanoFolder: 0.411 Positive Predictive Value Cylofold: 0.634 NanoFolder: 0.420 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.459 NanoFolder: 0.280 Sensitivity RNAalifold(seed): 0.289 NanoFolder: 0.298 Positive Predictive Value RNAalifold(seed): 0.733 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.514 NanoFolder: 0.366 Sensitivity RNAshapes: 0.447 NanoFolder: 0.376 Positive Predictive Value RNAshapes: 0.599 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.513 NanoFolder: 0.311 Sensitivity Afold: 0.481 NanoFolder: 0.349 Positive Predictive Value Afold: 0.554 NanoFolder: 0.285 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.474 NanoFolder: 0.366 Sensitivity McQFold: 0.412 NanoFolder: 0.376 Positive Predictive Value McQFold: 0.554 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.404 NanoFolder: 0.366 Sensitivity Pknots: 0.360 NanoFolder: 0.376 Positive Predictive Value Pknots: 0.461 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.461 NanoFolder: 0.366 Sensitivity RNAsubopt: 0.408 NanoFolder: 0.376 Positive Predictive Value RNAsubopt: 0.529 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.337 NanoFolder: 0.316 Sensitivity RSpredict(20): 0.243 NanoFolder: 0.324 Positive Predictive Value RSpredict(20): 0.474 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	9 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.393 NanoFolder: 0.366 Sensitivity Vsfold4: 0.325 NanoFolder: 0.376 Positive Predictive Value Vsfold4: 0.486 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.499 NanoFolder: 0.316 Sensitivity Mastr(20): 0.324 NanoFolder: 0.324 Positive Predictive Value Mastr(20): 0.774 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.475 NanoFolder: 0.366 Sensitivity RNASLOpt: 0.386 NanoFolder: 0.376 Positive Predictive Value RNASLOpt: 0.591 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.403 NanoFolder: 0.280 Sensitivity Murlet(seed): 0.237 NanoFolder: 0.298 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.272 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.366 Vsfold5: 0.327 Sensitivity NanoFolder: 0.376 Vsfold5: 0.280 Positive Predictive Value NanoFolder: 0.364 Vsfold5: 0.392 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.410 NanoFolder: 0.366 Sensitivity RNAwolf: 0.370 NanoFolder: 0.376 Positive Predictive Value RNAwolf: 0.464 NanoFolder: 0.364 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	4 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.417 RDfolder: 0.257 Sensitivity NanoFolder: 0.405 RDfolder: 0.198 Positive Predictive Value NanoFolder: 0.441 RDfolder: 0.349 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.529 NanoFolder: 0.373 Sensitivity MCFold: 0.552 NanoFolder: 0.397 Positive Predictive Value MCFold: 0.514 NanoFolder: 0.359 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.346 RSpredict(seed): 0.090 Sensitivity NanoFolder: 0.353 RSpredict(seed): 0.038 Positive Predictive Value NanoFolder: 0.349 RSpredict(seed): 0.225 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.346 PPfold(seed): 0.125 Sensitivity NanoFolder: 0.353 PPfold(seed): 0.030 Positive Predictive Value NanoFolder: 0.349 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.341 Carnac(seed): 0.154 Sensitivity NanoFolder: 0.351 Carnac(seed): 0.024 Positive Predictive Value NanoFolder: 0.339 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? 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	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.403 NanoFolder: 0.395 Sensitivity Multilign(seed): 0.306 NanoFolder: 0.371 Positive Predictive Value Multilign(seed): 0.543 NanoFolder: 0.434 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.490 NanoFolder: 0.316 Sensitivity Multilign(20): 0.419 NanoFolder: 0.324 Positive Predictive Value Multilign(20): 0.579 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.694 NanoFolder: 0.346 Sensitivity PETfold_pre2.0(seed): 0.562 NanoFolder: 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.863 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.526 NanoFolder: 0.316 Sensitivity TurboFold(20): 0.419 NanoFolder: 0.324 Positive Predictive Value TurboFold(20): 0.667 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs CMfinder(20) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(20): N/A Sensitivity NanoFolder: N/A CMfinder(20): N/A Positive Predictive Value NanoFolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.627 NanoFolder: 0.316 Sensitivity PETfold_pre2.0(20): 0.507 NanoFolder: 0.324 Positive Predictive Value PETfold_pre2.0(20): 0.781 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.439 NanoFolder: 0.341 Sensitivity TurboFold(seed): 0.369 NanoFolder: 0.351 Positive Predictive Value TurboFold(seed): 0.530 NanoFolder: 0.339 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.198 NanoFolder: 0.171 Sensitivity RNASampler(seed): 0.151 NanoFolder: 0.208 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.622 NanoFolder: 0.316 Sensitivity PPfold(20): 0.486 NanoFolder: 0.324 Positive Predictive Value PPfold(20): 0.800 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.346 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.353 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.349 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
CMfinder(seed)	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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	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 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		? 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	? 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	? 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	? 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	? 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_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	? 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	? 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	? 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	? 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
Multilign(seed)	4 MXScarna(seed) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(seed): 0.577 Multilign(seed): 0.538 Sensitivity MXScarna(seed): 0.464 Multilign(seed): 0.420 Positive Predictive Value MXScarna(seed): 0.727 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.729 Multilign(seed): 0.631 Sensitivity CentroidAlifold(20): 0.542 Multilign(seed): 0.492 Positive Predictive Value CentroidAlifold(20): 0.985 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.702 Multilign(seed): 0.631 Sensitivity RNAalifold(20): 0.542 Multilign(seed): 0.492 Positive Predictive Value RNAalifold(20): 0.914 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.669 Multilign(seed): 0.631 Sensitivity RNASampler(20): 0.483 Multilign(seed): 0.492 Positive Predictive Value RNASampler(20): 0.934 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.573 Multilign(seed): 0.538 Sensitivity CentroidFold: 0.442 Multilign(seed): 0.420 Positive Predictive Value CentroidFold: 0.753 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.652 Multilign(seed): 0.631 Sensitivity MXScarna(20): 0.542 Multilign(seed): 0.492 Positive Predictive Value MXScarna(20): 0.790 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.684 Multilign(seed): 0.538 Sensitivity CentroidAlifold(seed): 0.478 Multilign(seed): 0.420 Positive Predictive Value CentroidAlifold(seed): 0.985 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.552 Multilign(seed): 0.538 Sensitivity Contrafold: 0.449 Multilign(seed): 0.420 Positive Predictive Value Contrafold: 0.689 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.600 Multilign(seed): 0.538 Sensitivity Sfold: 0.471 Multilign(seed): 0.420 Positive Predictive Value Sfold: 0.774 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.538 MaxExpect: 0.507 Sensitivity Multilign(seed): 0.420 MaxExpect: 0.413 Positive Predictive Value Multilign(seed): 0.699 MaxExpect: 0.633 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.560 Multilign(seed): 0.538 Sensitivity IPknot: 0.435 Multilign(seed): 0.420 Positive Predictive Value IPknot: 0.732 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Multilign(seed): 0.538 Sensitivity CentroidHomfold‑LAST: 0.420 Multilign(seed): 0.420 Positive Predictive Value CentroidHomfold‑LAST: 0.817 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.621 Multilign(seed): 0.538 Sensitivity HotKnots: 0.507 Multilign(seed): 0.420 Positive Predictive Value HotKnots: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.631 Carnac(20): 0.612 Sensitivity Multilign(seed): 0.492 Carnac(20): 0.424 Positive Predictive Value Multilign(seed): 0.817 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	2 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.532 Multilign(seed): 0.403 Sensitivity ContextFold: 0.435 Multilign(seed): 0.306 Positive Predictive Value ContextFold: 0.659 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.538 ProbKnot: 0.493 Sensitivity Multilign(seed): 0.420 ProbKnot: 0.413 Positive Predictive Value Multilign(seed): 0.699 ProbKnot: 0.600 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.696 Multilign(seed): 0.631 Sensitivity Murlet(20): 0.534 Multilign(seed): 0.492 Positive Predictive Value Murlet(20): 0.913 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.538 UNAFold: 0.525 Sensitivity Multilign(seed): 0.420 UNAFold: 0.428 Positive Predictive Value Multilign(seed): 0.699 UNAFold: 0.656 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.538 Fold: 0.504 Sensitivity Multilign(seed): 0.420 Fold: 0.413 Positive Predictive Value Multilign(seed): 0.699 Fold: 0.626 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAfold vs Multilign(seed) Matthews Correlation Coefficient RNAfold: 0.621 Multilign(seed): 0.538 Sensitivity RNAfold: 0.507 Multilign(seed): 0.420 Positive Predictive Value RNAfold: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.616 Multilign(seed): 0.538 Sensitivity PknotsRG: 0.500 Multilign(seed): 0.420 Positive Predictive Value PknotsRG: 0.767 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.575 Multilign(seed): 0.538 Sensitivity Cylofold: 0.457 Multilign(seed): 0.420 Positive Predictive Value Cylofold: 0.733 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.544 Multilign(seed): 0.538 Sensitivity RNAalifold(seed): 0.399 Multilign(seed): 0.420 Positive Predictive Value RNAalifold(seed): 0.753 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAshapes vs Multilign(seed) Matthews Correlation Coefficient RNAshapes: 0.621 Multilign(seed): 0.538 Sensitivity RNAshapes: 0.507 Multilign(seed): 0.420 Positive Predictive Value RNAshapes: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 Afold vs Multilign(seed) Matthews Correlation Coefficient Afold: 0.700 Multilign(seed): 0.476 Sensitivity Afold: 0.574 Multilign(seed): 0.370 Positive Predictive Value Afold: 0.861 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.621 Multilign(seed): 0.538 Sensitivity McQFold: 0.507 Multilign(seed): 0.420 Positive Predictive Value McQFold: 0.769 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.555 Multilign(seed): 0.538 Sensitivity Pknots: 0.464 Multilign(seed): 0.420 Positive Predictive Value Pknots: 0.674 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.538 RNAsubopt: 0.522 Sensitivity Multilign(seed): 0.420 RNAsubopt: 0.428 Positive Predictive Value Multilign(seed): 0.699 RNAsubopt: 0.648 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.631 RSpredict(20): 0.591 Sensitivity Multilign(seed): 0.492 RSpredict(20): 0.441 Positive Predictive Value Multilign(seed): 0.817 RSpredict(20): 0.800 Number of pairs reference - predicted secondary structure: 3 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	4 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.538 Vsfold4: 0.366 Sensitivity Multilign(seed): 0.420 Vsfold4: 0.297 Positive Predictive Value Multilign(seed): 0.699 Vsfold4: 0.466 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.631 Mastr(20): 0.560 Sensitivity Multilign(seed): 0.492 Mastr(20): 0.415 Positive Predictive Value Multilign(seed): 0.817 Mastr(20): 0.766 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	2 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.403 RNASLOpt: 0.332 Sensitivity Multilign(seed): 0.306 RNASLOpt: 0.242 Positive Predictive Value Multilign(seed): 0.543 RNASLOpt: 0.469 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 Murlet(seed): 0.425 Sensitivity Multilign(seed): 0.420 Murlet(seed): 0.268 Positive Predictive Value Multilign(seed): 0.699 Murlet(seed): 0.685 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.538 Vsfold5: 0.284 Sensitivity Multilign(seed): 0.420 Vsfold5: 0.232 Positive Predictive Value Multilign(seed): 0.699 Vsfold5: 0.364 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.538 RNAwolf: 0.466 Sensitivity Multilign(seed): 0.420 RNAwolf: 0.413 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	4 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.538 RDfolder: 0.382 Sensitivity Multilign(seed): 0.420 RDfolder: 0.275 Positive Predictive Value Multilign(seed): 0.699 RDfolder: 0.543 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.509 MCFold: 0.472 Sensitivity Multilign(seed): 0.406 MCFold: 0.469 Positive Predictive Value Multilign(seed): 0.650 MCFold: 0.489 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 RSpredict(seed): 0.323 Sensitivity Multilign(seed): 0.420 RSpredict(seed): 0.174 Positive Predictive Value Multilign(seed): 0.699 RSpredict(seed): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 PPfold(seed): 0.179 Sensitivity Multilign(seed): 0.420 PPfold(seed): 0.043 Positive Predictive Value Multilign(seed): 0.699 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 Carnac(seed): 0.169 Sensitivity Multilign(seed): 0.420 Carnac(seed): 0.029 Positive Predictive Value Multilign(seed): 0.699 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.403 NanoFolder: 0.395 Sensitivity Multilign(seed): 0.306 NanoFolder: 0.371 Positive Predictive Value Multilign(seed): 0.543 NanoFolder: 0.434 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	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		? Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.631 Multilign(20): 0.598 Sensitivity Multilign(seed): 0.492 Multilign(20): 0.483 Positive Predictive Value Multilign(seed): 0.817 Multilign(20): 0.750 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.623 Multilign(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.484 Multilign(seed): 0.306 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.631 TurboFold(20): 0.629 Sensitivity Multilign(seed): 0.492 TurboFold(20): 0.483 Positive Predictive Value Multilign(seed): 0.817 TurboFold(20): 0.826 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 Multilign(seed): 0.609 Sensitivity PETfold_pre2.0(20): 0.595 Multilign(seed): 0.452 Positive Predictive Value PETfold_pre2.0(20): 0.926 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs TurboFold(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 TurboFold(seed): 0.525 Sensitivity Multilign(seed): 0.420 TurboFold(seed): 0.413 Positive Predictive Value Multilign(seed): 0.699 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(seed): 0.532 Multilign(seed): 0.509 Sensitivity RNASampler(seed): 0.375 Multilign(seed): 0.406 Positive Predictive Value RNASampler(seed): 0.766 Multilign(seed): 0.650 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.714 Multilign(seed): 0.631 Sensitivity PPfold(20): 0.559 Multilign(seed): 0.492 Positive Predictive Value PPfold(20): 0.917 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.420 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.699 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0
Multilign(20)	8 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.640 Multilign(20): 0.540 Sensitivity MXScarna(seed): 0.511 Multilign(20): 0.456 Positive Predictive Value MXScarna(seed): 0.807 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 Multilign(20): 0.540 Sensitivity CentroidAlifold(20): 0.515 Multilign(20): 0.456 Positive Predictive Value CentroidAlifold(20): 0.933 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.627 Multilign(20): 0.540 Sensitivity RNAalifold(20): 0.481 Multilign(20): 0.456 Positive Predictive Value RNAalifold(20): 0.823 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.637 Multilign(20): 0.540 Sensitivity RNASampler(20): 0.478 Multilign(20): 0.456 Positive Predictive Value RNASampler(20): 0.854 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.575 Multilign(20): 0.540 Sensitivity CentroidFold: 0.470 Multilign(20): 0.456 Positive Predictive Value CentroidFold: 0.709 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.586 Multilign(20): 0.540 Sensitivity MXScarna(20): 0.474 Multilign(20): 0.456 Positive Predictive Value MXScarna(20): 0.731 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.637 Multilign(20): 0.540 Sensitivity CentroidAlifold(seed): 0.415 Multilign(20): 0.456 Positive Predictive Value CentroidAlifold(seed): 0.982 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.561 Multilign(20): 0.540 Sensitivity Contrafold: 0.478 Multilign(20): 0.456 Positive Predictive Value Contrafold: 0.665 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.579 Multilign(20): 0.540 Sensitivity Sfold: 0.467 Multilign(20): 0.456 Positive Predictive Value Sfold: 0.724 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 MaxExpect vs Multilign(20) Matthews Correlation Coefficient MaxExpect: 0.543 Multilign(20): 0.540 Sensitivity MaxExpect: 0.463 Multilign(20): 0.456 Positive Predictive Value MaxExpect: 0.644 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.571 Multilign(20): 0.540 Sensitivity IPknot: 0.463 Multilign(20): 0.456 Positive Predictive Value IPknot: 0.710 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 Multilign(20): 0.540 Sensitivity CentroidHomfold‑LAST: 0.496 Multilign(20): 0.456 Positive Predictive Value CentroidHomfold‑LAST: 0.807 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.609 Multilign(20): 0.540 Sensitivity HotKnots: 0.526 Multilign(20): 0.456 Positive Predictive Value HotKnots: 0.710 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Carnac(20) vs Multilign(20) Matthews Correlation Coefficient Carnac(20): 0.560 Multilign(20): 0.540 Sensitivity Carnac(20): 0.367 Multilign(20): 0.456 Positive Predictive Value Carnac(20): 0.861 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.579 Multilign(20): 0.474 Sensitivity ContextFold: 0.443 Multilign(20): 0.401 Positive Predictive Value ContextFold: 0.763 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 ProbKnot vs Multilign(20) Matthews Correlation Coefficient ProbKnot: 0.542 Multilign(20): 0.540 Sensitivity ProbKnot: 0.481 Multilign(20): 0.456 Positive Predictive Value ProbKnot: 0.616 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.581 Multilign(20): 0.540 Sensitivity Murlet(20): 0.433 Multilign(20): 0.456 Positive Predictive Value Murlet(20): 0.785 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.556 Multilign(20): 0.540 Sensitivity UNAFold: 0.474 Multilign(20): 0.456 Positive Predictive Value UNAFold: 0.660 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.540 Fold: 0.510 Sensitivity Multilign(20): 0.456 Fold: 0.441 Positive Predictive Value Multilign(20): 0.647 Fold: 0.598 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.555 Multilign(20): 0.540 Sensitivity RNAfold: 0.474 Multilign(20): 0.456 Positive Predictive Value RNAfold: 0.656 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.600 Multilign(20): 0.540 Sensitivity PknotsRG: 0.522 Multilign(20): 0.456 Positive Predictive Value PknotsRG: 0.695 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.653 Multilign(20): 0.582 Sensitivity Cylofold: 0.536 Multilign(20): 0.470 Positive Predictive Value Cylofold: 0.803 Multilign(20): 0.729 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 Multilign(20): 0.480 Sensitivity RNAalifold(seed): 0.381 Multilign(20): 0.402 Positive Predictive Value RNAalifold(seed): 0.923 Multilign(20): 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.555 Multilign(20): 0.540 Sensitivity RNAshapes: 0.470 Multilign(20): 0.456 Positive Predictive Value RNAshapes: 0.661 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.461 Multilign(20): 0.405 Sensitivity Afold: 0.419 Multilign(20): 0.360 Positive Predictive Value Afold: 0.514 Multilign(20): 0.463 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.540 McQFold: 0.526 Sensitivity Multilign(20): 0.456 McQFold: 0.452 Positive Predictive Value Multilign(20): 0.647 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.540 Pknots: 0.505 Sensitivity Multilign(20): 0.456 Pknots: 0.441 Positive Predictive Value Multilign(20): 0.647 Pknots: 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.551 Multilign(20): 0.540 Sensitivity RNAsubopt: 0.474 Multilign(20): 0.456 Positive Predictive Value RNAsubopt: 0.646 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.540 RSpredict(20): 0.489 Sensitivity Multilign(20): 0.456 RSpredict(20): 0.367 Positive Predictive Value Multilign(20): 0.647 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	8 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.540 Vsfold4: 0.437 Sensitivity Multilign(20): 0.456 Vsfold4: 0.356 Positive Predictive Value Multilign(20): 0.647 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.567 Multilign(20): 0.540 Sensitivity Mastr(20): 0.389 Multilign(20): 0.456 Positive Predictive Value Mastr(20): 0.833 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.474 RNASLOpt: 0.467 Sensitivity Multilign(20): 0.401 RNASLOpt: 0.383 Positive Predictive Value Multilign(20): 0.568 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.520 Multilign(20): 0.480 Sensitivity Murlet(seed): 0.296 Multilign(20): 0.402 Positive Predictive Value Murlet(seed): 0.918 Multilign(20): 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.540 Vsfold5: 0.421 Sensitivity Multilign(20): 0.456 Vsfold5: 0.363 Positive Predictive Value Multilign(20): 0.647 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.540 RNAwolf: 0.364 Sensitivity Multilign(20): 0.456 RNAwolf: 0.333 Positive Predictive Value Multilign(20): 0.647 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	6 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.582 RDfolder: 0.407 Sensitivity Multilign(20): 0.470 RDfolder: 0.295 Positive Predictive Value Multilign(20): 0.729 RDfolder: 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.549 MCFold: 0.459 Sensitivity Multilign(20): 0.469 MCFold: 0.474 Positive Predictive Value Multilign(20): 0.648 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.540 RSpredict(seed): 0.267 Sensitivity Multilign(20): 0.456 RSpredict(seed): 0.111 Positive Predictive Value Multilign(20): 0.647 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.540 PPfold(seed): 0.026 Sensitivity Multilign(20): 0.456 PPfold(seed): 0.004 Positive Predictive Value Multilign(20): 0.647 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.530 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.444 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.639 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.490 NanoFolder: 0.316 Sensitivity Multilign(20): 0.419 NanoFolder: 0.324 Positive Predictive Value Multilign(20): 0.579 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	3 Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.631 Multilign(20): 0.598 Sensitivity Multilign(seed): 0.492 Multilign(20): 0.483 Positive Predictive Value Multilign(seed): 0.817 Multilign(20): 0.750 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0		? PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(seed): 0.557 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Multilign(20): 0.540 Sensitivity TurboFold(20): 0.470 Multilign(20): 0.456 Positive Predictive Value TurboFold(20): 0.756 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): N/A CMfinder(20): N/A Sensitivity Multilign(20): N/A CMfinder(20): N/A Positive Predictive Value Multilign(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(20): 0.497 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Multilign(20): 0.530 Sensitivity TurboFold(seed): 0.457 Multilign(20): 0.444 Positive Predictive Value TurboFold(seed): 0.703 Multilign(20): 0.639 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.556 Multilign(20): 0.475 Sensitivity RNASampler(seed): 0.404 Multilign(20): 0.422 Positive Predictive Value RNASampler(seed): 0.772 Multilign(20): 0.541 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.665 Multilign(20): 0.540 Sensitivity PPfold(20): 0.519 Multilign(20): 0.456 Positive Predictive Value PPfold(20): 0.859 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.540 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.456 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.647 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
PETfold_pre2.0(seed)	8 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MXScarna(seed): 0.586 Sensitivity PETfold_pre2.0(seed): 0.551 MXScarna(seed): 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MXScarna(seed): 0.758 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 CentroidAlifold(20): 0.650 Sensitivity PETfold_pre2.0(seed): 0.557 CentroidAlifold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 CentroidAlifold(20): 0.898 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(seed): 0.557 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(seed): 0.557 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidFold: 0.540 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidFold: 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidFold: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(seed): 0.557 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidAlifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidAlifold(seed): 0.299 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidAlifold(seed): 0.987 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Contrafold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.551 Contrafold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Contrafold: 0.633 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Sfold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 Sfold: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Sfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 MaxExpect: 0.458 Sensitivity PETfold_pre2.0(seed): 0.551 MaxExpect: 0.390 Positive Predictive Value PETfold_pre2.0(seed): 0.843 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 IPknot: 0.551 Sensitivity PETfold_pre2.0(seed): 0.551 IPknot: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 IPknot: 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 CentroidHomfold‑LAST: 0.575 Sensitivity PETfold_pre2.0(seed): 0.551 CentroidHomfold‑LAST: 0.453 Positive Predictive Value PETfold_pre2.0(seed): 0.843 CentroidHomfold‑LAST: 0.737 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 HotKnots: 0.518 Sensitivity PETfold_pre2.0(seed): 0.551 HotKnots: 0.457 Positive Predictive Value PETfold_pre2.0(seed): 0.843 HotKnots: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(seed): 0.557 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ContextFold: 0.616 Sensitivity PETfold_pre2.0(seed): 0.551 ContextFold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ContextFold: 0.801 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 ProbKnot: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 ProbKnot: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.843 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(seed): 0.557 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 UNAFold: 0.413 Sensitivity PETfold_pre2.0(seed): 0.551 UNAFold: 0.358 Positive Predictive Value PETfold_pre2.0(seed): 0.843 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Fold: 0.465 Sensitivity PETfold_pre2.0(seed): 0.551 Fold: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Fold: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAfold: 0.515 Sensitivity PETfold_pre2.0(seed): 0.551 RNAfold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PknotsRG: 0.569 Sensitivity PETfold_pre2.0(seed): 0.551 PknotsRG: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PknotsRG: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Cylofold: 0.601 Sensitivity PETfold_pre2.0(seed): 0.521 Cylofold: 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.821 Cylofold: 0.735 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 RNAalifold(seed): 0.472 Sensitivity PETfold_pre2.0(seed): 0.459 RNAalifold(seed): 0.293 Positive Predictive Value PETfold_pre2.0(seed): 0.726 RNAalifold(seed): 0.765 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAshapes: 0.476 Sensitivity PETfold_pre2.0(seed): 0.551 RNAshapes: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAshapes: 0.562 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 Afold: 0.389 Sensitivity PETfold_pre2.0(seed): 0.403 Afold: 0.375 Positive Predictive Value PETfold_pre2.0(seed): 0.644 Afold: 0.409 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 McQFold: 0.466 Sensitivity PETfold_pre2.0(seed): 0.551 McQFold: 0.409 Positive Predictive Value PETfold_pre2.0(seed): 0.843 McQFold: 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Pknots: 0.452 Sensitivity PETfold_pre2.0(seed): 0.551 Pknots: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Pknots: 0.518 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAsubopt: 0.431 Sensitivity PETfold_pre2.0(seed): 0.551 RNAsubopt: 0.378 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAsubopt: 0.500 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(seed): 0.557 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(seed): 0.830 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 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	8 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold4: 0.437 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold4: 0.350 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold4: 0.553 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(seed): 0.557 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNASLOpt: 0.474 Sensitivity PETfold_pre2.0(seed): 0.551 RNASLOpt: 0.374 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNASLOpt: 0.609 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.575 Murlet(seed): 0.425 Sensitivity PETfold_pre2.0(seed): 0.459 Murlet(seed): 0.248 Positive Predictive Value PETfold_pre2.0(seed): 0.726 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Vsfold5: 0.372 Sensitivity PETfold_pre2.0(seed): 0.551 Vsfold5: 0.319 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Vsfold5: 0.443 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RNAwolf: 0.339 Sensitivity PETfold_pre2.0(seed): 0.551 RNAwolf: 0.307 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RNAwolf: 0.384 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	5 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.634 RDfolder: 0.281 Sensitivity PETfold_pre2.0(seed): 0.515 RDfolder: 0.215 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RDfolder: 0.384 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.663 MCFold: 0.441 Sensitivity PETfold_pre2.0(seed): 0.549 MCFold: 0.469 Positive Predictive Value PETfold_pre2.0(seed): 0.807 MCFold: 0.423 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 RSpredict(seed): 0.110 Sensitivity PETfold_pre2.0(seed): 0.551 RSpredict(seed): 0.047 Positive Predictive Value PETfold_pre2.0(seed): 0.843 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 PPfold(seed): 0.121 Sensitivity PETfold_pre2.0(seed): 0.551 PPfold(seed): 0.028 Positive Predictive Value PETfold_pre2.0(seed): 0.843 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 Carnac(seed): 0.146 Sensitivity PETfold_pre2.0(seed): 0.529 Carnac(seed): 0.021 Positive Predictive Value PETfold_pre2.0(seed): 0.805 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.694 NanoFolder: 0.346 Sensitivity PETfold_pre2.0(seed): 0.562 NanoFolder: 0.353 Positive Predictive Value PETfold_pre2.0(seed): 0.863 NanoFolder: 0.349 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	2 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.623 Multilign(seed): 0.403 Sensitivity PETfold_pre2.0(seed): 0.484 Multilign(seed): 0.306 Positive Predictive Value PETfold_pre2.0(seed): 0.811 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(seed): 0.557 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(seed): 0.830 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(seed): 0.557 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.830 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(seed): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A CMfinder(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_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PETfold_pre2.0(20): 0.625 Sensitivity PETfold_pre2.0(seed): 0.557 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 TurboFold(seed): 0.460 Sensitivity PETfold_pre2.0(seed): 0.529 TurboFold(seed): 0.380 Positive Predictive Value PETfold_pre2.0(seed): 0.805 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 RNASampler(seed): 0.198 Sensitivity PETfold_pre2.0(seed): 0.396 RNASampler(seed): 0.151 Positive Predictive Value PETfold_pre2.0(seed): 0.656 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(seed): 0.557 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.551 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
TurboFold(20)	8 MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.640 TurboFold(20): 0.594 Sensitivity MXScarna(seed): 0.511 TurboFold(20): 0.470 Positive Predictive Value MXScarna(seed): 0.807 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 TurboFold(20): 0.594 Sensitivity CentroidAlifold(20): 0.515 TurboFold(20): 0.470 Positive Predictive Value CentroidAlifold(20): 0.933 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.627 TurboFold(20): 0.594 Sensitivity RNAalifold(20): 0.481 TurboFold(20): 0.470 Positive Predictive Value RNAalifold(20): 0.823 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.637 TurboFold(20): 0.594 Sensitivity RNASampler(20): 0.478 TurboFold(20): 0.470 Positive Predictive Value RNASampler(20): 0.854 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.594 CentroidFold: 0.575 Sensitivity TurboFold(20): 0.470 CentroidFold: 0.470 Positive Predictive Value TurboFold(20): 0.756 CentroidFold: 0.709 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.594 MXScarna(20): 0.586 Sensitivity TurboFold(20): 0.470 MXScarna(20): 0.474 Positive Predictive Value TurboFold(20): 0.756 MXScarna(20): 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.637 TurboFold(20): 0.594 Sensitivity CentroidAlifold(seed): 0.415 TurboFold(20): 0.470 Positive Predictive Value CentroidAlifold(seed): 0.982 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.594 Contrafold: 0.561 Sensitivity TurboFold(20): 0.470 Contrafold: 0.478 Positive Predictive Value TurboFold(20): 0.756 Contrafold: 0.665 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.594 Sfold: 0.579 Sensitivity TurboFold(20): 0.470 Sfold: 0.467 Positive Predictive Value TurboFold(20): 0.756 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.594 MaxExpect: 0.543 Sensitivity TurboFold(20): 0.470 MaxExpect: 0.463 Positive Predictive Value TurboFold(20): 0.756 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.594 IPknot: 0.571 Sensitivity TurboFold(20): 0.470 IPknot: 0.463 Positive Predictive Value TurboFold(20): 0.756 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.631 TurboFold(20): 0.594 Sensitivity CentroidHomfold‑LAST: 0.496 TurboFold(20): 0.470 Positive Predictive Value CentroidHomfold‑LAST: 0.807 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.609 TurboFold(20): 0.594 Sensitivity HotKnots: 0.526 TurboFold(20): 0.470 Positive Predictive Value HotKnots: 0.710 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Carnac(20): 0.560 Sensitivity TurboFold(20): 0.470 Carnac(20): 0.367 Positive Predictive Value TurboFold(20): 0.756 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.579 TurboFold(20): 0.542 Sensitivity ContextFold: 0.443 TurboFold(20): 0.425 Positive Predictive Value ContextFold: 0.763 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.594 ProbKnot: 0.542 Sensitivity TurboFold(20): 0.470 ProbKnot: 0.481 Positive Predictive Value TurboFold(20): 0.756 ProbKnot: 0.616 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Murlet(20): 0.581 Sensitivity TurboFold(20): 0.470 Murlet(20): 0.433 Positive Predictive Value TurboFold(20): 0.756 Murlet(20): 0.785 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.594 UNAFold: 0.556 Sensitivity TurboFold(20): 0.470 UNAFold: 0.474 Positive Predictive Value TurboFold(20): 0.756 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.594 Fold: 0.510 Sensitivity TurboFold(20): 0.470 Fold: 0.441 Positive Predictive Value TurboFold(20): 0.756 Fold: 0.598 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.594 RNAfold: 0.555 Sensitivity TurboFold(20): 0.470 RNAfold: 0.474 Positive Predictive Value TurboFold(20): 0.756 RNAfold: 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.600 TurboFold(20): 0.594 Sensitivity PknotsRG: 0.522 TurboFold(20): 0.470 Positive Predictive Value PknotsRG: 0.695 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.653 TurboFold(20): 0.647 Sensitivity Cylofold: 0.536 TurboFold(20): 0.497 Positive Predictive Value Cylofold: 0.803 TurboFold(20): 0.850 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(seed) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(seed): 0.591 TurboFold(20): 0.547 Sensitivity RNAalifold(seed): 0.381 TurboFold(20): 0.423 Positive Predictive Value RNAalifold(seed): 0.923 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.594 RNAshapes: 0.555 Sensitivity TurboFold(20): 0.470 RNAshapes: 0.470 Positive Predictive Value TurboFold(20): 0.756 RNAshapes: 0.661 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.501 Afold: 0.461 Sensitivity TurboFold(20): 0.395 Afold: 0.419 Positive Predictive Value TurboFold(20): 0.642 Afold: 0.514 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.594 McQFold: 0.526 Sensitivity TurboFold(20): 0.470 McQFold: 0.452 Positive Predictive Value TurboFold(20): 0.756 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.594 Pknots: 0.505 Sensitivity TurboFold(20): 0.470 Pknots: 0.441 Positive Predictive Value TurboFold(20): 0.756 Pknots: 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.594 RNAsubopt: 0.551 Sensitivity TurboFold(20): 0.470 RNAsubopt: 0.474 Positive Predictive Value TurboFold(20): 0.756 RNAsubopt: 0.646 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.594 RSpredict(20): 0.489 Sensitivity TurboFold(20): 0.470 RSpredict(20): 0.367 Positive Predictive Value TurboFold(20): 0.756 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 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	8 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.594 Vsfold4: 0.437 Sensitivity TurboFold(20): 0.470 Vsfold4: 0.356 Positive Predictive Value TurboFold(20): 0.756 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Mastr(20): 0.567 Sensitivity TurboFold(20): 0.470 Mastr(20): 0.389 Positive Predictive Value TurboFold(20): 0.756 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.542 RNASLOpt: 0.467 Sensitivity TurboFold(20): 0.425 RNASLOpt: 0.383 Positive Predictive Value TurboFold(20): 0.696 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.547 Murlet(seed): 0.520 Sensitivity TurboFold(20): 0.423 Murlet(seed): 0.296 Positive Predictive Value TurboFold(20): 0.714 Murlet(seed): 0.918 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.594 Vsfold5: 0.421 Sensitivity TurboFold(20): 0.470 Vsfold5: 0.363 Positive Predictive Value TurboFold(20): 0.756 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.594 RNAwolf: 0.364 Sensitivity TurboFold(20): 0.470 RNAwolf: 0.333 Positive Predictive Value TurboFold(20): 0.756 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	6 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.647 RDfolder: 0.407 Sensitivity TurboFold(20): 0.497 RDfolder: 0.295 Positive Predictive Value TurboFold(20): 0.850 RDfolder: 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.601 MCFold: 0.459 Sensitivity TurboFold(20): 0.482 MCFold: 0.474 Positive Predictive Value TurboFold(20): 0.753 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 RSpredict(seed): 0.267 Sensitivity TurboFold(20): 0.470 RSpredict(seed): 0.111 Positive Predictive Value TurboFold(20): 0.756 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 PPfold(seed): 0.026 Sensitivity TurboFold(20): 0.470 PPfold(seed): 0.004 Positive Predictive Value TurboFold(20): 0.756 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.581 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.457 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.745 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.526 NanoFolder: 0.316 Sensitivity TurboFold(20): 0.419 NanoFolder: 0.324 Positive Predictive Value TurboFold(20): 0.667 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	3 Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.631 TurboFold(20): 0.629 Sensitivity Multilign(seed): 0.492 TurboFold(20): 0.483 Positive Predictive Value Multilign(seed): 0.817 TurboFold(20): 0.826 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.594 Multilign(20): 0.540 Sensitivity TurboFold(20): 0.470 Multilign(20): 0.456 Positive Predictive Value TurboFold(20): 0.756 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(seed): 0.557 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.830 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(20): N/A Sensitivity TurboFold(20): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.581 TurboFold(seed): 0.564 Sensitivity TurboFold(20): 0.457 TurboFold(seed): 0.457 Positive Predictive Value TurboFold(20): 0.745 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): 0.556 TurboFold(20): 0.509 Sensitivity RNASampler(seed): 0.404 TurboFold(20): 0.413 Positive Predictive Value RNASampler(seed): 0.772 TurboFold(20): 0.634 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.665 TurboFold(20): 0.594 Sensitivity PPfold(20): 0.519 TurboFold(20): 0.470 Positive Predictive Value PPfold(20): 0.859 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.470 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.756 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
CMfinder(20)	0 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): N/A CMfinder(20): N/A Sensitivity MXScarna(seed): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(20): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(20): N/A Sensitivity RNAalifold(20): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(20): N/A Sensitivity RNASampler(20): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: N/A CMfinder(20): N/A Sensitivity CentroidFold: N/A CMfinder(20): N/A Positive Predictive Value CentroidFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): N/A CMfinder(20): N/A Sensitivity MXScarna(20): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: N/A CMfinder(20): N/A Sensitivity Contrafold: N/A CMfinder(20): N/A Positive Predictive Value Contrafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: N/A CMfinder(20): N/A Sensitivity Sfold: N/A CMfinder(20): N/A Positive Predictive Value Sfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(20): N/A Sensitivity MaxExpect: N/A CMfinder(20): N/A Positive Predictive Value MaxExpect: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: N/A CMfinder(20): N/A Sensitivity IPknot: N/A CMfinder(20): N/A Positive Predictive Value IPknot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(20): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): N/A CMfinder(20): N/A Sensitivity Carnac(20): N/A CMfinder(20): N/A Positive Predictive Value Carnac(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: N/A CMfinder(20): N/A Sensitivity ContextFold: N/A CMfinder(20): N/A Positive Predictive Value ContextFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(20): N/A Sensitivity ProbKnot: N/A CMfinder(20): N/A Positive Predictive Value ProbKnot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(20): N/A Sensitivity Murlet(20): N/A CMfinder(20): N/A Positive Predictive Value Murlet(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 CMfinder(20) Matthews Correlation Coefficient UNAFold: N/A CMfinder(20): N/A Sensitivity UNAFold: N/A CMfinder(20): N/A Positive Predictive Value UNAFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: N/A CMfinder(20): N/A Sensitivity Fold: N/A CMfinder(20): N/A Positive Predictive Value Fold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: N/A CMfinder(20): N/A Sensitivity RNAfold: N/A CMfinder(20): N/A Positive Predictive Value RNAfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(20): N/A Sensitivity PknotsRG: N/A CMfinder(20): N/A Positive Predictive Value PknotsRG: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(20): N/A Sensitivity RNAalifold(seed): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: N/A CMfinder(20): N/A Sensitivity RNAshapes: N/A CMfinder(20): N/A Positive Predictive Value RNAshapes: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: N/A CMfinder(20): N/A Sensitivity Afold: N/A CMfinder(20): N/A Positive Predictive Value Afold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: N/A CMfinder(20): N/A Sensitivity McQFold: N/A CMfinder(20): N/A Positive Predictive Value McQFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: N/A CMfinder(20): N/A Sensitivity RNAsubopt: N/A CMfinder(20): N/A Positive Predictive Value RNAsubopt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(20): N/A Sensitivity RSpredict(20): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(20): N/A Sensitivity Vsfold4: N/A CMfinder(20): N/A Positive Predictive Value Vsfold4: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(20): N/A Sensitivity Mastr(20): N/A CMfinder(20): N/A Positive Predictive Value Mastr(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: N/A CMfinder(20): N/A Sensitivity RNASLOpt: N/A CMfinder(20): N/A Positive Predictive Value RNASLOpt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs CMfinder(20) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(20): N/A Sensitivity Vsfold5: N/A CMfinder(20): N/A Positive Predictive Value Vsfold5: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAwolf vs CMfinder(20) Matthews Correlation Coefficient RNAwolf: N/A CMfinder(20): N/A Sensitivity RNAwolf: N/A CMfinder(20): N/A Positive Predictive Value RNAwolf: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(20): N/A Sensitivity RSpredict(seed): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(seed) vs CMfinder(20) Matthews Correlation Coefficient Carnac(seed): N/A CMfinder(20): N/A Sensitivity Carnac(seed): N/A CMfinder(20): N/A Positive Predictive Value Carnac(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs CMfinder(20) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(20): N/A Sensitivity NanoFolder: N/A CMfinder(20): N/A Positive Predictive Value NanoFolder: N/A CMfinder(20): 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 Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): N/A CMfinder(20): N/A Sensitivity Multilign(20): N/A CMfinder(20): N/A Positive Predictive Value Multilign(20): N/A CMfinder(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 CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(seed): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(20): N/A Sensitivity TurboFold(20): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(20): N/A Sensitivity PPfold(20): N/A CMfinder(20): N/A Positive Predictive Value PPfold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs CMfinder(20) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(20): N/A Sensitivity Mastr(seed): N/A CMfinder(20): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_pre2.0(20)	5 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(seed): 0.593 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(seed): 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(seed): 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.650 PETfold_pre2.0(20): 0.625 Sensitivity CentroidAlifold(20): 0.473 PETfold_pre2.0(20): 0.497 Positive Predictive Value CentroidAlifold(20): 0.898 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAalifold(20): 0.553 Sensitivity PETfold_pre2.0(20): 0.497 RNAalifold(20): 0.407 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAalifold(20): 0.756 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASampler(20): 0.569 Sensitivity PETfold_pre2.0(20): 0.497 RNASampler(20): 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASampler(20): 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidFold: 0.517 Sensitivity PETfold_pre2.0(20): 0.497 CentroidFold: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidFold: 0.634 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MXScarna(20): 0.501 Sensitivity PETfold_pre2.0(20): 0.497 MXScarna(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 MXScarna(20): 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidAlifold(seed): 0.613 Sensitivity PETfold_pre2.0(20): 0.497 CentroidAlifold(seed): 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidAlifold(seed): 0.985 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Contrafold: 0.511 Sensitivity PETfold_pre2.0(20): 0.497 Contrafold: 0.437 Positive Predictive Value PETfold_pre2.0(20): 0.790 Contrafold: 0.603 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Sfold: 0.507 Sensitivity PETfold_pre2.0(20): 0.497 Sfold: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 Sfold: 0.627 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 MaxExpect: 0.479 Sensitivity PETfold_pre2.0(20): 0.497 MaxExpect: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 MaxExpect: 0.561 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 IPknot: 0.502 Sensitivity PETfold_pre2.0(20): 0.497 IPknot: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 IPknot: 0.616 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 CentroidHomfold‑LAST: 0.581 Sensitivity PETfold_pre2.0(20): 0.497 CentroidHomfold‑LAST: 0.467 Positive Predictive Value PETfold_pre2.0(20): 0.790 CentroidHomfold‑LAST: 0.729 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 HotKnots: 0.561 Sensitivity PETfold_pre2.0(20): 0.497 HotKnots: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 HotKnots: 0.632 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(20): 0.476 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(20): 0.281 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(20): 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ContextFold: 0.579 Sensitivity PETfold_pre2.0(20): 0.497 ContextFold: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 ProbKnot: 0.488 Sensitivity PETfold_pre2.0(20): 0.497 ProbKnot: 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.790 ProbKnot: 0.544 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Murlet(20): 0.496 Sensitivity PETfold_pre2.0(20): 0.497 Murlet(20): 0.353 Positive Predictive Value PETfold_pre2.0(20): 0.790 Murlet(20): 0.702 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 UNAFold: 0.478 Sensitivity PETfold_pre2.0(20): 0.497 UNAFold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 UNAFold: 0.551 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Fold: 0.429 Sensitivity PETfold_pre2.0(20): 0.497 Fold: 0.377 Positive Predictive Value PETfold_pre2.0(20): 0.790 Fold: 0.496 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAfold: 0.476 Sensitivity PETfold_pre2.0(20): 0.497 RNAfold: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PknotsRG: 0.555 Sensitivity PETfold_pre2.0(20): 0.497 PknotsRG: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.790 PknotsRG: 0.618 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.666 Cylofold: 0.620 Sensitivity PETfold_pre2.0(20): 0.513 Cylofold: 0.513 Positive Predictive Value PETfold_pre2.0(20): 0.872 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.586 PETfold_pre2.0(20): 0.527 Sensitivity RNAalifold(seed): 0.345 PETfold_pre2.0(20): 0.407 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAshapes: 0.475 Sensitivity PETfold_pre2.0(20): 0.497 RNAshapes: 0.413 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAshapes: 0.552 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.333 Afold: 0.311 Sensitivity PETfold_pre2.0(20): 0.250 Afold: 0.308 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.320 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 McQFold: 0.409 Sensitivity PETfold_pre2.0(20): 0.497 McQFold: 0.365 Positive Predictive Value PETfold_pre2.0(20): 0.790 McQFold: 0.466 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Pknots: 0.371 Sensitivity PETfold_pre2.0(20): 0.497 Pknots: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Pknots: 0.418 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAsubopt: 0.477 Sensitivity PETfold_pre2.0(20): 0.497 RNAsubopt: 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAsubopt: 0.542 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(20): 0.352 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(20): 0.251 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(20): 0.500 Number of pairs reference - predicted secondary structure: 5 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	5 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold4: 0.401 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold4: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold4: 0.505 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Mastr(20): 0.488 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(20): 0.305 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(20): 0.785 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNASLOpt: 0.467 Sensitivity PETfold_pre2.0(20): 0.497 RNASLOpt: 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Murlet(seed): 0.539 PETfold_pre2.0(20): 0.527 Sensitivity Murlet(seed): 0.292 PETfold_pre2.0(20): 0.407 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.687 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Vsfold5: 0.384 Sensitivity PETfold_pre2.0(20): 0.497 Vsfold5: 0.335 Positive Predictive Value PETfold_pre2.0(20): 0.790 Vsfold5: 0.448 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RNAwolf: 0.220 Sensitivity PETfold_pre2.0(20): 0.497 RNAwolf: 0.204 Positive Predictive Value PETfold_pre2.0(20): 0.790 RNAwolf: 0.248 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.666 RDfolder: 0.387 Sensitivity PETfold_pre2.0(20): 0.513 RDfolder: 0.288 Positive Predictive Value PETfold_pre2.0(20): 0.872 RDfolder: 0.535 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.586 MCFold: 0.444 Sensitivity PETfold_pre2.0(20): 0.464 MCFold: 0.472 Positive Predictive Value PETfold_pre2.0(20): 0.744 MCFold: 0.424 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 RSpredict(seed): 0.184 Sensitivity PETfold_pre2.0(20): 0.497 RSpredict(seed): 0.072 Positive Predictive Value PETfold_pre2.0(20): 0.790 RSpredict(seed): 0.480 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(seed): 0.034 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(seed): 0.006 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.627 NanoFolder: 0.316 Sensitivity PETfold_pre2.0(20): 0.507 NanoFolder: 0.324 Positive Predictive Value PETfold_pre2.0(20): 0.781 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	1 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 Multilign(seed): 0.609 Sensitivity PETfold_pre2.0(20): 0.595 Multilign(seed): 0.452 Positive Predictive Value PETfold_pre2.0(20): 0.926 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Multilign(20): 0.474 Sensitivity PETfold_pre2.0(20): 0.497 Multilign(20): 0.401 Positive Predictive Value PETfold_pre2.0(20): 0.790 Multilign(20): 0.568 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PETfold_pre2.0(20): 0.625 Sensitivity PETfold_pre2.0(seed): 0.557 PETfold_pre2.0(20): 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PETfold_pre2.0(20): 0.790 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(20): 0.542 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(20): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(20): 0.696 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(seed): 0.519 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(seed): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(seed): 0.640 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.310 PETfold_pre2.0(20): 0.193 Sensitivity RNASampler(seed): 0.242 PETfold_pre2.0(20): 0.152 Positive Predictive Value RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
TurboFold(seed)	8 MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.574 TurboFold(seed): 0.517 Sensitivity MXScarna(seed): 0.452 TurboFold(seed): 0.422 Positive Predictive Value MXScarna(seed): 0.735 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.670 TurboFold(seed): 0.564 Sensitivity CentroidAlifold(20): 0.490 TurboFold(seed): 0.457 Positive Predictive Value CentroidAlifold(20): 0.922 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(20) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.599 TurboFold(seed): 0.564 Sensitivity RNAalifold(20): 0.453 TurboFold(seed): 0.457 Positive Predictive Value RNAalifold(20): 0.797 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.615 TurboFold(seed): 0.564 Sensitivity RNASampler(20): 0.453 TurboFold(seed): 0.457 Positive Predictive Value RNASampler(20): 0.840 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.555 TurboFold(seed): 0.517 Sensitivity CentroidFold: 0.449 TurboFold(seed): 0.422 Positive Predictive Value CentroidFold: 0.694 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 MXScarna(20): 0.554 Sensitivity TurboFold(seed): 0.457 MXScarna(20): 0.444 Positive Predictive Value TurboFold(seed): 0.703 MXScarna(20): 0.697 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.627 TurboFold(seed): 0.517 Sensitivity CentroidAlifold(seed): 0.403 TurboFold(seed): 0.422 Positive Predictive Value CentroidAlifold(seed): 0.981 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.543 TurboFold(seed): 0.517 Sensitivity Contrafold: 0.456 TurboFold(seed): 0.422 Positive Predictive Value Contrafold: 0.652 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.556 TurboFold(seed): 0.517 Sensitivity Sfold: 0.445 TurboFold(seed): 0.422 Positive Predictive Value Sfold: 0.701 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.517 MaxExpect: 0.490 Sensitivity TurboFold(seed): 0.422 MaxExpect: 0.414 Positive Predictive Value TurboFold(seed): 0.642 MaxExpect: 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.544 TurboFold(seed): 0.517 Sensitivity IPknot: 0.437 TurboFold(seed): 0.422 Positive Predictive Value IPknot: 0.685 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.563 TurboFold(seed): 0.517 Sensitivity CentroidHomfold‑LAST: 0.437 TurboFold(seed): 0.422 Positive Predictive Value CentroidHomfold‑LAST: 0.732 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.599 TurboFold(seed): 0.517 Sensitivity HotKnots: 0.521 TurboFold(seed): 0.422 Positive Predictive Value HotKnots: 0.695 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Carnac(20): 0.544 Sensitivity TurboFold(seed): 0.457 Carnac(20): 0.342 Positive Predictive Value TurboFold(seed): 0.703 Carnac(20): 0.874 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.576 TurboFold(seed): 0.460 Sensitivity ContextFold: 0.449 TurboFold(seed): 0.380 Positive Predictive Value ContextFold: 0.743 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.517 ProbKnot: 0.489 Sensitivity TurboFold(seed): 0.422 ProbKnot: 0.433 Positive Predictive Value TurboFold(seed): 0.642 ProbKnot: 0.559 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Murlet(20): 0.557 Sensitivity TurboFold(seed): 0.457 Murlet(20): 0.407 Positive Predictive Value TurboFold(seed): 0.703 Murlet(20): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.517 UNAFold: 0.498 Sensitivity TurboFold(seed): 0.422 UNAFold: 0.426 Positive Predictive Value TurboFold(seed): 0.642 UNAFold: 0.589 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.517 Fold: 0.456 Sensitivity TurboFold(seed): 0.422 Fold: 0.392 Positive Predictive Value TurboFold(seed): 0.642 Fold: 0.539 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.544 TurboFold(seed): 0.517 Sensitivity RNAfold: 0.468 TurboFold(seed): 0.422 Positive Predictive Value RNAfold: 0.641 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.592 TurboFold(seed): 0.517 Sensitivity PknotsRG: 0.517 TurboFold(seed): 0.422 Positive Predictive Value PknotsRG: 0.683 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.645 TurboFold(seed): 0.553 Sensitivity Cylofold: 0.528 TurboFold(seed): 0.426 Positive Predictive Value Cylofold: 0.795 TurboFold(seed): 0.728 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.523 TurboFold(seed): 0.471 Sensitivity RNAalifold(seed): 0.344 TurboFold(seed): 0.383 Positive Predictive Value RNAalifold(seed): 0.800 TurboFold(seed): 0.588 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.544 TurboFold(seed): 0.517 Sensitivity RNAshapes: 0.464 TurboFold(seed): 0.422 Positive Predictive Value RNAshapes: 0.646 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	4 Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.489 TurboFold(seed): 0.373 Sensitivity Afold: 0.443 TurboFold(seed): 0.321 Positive Predictive Value Afold: 0.547 TurboFold(seed): 0.442 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.517 McQFold: 0.512 Sensitivity TurboFold(seed): 0.422 McQFold: 0.445 Positive Predictive Value TurboFold(seed): 0.642 McQFold: 0.597 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.517 Pknots: 0.492 Sensitivity TurboFold(seed): 0.422 Pknots: 0.433 Positive Predictive Value TurboFold(seed): 0.642 Pknots: 0.567 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.517 RNAsubopt: 0.492 Sensitivity TurboFold(seed): 0.422 RNAsubopt: 0.426 Positive Predictive Value TurboFold(seed): 0.642 RNAsubopt: 0.577 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 RSpredict(20): 0.478 Sensitivity TurboFold(seed): 0.457 RSpredict(20): 0.362 Positive Predictive Value TurboFold(seed): 0.703 RSpredict(20): 0.638 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	8 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.517 Vsfold4: 0.380 Sensitivity TurboFold(seed): 0.422 Vsfold4: 0.308 Positive Predictive Value TurboFold(seed): 0.642 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Mastr(20): 0.542 Sensitivity TurboFold(seed): 0.457 Mastr(20): 0.366 Positive Predictive Value TurboFold(seed): 0.703 Mastr(20): 0.809 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNASLOpt vs TurboFold(seed) Matthews Correlation Coefficient RNASLOpt: 0.467 TurboFold(seed): 0.460 Sensitivity RNASLOpt: 0.380 TurboFold(seed): 0.380 Positive Predictive Value RNASLOpt: 0.582 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.471 Murlet(seed): 0.451 Sensitivity TurboFold(seed): 0.383 Murlet(seed): 0.268 Positive Predictive Value TurboFold(seed): 0.588 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.517 Vsfold5: 0.364 Sensitivity TurboFold(seed): 0.422 Vsfold5: 0.312 Positive Predictive Value TurboFold(seed): 0.642 Vsfold5: 0.434 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.517 RNAwolf: 0.344 Sensitivity TurboFold(seed): 0.422 RNAwolf: 0.316 Positive Predictive Value TurboFold(seed): 0.642 RNAwolf: 0.384 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	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	7 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.512 MCFold: 0.456 Sensitivity TurboFold(seed): 0.425 MCFold: 0.471 Positive Predictive Value TurboFold(seed): 0.623 MCFold: 0.450 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 RSpredict(seed): 0.243 Sensitivity TurboFold(seed): 0.422 RSpredict(seed): 0.114 Positive Predictive Value TurboFold(seed): 0.642 RSpredict(seed): 0.526 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 PPfold(seed): 0.118 Sensitivity TurboFold(seed): 0.422 PPfold(seed): 0.027 Positive Predictive Value TurboFold(seed): 0.642 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 Carnac(seed): 0.123 Sensitivity TurboFold(seed): 0.422 Carnac(seed): 0.015 Positive Predictive Value TurboFold(seed): 0.642 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.439 NanoFolder: 0.341 Sensitivity TurboFold(seed): 0.369 NanoFolder: 0.351 Positive Predictive Value TurboFold(seed): 0.530 NanoFolder: 0.339 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	4 Multilign(seed) vs TurboFold(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 TurboFold(seed): 0.525 Sensitivity Multilign(seed): 0.420 TurboFold(seed): 0.413 Positive Predictive Value Multilign(seed): 0.699 TurboFold(seed): 0.679 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.564 Multilign(20): 0.530 Sensitivity TurboFold(seed): 0.457 Multilign(20): 0.444 Positive Predictive Value TurboFold(seed): 0.703 Multilign(20): 0.639 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.651 TurboFold(seed): 0.460 Sensitivity PETfold_pre2.0(seed): 0.529 TurboFold(seed): 0.380 Positive Predictive Value PETfold_pre2.0(seed): 0.805 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.581 TurboFold(seed): 0.564 Sensitivity TurboFold(20): 0.457 TurboFold(seed): 0.457 Positive Predictive Value TurboFold(20): 0.745 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 TurboFold(seed): 0.519 Sensitivity PETfold_pre2.0(20): 0.497 TurboFold(seed): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.790 TurboFold(seed): 0.640 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.471 TurboFold(seed): 0.403 Sensitivity RNASampler(seed): 0.341 TurboFold(seed): 0.349 Positive Predictive Value RNASampler(seed): 0.657 TurboFold(seed): 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.642 TurboFold(seed): 0.564 Sensitivity PPfold(20): 0.494 TurboFold(seed): 0.457 Positive Predictive Value PPfold(20): 0.839 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.422 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.642 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
RNASampler(seed)	9 MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.552 RNASampler(seed): 0.546 Sensitivity MXScarna(seed): 0.431 RNASampler(seed): 0.409 Positive Predictive Value MXScarna(seed): 0.713 RNASampler(seed): 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.585 RNASampler(seed): 0.546 Sensitivity CentroidAlifold(20): 0.409 RNASampler(seed): 0.409 Positive Predictive Value CentroidAlifold(20): 0.842 RNASampler(seed): 0.733 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 RNAalifold(20): 0.512 Sensitivity RNASampler(seed): 0.434 RNAalifold(20): 0.402 Positive Predictive Value RNASampler(seed): 0.754 RNAalifold(20): 0.657 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 RNASampler(20): 0.541 Sensitivity RNASampler(seed): 0.434 RNASampler(20): 0.438 Positive Predictive Value RNASampler(seed): 0.754 RNASampler(20): 0.671 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.526 RNASampler(seed): 0.526 Sensitivity CentroidFold: 0.438 RNASampler(seed): 0.389 Positive Predictive Value CentroidFold: 0.637 RNASampler(seed): 0.715 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 MXScarna(20): 0.539 Sensitivity RNASampler(seed): 0.434 MXScarna(20): 0.447 Positive Predictive Value RNASampler(seed): 0.754 MXScarna(20): 0.653 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.655 RNASampler(seed): 0.526 Sensitivity CentroidAlifold(seed): 0.449 RNASampler(seed): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.960 RNASampler(seed): 0.715 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.546 Contrafold: 0.512 Sensitivity RNASampler(seed): 0.409 Contrafold: 0.453 Positive Predictive Value RNASampler(seed): 0.734 Contrafold: 0.584 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.575 RNASampler(seed): 0.546 Sensitivity Sfold: 0.478 RNASampler(seed): 0.409 Positive Predictive Value Sfold: 0.695 RNASampler(seed): 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.500 MaxExpect: 0.418 Sensitivity RNASampler(seed): 0.373 MaxExpect: 0.377 Positive Predictive Value RNASampler(seed): 0.675 MaxExpect: 0.470 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.493 RNASampler(seed): 0.471 Sensitivity IPknot: 0.395 RNASampler(seed): 0.341 Positive Predictive Value IPknot: 0.622 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.471 CentroidHomfold‑LAST: 0.416 Sensitivity RNASampler(seed): 0.341 CentroidHomfold‑LAST: 0.326 Positive Predictive Value RNASampler(seed): 0.657 CentroidHomfold‑LAST: 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.546 HotKnots: 0.530 Sensitivity RNASampler(seed): 0.409 HotKnots: 0.486 Positive Predictive Value RNASampler(seed): 0.734 HotKnots: 0.583 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 Carnac(20) vs RNASampler(seed) Matthews Correlation Coefficient Carnac(20): 0.600 RNASampler(seed): 0.570 Sensitivity Carnac(20): 0.374 RNASampler(seed): 0.434 Positive Predictive Value Carnac(20): 0.965 RNASampler(seed): 0.754 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	2 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.351 RNASampler(seed): 0.198 Sensitivity ContextFold: 0.283 RNASampler(seed): 0.151 Positive Predictive Value ContextFold: 0.441 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.467 ProbKnot: 0.358 Sensitivity RNASampler(seed): 0.341 ProbKnot: 0.348 Positive Predictive Value RNASampler(seed): 0.644 ProbKnot: 0.375 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 Murlet(20): 0.492 Sensitivity RNASampler(seed): 0.434 Murlet(20): 0.374 Positive Predictive Value RNASampler(seed): 0.754 Murlet(20): 0.651 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.546 UNAFold: 0.510 Sensitivity RNASampler(seed): 0.409 UNAFold: 0.457 Positive Predictive Value RNASampler(seed): 0.734 UNAFold: 0.575 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.467 Fold: 0.365 Sensitivity RNASampler(seed): 0.341 Fold: 0.341 Positive Predictive Value RNASampler(seed): 0.644 Fold: 0.397 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.549 RNASampler(seed): 0.546 Sensitivity RNAfold: 0.496 RNASampler(seed): 0.409 Positive Predictive Value RNAfold: 0.612 RNASampler(seed): 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs PknotsRG Matthews Correlation Coefficient RNASampler(seed): 0.546 PknotsRG: 0.544 Sensitivity RNASampler(seed): 0.409 PknotsRG: 0.493 Positive Predictive Value RNASampler(seed): 0.734 PknotsRG: 0.604 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.571 RNASampler(seed): 0.510 Sensitivity Cylofold: 0.489 RNASampler(seed): 0.366 Positive Predictive Value Cylofold: 0.674 RNASampler(seed): 0.716 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 RNAalifold(seed): 0.514 Sensitivity RNASampler(seed): 0.409 RNAalifold(seed): 0.330 Positive Predictive Value RNASampler(seed): 0.734 RNAalifold(seed): 0.805 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.546 RNAshapes: 0.535 Sensitivity RNASampler(seed): 0.409 RNAshapes: 0.482 Positive Predictive Value RNASampler(seed): 0.734 RNAshapes: 0.599 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.540 Afold: 0.528 Sensitivity RNASampler(seed): 0.415 Afold: 0.483 Positive Predictive Value RNASampler(seed): 0.708 Afold: 0.582 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.546 McQFold: 0.534 Sensitivity RNASampler(seed): 0.409 McQFold: 0.486 Positive Predictive Value RNASampler(seed): 0.734 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.546 Pknots: 0.541 Sensitivity RNASampler(seed): 0.409 Pknots: 0.514 Positive Predictive Value RNASampler(seed): 0.734 Pknots: 0.575 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.546 RNAsubopt: 0.472 Sensitivity RNASampler(seed): 0.409 RNAsubopt: 0.438 Positive Predictive Value RNASampler(seed): 0.734 RNAsubopt: 0.515 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 RSpredict(20): 0.502 Sensitivity RNASampler(seed): 0.434 RSpredict(20): 0.461 Positive Predictive Value RNASampler(seed): 0.754 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	9 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.546 Vsfold4: 0.412 Sensitivity RNASampler(seed): 0.409 Vsfold4: 0.351 Positive Predictive Value RNASampler(seed): 0.734 Vsfold4: 0.490 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.570 Mastr(20): 0.526 Sensitivity RNASampler(seed): 0.434 Mastr(20): 0.311 Positive Predictive Value RNASampler(seed): 0.754 Mastr(20): 0.895 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	2 RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.295 RNASampler(seed): 0.198 Sensitivity RNASLOpt: 0.283 RNASampler(seed): 0.151 Positive Predictive Value RNASLOpt: 0.313 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 Murlet(seed): 0.424 Sensitivity RNASampler(seed): 0.409 Murlet(seed): 0.243 Positive Predictive Value RNASampler(seed): 0.734 Murlet(seed): 0.744 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.546 Vsfold5: 0.453 Sensitivity RNASampler(seed): 0.409 Vsfold5: 0.402 Positive Predictive Value RNASampler(seed): 0.734 Vsfold5: 0.516 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.471 RNAwolf: 0.416 Sensitivity RNASampler(seed): 0.341 RNAwolf: 0.403 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.437 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	6 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.644 RDfolder: 0.541 Sensitivity RNASampler(seed): 0.474 RDfolder: 0.406 Positive Predictive Value RNASampler(seed): 0.883 RDfolder: 0.732 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.546 MCFold: 0.412 Sensitivity RNASampler(seed): 0.409 MCFold: 0.438 Positive Predictive Value RNASampler(seed): 0.734 MCFold: 0.393 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 RSpredict(seed): 0.364 Sensitivity RNASampler(seed): 0.409 RSpredict(seed): 0.203 Positive Predictive Value RNASampler(seed): 0.734 RSpredict(seed): 0.659 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.471 PPfold(seed): 0.169 Sensitivity RNASampler(seed): 0.341 PPfold(seed): 0.054 Positive Predictive Value RNASampler(seed): 0.657 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 Carnac(seed): 0.225 Sensitivity RNASampler(seed): 0.409 Carnac(seed): 0.051 Positive Predictive Value RNASampler(seed): 0.734 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	2 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.198 NanoFolder: 0.171 Sensitivity RNASampler(seed): 0.151 NanoFolder: 0.208 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	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	3 RNASampler(seed) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(seed): 0.532 Multilign(seed): 0.509 Sensitivity RNASampler(seed): 0.375 Multilign(seed): 0.406 Positive Predictive Value RNASampler(seed): 0.766 Multilign(seed): 0.650 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.556 Multilign(20): 0.475 Sensitivity RNASampler(seed): 0.404 Multilign(20): 0.422 Positive Predictive Value RNASampler(seed): 0.772 Multilign(20): 0.541 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.508 RNASampler(seed): 0.198 Sensitivity PETfold_pre2.0(seed): 0.396 RNASampler(seed): 0.151 Positive Predictive Value PETfold_pre2.0(seed): 0.656 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): 0.556 TurboFold(20): 0.509 Sensitivity RNASampler(seed): 0.404 TurboFold(20): 0.413 Positive Predictive Value RNASampler(seed): 0.772 TurboFold(20): 0.634 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.310 PETfold_pre2.0(20): 0.193 Sensitivity RNASampler(seed): 0.242 PETfold_pre2.0(20): 0.152 Positive Predictive Value RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.471 TurboFold(seed): 0.403 Sensitivity RNASampler(seed): 0.341 TurboFold(seed): 0.349 Positive Predictive Value RNASampler(seed): 0.657 TurboFold(seed): 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.558 RNASampler(seed): 0.556 Sensitivity PPfold(20): 0.422 RNASampler(seed): 0.404 Positive Predictive Value PPfold(20): 0.742 RNASampler(seed): 0.772 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 Mastr(seed): 0.000 Sensitivity RNASampler(seed): 0.409 Mastr(seed): 0.000 Positive Predictive Value RNASampler(seed): 0.734 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
PPfold(20)	8 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.665 MXScarna(seed): 0.640 Sensitivity PPfold(20): 0.519 MXScarna(seed): 0.511 Positive Predictive Value PPfold(20): 0.859 MXScarna(seed): 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.691 PPfold(20): 0.665 Sensitivity CentroidAlifold(20): 0.515 PPfold(20): 0.519 Positive Predictive Value CentroidAlifold(20): 0.933 PPfold(20): 0.859 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.665 RNAalifold(20): 0.627 Sensitivity PPfold(20): 0.519 RNAalifold(20): 0.481 Positive Predictive Value PPfold(20): 0.859 RNAalifold(20): 0.823 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.665 RNASampler(20): 0.637 Sensitivity PPfold(20): 0.519 RNASampler(20): 0.478 Positive Predictive Value PPfold(20): 0.859 RNASampler(20): 0.854 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.665 CentroidFold: 0.575 Sensitivity PPfold(20): 0.519 CentroidFold: 0.470 Positive Predictive Value PPfold(20): 0.859 CentroidFold: 0.709 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.665 MXScarna(20): 0.586 Sensitivity PPfold(20): 0.519 MXScarna(20): 0.474 Positive Predictive Value PPfold(20): 0.859 MXScarna(20): 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.665 CentroidAlifold(seed): 0.637 Sensitivity PPfold(20): 0.519 CentroidAlifold(seed): 0.415 Positive Predictive Value PPfold(20): 0.859 CentroidAlifold(seed): 0.982 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.665 Contrafold: 0.561 Sensitivity PPfold(20): 0.519 Contrafold: 0.478 Positive Predictive Value PPfold(20): 0.859 Contrafold: 0.665 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.665 Sfold: 0.579 Sensitivity PPfold(20): 0.519 Sfold: 0.467 Positive Predictive Value PPfold(20): 0.859 Sfold: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.665 MaxExpect: 0.543 Sensitivity PPfold(20): 0.519 MaxExpect: 0.463 Positive Predictive Value PPfold(20): 0.859 MaxExpect: 0.644 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.665 IPknot: 0.571 Sensitivity PPfold(20): 0.519 IPknot: 0.463 Positive Predictive Value PPfold(20): 0.859 IPknot: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.665 CentroidHomfold‑LAST: 0.631 Sensitivity PPfold(20): 0.519 CentroidHomfold‑LAST: 0.496 Positive Predictive Value PPfold(20): 0.859 CentroidHomfold‑LAST: 0.807 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.665 HotKnots: 0.609 Sensitivity PPfold(20): 0.519 HotKnots: 0.526 Positive Predictive Value PPfold(20): 0.859 HotKnots: 0.710 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.665 Carnac(20): 0.560 Sensitivity PPfold(20): 0.519 Carnac(20): 0.367 Positive Predictive Value PPfold(20): 0.859 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.616 ContextFold: 0.579 Sensitivity PPfold(20): 0.473 ContextFold: 0.443 Positive Predictive Value PPfold(20): 0.806 ContextFold: 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.665 ProbKnot: 0.542 Sensitivity PPfold(20): 0.519 ProbKnot: 0.481 Positive Predictive Value PPfold(20): 0.859 ProbKnot: 0.616 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.665 Murlet(20): 0.581 Sensitivity PPfold(20): 0.519 Murlet(20): 0.433 Positive Predictive Value PPfold(20): 0.859 Murlet(20): 0.785 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.665 UNAFold: 0.556 Sensitivity PPfold(20): 0.519 UNAFold: 0.474 Positive Predictive Value PPfold(20): 0.859 UNAFold: 0.660 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.665 Fold: 0.510 Sensitivity PPfold(20): 0.519 Fold: 0.441 Positive Predictive Value PPfold(20): 0.859 Fold: 0.598 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.665 RNAfold: 0.555 Sensitivity PPfold(20): 0.519 RNAfold: 0.474 Positive Predictive Value PPfold(20): 0.859 RNAfold: 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.665 PknotsRG: 0.600 Sensitivity PPfold(20): 0.519 PknotsRG: 0.522 Positive Predictive Value PPfold(20): 0.859 PknotsRG: 0.695 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.710 Cylofold: 0.653 Sensitivity PPfold(20): 0.552 Cylofold: 0.536 Positive Predictive Value PPfold(20): 0.918 Cylofold: 0.803 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.603 RNAalifold(seed): 0.591 Sensitivity PPfold(20): 0.455 RNAalifold(seed): 0.381 Positive Predictive Value PPfold(20): 0.804 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.665 RNAshapes: 0.555 Sensitivity PPfold(20): 0.519 RNAshapes: 0.470 Positive Predictive Value PPfold(20): 0.859 RNAshapes: 0.661 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.496 Afold: 0.461 Sensitivity PPfold(20): 0.360 Afold: 0.419 Positive Predictive Value PPfold(20): 0.689 Afold: 0.514 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.665 McQFold: 0.526 Sensitivity PPfold(20): 0.519 McQFold: 0.452 Positive Predictive Value PPfold(20): 0.859 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.665 Pknots: 0.505 Sensitivity PPfold(20): 0.519 Pknots: 0.441 Positive Predictive Value PPfold(20): 0.859 Pknots: 0.586 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.665 RNAsubopt: 0.551 Sensitivity PPfold(20): 0.519 RNAsubopt: 0.474 Positive Predictive Value PPfold(20): 0.859 RNAsubopt: 0.646 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.665 RSpredict(20): 0.489 Sensitivity PPfold(20): 0.519 RSpredict(20): 0.367 Positive Predictive Value PPfold(20): 0.859 RSpredict(20): 0.660 Number of pairs reference - predicted secondary structure: 8 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	8 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.665 Vsfold4: 0.437 Sensitivity PPfold(20): 0.519 Vsfold4: 0.356 Positive Predictive Value PPfold(20): 0.859 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.665 Mastr(20): 0.567 Sensitivity PPfold(20): 0.519 Mastr(20): 0.389 Positive Predictive Value PPfold(20): 0.859 Mastr(20): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.616 RNASLOpt: 0.467 Sensitivity PPfold(20): 0.473 RNASLOpt: 0.383 Positive Predictive Value PPfold(20): 0.806 RNASLOpt: 0.577 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.603 Murlet(seed): 0.520 Sensitivity PPfold(20): 0.455 Murlet(seed): 0.296 Positive Predictive Value PPfold(20): 0.804 Murlet(seed): 0.918 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.665 Vsfold5: 0.421 Sensitivity PPfold(20): 0.519 Vsfold5: 0.363 Positive Predictive Value PPfold(20): 0.859 Vsfold5: 0.497 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.665 RNAwolf: 0.364 Sensitivity PPfold(20): 0.519 RNAwolf: 0.333 Positive Predictive Value PPfold(20): 0.859 RNAwolf: 0.407 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.710 RDfolder: 0.407 Sensitivity PPfold(20): 0.552 RDfolder: 0.295 Positive Predictive Value PPfold(20): 0.918 RDfolder: 0.574 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.651 MCFold: 0.459 Sensitivity PPfold(20): 0.504 MCFold: 0.474 Positive Predictive Value PPfold(20): 0.846 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.665 RSpredict(seed): 0.267 Sensitivity PPfold(20): 0.519 RSpredict(seed): 0.111 Positive Predictive Value PPfold(20): 0.859 RSpredict(seed): 0.652 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.665 PPfold(seed): 0.026 Sensitivity PPfold(20): 0.519 PPfold(seed): 0.004 Positive Predictive Value PPfold(20): 0.859 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.642 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.494 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.839 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.622 NanoFolder: 0.316 Sensitivity PPfold(20): 0.486 NanoFolder: 0.324 Positive Predictive Value PPfold(20): 0.800 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	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	3 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.714 Multilign(seed): 0.631 Sensitivity PPfold(20): 0.559 Multilign(seed): 0.492 Positive Predictive Value PPfold(20): 0.917 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.665 Multilign(20): 0.540 Sensitivity PPfold(20): 0.519 Multilign(20): 0.456 Positive Predictive Value PPfold(20): 0.859 Multilign(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.678 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(seed): 0.557 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.830 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.665 TurboFold(20): 0.594 Sensitivity PPfold(20): 0.519 TurboFold(20): 0.470 Positive Predictive Value PPfold(20): 0.859 TurboFold(20): 0.756 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(20): N/A Sensitivity PPfold(20): N/A CMfinder(20): N/A Positive Predictive Value PPfold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 PPfold(20): 0.616 Sensitivity PETfold_pre2.0(20): 0.497 PPfold(20): 0.473 Positive Predictive Value PETfold_pre2.0(20): 0.790 PPfold(20): 0.806 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.642 TurboFold(seed): 0.564 Sensitivity PPfold(20): 0.494 TurboFold(seed): 0.457 Positive Predictive Value PPfold(20): 0.839 TurboFold(seed): 0.703 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	3 PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.558 RNASampler(seed): 0.556 Sensitivity PPfold(20): 0.422 RNASampler(seed): 0.404 Positive Predictive Value PPfold(20): 0.742 RNASampler(seed): 0.772 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.665 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.519 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.859 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Mastr(seed)	34 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.650 Mastr(seed): 0.000 Sensitivity MXScarna(seed): 0.533 Mastr(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.796 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.695 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.540 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.897 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	25 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.659 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.510 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.854 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.491 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.839 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	33 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.592 Mastr(seed): 0.000 Sensitivity CentroidFold: 0.510 Mastr(seed): 0.000 Positive Predictive Value CentroidFold: 0.690 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.621 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	33 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.590 Mastr(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.377 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.925 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	35 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.555 Mastr(seed): 0.000 Sensitivity Contrafold: 0.497 Mastr(seed): 0.000 Positive Predictive Value Contrafold: 0.623 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.568 Mastr(seed): 0.000 Sensitivity Sfold: 0.479 Mastr(seed): 0.000 Positive Predictive Value Sfold: 0.676 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.569 Mastr(seed): 0.000 Sensitivity MaxExpect: 0.504 Mastr(seed): 0.000 Positive Predictive Value MaxExpect: 0.646 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.590 Mastr(seed): 0.000 Sensitivity IPknot: 0.471 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.747 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	11 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.615 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.479 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.795 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.9460272886e-09	35 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.558 Mastr(seed): 0.000 Sensitivity HotKnots: 0.503 Mastr(seed): 0.000 Positive Predictive Value HotKnots: 0.623 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.601 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.397 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.914 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	8 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.616 Mastr(seed): 0.000 Sensitivity ContextFold: 0.476 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.801 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	21 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.553 Mastr(seed): 0.000 Sensitivity ProbKnot: 0.511 Mastr(seed): 0.000 Positive Predictive Value ProbKnot: 0.603 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	25 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.592 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.437 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.807 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.98172311752e-08	35 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.555 Mastr(seed): 0.000 Sensitivity UNAFold: 0.493 Mastr(seed): 0.000 Positive Predictive Value UNAFold: 0.628 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.560 Mastr(seed): 0.000 Sensitivity Fold: 0.504 Mastr(seed): 0.000 Positive Predictive Value Fold: 0.627 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	35 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.559 Mastr(seed): 0.000 Sensitivity RNAfold: 0.501 Mastr(seed): 0.000 Positive Predictive Value RNAfold: 0.629 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.568 Mastr(seed): 0.000 Sensitivity PknotsRG: 0.511 Mastr(seed): 0.000 Positive Predictive Value PknotsRG: 0.636 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	16 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.659 Mastr(seed): 0.000 Sensitivity Cylofold: 0.554 Mastr(seed): 0.000 Positive Predictive Value Cylofold: 0.789 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.41358941668e-08	19 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.539 Mastr(seed): 0.000 Sensitivity RNAalifold(seed): 0.336 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.866 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	35 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.533 Mastr(seed): 0.000 Sensitivity RNAshapes: 0.472 Mastr(seed): 0.000 Positive Predictive Value RNAshapes: 0.606 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.499 Mastr(seed): 0.000 Sensitivity Afold: 0.460 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.546 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	35 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.520 Mastr(seed): 0.000 Sensitivity McQFold: 0.455 Mastr(seed): 0.000 Positive Predictive Value McQFold: 0.599 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.562 Mastr(seed): 0.000 Sensitivity Pknots: 0.504 Mastr(seed): 0.000 Positive Predictive Value Pknots: 0.632 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	35 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.519 Mastr(seed): 0.000 Sensitivity RNAsubopt: 0.470 Mastr(seed): 0.000 Positive Predictive Value RNAsubopt: 0.578 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.559 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.446 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.705 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-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	35 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.486 Mastr(seed): 0.000 Sensitivity Vsfold4: 0.411 Mastr(seed): 0.000 Positive Predictive Value Vsfold4: 0.580 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.523 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.348 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.790 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.374 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.609 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	16 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.475 Mastr(seed): 0.000 Sensitivity Murlet(seed): 0.270 Mastr(seed): 0.000 Positive Predictive Value Murlet(seed): 0.841 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.50323628132e-08	35 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.447 Mastr(seed): 0.000 Sensitivity Vsfold5: 0.381 Mastr(seed): 0.000 Positive Predictive Value Vsfold5: 0.530 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.414 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.375 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.467 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-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: 5.1503931209e-08	22 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.509 Mastr(seed): 0.000 Sensitivity RDfolder: 0.411 Mastr(seed): 0.000 Positive Predictive Value RDfolder: 0.640 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.448 Mastr(seed): 0.000 Sensitivity MCFold: 0.472 Mastr(seed): 0.000 Positive Predictive Value MCFold: 0.433 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	34 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.204 Mastr(seed): 0.000 Sensitivity RSpredict(seed): 0.088 Mastr(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.477 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.102 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.020 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.1568170475e-08	20 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.139 Mastr(seed): 0.000 Sensitivity Carnac(seed): 0.019 Mastr(seed): 0.000 Positive Predictive Value Carnac(seed): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	7 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.346 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.353 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.349 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	4 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.538 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.420 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.699 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.540 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.456 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.647 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.680 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.551 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.594 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.470 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.756 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Mastr(seed) vs CMfinder(20) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(20): N/A Sensitivity Mastr(seed): N/A CMfinder(20): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.625 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.497 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.790 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.517 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.422 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.642 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.546 Mastr(seed): 0.000 Sensitivity RNASampler(seed): 0.409 Mastr(seed): 0.000 Positive Predictive Value RNASampler(seed): 0.734 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.665 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.519 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.859 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0

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