CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Pseudoknotted RNAs
standard base pair definition

	Only pseudoknotted RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. Standard base pair definition is used - it corresponds to the Leontis and Westhof classification i.e. the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry are considered as the secondary structure. 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: standard
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 30000
Number of RNA sequences: 31
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	CentroidAlifold(20)	yes	2009-07-01	33	0	0	20	15	15
2	CentroidAlifold(seed)	yes	2009-07-01	33	1	0	19	19	19
3	RNAalifold(20)	no	2009-02-18	31	2	0	20	15	15
4	MXScarna(seed)	no	2009-06-15	31	3	0	19	19	19
5	CentroidFold	yes	2009-08-01	30	5	0	18	27	27
6	RNASampler(20)	no	2009-02-18	29	4	0	20	15	15
7	MXScarna(20)	no	2009-02-18	26	6	1	20	15	15
8	Contrafold	yes	2009-02-18	26	9	0	18	31	31
9	Sfold	no	2009-02-18	24	9	2	18	31	31
10	MaxExpect	yes	2009-10-15	24	10	1	18	25	24
11	HotKnots	no	2009-02-18	21	12	2	18	31	28
12	RNAalifold(seed)	no	2009-02-18	20	10	3	20	19	16
13	Murlet(20)	yes	2009-02-18	19	9	5	20	15	15
14	UNAFold	no	2009-02-18	19	14	2	18	31	31
15	Carnac(20)	no	2009-02-18	17	11	5	20	15	15
16	McQFold	yes	2009-02-18	17	17	1	18	31	31
17	RNAshapes	no	2009-02-18	16	17	2	18	31	28
18	RNAfold	no	2009-02-18	16	18	1	18	31	31
19	PknotsRG	no	2009-02-18	15	15	5	18	31	31
20	Pknots	no	2009-02-18	15	17	3	18	31	26
21	Afold	no	2009-02-18	13	16	3	21	31	24
22	ProbKnot	yes	2010-08-10	13	19	1	20	16	16
23	RNAsubopt	no	2009-02-18	10	22	3	18	31	28
24	Fold	no	2010-03-15	9	22	2	20	17	17
25	RSpredict(20)	no	2009-06-03	9	23	1	20	15	15
26	Vsfold4	no	2009-02-18	8	26	1	18	31	28
27	Murlet(seed)	yes	2009-02-18	6	24	2	21	19	14
28	Alterna	no	2009-02-18	5	12	4	32	31	17
29	Mastr(20)	yes	2009-02-18	5	26	2	20	15	15
30	Vsfold5	no	2009-02-18	5	29	1	18	31	28
31	RDfolder	no	2009-02-18	4	27	1	21	31	20
32	MCFold	yes	2009-02-18	3	30	2	18	31	22
33	RSpredict(seed)	no	2009-06-03	2	32	0	19	19	19
34	Carnac(seed)	no	2009-02-18	1	31	0	21	19	14
35	Mastr(seed)	yes	2009-02-18	0	34	0	19	19	19
N/A	Cylofold	no	2010-06-08	12	5	0	36	17	13
N/A	RNASampler(seed)	no	2009-02-18	0	0	0	53	19	7
N/A	RNAwolf	yes	2011-07-01	0	0	0	53	9	9
N/A	CentroidHomfold‑LAST	yes	2011-05-11	0	0	0	53	9	9
N/A	IPknot	yes	2011-07-01	0	0	0	53	9	9
N/A	CRWrnafold	yes	2011-08-23	0	0	0	53	8	8
N/A	TurboFold(seed)	no	2011-04-20	0	0	0	53	7	7
N/A	PPfold(seed)	yes	2011-04-18	0	0	0	53	7	7
N/A	RNASLOpt	no	2011-11-01	0	0	0	53	7	7
N/A	ContextFold	yes	2011-11-15	0	0	0	53	7	7
N/A	Multilign(seed)	no	2011-03-01	0	0	0	53	7	4
N/A	Multilign(20)	no	2011-03-01	0	0	0	53	6	6
N/A	PPfold(20)	yes	2011-04-18	0	0	0	53	6	6
N/A	TurboFold(20)	no	2011-04-20	0	0	0	53	6	6
N/A	NanoFolder	yes	2011-11-17	0	0	0	53	6	5
N/A	PETfold_pre2.0(seed)	no	2011-11-03	0	0	0	53	5	5
N/A	PETfold_pre2.0(20)	no	2011-11-03	0	0	0	53	4	4
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.


CentroidAlifold(20)		+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 CentroidAlifold(seed): 0.761 Sensitivity CentroidAlifold(20): 0.694 CentroidAlifold(seed): 0.623 Positive Predictive Value CentroidAlifold(20): 0.932 CentroidAlifold(seed): 0.934 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAalifold(20): 0.753 Sensitivity CentroidAlifold(20): 0.694 RNAalifold(20): 0.656 Positive Predictive Value CentroidAlifold(20): 0.932 RNAalifold(20): 0.869 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 MXScarna(seed): 0.751 Sensitivity CentroidAlifold(20): 0.694 MXScarna(seed): 0.692 Positive Predictive Value CentroidAlifold(20): 0.932 MXScarna(seed): 0.820 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 CentroidFold: 0.716 Sensitivity CentroidAlifold(20): 0.694 CentroidFold: 0.687 Positive Predictive Value CentroidAlifold(20): 0.932 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNASampler(20): 0.732 Sensitivity CentroidAlifold(20): 0.694 RNASampler(20): 0.639 Positive Predictive Value CentroidAlifold(20): 0.932 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.84361416392e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 MXScarna(20): 0.703 Sensitivity CentroidAlifold(20): 0.694 MXScarna(20): 0.659 Positive Predictive Value CentroidAlifold(20): 0.932 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 8.09700314043e-09	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Contrafold: 0.650 Sensitivity CentroidAlifold(20): 0.694 Contrafold: 0.652 Positive Predictive Value CentroidAlifold(20): 0.932 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Sfold: 0.665 Sensitivity CentroidAlifold(20): 0.694 Sfold: 0.628 Positive Predictive Value CentroidAlifold(20): 0.932 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.803 MaxExpect: 0.674 Sensitivity CentroidAlifold(20): 0.694 MaxExpect: 0.670 Positive Predictive Value CentroidAlifold(20): 0.932 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.803 HotKnots: 0.640 Sensitivity CentroidAlifold(20): 0.694 HotKnots: 0.663 Positive Predictive Value CentroidAlifold(20): 0.932 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.783 RNAalifold(seed): 0.685 Sensitivity CentroidAlifold(20): 0.667 RNAalifold(seed): 0.515 Positive Predictive Value CentroidAlifold(20): 0.923 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Murlet(20): 0.666 Sensitivity CentroidAlifold(20): 0.694 Murlet(20): 0.548 Positive Predictive Value CentroidAlifold(20): 0.932 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 UNAFold: 0.662 Sensitivity CentroidAlifold(20): 0.694 UNAFold: 0.663 Positive Predictive Value CentroidAlifold(20): 0.932 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Carnac(20): 0.662 Sensitivity CentroidAlifold(20): 0.694 Carnac(20): 0.469 Positive Predictive Value CentroidAlifold(20): 0.932 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 McQFold: 0.644 Sensitivity CentroidAlifold(20): 0.694 McQFold: 0.643 Positive Predictive Value CentroidAlifold(20): 0.932 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAshapes: 0.637 Sensitivity CentroidAlifold(20): 0.694 RNAshapes: 0.637 Positive Predictive Value CentroidAlifold(20): 0.932 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAfold: 0.643 Sensitivity CentroidAlifold(20): 0.694 RNAfold: 0.656 Positive Predictive Value CentroidAlifold(20): 0.932 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.803 PknotsRG: 0.664 Sensitivity CentroidAlifold(20): 0.694 PknotsRG: 0.685 Positive Predictive Value CentroidAlifold(20): 0.932 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.834 Pknots: 0.670 Sensitivity CentroidAlifold(20): 0.741 Pknots: 0.691 Positive Predictive Value CentroidAlifold(20): 0.943 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.762 Afold: 0.565 Sensitivity CentroidAlifold(20): 0.640 Afold: 0.591 Positive Predictive Value CentroidAlifold(20): 0.911 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.45489855545e-09	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.758 ProbKnot: 0.630 Sensitivity CentroidAlifold(20): 0.631 ProbKnot: 0.664 Positive Predictive Value CentroidAlifold(20): 0.914 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	? CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.836 Cylofold: 0.731 Sensitivity CentroidAlifold(20): 0.728 Cylofold: 0.712 Positive Predictive Value CentroidAlifold(20): 0.964 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAsubopt: 0.620 Sensitivity CentroidAlifold(20): 0.694 RNAsubopt: 0.632 Positive Predictive Value CentroidAlifold(20): 0.932 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.758 Fold: 0.621 Sensitivity CentroidAlifold(20): 0.631 Fold: 0.637 Positive Predictive Value CentroidAlifold(20): 0.914 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.09700314043e-09	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RSpredict(20): 0.624 Sensitivity CentroidAlifold(20): 0.694 RSpredict(20): 0.559 Positive Predictive Value CentroidAlifold(20): 0.932 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Vsfold4: 0.545 Sensitivity CentroidAlifold(20): 0.694 Vsfold4: 0.526 Positive Predictive Value CentroidAlifold(20): 0.932 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.814 Murlet(seed): 0.607 Sensitivity CentroidAlifold(20): 0.713 Murlet(seed): 0.407 Positive Predictive Value CentroidAlifold(20): 0.934 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.25253056981e-08	? CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.900 Alterna: 0.593 Sensitivity CentroidAlifold(20): 0.836 Alterna: 0.596 Positive Predictive Value CentroidAlifold(20): 0.973 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Mastr(20): 0.506 Sensitivity CentroidAlifold(20): 0.694 Mastr(20): 0.337 Positive Predictive Value CentroidAlifold(20): 0.932 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Vsfold5: 0.495 Sensitivity CentroidAlifold(20): 0.694 Vsfold5: 0.480 Positive Predictive Value CentroidAlifold(20): 0.932 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.878 RDfolder: 0.613 Sensitivity CentroidAlifold(20): 0.791 RDfolder: 0.552 Positive Predictive Value CentroidAlifold(20): 0.978 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.836 MCFold: 0.506 Sensitivity CentroidAlifold(20): 0.747 MCFold: 0.546 Positive Predictive Value CentroidAlifold(20): 0.940 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RSpredict(seed): 0.350 Sensitivity CentroidAlifold(20): 0.694 RSpredict(seed): 0.181 Positive Predictive Value CentroidAlifold(20): 0.932 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.814 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.713 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.934 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.70887622364e-08	? CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.681 NanoFolder: 0.285 Sensitivity CentroidAlifold(20): 0.547 NanoFolder: 0.359 Positive Predictive Value CentroidAlifold(20): 0.854 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.764 CentroidHomfold‑LAST: 0.726 Sensitivity CentroidAlifold(20): 0.636 CentroidHomfold‑LAST: 0.644 Positive Predictive Value CentroidAlifold(20): 0.923 CentroidHomfold‑LAST: 0.825 Number of pairs reference - predicted secondary structure: 6 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): 0.867 Multilign(seed): 0.755 Sensitivity CentroidAlifold(20): 0.768 Multilign(seed): 0.707 Positive Predictive Value CentroidAlifold(20): 0.984 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): 0.764 Multilign(20): 0.581 Sensitivity CentroidAlifold(20): 0.636 Multilign(20): 0.576 Positive Predictive Value CentroidAlifold(20): 0.923 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 CentroidAlifold(20): 0.698 Sensitivity PETfold_pre2.0(seed): 0.684 CentroidAlifold(20): 0.557 Positive Predictive Value PETfold_pre2.0(seed): 0.831 CentroidAlifold(20): 0.880 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 TurboFold(20): 0.653 Sensitivity CentroidAlifold(20): 0.636 TurboFold(20): 0.606 Positive Predictive Value CentroidAlifold(20): 0.923 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.764 RNAwolf: 0.442 Sensitivity CentroidAlifold(20): 0.636 RNAwolf: 0.439 Positive Predictive Value CentroidAlifold(20): 0.923 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.764 IPknot: 0.623 Sensitivity CentroidAlifold(20): 0.636 IPknot: 0.591 Positive Predictive Value CentroidAlifold(20): 0.923 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 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): 0.698 PETfold_pre2.0(20): 0.619 Sensitivity CentroidAlifold(20): 0.557 PETfold_pre2.0(20): 0.570 Positive Predictive Value CentroidAlifold(20): 0.880 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 PPfold(seed): 0.036 Sensitivity CentroidAlifold(20): 0.636 PPfold(seed): 0.008 Positive Predictive Value CentroidAlifold(20): 0.923 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.698 ContextFold: 0.567 Sensitivity CentroidAlifold(20): 0.557 ContextFold: 0.506 Positive Predictive Value CentroidAlifold(20): 0.880 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 TurboFold(seed): 0.636 Sensitivity CentroidAlifold(20): 0.636 TurboFold(seed): 0.606 Positive Predictive Value CentroidAlifold(20): 0.923 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.741 CRWrnafold: 0.592 Sensitivity CentroidAlifold(20): 0.611 CRWrnafold: 0.611 Positive Predictive Value CentroidAlifold(20): 0.904 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.741 RNASampler(seed): 0.696 Sensitivity CentroidAlifold(20): 0.627 RNASampler(seed): 0.627 Positive Predictive Value CentroidAlifold(20): 0.881 RNASampler(seed): 0.779 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.698 RNASLOpt: 0.459 Sensitivity CentroidAlifold(20): 0.557 RNASLOpt: 0.456 Positive Predictive Value CentroidAlifold(20): 0.880 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 PPfold(20): 0.715 Sensitivity CentroidAlifold(20): 0.636 PPfold(20): 0.644 Positive Predictive Value CentroidAlifold(20): 0.923 PPfold(20): 0.802 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.932 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08
CentroidAlifold(seed)	15 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 CentroidAlifold(seed): 0.761 Sensitivity CentroidAlifold(20): 0.694 CentroidAlifold(seed): 0.623 Positive Predictive Value CentroidAlifold(20): 0.932 CentroidAlifold(seed): 0.934 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08		+ CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 RNAalifold(20): 0.753 Sensitivity CentroidAlifold(seed): 0.623 RNAalifold(20): 0.656 Positive Predictive Value CentroidAlifold(seed): 0.934 RNAalifold(20): 0.869 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.72942716385e-07	+ CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 MXScarna(seed): 0.711 Sensitivity CentroidAlifold(seed): 0.598 MXScarna(seed): 0.663 Positive Predictive Value CentroidAlifold(seed): 0.894 MXScarna(seed): 0.768 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 CentroidFold: 0.675 Sensitivity CentroidAlifold(seed): 0.598 CentroidFold: 0.675 Positive Predictive Value CentroidAlifold(seed): 0.894 CentroidFold: 0.681 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 RNASampler(20): 0.732 Sensitivity CentroidAlifold(seed): 0.623 RNASampler(20): 0.639 Positive Predictive Value CentroidAlifold(seed): 0.934 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 MXScarna(20): 0.703 Sensitivity CentroidAlifold(seed): 0.623 MXScarna(20): 0.659 Positive Predictive Value CentroidAlifold(seed): 0.934 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Contrafold: 0.623 Sensitivity CentroidAlifold(seed): 0.598 Contrafold: 0.647 Positive Predictive Value CentroidAlifold(seed): 0.894 Contrafold: 0.606 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Sfold: 0.632 Sensitivity CentroidAlifold(seed): 0.598 Sfold: 0.623 Positive Predictive Value CentroidAlifold(seed): 0.894 Sfold: 0.646 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.723 MaxExpect: 0.591 Sensitivity CentroidAlifold(seed): 0.595 MaxExpect: 0.614 Positive Predictive Value CentroidAlifold(seed): 0.884 MaxExpect: 0.575 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 HotKnots: 0.616 Sensitivity CentroidAlifold(seed): 0.598 HotKnots: 0.657 Positive Predictive Value CentroidAlifold(seed): 0.894 HotKnots: 0.582 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.73174208038e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.753 RNAalifold(seed): 0.634 Sensitivity CentroidAlifold(seed): 0.640 RNAalifold(seed): 0.479 Positive Predictive Value CentroidAlifold(seed): 0.889 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 Murlet(20): 0.666 Sensitivity CentroidAlifold(seed): 0.623 Murlet(20): 0.548 Positive Predictive Value CentroidAlifold(seed): 0.934 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 UNAFold: 0.613 Sensitivity CentroidAlifold(seed): 0.598 UNAFold: 0.638 Positive Predictive Value CentroidAlifold(seed): 0.894 UNAFold: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 Carnac(20): 0.662 Sensitivity CentroidAlifold(seed): 0.623 Carnac(20): 0.469 Positive Predictive Value CentroidAlifold(seed): 0.934 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 McQFold: 0.613 Sensitivity CentroidAlifold(seed): 0.598 McQFold: 0.640 Positive Predictive Value CentroidAlifold(seed): 0.894 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNAshapes: 0.594 Sensitivity CentroidAlifold(seed): 0.598 RNAshapes: 0.617 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAshapes: 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNAfold: 0.618 Sensitivity CentroidAlifold(seed): 0.598 RNAfold: 0.652 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAfold: 0.591 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 PknotsRG: 0.634 Sensitivity CentroidAlifold(seed): 0.598 PknotsRG: 0.675 Positive Predictive Value CentroidAlifold(seed): 0.894 PknotsRG: 0.602 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.787 Pknots: 0.710 Sensitivity CentroidAlifold(seed): 0.641 Pknots: 0.727 Positive Predictive Value CentroidAlifold(seed): 0.972 Pknots: 0.701 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.668 Afold: 0.551 Sensitivity CentroidAlifold(seed): 0.526 Afold: 0.597 Positive Predictive Value CentroidAlifold(seed): 0.851 Afold: 0.514 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 ProbKnot: 0.542 Sensitivity CentroidAlifold(seed): 0.585 ProbKnot: 0.593 Positive Predictive Value CentroidAlifold(seed): 0.862 ProbKnot: 0.501 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.14531876181e-08	? CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 Cylofold: 0.723 Sensitivity CentroidAlifold(seed): 0.673 Cylofold: 0.703 Positive Predictive Value CentroidAlifold(seed): 0.978 Cylofold: 0.751 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNAsubopt: 0.573 Sensitivity CentroidAlifold(seed): 0.598 RNAsubopt: 0.603 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAsubopt: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Fold: 0.532 Sensitivity CentroidAlifold(seed): 0.585 Fold: 0.570 Positive Predictive Value CentroidAlifold(seed): 0.862 Fold: 0.502 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 RSpredict(20): 0.624 Sensitivity CentroidAlifold(seed): 0.623 RSpredict(20): 0.559 Positive Predictive Value CentroidAlifold(seed): 0.934 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Vsfold4: 0.531 Sensitivity CentroidAlifold(seed): 0.598 Vsfold4: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.894 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.826 Murlet(seed): 0.571 Sensitivity CentroidAlifold(seed): 0.707 Murlet(seed): 0.386 Positive Predictive Value CentroidAlifold(seed): 0.970 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.772 Alterna: 0.657 Sensitivity CentroidAlifold(seed): 0.618 Alterna: 0.651 Positive Predictive Value CentroidAlifold(seed): 0.974 Alterna: 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.05690340753e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 Mastr(20): 0.506 Sensitivity CentroidAlifold(seed): 0.623 Mastr(20): 0.337 Positive Predictive Value CentroidAlifold(seed): 0.934 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.66062906821e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Vsfold5: 0.498 Sensitivity CentroidAlifold(seed): 0.598 Vsfold5: 0.496 Positive Predictive Value CentroidAlifold(seed): 0.894 Vsfold5: 0.508 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.780 RDfolder: 0.600 Sensitivity CentroidAlifold(seed): 0.627 RDfolder: 0.543 Positive Predictive Value CentroidAlifold(seed): 0.979 RDfolder: 0.679 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.19192530585e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.778 MCFold: 0.551 Sensitivity CentroidAlifold(seed): 0.628 MCFold: 0.587 Positive Predictive Value CentroidAlifold(seed): 0.970 MCFold: 0.530 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RSpredict(seed): 0.324 Sensitivity CentroidAlifold(seed): 0.598 RSpredict(seed): 0.177 Positive Predictive Value CentroidAlifold(seed): 0.894 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.826 Carnac(seed): 0.104 Sensitivity CentroidAlifold(seed): 0.707 Carnac(seed): 0.011 Positive Predictive Value CentroidAlifold(seed): 0.970 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	? CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.679 NanoFolder: 0.336 Sensitivity CentroidAlifold(seed): 0.476 NanoFolder: 0.415 Positive Predictive Value CentroidAlifold(seed): 0.975 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 CentroidHomfold‑LAST: 0.645 Sensitivity CentroidAlifold(seed): 0.593 CentroidHomfold‑LAST: 0.567 Positive Predictive Value CentroidAlifold(seed): 0.978 CentroidHomfold‑LAST: 0.746 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): 0.797 Multilign(seed): 0.629 Sensitivity CentroidAlifold(seed): 0.650 Multilign(seed): 0.580 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): 0.810 Multilign(20): 0.581 Sensitivity CentroidAlifold(seed): 0.674 Multilign(20): 0.576 Positive Predictive Value CentroidAlifold(seed): 0.978 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CentroidAlifold(seed): 0.686 Sensitivity PETfold_pre2.0(seed): 0.619 CentroidAlifold(seed): 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CentroidAlifold(seed): 0.979 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 TurboFold(20): 0.653 Sensitivity CentroidAlifold(seed): 0.674 TurboFold(20): 0.606 Positive Predictive Value CentroidAlifold(seed): 0.978 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 RNAwolf: 0.451 Sensitivity CentroidAlifold(seed): 0.593 RNAwolf: 0.447 Positive Predictive Value CentroidAlifold(seed): 0.978 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 IPknot: 0.601 Sensitivity CentroidAlifold(seed): 0.593 IPknot: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.978 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 7 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	? CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 PETfold_pre2.0(20): 0.619 Sensitivity CentroidAlifold(seed): 0.595 PETfold_pre2.0(20): 0.570 Positive Predictive Value CentroidAlifold(seed): 0.979 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 PPfold(seed): 0.155 Sensitivity CentroidAlifold(seed): 0.593 PPfold(seed): 0.047 Positive Predictive Value CentroidAlifold(seed): 0.978 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 ContextFold: 0.570 Sensitivity CentroidAlifold(seed): 0.485 ContextFold: 0.515 Positive Predictive Value CentroidAlifold(seed): 0.979 ContextFold: 0.641 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): 0.759 TurboFold(seed): 0.560 Sensitivity CentroidAlifold(seed): 0.593 TurboFold(seed): 0.533 Positive Predictive Value CentroidAlifold(seed): 0.978 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.727 CRWrnafold: 0.513 Sensitivity CentroidAlifold(seed): 0.548 CRWrnafold: 0.524 Positive Predictive Value CentroidAlifold(seed): 0.972 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.783 RNASampler(seed): 0.640 Sensitivity CentroidAlifold(seed): 0.645 RNASampler(seed): 0.554 Positive Predictive Value CentroidAlifold(seed): 0.955 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 RNASLOpt: 0.461 Sensitivity CentroidAlifold(seed): 0.485 RNASLOpt: 0.443 Positive Predictive Value CentroidAlifold(seed): 0.979 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 PPfold(20): 0.715 Sensitivity CentroidAlifold(seed): 0.674 PPfold(20): 0.644 Positive Predictive Value CentroidAlifold(seed): 0.978 PPfold(20): 0.802 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Mastr(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.598 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.894 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08
RNAalifold(20)	15 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAalifold(20): 0.753 Sensitivity CentroidAlifold(20): 0.694 RNAalifold(20): 0.656 Positive Predictive Value CentroidAlifold(20): 0.932 RNAalifold(20): 0.869 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.39551335374e-08	15 CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 RNAalifold(20): 0.753 Sensitivity CentroidAlifold(seed): 0.623 RNAalifold(20): 0.656 Positive Predictive Value CentroidAlifold(seed): 0.934 RNAalifold(20): 0.869 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.72942716385e-07		+ RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.753 MXScarna(seed): 0.751 Sensitivity RNAalifold(20): 0.656 MXScarna(seed): 0.692 Positive Predictive Value RNAalifold(20): 0.869 MXScarna(seed): 0.820 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00088266202036	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.753 CentroidFold: 0.716 Sensitivity RNAalifold(20): 0.656 CentroidFold: 0.687 Positive Predictive Value RNAalifold(20): 0.869 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 RNASampler(20): 0.732 Sensitivity RNAalifold(20): 0.656 RNASampler(20): 0.639 Positive Predictive Value RNAalifold(20): 0.869 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.53919717921e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 MXScarna(20): 0.703 Sensitivity RNAalifold(20): 0.656 MXScarna(20): 0.659 Positive Predictive Value RNAalifold(20): 0.869 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.753 Contrafold: 0.650 Sensitivity RNAalifold(20): 0.656 Contrafold: 0.652 Positive Predictive Value RNAalifold(20): 0.869 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.753 Sfold: 0.665 Sensitivity RNAalifold(20): 0.656 Sfold: 0.628 Positive Predictive Value RNAalifold(20): 0.869 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.753 MaxExpect: 0.674 Sensitivity RNAalifold(20): 0.656 MaxExpect: 0.670 Positive Predictive Value RNAalifold(20): 0.869 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.66062906821e-08	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.753 HotKnots: 0.640 Sensitivity RNAalifold(20): 0.656 HotKnots: 0.663 Positive Predictive Value RNAalifold(20): 0.869 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.728 RNAalifold(seed): 0.685 Sensitivity RNAalifold(20): 0.626 RNAalifold(seed): 0.515 Positive Predictive Value RNAalifold(20): 0.851 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.19192530585e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 Murlet(20): 0.666 Sensitivity RNAalifold(20): 0.656 Murlet(20): 0.548 Positive Predictive Value RNAalifold(20): 0.869 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.753 UNAFold: 0.662 Sensitivity RNAalifold(20): 0.656 UNAFold: 0.663 Positive Predictive Value RNAalifold(20): 0.869 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 Carnac(20): 0.662 Sensitivity RNAalifold(20): 0.656 Carnac(20): 0.469 Positive Predictive Value RNAalifold(20): 0.869 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.753 McQFold: 0.644 Sensitivity RNAalifold(20): 0.656 McQFold: 0.643 Positive Predictive Value RNAalifold(20): 0.869 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.753 RNAshapes: 0.637 Sensitivity RNAalifold(20): 0.656 RNAshapes: 0.637 Positive Predictive Value RNAalifold(20): 0.869 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.753 RNAfold: 0.643 Sensitivity RNAalifold(20): 0.656 RNAfold: 0.656 Positive Predictive Value RNAalifold(20): 0.869 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.753 PknotsRG: 0.664 Sensitivity RNAalifold(20): 0.656 PknotsRG: 0.685 Positive Predictive Value RNAalifold(20): 0.869 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.778 Pknots: 0.670 Sensitivity RNAalifold(20): 0.702 Pknots: 0.691 Positive Predictive Value RNAalifold(20): 0.869 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.694 Afold: 0.565 Sensitivity RNAalifold(20): 0.587 Afold: 0.591 Positive Predictive Value RNAalifold(20): 0.824 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.690 ProbKnot: 0.630 Sensitivity RNAalifold(20): 0.586 ProbKnot: 0.664 Positive Predictive Value RNAalifold(20): 0.817 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.26710183075e-09	? RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.774 Cylofold: 0.731 Sensitivity RNAalifold(20): 0.679 Cylofold: 0.712 Positive Predictive Value RNAalifold(20): 0.887 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.753 RNAsubopt: 0.620 Sensitivity RNAalifold(20): 0.656 RNAsubopt: 0.632 Positive Predictive Value RNAalifold(20): 0.869 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.690 Fold: 0.621 Sensitivity RNAalifold(20): 0.586 Fold: 0.637 Positive Predictive Value RNAalifold(20): 0.817 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1568170475e-08	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 RSpredict(20): 0.624 Sensitivity RNAalifold(20): 0.656 RSpredict(20): 0.559 Positive Predictive Value RNAalifold(20): 0.869 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.753 Vsfold4: 0.545 Sensitivity RNAalifold(20): 0.656 Vsfold4: 0.526 Positive Predictive Value RNAalifold(20): 0.869 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.750 Murlet(seed): 0.607 Sensitivity RNAalifold(20): 0.669 Murlet(seed): 0.407 Positive Predictive Value RNAalifold(20): 0.848 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.87872347734e-08	? RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.891 Alterna: 0.593 Sensitivity RNAalifold(20): 0.836 Alterna: 0.596 Positive Predictive Value RNAalifold(20): 0.953 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 Mastr(20): 0.506 Sensitivity RNAalifold(20): 0.656 Mastr(20): 0.337 Positive Predictive Value RNAalifold(20): 0.869 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.753 Vsfold5: 0.495 Sensitivity RNAalifold(20): 0.656 Vsfold5: 0.480 Positive Predictive Value RNAalifold(20): 0.869 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.850 RDfolder: 0.613 Sensitivity RNAalifold(20): 0.757 RDfolder: 0.552 Positive Predictive Value RNAalifold(20): 0.961 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.776 MCFold: 0.506 Sensitivity RNAalifold(20): 0.717 MCFold: 0.546 Positive Predictive Value RNAalifold(20): 0.847 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.753 RSpredict(seed): 0.350 Sensitivity RNAalifold(20): 0.656 RSpredict(seed): 0.181 Positive Predictive Value RNAalifold(20): 0.869 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.750 Carnac(seed): 0.000 Sensitivity RNAalifold(20): 0.669 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.848 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.91441904741e-08	? RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.545 NanoFolder: 0.285 Sensitivity RNAalifold(20): 0.500 NanoFolder: 0.359 Positive Predictive Value RNAalifold(20): 0.604 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 RNAalifold(20): 0.658 Sensitivity CentroidHomfold‑LAST: 0.644 RNAalifold(20): 0.591 Positive Predictive Value CentroidHomfold‑LAST: 0.825 RNAalifold(20): 0.743 Number of pairs reference - predicted secondary structure: 6 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): 0.834 Multilign(seed): 0.755 Sensitivity RNAalifold(20): 0.768 Multilign(seed): 0.707 Positive Predictive Value RNAalifold(20): 0.913 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): 0.658 Multilign(20): 0.581 Sensitivity RNAalifold(20): 0.591 Multilign(20): 0.576 Positive Predictive Value RNAalifold(20): 0.743 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 RNAalifold(20): 0.532 Sensitivity PETfold_pre2.0(seed): 0.684 RNAalifold(20): 0.456 Positive Predictive Value PETfold_pre2.0(seed): 0.831 RNAalifold(20): 0.632 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.658 TurboFold(20): 0.653 Sensitivity RNAalifold(20): 0.591 TurboFold(20): 0.606 Positive Predictive Value RNAalifold(20): 0.743 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.658 RNAwolf: 0.442 Sensitivity RNAalifold(20): 0.591 RNAwolf: 0.439 Positive Predictive Value RNAalifold(20): 0.743 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.658 IPknot: 0.623 Sensitivity RNAalifold(20): 0.591 IPknot: 0.591 Positive Predictive Value RNAalifold(20): 0.743 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 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): 0.619 RNAalifold(20): 0.532 Sensitivity PETfold_pre2.0(20): 0.570 RNAalifold(20): 0.456 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAalifold(20): 0.632 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.658 PPfold(seed): 0.036 Sensitivity RNAalifold(20): 0.591 PPfold(seed): 0.008 Positive Predictive Value RNAalifold(20): 0.743 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.567 RNAalifold(20): 0.532 Sensitivity ContextFold: 0.506 RNAalifold(20): 0.456 Positive Predictive Value ContextFold: 0.645 RNAalifold(20): 0.632 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.658 TurboFold(seed): 0.636 Sensitivity RNAalifold(20): 0.591 TurboFold(seed): 0.606 Positive Predictive Value RNAalifold(20): 0.743 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.625 CRWrnafold: 0.592 Sensitivity RNAalifold(20): 0.565 CRWrnafold: 0.611 Positive Predictive Value RNAalifold(20): 0.701 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 RNAalifold(20): 0.640 Sensitivity RNASampler(seed): 0.627 RNAalifold(20): 0.619 Positive Predictive Value RNASampler(seed): 0.779 RNAalifold(20): 0.670 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.532 RNASLOpt: 0.459 Sensitivity RNAalifold(20): 0.456 RNASLOpt: 0.456 Positive Predictive Value RNAalifold(20): 0.632 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.715 RNAalifold(20): 0.658 Sensitivity PPfold(20): 0.644 RNAalifold(20): 0.591 Positive Predictive Value PPfold(20): 0.802 RNAalifold(20): 0.743 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.753 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.656 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.869 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-08
MXScarna(seed)	15 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 MXScarna(seed): 0.751 Sensitivity CentroidAlifold(20): 0.694 MXScarna(seed): 0.692 Positive Predictive Value CentroidAlifold(20): 0.932 MXScarna(seed): 0.820 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	19 CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 MXScarna(seed): 0.711 Sensitivity CentroidAlifold(seed): 0.598 MXScarna(seed): 0.663 Positive Predictive Value CentroidAlifold(seed): 0.894 MXScarna(seed): 0.768 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	15 RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.753 MXScarna(seed): 0.751 Sensitivity RNAalifold(20): 0.656 MXScarna(seed): 0.692 Positive Predictive Value RNAalifold(20): 0.869 MXScarna(seed): 0.820 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00088266202036		+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.711 CentroidFold: 0.675 Sensitivity MXScarna(seed): 0.663 CentroidFold: 0.675 Positive Predictive Value MXScarna(seed): 0.768 CentroidFold: 0.681 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 RNASampler(20): 0.732 Sensitivity MXScarna(seed): 0.692 RNASampler(20): 0.639 Positive Predictive Value MXScarna(seed): 0.820 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.40343002478e-05	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 MXScarna(20): 0.703 Sensitivity MXScarna(seed): 0.692 MXScarna(20): 0.659 Positive Predictive Value MXScarna(seed): 0.820 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.40919803867e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.711 Contrafold: 0.623 Sensitivity MXScarna(seed): 0.663 Contrafold: 0.647 Positive Predictive Value MXScarna(seed): 0.768 Contrafold: 0.606 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.711 Sfold: 0.632 Sensitivity MXScarna(seed): 0.663 Sfold: 0.623 Positive Predictive Value MXScarna(seed): 0.768 Sfold: 0.646 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.694 MaxExpect: 0.591 Sensitivity MXScarna(seed): 0.646 MaxExpect: 0.614 Positive Predictive Value MXScarna(seed): 0.749 MaxExpect: 0.575 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.711 HotKnots: 0.616 Sensitivity MXScarna(seed): 0.663 HotKnots: 0.657 Positive Predictive Value MXScarna(seed): 0.768 HotKnots: 0.582 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.681 RNAalifold(seed): 0.634 Sensitivity MXScarna(seed): 0.632 RNAalifold(seed): 0.479 Positive Predictive Value MXScarna(seed): 0.737 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 Murlet(20): 0.666 Sensitivity MXScarna(seed): 0.692 Murlet(20): 0.548 Positive Predictive Value MXScarna(seed): 0.820 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.711 UNAFold: 0.613 Sensitivity MXScarna(seed): 0.663 UNAFold: 0.638 Positive Predictive Value MXScarna(seed): 0.768 UNAFold: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.63594052159e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 Carnac(20): 0.662 Sensitivity MXScarna(seed): 0.692 Carnac(20): 0.469 Positive Predictive Value MXScarna(seed): 0.820 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.13392142882e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.711 McQFold: 0.613 Sensitivity MXScarna(seed): 0.663 McQFold: 0.640 Positive Predictive Value MXScarna(seed): 0.768 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.60448791174e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.711 RNAshapes: 0.594 Sensitivity MXScarna(seed): 0.663 RNAshapes: 0.617 Positive Predictive Value MXScarna(seed): 0.768 RNAshapes: 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.711 RNAfold: 0.618 Sensitivity MXScarna(seed): 0.663 RNAfold: 0.652 Positive Predictive Value MXScarna(seed): 0.768 RNAfold: 0.591 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.711 PknotsRG: 0.634 Sensitivity MXScarna(seed): 0.663 PknotsRG: 0.675 Positive Predictive Value MXScarna(seed): 0.768 PknotsRG: 0.602 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.746 Pknots: 0.710 Sensitivity MXScarna(seed): 0.690 Pknots: 0.727 Positive Predictive Value MXScarna(seed): 0.813 Pknots: 0.701 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.688 Afold: 0.551 Sensitivity MXScarna(seed): 0.627 Afold: 0.597 Positive Predictive Value MXScarna(seed): 0.758 Afold: 0.514 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.650 ProbKnot: 0.542 Sensitivity MXScarna(seed): 0.607 ProbKnot: 0.593 Positive Predictive Value MXScarna(seed): 0.699 ProbKnot: 0.501 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	? Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.723 MXScarna(seed): 0.675 Sensitivity Cylofold: 0.703 MXScarna(seed): 0.629 Positive Predictive Value Cylofold: 0.751 MXScarna(seed): 0.734 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.711 RNAsubopt: 0.573 Sensitivity MXScarna(seed): 0.663 RNAsubopt: 0.603 Positive Predictive Value MXScarna(seed): 0.768 RNAsubopt: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.650 Fold: 0.532 Sensitivity MXScarna(seed): 0.607 Fold: 0.570 Positive Predictive Value MXScarna(seed): 0.699 Fold: 0.502 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.84361416392e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 RSpredict(20): 0.624 Sensitivity MXScarna(seed): 0.692 RSpredict(20): 0.559 Positive Predictive Value MXScarna(seed): 0.820 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.711 Vsfold4: 0.531 Sensitivity MXScarna(seed): 0.663 Vsfold4: 0.530 Positive Predictive Value MXScarna(seed): 0.768 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.709 Murlet(seed): 0.571 Sensitivity MXScarna(seed): 0.652 Murlet(seed): 0.386 Positive Predictive Value MXScarna(seed): 0.778 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.789 Alterna: 0.657 Sensitivity MXScarna(seed): 0.726 Alterna: 0.651 Positive Predictive Value MXScarna(seed): 0.866 Alterna: 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.09700314043e-09	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 Mastr(20): 0.506 Sensitivity MXScarna(seed): 0.692 Mastr(20): 0.337 Positive Predictive Value MXScarna(seed): 0.820 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 9.35568223474e-09	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.711 Vsfold5: 0.498 Sensitivity MXScarna(seed): 0.663 Vsfold5: 0.496 Positive Predictive Value MXScarna(seed): 0.768 Vsfold5: 0.508 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.756 RDfolder: 0.600 Sensitivity MXScarna(seed): 0.690 RDfolder: 0.543 Positive Predictive Value MXScarna(seed): 0.838 RDfolder: 0.679 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.40919803867e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.747 MCFold: 0.551 Sensitivity MXScarna(seed): 0.689 MCFold: 0.587 Positive Predictive Value MXScarna(seed): 0.817 MCFold: 0.530 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.711 RSpredict(seed): 0.324 Sensitivity MXScarna(seed): 0.663 RSpredict(seed): 0.177 Positive Predictive Value MXScarna(seed): 0.768 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.709 Carnac(seed): 0.104 Sensitivity MXScarna(seed): 0.652 Carnac(seed): 0.011 Positive Predictive Value MXScarna(seed): 0.778 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	? MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.468 NanoFolder: 0.336 Sensitivity MXScarna(seed): 0.415 NanoFolder: 0.415 Positive Predictive Value MXScarna(seed): 0.540 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 MXScarna(seed): 0.593 Sensitivity CentroidHomfold‑LAST: 0.567 MXScarna(seed): 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.746 MXScarna(seed): 0.672 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): 0.643 Multilign(seed): 0.629 Sensitivity MXScarna(seed): 0.600 Multilign(seed): 0.580 Positive Predictive Value MXScarna(seed): 0.706 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): 0.663 Multilign(20): 0.581 Sensitivity MXScarna(seed): 0.606 Multilign(20): 0.576 Positive Predictive Value MXScarna(seed): 0.734 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 MXScarna(seed): 0.476 Sensitivity PETfold_pre2.0(seed): 0.619 MXScarna(seed): 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 MXScarna(seed): 0.563 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.663 TurboFold(20): 0.653 Sensitivity MXScarna(seed): 0.606 TurboFold(20): 0.606 Positive Predictive Value MXScarna(seed): 0.734 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.593 RNAwolf: 0.451 Sensitivity MXScarna(seed): 0.533 RNAwolf: 0.447 Positive Predictive Value MXScarna(seed): 0.672 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.601 MXScarna(seed): 0.593 Sensitivity IPknot: 0.560 MXScarna(seed): 0.533 Positive Predictive Value IPknot: 0.656 MXScarna(seed): 0.672 Number of pairs reference - predicted secondary structure: 7 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): 0.619 MXScarna(seed): 0.572 Sensitivity PETfold_pre2.0(20): 0.570 MXScarna(seed): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 MXScarna(seed): 0.656 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.593 PPfold(seed): 0.155 Sensitivity MXScarna(seed): 0.533 PPfold(seed): 0.047 Positive Predictive Value MXScarna(seed): 0.672 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.570 MXScarna(seed): 0.476 Sensitivity ContextFold: 0.515 MXScarna(seed): 0.412 Positive Predictive Value ContextFold: 0.641 MXScarna(seed): 0.563 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): 0.593 TurboFold(seed): 0.560 Sensitivity MXScarna(seed): 0.533 TurboFold(seed): 0.533 Positive Predictive Value MXScarna(seed): 0.672 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.544 CRWrnafold: 0.513 Sensitivity MXScarna(seed): 0.492 CRWrnafold: 0.524 Positive Predictive Value MXScarna(seed): 0.614 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 MXScarna(seed): 0.636 Sensitivity RNASampler(seed): 0.554 MXScarna(seed): 0.572 Positive Predictive Value RNASampler(seed): 0.748 MXScarna(seed): 0.714 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.476 RNASLOpt: 0.461 Sensitivity MXScarna(seed): 0.412 RNASLOpt: 0.443 Positive Predictive Value MXScarna(seed): 0.563 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.715 MXScarna(seed): 0.663 Sensitivity PPfold(20): 0.644 MXScarna(seed): 0.606 Positive Predictive Value PPfold(20): 0.802 MXScarna(seed): 0.734 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.711 Mastr(seed): 0.000 Sensitivity MXScarna(seed): 0.663 Mastr(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.768 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08
CentroidFold	15 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 CentroidFold: 0.716 Sensitivity CentroidAlifold(20): 0.694 CentroidFold: 0.687 Positive Predictive Value CentroidAlifold(20): 0.932 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.52299983238e-08	19 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 CentroidFold: 0.675 Sensitivity CentroidAlifold(seed): 0.598 CentroidFold: 0.675 Positive Predictive Value CentroidAlifold(seed): 0.894 CentroidFold: 0.681 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	15 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.753 CentroidFold: 0.716 Sensitivity RNAalifold(20): 0.656 CentroidFold: 0.687 Positive Predictive Value RNAalifold(20): 0.869 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	19 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.711 CentroidFold: 0.675 Sensitivity MXScarna(seed): 0.663 CentroidFold: 0.675 Positive Predictive Value MXScarna(seed): 0.768 CentroidFold: 0.681 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08		- RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.732 CentroidFold: 0.716 Sensitivity RNASampler(20): 0.639 CentroidFold: 0.687 Positive Predictive Value RNASampler(20): 0.843 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.98630365413e-08	+ CentroidFold vs MXScarna(20) Matthews Correlation Coefficient CentroidFold: 0.716 MXScarna(20): 0.703 Sensitivity CentroidFold: 0.687 MXScarna(20): 0.659 Positive Predictive Value CentroidFold: 0.750 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.187960932e-08	+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.641 Contrafold: 0.616 Sensitivity CentroidFold: 0.639 Contrafold: 0.649 Positive Predictive Value CentroidFold: 0.644 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.641 Sfold: 0.541 Sensitivity CentroidFold: 0.639 Sfold: 0.544 Positive Predictive Value CentroidFold: 0.644 Sfold: 0.539 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.701 MaxExpect: 0.648 Sensitivity CentroidFold: 0.680 MaxExpect: 0.660 Positive Predictive Value CentroidFold: 0.723 MaxExpect: 0.637 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.704 HotKnots: 0.635 Sensitivity CentroidFold: 0.698 HotKnots: 0.672 Positive Predictive Value CentroidFold: 0.715 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.664 RNAalifold(seed): 0.634 Sensitivity CentroidFold: 0.661 RNAalifold(seed): 0.479 Positive Predictive Value CentroidFold: 0.671 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.716 Murlet(20): 0.666 Sensitivity CentroidFold: 0.687 Murlet(20): 0.548 Positive Predictive Value CentroidFold: 0.750 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.641 UNAFold: 0.509 Sensitivity CentroidFold: 0.639 UNAFold: 0.554 Positive Predictive Value CentroidFold: 0.644 UNAFold: 0.467 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.716 Carnac(20): 0.662 Sensitivity CentroidFold: 0.687 Carnac(20): 0.469 Positive Predictive Value CentroidFold: 0.750 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.16131455263e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.641 McQFold: 0.433 Sensitivity CentroidFold: 0.639 McQFold: 0.383 Positive Predictive Value CentroidFold: 0.644 McQFold: 0.491 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.704 RNAshapes: 0.613 Sensitivity CentroidFold: 0.698 RNAshapes: 0.630 Positive Predictive Value CentroidFold: 0.715 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.641 RNAfold: 0.499 Sensitivity CentroidFold: 0.639 RNAfold: 0.550 Positive Predictive Value CentroidFold: 0.644 RNAfold: 0.454 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.641 PknotsRG: 0.489 Sensitivity CentroidFold: 0.639 PknotsRG: 0.539 Positive Predictive Value CentroidFold: 0.644 PknotsRG: 0.443 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.778 Pknots: 0.682 Sensitivity CentroidFold: 0.747 Pknots: 0.697 Positive Predictive Value CentroidFold: 0.818 Pknots: 0.676 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.628 Afold: 0.484 Sensitivity CentroidFold: 0.629 Afold: 0.539 Positive Predictive Value CentroidFold: 0.627 Afold: 0.435 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.620 ProbKnot: 0.564 Sensitivity CentroidFold: 0.623 ProbKnot: 0.613 Positive Predictive Value CentroidFold: 0.623 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.755 Cylofold: 0.693 Sensitivity CentroidFold: 0.713 Cylofold: 0.681 Positive Predictive Value CentroidFold: 0.807 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.704 RNAsubopt: 0.593 Sensitivity CentroidFold: 0.698 RNAsubopt: 0.620 Positive Predictive Value CentroidFold: 0.715 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.643 Fold: 0.557 Sensitivity CentroidFold: 0.645 Fold: 0.589 Positive Predictive Value CentroidFold: 0.646 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.716 RSpredict(20): 0.624 Sensitivity CentroidFold: 0.687 RSpredict(20): 0.559 Positive Predictive Value CentroidFold: 0.750 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.704 Vsfold4: 0.553 Sensitivity CentroidFold: 0.698 Vsfold4: 0.550 Positive Predictive Value CentroidFold: 0.715 Vsfold4: 0.563 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.762 Murlet(seed): 0.571 Sensitivity CentroidFold: 0.723 Murlet(seed): 0.386 Positive Predictive Value CentroidFold: 0.810 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.823 Alterna: 0.638 Sensitivity CentroidFold: 0.786 Alterna: 0.633 Positive Predictive Value CentroidFold: 0.870 Alterna: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.716 Mastr(20): 0.506 Sensitivity CentroidFold: 0.687 Mastr(20): 0.337 Positive Predictive Value CentroidFold: 0.750 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.704 Vsfold5: 0.510 Sensitivity CentroidFold: 0.698 Vsfold5: 0.506 Positive Predictive Value CentroidFold: 0.715 Vsfold5: 0.521 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.801 RDfolder: 0.535 Sensitivity CentroidFold: 0.760 RDfolder: 0.476 Positive Predictive Value CentroidFold: 0.853 RDfolder: 0.622 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.766 MCFold: 0.533 Sensitivity CentroidFold: 0.734 MCFold: 0.569 Positive Predictive Value CentroidFold: 0.806 MCFold: 0.513 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.675 RSpredict(seed): 0.324 Sensitivity CentroidFold: 0.675 RSpredict(seed): 0.177 Positive Predictive Value CentroidFold: 0.681 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.762 Carnac(seed): 0.104 Sensitivity CentroidFold: 0.723 Carnac(seed): 0.011 Positive Predictive Value CentroidFold: 0.810 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	? CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.544 NanoFolder: 0.427 Sensitivity CentroidFold: 0.519 NanoFolder: 0.519 Positive Predictive Value CentroidFold: 0.581 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 CentroidFold: 0.632 Sensitivity CentroidHomfold‑LAST: 0.552 CentroidFold: 0.596 Positive Predictive Value CentroidHomfold‑LAST: 0.743 CentroidFold: 0.681 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: 0.659 Multilign(seed): 0.629 Sensitivity CentroidFold: 0.610 Multilign(seed): 0.580 Positive Predictive Value CentroidFold: 0.726 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: 0.633 Multilign(20): 0.581 Sensitivity CentroidFold: 0.614 Multilign(20): 0.576 Positive Predictive Value CentroidFold: 0.664 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CentroidFold: 0.526 Sensitivity PETfold_pre2.0(seed): 0.619 CentroidFold: 0.495 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CentroidFold: 0.571 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.653 CentroidFold: 0.633 Sensitivity TurboFold(20): 0.606 CentroidFold: 0.614 Positive Predictive Value TurboFold(20): 0.714 CentroidFold: 0.664 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.632 RNAwolf: 0.436 Sensitivity CentroidFold: 0.596 RNAwolf: 0.437 Positive Predictive Value CentroidFold: 0.681 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs IPknot Matthews Correlation Coefficient CentroidFold: 0.632 IPknot: 0.612 Sensitivity CentroidFold: 0.596 IPknot: 0.579 Positive Predictive Value CentroidFold: 0.681 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 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): 0.619 CentroidFold: 0.531 Sensitivity PETfold_pre2.0(20): 0.570 CentroidFold: 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.682 CentroidFold: 0.554 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.620 PPfold(seed): 0.155 Sensitivity CentroidFold: 0.587 PPfold(seed): 0.047 Positive Predictive Value CentroidFold: 0.667 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.662 CentroidFold: 0.566 Sensitivity ContextFold: 0.608 CentroidFold: 0.531 Positive Predictive Value ContextFold: 0.731 CentroidFold: 0.616 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.620 TurboFold(seed): 0.560 Sensitivity CentroidFold: 0.587 TurboFold(seed): 0.533 Positive Predictive Value CentroidFold: 0.667 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.591 CRWrnafold: 0.502 Sensitivity CentroidFold: 0.560 CRWrnafold: 0.516 Positive Predictive Value CentroidFold: 0.636 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.681 RNASampler(seed): 0.640 Sensitivity CentroidFold: 0.651 RNASampler(seed): 0.554 Positive Predictive Value CentroidFold: 0.720 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.566 RNASLOpt: 0.449 Sensitivity CentroidFold: 0.531 RNASLOpt: 0.438 Positive Predictive Value CentroidFold: 0.616 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.715 CentroidFold: 0.633 Sensitivity PPfold(20): 0.644 CentroidFold: 0.614 Positive Predictive Value PPfold(20): 0.802 CentroidFold: 0.664 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.675 Mastr(seed): 0.000 Sensitivity CentroidFold: 0.675 Mastr(seed): 0.000 Positive Predictive Value CentroidFold: 0.681 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08
RNASampler(20)	15 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNASampler(20): 0.732 Sensitivity CentroidAlifold(20): 0.694 RNASampler(20): 0.639 Positive Predictive Value CentroidAlifold(20): 0.932 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.84361416392e-08	15 CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 RNASampler(20): 0.732 Sensitivity CentroidAlifold(seed): 0.623 RNASampler(20): 0.639 Positive Predictive Value CentroidAlifold(seed): 0.934 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	15 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 RNASampler(20): 0.732 Sensitivity RNAalifold(20): 0.656 RNASampler(20): 0.639 Positive Predictive Value RNAalifold(20): 0.869 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.53919717921e-08	15 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 RNASampler(20): 0.732 Sensitivity MXScarna(seed): 0.692 RNASampler(20): 0.639 Positive Predictive Value MXScarna(seed): 0.820 RNASampler(20): 0.843 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.40343002478e-05	15 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.732 CentroidFold: 0.716 Sensitivity RNASampler(20): 0.639 CentroidFold: 0.687 Positive Predictive Value RNASampler(20): 0.843 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.98630365413e-08		+ RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.732 MXScarna(20): 0.703 Sensitivity RNASampler(20): 0.639 MXScarna(20): 0.659 Positive Predictive Value RNASampler(20): 0.843 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.732 Contrafold: 0.650 Sensitivity RNASampler(20): 0.639 Contrafold: 0.652 Positive Predictive Value RNASampler(20): 0.843 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.732 Sfold: 0.665 Sensitivity RNASampler(20): 0.639 Sfold: 0.628 Positive Predictive Value RNASampler(20): 0.843 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.732 MaxExpect: 0.674 Sensitivity RNASampler(20): 0.639 MaxExpect: 0.670 Positive Predictive Value RNASampler(20): 0.843 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.732 HotKnots: 0.640 Sensitivity RNASampler(20): 0.639 HotKnots: 0.663 Positive Predictive Value RNASampler(20): 0.843 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.704 RNAalifold(seed): 0.685 Sensitivity RNASampler(20): 0.607 RNAalifold(seed): 0.515 Positive Predictive Value RNASampler(20): 0.822 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.732 Murlet(20): 0.666 Sensitivity RNASampler(20): 0.639 Murlet(20): 0.548 Positive Predictive Value RNASampler(20): 0.843 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.732 UNAFold: 0.662 Sensitivity RNASampler(20): 0.639 UNAFold: 0.663 Positive Predictive Value RNASampler(20): 0.843 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.732 Carnac(20): 0.662 Sensitivity RNASampler(20): 0.639 Carnac(20): 0.469 Positive Predictive Value RNASampler(20): 0.843 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.732 McQFold: 0.644 Sensitivity RNASampler(20): 0.639 McQFold: 0.643 Positive Predictive Value RNASampler(20): 0.843 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.732 RNAshapes: 0.637 Sensitivity RNASampler(20): 0.639 RNAshapes: 0.637 Positive Predictive Value RNASampler(20): 0.843 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.732 RNAfold: 0.643 Sensitivity RNASampler(20): 0.639 RNAfold: 0.656 Positive Predictive Value RNASampler(20): 0.843 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.732 PknotsRG: 0.664 Sensitivity RNASampler(20): 0.639 PknotsRG: 0.685 Positive Predictive Value RNASampler(20): 0.843 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.784 Pknots: 0.670 Sensitivity RNASampler(20): 0.699 Pknots: 0.691 Positive Predictive Value RNASampler(20): 0.884 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.689 Afold: 0.565 Sensitivity RNASampler(20): 0.601 Afold: 0.591 Positive Predictive Value RNASampler(20): 0.795 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.659 ProbKnot: 0.630 Sensitivity RNASampler(20): 0.563 ProbKnot: 0.664 Positive Predictive Value RNASampler(20): 0.778 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.45186852942e-09	? RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.767 Cylofold: 0.731 Sensitivity RNASampler(20): 0.674 Cylofold: 0.712 Positive Predictive Value RNASampler(20): 0.879 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.732 RNAsubopt: 0.620 Sensitivity RNASampler(20): 0.639 RNAsubopt: 0.632 Positive Predictive Value RNASampler(20): 0.843 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.659 Fold: 0.621 Sensitivity RNASampler(20): 0.563 Fold: 0.637 Positive Predictive Value RNASampler(20): 0.778 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.732 RSpredict(20): 0.624 Sensitivity RNASampler(20): 0.639 RSpredict(20): 0.559 Positive Predictive Value RNASampler(20): 0.843 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.732 Vsfold4: 0.545 Sensitivity RNASampler(20): 0.639 Vsfold4: 0.526 Positive Predictive Value RNASampler(20): 0.843 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.756 Murlet(seed): 0.607 Sensitivity RNASampler(20): 0.666 Murlet(seed): 0.407 Positive Predictive Value RNASampler(20): 0.865 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.50834591464e-08	? RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.903 Alterna: 0.593 Sensitivity RNASampler(20): 0.825 Alterna: 0.596 Positive Predictive Value RNASampler(20): 0.993 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.732 Mastr(20): 0.506 Sensitivity RNASampler(20): 0.639 Mastr(20): 0.337 Positive Predictive Value RNASampler(20): 0.843 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.732 Vsfold5: 0.495 Sensitivity RNASampler(20): 0.639 Vsfold5: 0.480 Positive Predictive Value RNASampler(20): 0.843 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.84361416392e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.862 RDfolder: 0.613 Sensitivity RNASampler(20): 0.765 RDfolder: 0.552 Positive Predictive Value RNASampler(20): 0.978 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.796 MCFold: 0.506 Sensitivity RNASampler(20): 0.727 MCFold: 0.546 Positive Predictive Value RNASampler(20): 0.877 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.732 RSpredict(seed): 0.350 Sensitivity RNASampler(20): 0.639 RSpredict(seed): 0.181 Positive Predictive Value RNASampler(20): 0.843 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.756 Carnac(seed): 0.000 Sensitivity RNASampler(20): 0.666 Carnac(seed): 0.000 Positive Predictive Value RNASampler(20): 0.865 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 6.84390417318e-09	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.568 NanoFolder: 0.285 Sensitivity RNASampler(20): 0.516 NanoFolder: 0.359 Positive Predictive Value RNASampler(20): 0.635 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 RNASampler(20): 0.693 Sensitivity CentroidHomfold‑LAST: 0.644 RNASampler(20): 0.606 Positive Predictive Value CentroidHomfold‑LAST: 0.825 RNASampler(20): 0.800 Number of pairs reference - predicted secondary structure: 6 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): 0.802 Multilign(seed): 0.755 Sensitivity RNASampler(20): 0.695 Multilign(seed): 0.707 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): 0.693 Multilign(20): 0.581 Sensitivity RNASampler(20): 0.606 Multilign(20): 0.576 Positive Predictive Value RNASampler(20): 0.800 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 RNASampler(20): 0.582 Sensitivity PETfold_pre2.0(seed): 0.684 RNASampler(20): 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.831 RNASampler(20): 0.678 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.693 TurboFold(20): 0.653 Sensitivity RNASampler(20): 0.606 TurboFold(20): 0.606 Positive Predictive Value RNASampler(20): 0.800 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.693 RNAwolf: 0.442 Sensitivity RNASampler(20): 0.606 RNAwolf: 0.439 Positive Predictive Value RNASampler(20): 0.800 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.693 IPknot: 0.623 Sensitivity RNASampler(20): 0.606 IPknot: 0.591 Positive Predictive Value RNASampler(20): 0.800 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 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): 0.619 RNASampler(20): 0.582 Sensitivity PETfold_pre2.0(20): 0.570 RNASampler(20): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNASampler(20): 0.678 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.693 PPfold(seed): 0.036 Sensitivity RNASampler(20): 0.606 PPfold(seed): 0.008 Positive Predictive Value RNASampler(20): 0.800 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs ContextFold Matthews Correlation Coefficient RNASampler(20): 0.582 ContextFold: 0.567 Sensitivity RNASampler(20): 0.506 ContextFold: 0.506 Positive Predictive Value RNASampler(20): 0.678 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.693 TurboFold(seed): 0.636 Sensitivity RNASampler(20): 0.606 TurboFold(seed): 0.606 Positive Predictive Value RNASampler(20): 0.800 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.642 CRWrnafold: 0.592 Sensitivity RNASampler(20): 0.556 CRWrnafold: 0.611 Positive Predictive Value RNASampler(20): 0.750 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 RNASampler(20): 0.681 Sensitivity RNASampler(seed): 0.627 RNASampler(20): 0.636 Positive Predictive Value RNASampler(seed): 0.779 RNASampler(20): 0.735 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.582 RNASLOpt: 0.459 Sensitivity RNASampler(20): 0.506 RNASLOpt: 0.456 Positive Predictive Value RNASampler(20): 0.678 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.715 RNASampler(20): 0.693 Sensitivity PPfold(20): 0.644 RNASampler(20): 0.606 Positive Predictive Value PPfold(20): 0.802 RNASampler(20): 0.800 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.732 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.639 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08
MXScarna(20)	15 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 MXScarna(20): 0.703 Sensitivity CentroidAlifold(20): 0.694 MXScarna(20): 0.659 Positive Predictive Value CentroidAlifold(20): 0.932 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 8.09700314043e-09	15 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 MXScarna(20): 0.703 Sensitivity CentroidAlifold(seed): 0.623 MXScarna(20): 0.659 Positive Predictive Value CentroidAlifold(seed): 0.934 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	15 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 MXScarna(20): 0.703 Sensitivity RNAalifold(20): 0.656 MXScarna(20): 0.659 Positive Predictive Value RNAalifold(20): 0.869 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.27388928538e-08	15 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 MXScarna(20): 0.703 Sensitivity MXScarna(seed): 0.692 MXScarna(20): 0.659 Positive Predictive Value MXScarna(seed): 0.820 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.40919803867e-08	15 CentroidFold vs MXScarna(20) Matthews Correlation Coefficient CentroidFold: 0.716 MXScarna(20): 0.703 Sensitivity CentroidFold: 0.687 MXScarna(20): 0.659 Positive Predictive Value CentroidFold: 0.750 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.187960932e-08	15 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.732 MXScarna(20): 0.703 Sensitivity RNASampler(20): 0.639 MXScarna(20): 0.659 Positive Predictive Value RNASampler(20): 0.843 MXScarna(20): 0.755 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08		+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.703 Contrafold: 0.650 Sensitivity MXScarna(20): 0.659 Contrafold: 0.652 Positive Predictive Value MXScarna(20): 0.755 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.703 Sfold: 0.665 Sensitivity MXScarna(20): 0.659 Sfold: 0.628 Positive Predictive Value MXScarna(20): 0.755 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.75627809383e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.703 MaxExpect: 0.674 Sensitivity MXScarna(20): 0.659 MaxExpect: 0.670 Positive Predictive Value MXScarna(20): 0.755 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.703 HotKnots: 0.640 Sensitivity MXScarna(20): 0.659 HotKnots: 0.663 Positive Predictive Value MXScarna(20): 0.755 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08	= MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 RNAalifold(seed): 0.685 Sensitivity MXScarna(20): 0.643 RNAalifold(seed): 0.515 Positive Predictive Value MXScarna(20): 0.742 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00524908862044	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.703 Murlet(20): 0.666 Sensitivity MXScarna(20): 0.659 Murlet(20): 0.548 Positive Predictive Value MXScarna(20): 0.755 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.703 UNAFold: 0.662 Sensitivity MXScarna(20): 0.659 UNAFold: 0.663 Positive Predictive Value MXScarna(20): 0.755 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.703 Carnac(20): 0.662 Sensitivity MXScarna(20): 0.659 Carnac(20): 0.469 Positive Predictive Value MXScarna(20): 0.755 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.703 McQFold: 0.644 Sensitivity MXScarna(20): 0.659 McQFold: 0.643 Positive Predictive Value MXScarna(20): 0.755 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.703 RNAshapes: 0.637 Sensitivity MXScarna(20): 0.659 RNAshapes: 0.637 Positive Predictive Value MXScarna(20): 0.755 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.703 RNAfold: 0.643 Sensitivity MXScarna(20): 0.659 RNAfold: 0.656 Positive Predictive Value MXScarna(20): 0.755 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.703 PknotsRG: 0.664 Sensitivity MXScarna(20): 0.659 PknotsRG: 0.685 Positive Predictive Value MXScarna(20): 0.755 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.83658036805e-08	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.734 Pknots: 0.670 Sensitivity MXScarna(20): 0.691 Pknots: 0.691 Positive Predictive Value MXScarna(20): 0.787 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.66062906821e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.667 Afold: 0.565 Sensitivity MXScarna(20): 0.617 Afold: 0.591 Positive Predictive Value MXScarna(20): 0.725 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.35199149577e-09	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.657 ProbKnot: 0.630 Sensitivity MXScarna(20): 0.613 ProbKnot: 0.664 Positive Predictive Value MXScarna(20): 0.708 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.02533530638e-08	? Cylofold vs MXScarna(20) Matthews Correlation Coefficient Cylofold: 0.731 MXScarna(20): 0.730 Sensitivity Cylofold: 0.712 MXScarna(20): 0.668 Positive Predictive Value Cylofold: 0.757 MXScarna(20): 0.804 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.703 RNAsubopt: 0.620 Sensitivity MXScarna(20): 0.659 RNAsubopt: 0.632 Positive Predictive Value MXScarna(20): 0.755 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.657 Fold: 0.621 Sensitivity MXScarna(20): 0.613 Fold: 0.637 Positive Predictive Value MXScarna(20): 0.708 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.45186852942e-09	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.703 RSpredict(20): 0.624 Sensitivity MXScarna(20): 0.659 RSpredict(20): 0.559 Positive Predictive Value MXScarna(20): 0.755 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.703 Vsfold4: 0.545 Sensitivity MXScarna(20): 0.659 Vsfold4: 0.526 Positive Predictive Value MXScarna(20): 0.755 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.720 Murlet(seed): 0.607 Sensitivity MXScarna(20): 0.675 Murlet(seed): 0.407 Positive Predictive Value MXScarna(20): 0.775 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.67657656842e-08	? MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.819 Alterna: 0.593 Sensitivity MXScarna(20): 0.778 Alterna: 0.596 Positive Predictive Value MXScarna(20): 0.869 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.703 Mastr(20): 0.506 Sensitivity MXScarna(20): 0.659 Mastr(20): 0.337 Positive Predictive Value MXScarna(20): 0.755 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.703 Vsfold5: 0.495 Sensitivity MXScarna(20): 0.659 Vsfold5: 0.480 Positive Predictive Value MXScarna(20): 0.755 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.766 RDfolder: 0.613 Sensitivity MXScarna(20): 0.704 RDfolder: 0.552 Positive Predictive Value MXScarna(20): 0.844 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.69265863073e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.735 MCFold: 0.506 Sensitivity MXScarna(20): 0.686 MCFold: 0.546 Positive Predictive Value MXScarna(20): 0.794 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.703 RSpredict(seed): 0.350 Sensitivity MXScarna(20): 0.659 RSpredict(seed): 0.181 Positive Predictive Value MXScarna(20): 0.755 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.720 Carnac(seed): 0.000 Sensitivity MXScarna(20): 0.675 Carnac(seed): 0.000 Positive Predictive Value MXScarna(20): 0.775 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	? MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.512 NanoFolder: 0.285 Sensitivity MXScarna(20): 0.500 NanoFolder: 0.359 Positive Predictive Value MXScarna(20): 0.533 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 MXScarna(20): 0.606 Sensitivity CentroidHomfold‑LAST: 0.644 MXScarna(20): 0.561 Positive Predictive Value CentroidHomfold‑LAST: 0.825 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 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	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.755 MXScarna(20): 0.750 Sensitivity Multilign(seed): 0.707 MXScarna(20): 0.732 Positive Predictive Value Multilign(seed): 0.817 MXScarna(20): 0.779 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): 0.606 Multilign(20): 0.581 Sensitivity MXScarna(20): 0.561 Multilign(20): 0.576 Positive Predictive Value MXScarna(20): 0.667 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 MXScarna(20): 0.477 Sensitivity PETfold_pre2.0(seed): 0.684 MXScarna(20): 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.831 MXScarna(20): 0.540 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.653 MXScarna(20): 0.606 Sensitivity TurboFold(20): 0.606 MXScarna(20): 0.561 Positive Predictive Value TurboFold(20): 0.714 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.606 RNAwolf: 0.442 Sensitivity MXScarna(20): 0.561 RNAwolf: 0.439 Positive Predictive Value MXScarna(20): 0.667 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.623 MXScarna(20): 0.606 Sensitivity IPknot: 0.591 MXScarna(20): 0.561 Positive Predictive Value IPknot: 0.667 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 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): 0.619 MXScarna(20): 0.477 Sensitivity PETfold_pre2.0(20): 0.570 MXScarna(20): 0.430 Positive Predictive Value PETfold_pre2.0(20): 0.682 MXScarna(20): 0.540 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.606 PPfold(seed): 0.036 Sensitivity MXScarna(20): 0.561 PPfold(seed): 0.008 Positive Predictive Value MXScarna(20): 0.667 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.567 MXScarna(20): 0.477 Sensitivity ContextFold: 0.506 MXScarna(20): 0.430 Positive Predictive Value ContextFold: 0.645 MXScarna(20): 0.540 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 MXScarna(20): 0.606 Sensitivity TurboFold(seed): 0.606 MXScarna(20): 0.561 Positive Predictive Value TurboFold(seed): 0.678 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs MXScarna(20) Matthews Correlation Coefficient CRWrnafold: 0.592 MXScarna(20): 0.554 Sensitivity CRWrnafold: 0.611 MXScarna(20): 0.519 Positive Predictive Value CRWrnafold: 0.584 MXScarna(20): 0.602 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 MXScarna(20): 0.652 Sensitivity RNASampler(seed): 0.627 MXScarna(20): 0.636 Positive Predictive Value RNASampler(seed): 0.779 MXScarna(20): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.477 RNASLOpt: 0.459 Sensitivity MXScarna(20): 0.430 RNASLOpt: 0.456 Positive Predictive Value MXScarna(20): 0.540 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.715 MXScarna(20): 0.606 Sensitivity PPfold(20): 0.644 MXScarna(20): 0.561 Positive Predictive Value PPfold(20): 0.802 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.703 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.659 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.755 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.39551335374e-08
Contrafold	15 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Contrafold: 0.650 Sensitivity CentroidAlifold(20): 0.694 Contrafold: 0.652 Positive Predictive Value CentroidAlifold(20): 0.932 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.33194562506e-08	19 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Contrafold: 0.623 Sensitivity CentroidAlifold(seed): 0.598 Contrafold: 0.647 Positive Predictive Value CentroidAlifold(seed): 0.894 Contrafold: 0.606 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	15 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.753 Contrafold: 0.650 Sensitivity RNAalifold(20): 0.656 Contrafold: 0.652 Positive Predictive Value RNAalifold(20): 0.869 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	19 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.711 Contrafold: 0.623 Sensitivity MXScarna(seed): 0.663 Contrafold: 0.647 Positive Predictive Value MXScarna(seed): 0.768 Contrafold: 0.606 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	27 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.641 Contrafold: 0.616 Sensitivity CentroidFold: 0.639 Contrafold: 0.649 Positive Predictive Value CentroidFold: 0.644 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.732 Contrafold: 0.650 Sensitivity RNASampler(20): 0.639 Contrafold: 0.652 Positive Predictive Value RNASampler(20): 0.843 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	15 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.703 Contrafold: 0.650 Sensitivity MXScarna(20): 0.659 Contrafold: 0.652 Positive Predictive Value MXScarna(20): 0.755 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08		+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.638 Sfold: 0.530 Sensitivity Contrafold: 0.665 Sfold: 0.530 Positive Predictive Value Contrafold: 0.613 Sfold: 0.529 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.675 MaxExpect: 0.648 Sensitivity Contrafold: 0.688 MaxExpect: 0.660 Positive Predictive Value Contrafold: 0.663 MaxExpect: 0.637 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.663 HotKnots: 0.631 Sensitivity Contrafold: 0.678 HotKnots: 0.666 Positive Predictive Value Contrafold: 0.654 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.640 RNAalifold(seed): 0.634 Sensitivity Contrafold: 0.663 RNAalifold(seed): 0.479 Positive Predictive Value Contrafold: 0.622 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.000512952720519	- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.666 Contrafold: 0.650 Sensitivity Murlet(20): 0.548 Contrafold: 0.652 Positive Predictive Value Murlet(20): 0.814 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.42587965167e-05	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.638 UNAFold: 0.502 Sensitivity Contrafold: 0.665 UNAFold: 0.539 Positive Predictive Value Contrafold: 0.613 UNAFold: 0.469 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.662 Contrafold: 0.650 Sensitivity Carnac(20): 0.469 Contrafold: 0.652 Positive Predictive Value Carnac(20): 0.938 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000793683551711	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.638 McQFold: 0.415 Sensitivity Contrafold: 0.665 McQFold: 0.382 Positive Predictive Value Contrafold: 0.613 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.663 RNAshapes: 0.610 Sensitivity Contrafold: 0.678 RNAshapes: 0.625 Positive Predictive Value Contrafold: 0.654 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.638 RNAfold: 0.498 Sensitivity Contrafold: 0.665 RNAfold: 0.540 Positive Predictive Value Contrafold: 0.613 RNAfold: 0.460 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.638 PknotsRG: 0.486 Sensitivity Contrafold: 0.665 PknotsRG: 0.529 Positive Predictive Value Contrafold: 0.613 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.729 Pknots: 0.676 Sensitivity Contrafold: 0.719 Pknots: 0.693 Positive Predictive Value Contrafold: 0.747 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.630 Afold: 0.493 Sensitivity Contrafold: 0.658 Afold: 0.537 Positive Predictive Value Contrafold: 0.602 Afold: 0.453 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.599 ProbKnot: 0.564 Sensitivity Contrafold: 0.629 ProbKnot: 0.613 Positive Predictive Value Contrafold: 0.575 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.727 Cylofold: 0.693 Sensitivity Contrafold: 0.719 Cylofold: 0.681 Positive Predictive Value Contrafold: 0.743 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.663 RNAsubopt: 0.591 Sensitivity Contrafold: 0.678 RNAsubopt: 0.615 Positive Predictive Value Contrafold: 0.654 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.622 Fold: 0.557 Sensitivity Contrafold: 0.651 Fold: 0.589 Positive Predictive Value Contrafold: 0.600 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.63594052159e-08	+ Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.650 RSpredict(20): 0.624 Sensitivity Contrafold: 0.652 RSpredict(20): 0.559 Positive Predictive Value Contrafold: 0.655 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.0326876712e-07	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.663 Vsfold4: 0.559 Sensitivity Contrafold: 0.678 Vsfold4: 0.554 Positive Predictive Value Contrafold: 0.654 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.735 Murlet(seed): 0.571 Sensitivity Contrafold: 0.723 Murlet(seed): 0.386 Positive Predictive Value Contrafold: 0.754 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.757 Alterna: 0.647 Sensitivity Contrafold: 0.737 Alterna: 0.636 Positive Predictive Value Contrafold: 0.789 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.650 Mastr(20): 0.506 Sensitivity Contrafold: 0.652 Mastr(20): 0.337 Positive Predictive Value Contrafold: 0.655 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.663 Vsfold5: 0.518 Sensitivity Contrafold: 0.678 Vsfold5: 0.514 Positive Predictive Value Contrafold: 0.654 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.747 RDfolder: 0.549 Sensitivity Contrafold: 0.722 RDfolder: 0.487 Positive Predictive Value Contrafold: 0.784 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.704 MCFold: 0.527 Sensitivity Contrafold: 0.697 MCFold: 0.563 Positive Predictive Value Contrafold: 0.720 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.623 RSpredict(seed): 0.324 Sensitivity Contrafold: 0.647 RSpredict(seed): 0.177 Positive Predictive Value Contrafold: 0.606 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.735 Carnac(seed): 0.104 Sensitivity Contrafold: 0.723 Carnac(seed): 0.011 Positive Predictive Value Contrafold: 0.754 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.78993384543e-08	? Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.542 NanoFolder: 0.427 Sensitivity Contrafold: 0.529 NanoFolder: 0.519 Positive Predictive Value Contrafold: 0.567 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Contrafold: 0.629 Sensitivity CentroidHomfold‑LAST: 0.552 Contrafold: 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Contrafold: 0.659 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: 0.646 Multilign(seed): 0.629 Sensitivity Contrafold: 0.620 Multilign(seed): 0.580 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: 0.628 Multilign(20): 0.581 Sensitivity Contrafold: 0.621 Multilign(20): 0.576 Positive Predictive Value Contrafold: 0.646 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Contrafold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.619 Contrafold: 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Contrafold: 0.557 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.653 Contrafold: 0.628 Sensitivity TurboFold(20): 0.606 Contrafold: 0.621 Positive Predictive Value TurboFold(20): 0.714 Contrafold: 0.646 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.629 RNAwolf: 0.436 Sensitivity Contrafold: 0.612 RNAwolf: 0.437 Positive Predictive Value Contrafold: 0.659 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs IPknot Matthews Correlation Coefficient Contrafold: 0.629 IPknot: 0.612 Sensitivity Contrafold: 0.612 IPknot: 0.579 Positive Predictive Value Contrafold: 0.659 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 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): 0.619 Contrafold: 0.537 Sensitivity PETfold_pre2.0(20): 0.570 Contrafold: 0.532 Positive Predictive Value PETfold_pre2.0(20): 0.682 Contrafold: 0.553 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.611 PPfold(seed): 0.155 Sensitivity Contrafold: 0.593 PPfold(seed): 0.047 Positive Predictive Value Contrafold: 0.640 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.662 Contrafold: 0.573 Sensitivity ContextFold: 0.608 Contrafold: 0.554 Positive Predictive Value ContextFold: 0.731 Contrafold: 0.605 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.611 TurboFold(seed): 0.560 Sensitivity Contrafold: 0.593 TurboFold(seed): 0.533 Positive Predictive Value Contrafold: 0.640 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.594 CRWrnafold: 0.502 Sensitivity Contrafold: 0.579 CRWrnafold: 0.516 Positive Predictive Value Contrafold: 0.622 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.642 RNASampler(seed): 0.640 Sensitivity Contrafold: 0.645 RNASampler(seed): 0.554 Positive Predictive Value Contrafold: 0.648 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.573 RNASLOpt: 0.449 Sensitivity Contrafold: 0.554 RNASLOpt: 0.438 Positive Predictive Value Contrafold: 0.605 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.715 Contrafold: 0.628 Sensitivity PPfold(20): 0.644 Contrafold: 0.621 Positive Predictive Value PPfold(20): 0.802 Contrafold: 0.646 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.623 Mastr(seed): 0.000 Sensitivity Contrafold: 0.647 Mastr(seed): 0.000 Positive Predictive Value Contrafold: 0.606 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08
Sfold	15 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Sfold: 0.665 Sensitivity CentroidAlifold(20): 0.694 Sfold: 0.628 Positive Predictive Value CentroidAlifold(20): 0.932 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.72523032126e-08	19 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Sfold: 0.632 Sensitivity CentroidAlifold(seed): 0.598 Sfold: 0.623 Positive Predictive Value CentroidAlifold(seed): 0.894 Sfold: 0.646 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	15 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.753 Sfold: 0.665 Sensitivity RNAalifold(20): 0.656 Sfold: 0.628 Positive Predictive Value RNAalifold(20): 0.869 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	19 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.711 Sfold: 0.632 Sensitivity MXScarna(seed): 0.663 Sfold: 0.623 Positive Predictive Value MXScarna(seed): 0.768 Sfold: 0.646 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.45076534967e-08	27 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.641 Sfold: 0.541 Sensitivity CentroidFold: 0.639 Sfold: 0.544 Positive Predictive Value CentroidFold: 0.644 Sfold: 0.539 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.732 Sfold: 0.665 Sensitivity RNASampler(20): 0.639 Sfold: 0.628 Positive Predictive Value RNASampler(20): 0.843 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.703 Sfold: 0.665 Sensitivity MXScarna(20): 0.659 Sfold: 0.628 Positive Predictive Value MXScarna(20): 0.755 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.75627809383e-08	31 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.638 Sfold: 0.530 Sensitivity Contrafold: 0.665 Sfold: 0.530 Positive Predictive Value Contrafold: 0.613 Sfold: 0.529 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08		- MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.648 Sfold: 0.573 Sensitivity MaxExpect: 0.660 Sfold: 0.557 Positive Predictive Value MaxExpect: 0.637 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.638 HotKnots: 0.631 Sensitivity Sfold: 0.629 HotKnots: 0.666 Positive Predictive Value Sfold: 0.653 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.9225991223e-05	+ Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.648 RNAalifold(seed): 0.634 Sensitivity Sfold: 0.638 RNAalifold(seed): 0.479 Positive Predictive Value Sfold: 0.664 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.9039628243e-08	= Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.666 Sfold: 0.665 Sensitivity Murlet(20): 0.548 Sfold: 0.628 Positive Predictive Value Murlet(20): 0.814 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.402525058148	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.530 UNAFold: 0.502 Sensitivity Sfold: 0.530 UNAFold: 0.539 Positive Predictive Value Sfold: 0.529 UNAFold: 0.469 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.665 Carnac(20): 0.662 Sensitivity Sfold: 0.628 Carnac(20): 0.469 Positive Predictive Value Sfold: 0.711 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0255587090362	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.530 McQFold: 0.415 Sensitivity Sfold: 0.530 McQFold: 0.382 Positive Predictive Value Sfold: 0.529 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.638 RNAshapes: 0.610 Sensitivity Sfold: 0.629 RNAshapes: 0.625 Positive Predictive Value Sfold: 0.653 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.530 RNAfold: 0.498 Sensitivity Sfold: 0.530 RNAfold: 0.540 Positive Predictive Value Sfold: 0.529 RNAfold: 0.460 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.530 PknotsRG: 0.486 Sensitivity Sfold: 0.530 PknotsRG: 0.529 Positive Predictive Value Sfold: 0.529 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.695 Pknots: 0.676 Sensitivity Sfold: 0.666 Pknots: 0.693 Positive Predictive Value Sfold: 0.735 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 8.58720925105e-07	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.514 Afold: 0.493 Sensitivity Sfold: 0.517 Afold: 0.537 Positive Predictive Value Sfold: 0.512 Afold: 0.453 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.600 ProbKnot: 0.564 Sensitivity Sfold: 0.602 ProbKnot: 0.613 Positive Predictive Value Sfold: 0.603 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.700 Cylofold: 0.693 Sensitivity Sfold: 0.665 Cylofold: 0.681 Positive Predictive Value Sfold: 0.746 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000109045993861	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.638 RNAsubopt: 0.591 Sensitivity Sfold: 0.629 RNAsubopt: 0.615 Positive Predictive Value Sfold: 0.653 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.605 Fold: 0.557 Sensitivity Sfold: 0.604 Fold: 0.589 Positive Predictive Value Sfold: 0.610 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.665 RSpredict(20): 0.624 Sensitivity Sfold: 0.628 RSpredict(20): 0.559 Positive Predictive Value Sfold: 0.711 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.16236719691e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.638 Vsfold4: 0.559 Sensitivity Sfold: 0.629 Vsfold4: 0.554 Positive Predictive Value Sfold: 0.653 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.89920829651e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.749 Murlet(seed): 0.571 Sensitivity Sfold: 0.701 Murlet(seed): 0.386 Positive Predictive Value Sfold: 0.808 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.715 Alterna: 0.647 Sensitivity Sfold: 0.681 Alterna: 0.636 Positive Predictive Value Sfold: 0.763 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.665 Mastr(20): 0.506 Sensitivity Sfold: 0.628 Mastr(20): 0.337 Positive Predictive Value Sfold: 0.711 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.638 Vsfold5: 0.518 Sensitivity Sfold: 0.629 Vsfold5: 0.514 Positive Predictive Value Sfold: 0.653 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.705 RDfolder: 0.549 Sensitivity Sfold: 0.663 RDfolder: 0.487 Positive Predictive Value Sfold: 0.763 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.680 MCFold: 0.527 Sensitivity Sfold: 0.654 MCFold: 0.563 Positive Predictive Value Sfold: 0.717 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.632 RSpredict(seed): 0.324 Sensitivity Sfold: 0.623 RSpredict(seed): 0.177 Positive Predictive Value Sfold: 0.646 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.749 Carnac(seed): 0.104 Sensitivity Sfold: 0.701 Carnac(seed): 0.011 Positive Predictive Value Sfold: 0.808 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	? Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.451 NanoFolder: 0.427 Sensitivity Sfold: 0.442 NanoFolder: 0.519 Positive Predictive Value Sfold: 0.474 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Sfold: 0.595 Sensitivity CentroidHomfold‑LAST: 0.552 Sfold: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Sfold: 0.629 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: 0.703 Multilign(seed): 0.629 Sensitivity Sfold: 0.650 Multilign(seed): 0.580 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: 0.636 Multilign(20): 0.581 Sensitivity Sfold: 0.598 Multilign(20): 0.576 Positive Predictive Value Sfold: 0.687 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Sfold: 0.499 Sensitivity PETfold_pre2.0(seed): 0.619 Sfold: 0.464 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Sfold: 0.549 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.653 Sfold: 0.636 Sensitivity TurboFold(20): 0.606 Sfold: 0.598 Positive Predictive Value TurboFold(20): 0.714 Sfold: 0.687 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.595 RNAwolf: 0.436 Sensitivity Sfold: 0.574 RNAwolf: 0.437 Positive Predictive Value Sfold: 0.629 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.612 Sfold: 0.595 Sensitivity IPknot: 0.579 Sfold: 0.574 Positive Predictive Value IPknot: 0.658 Sfold: 0.629 Number of pairs reference - predicted secondary structure: 9 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): 0.619 Sfold: 0.506 Sensitivity PETfold_pre2.0(20): 0.570 Sfold: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 Sfold: 0.543 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.618 PPfold(seed): 0.155 Sensitivity Sfold: 0.573 PPfold(seed): 0.047 Positive Predictive Value Sfold: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.662 Sfold: 0.501 Sensitivity ContextFold: 0.608 Sfold: 0.492 Positive Predictive Value ContextFold: 0.731 Sfold: 0.525 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.618 TurboFold(seed): 0.560 Sensitivity Sfold: 0.573 TurboFold(seed): 0.533 Positive Predictive Value Sfold: 0.677 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.550 CRWrnafold: 0.502 Sensitivity Sfold: 0.535 CRWrnafold: 0.516 Positive Predictive Value Sfold: 0.578 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.695 RNASampler(seed): 0.640 Sensitivity Sfold: 0.669 RNASampler(seed): 0.554 Positive Predictive Value Sfold: 0.730 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.501 RNASLOpt: 0.449 Sensitivity Sfold: 0.492 RNASLOpt: 0.438 Positive Predictive Value Sfold: 0.525 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.715 Sfold: 0.636 Sensitivity PPfold(20): 0.644 Sfold: 0.598 Positive Predictive Value PPfold(20): 0.802 Sfold: 0.687 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.632 Mastr(seed): 0.000 Sensitivity Sfold: 0.623 Mastr(seed): 0.000 Positive Predictive Value Sfold: 0.646 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08
MaxExpect	15 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.803 MaxExpect: 0.674 Sensitivity CentroidAlifold(20): 0.694 MaxExpect: 0.670 Positive Predictive Value CentroidAlifold(20): 0.932 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	17 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.723 MaxExpect: 0.591 Sensitivity CentroidAlifold(seed): 0.595 MaxExpect: 0.614 Positive Predictive Value CentroidAlifold(seed): 0.884 MaxExpect: 0.575 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	15 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.753 MaxExpect: 0.674 Sensitivity RNAalifold(20): 0.656 MaxExpect: 0.670 Positive Predictive Value RNAalifold(20): 0.869 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.66062906821e-08	17 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.694 MaxExpect: 0.591 Sensitivity MXScarna(seed): 0.646 MaxExpect: 0.614 Positive Predictive Value MXScarna(seed): 0.749 MaxExpect: 0.575 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	24 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.701 MaxExpect: 0.648 Sensitivity CentroidFold: 0.680 MaxExpect: 0.660 Positive Predictive Value CentroidFold: 0.723 MaxExpect: 0.637 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	15 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.732 MaxExpect: 0.674 Sensitivity RNASampler(20): 0.639 MaxExpect: 0.670 Positive Predictive Value RNASampler(20): 0.843 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	15 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.703 MaxExpect: 0.674 Sensitivity MXScarna(20): 0.659 MaxExpect: 0.670 Positive Predictive Value MXScarna(20): 0.755 MaxExpect: 0.683 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.50323628132e-08	24 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.675 MaxExpect: 0.648 Sensitivity Contrafold: 0.688 MaxExpect: 0.660 Positive Predictive Value Contrafold: 0.663 MaxExpect: 0.637 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.648 Sfold: 0.573 Sensitivity MaxExpect: 0.660 Sfold: 0.557 Positive Predictive Value MaxExpect: 0.637 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08		+ MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.623 HotKnots: 0.611 Sensitivity MaxExpect: 0.640 HotKnots: 0.651 Positive Predictive Value MaxExpect: 0.612 HotKnots: 0.581 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 2.05363013301e-06	- RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.623 MaxExpect: 0.601 Sensitivity RNAalifold(seed): 0.470 MaxExpect: 0.626 Positive Predictive Value RNAalifold(seed): 0.831 MaxExpect: 0.582 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.82294361511e-07	= MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.674 Murlet(20): 0.666 Sensitivity MaxExpect: 0.670 Murlet(20): 0.548 Positive Predictive Value MaxExpect: 0.683 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00189913880948	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.648 UNAFold: 0.554 Sensitivity MaxExpect: 0.660 UNAFold: 0.575 Positive Predictive Value MaxExpect: 0.637 UNAFold: 0.535 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.674 Carnac(20): 0.662 Sensitivity MaxExpect: 0.670 Carnac(20): 0.469 Positive Predictive Value MaxExpect: 0.683 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000120909053629	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.648 McQFold: 0.482 Sensitivity MaxExpect: 0.660 McQFold: 0.490 Positive Predictive Value MaxExpect: 0.637 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.623 RNAshapes: 0.598 Sensitivity MaxExpect: 0.640 RNAshapes: 0.618 Positive Predictive Value MaxExpect: 0.612 RNAshapes: 0.586 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.648 RNAfold: 0.540 Sensitivity MaxExpect: 0.660 RNAfold: 0.567 Positive Predictive Value MaxExpect: 0.637 RNAfold: 0.516 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.648 PknotsRG: 0.524 Sensitivity MaxExpect: 0.660 PknotsRG: 0.552 Positive Predictive Value MaxExpect: 0.637 PknotsRG: 0.498 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.682 Pknots: 0.655 Sensitivity MaxExpect: 0.676 Pknots: 0.673 Positive Predictive Value MaxExpect: 0.697 Pknots: 0.647 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 3.32276783474e-07	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.632 Afold: 0.534 Sensitivity MaxExpect: 0.648 Afold: 0.563 Positive Predictive Value MaxExpect: 0.616 Afold: 0.507 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.569 ProbKnot: 0.564 Sensitivity MaxExpect: 0.598 ProbKnot: 0.613 Positive Predictive Value MaxExpect: 0.548 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	- Cylofold vs MaxExpect Matthews Correlation Coefficient Cylofold: 0.693 MaxExpect: 0.679 Sensitivity Cylofold: 0.681 MaxExpect: 0.671 Positive Predictive Value Cylofold: 0.715 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.06154098047e-05	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.623 RNAsubopt: 0.579 Sensitivity MaxExpect: 0.640 RNAsubopt: 0.608 Positive Predictive Value MaxExpect: 0.612 RNAsubopt: 0.558 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.587 Fold: 0.557 Sensitivity MaxExpect: 0.614 Fold: 0.589 Positive Predictive Value MaxExpect: 0.567 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.674 RSpredict(20): 0.624 Sensitivity MaxExpect: 0.670 RSpredict(20): 0.559 Positive Predictive Value MaxExpect: 0.683 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.623 Vsfold4: 0.522 Sensitivity MaxExpect: 0.640 Vsfold4: 0.520 Positive Predictive Value MaxExpect: 0.612 Vsfold4: 0.531 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.681 Murlet(seed): 0.566 Sensitivity MaxExpect: 0.675 Murlet(seed): 0.385 Positive Predictive Value MaxExpect: 0.695 Murlet(seed): 0.843 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.711 Alterna: 0.584 Sensitivity MaxExpect: 0.689 Alterna: 0.582 Positive Predictive Value MaxExpect: 0.745 Alterna: 0.604 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.674 Mastr(20): 0.506 Sensitivity MaxExpect: 0.670 Mastr(20): 0.337 Positive Predictive Value MaxExpect: 0.683 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.623 Vsfold5: 0.476 Sensitivity MaxExpect: 0.640 Vsfold5: 0.473 Positive Predictive Value MaxExpect: 0.612 Vsfold5: 0.486 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.692 RDfolder: 0.501 Sensitivity MaxExpect: 0.667 RDfolder: 0.442 Positive Predictive Value MaxExpect: 0.731 RDfolder: 0.588 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.652 MCFold: 0.493 Sensitivity MaxExpect: 0.652 MCFold: 0.529 Positive Predictive Value MaxExpect: 0.662 MCFold: 0.473 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.591 RSpredict(seed): 0.307 Sensitivity MaxExpect: 0.614 RSpredict(seed): 0.166 Positive Predictive Value MaxExpect: 0.575 RSpredict(seed): 0.576 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.681 Carnac(seed): 0.109 Sensitivity MaxExpect: 0.675 Carnac(seed): 0.012 Positive Predictive Value MaxExpect: 0.695 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	? NanoFolder vs MaxExpect Matthews Correlation Coefficient NanoFolder: 0.427 MaxExpect: 0.369 Sensitivity NanoFolder: 0.519 MaxExpect: 0.385 Positive Predictive Value NanoFolder: 0.365 MaxExpect: 0.370 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 MaxExpect: 0.522 Sensitivity CentroidHomfold‑LAST: 0.552 MaxExpect: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.743 MaxExpect: 0.540 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): 0.629 MaxExpect: 0.592 Sensitivity Multilign(seed): 0.580 MaxExpect: 0.570 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: 0.590 Multilign(20): 0.581 Sensitivity MaxExpect: 0.591 Multilign(20): 0.576 Positive Predictive Value MaxExpect: 0.600 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 MaxExpect: 0.384 Sensitivity PETfold_pre2.0(seed): 0.619 MaxExpect: 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 MaxExpect: 0.392 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.653 MaxExpect: 0.590 Sensitivity TurboFold(20): 0.606 MaxExpect: 0.591 Positive Predictive Value TurboFold(20): 0.714 MaxExpect: 0.600 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.522 RNAwolf: 0.436 Sensitivity MaxExpect: 0.519 RNAwolf: 0.437 Positive Predictive Value MaxExpect: 0.540 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.612 MaxExpect: 0.522 Sensitivity IPknot: 0.579 MaxExpect: 0.519 Positive Predictive Value IPknot: 0.658 MaxExpect: 0.540 Number of pairs reference - predicted secondary structure: 9 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): 0.619 MaxExpect: 0.466 Sensitivity PETfold_pre2.0(20): 0.570 MaxExpect: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 MaxExpect: 0.463 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.522 PPfold(seed): 0.155 Sensitivity MaxExpect: 0.520 PPfold(seed): 0.047 Positive Predictive Value MaxExpect: 0.538 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.662 MaxExpect: 0.418 Sensitivity ContextFold: 0.608 MaxExpect: 0.423 Positive Predictive Value ContextFold: 0.731 MaxExpect: 0.430 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.560 MaxExpect: 0.522 Sensitivity TurboFold(seed): 0.533 MaxExpect: 0.520 Positive Predictive Value TurboFold(seed): 0.602 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.502 MaxExpect: 0.468 Sensitivity CRWrnafold: 0.516 MaxExpect: 0.472 Positive Predictive Value CRWrnafold: 0.503 MaxExpect: 0.481 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): 0.616 MaxExpect: 0.525 Sensitivity RNASampler(seed): 0.544 MaxExpect: 0.551 Positive Predictive Value RNASampler(seed): 0.705 MaxExpect: 0.510 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs MaxExpect Matthews Correlation Coefficient RNASLOpt: 0.449 MaxExpect: 0.418 Sensitivity RNASLOpt: 0.438 MaxExpect: 0.423 Positive Predictive Value RNASLOpt: 0.475 MaxExpect: 0.430 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): 0.715 MaxExpect: 0.590 Sensitivity PPfold(20): 0.644 MaxExpect: 0.591 Positive Predictive Value PPfold(20): 0.802 MaxExpect: 0.600 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.591 Mastr(seed): 0.000 Sensitivity MaxExpect: 0.614 Mastr(seed): 0.000 Positive Predictive Value MaxExpect: 0.575 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08
HotKnots	15 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.803 HotKnots: 0.640 Sensitivity CentroidAlifold(20): 0.694 HotKnots: 0.663 Positive Predictive Value CentroidAlifold(20): 0.932 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.64318034126e-08	19 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 HotKnots: 0.616 Sensitivity CentroidAlifold(seed): 0.598 HotKnots: 0.657 Positive Predictive Value CentroidAlifold(seed): 0.894 HotKnots: 0.582 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.73174208038e-08	15 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.753 HotKnots: 0.640 Sensitivity RNAalifold(20): 0.656 HotKnots: 0.663 Positive Predictive Value RNAalifold(20): 0.869 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	19 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.711 HotKnots: 0.616 Sensitivity MXScarna(seed): 0.663 HotKnots: 0.657 Positive Predictive Value MXScarna(seed): 0.768 HotKnots: 0.582 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.39090039918e-08	25 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.704 HotKnots: 0.635 Sensitivity CentroidFold: 0.698 HotKnots: 0.672 Positive Predictive Value CentroidFold: 0.715 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.732 HotKnots: 0.640 Sensitivity RNASampler(20): 0.639 HotKnots: 0.663 Positive Predictive Value RNASampler(20): 0.843 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	15 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.703 HotKnots: 0.640 Sensitivity MXScarna(20): 0.659 HotKnots: 0.663 Positive Predictive Value MXScarna(20): 0.755 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08	28 Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.663 HotKnots: 0.631 Sensitivity Contrafold: 0.678 HotKnots: 0.666 Positive Predictive Value Contrafold: 0.654 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.638 HotKnots: 0.631 Sensitivity Sfold: 0.629 HotKnots: 0.666 Positive Predictive Value Sfold: 0.653 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.9225991223e-05	23 MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.623 HotKnots: 0.611 Sensitivity MaxExpect: 0.640 HotKnots: 0.651 Positive Predictive Value MaxExpect: 0.612 HotKnots: 0.581 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 2.05363013301e-06		= RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.634 HotKnots: 0.633 Sensitivity RNAalifold(seed): 0.479 HotKnots: 0.677 Positive Predictive Value RNAalifold(seed): 0.842 HotKnots: 0.597 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.00677354341424	- Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.666 HotKnots: 0.640 Sensitivity Murlet(20): 0.548 HotKnots: 0.663 Positive Predictive Value Murlet(20): 0.814 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.40910484167e-08	= UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.633 HotKnots: 0.631 Sensitivity UNAFold: 0.655 HotKnots: 0.666 Positive Predictive Value UNAFold: 0.619 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.193426068958	- Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.662 HotKnots: 0.640 Sensitivity Carnac(20): 0.469 HotKnots: 0.663 Positive Predictive Value Carnac(20): 0.938 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.03796748738e-07	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.631 McQFold: 0.624 Sensitivity HotKnots: 0.666 McQFold: 0.641 Positive Predictive Value HotKnots: 0.605 McQFold: 0.614 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000493106477465	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.631 RNAshapes: 0.610 Sensitivity HotKnots: 0.666 RNAshapes: 0.625 Positive Predictive Value HotKnots: 0.605 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.631 RNAfold: 0.607 Sensitivity HotKnots: 0.666 RNAfold: 0.633 Positive Predictive Value HotKnots: 0.605 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.631 PknotsRG: 0.612 Sensitivity HotKnots: 0.666 PknotsRG: 0.645 Positive Predictive Value HotKnots: 0.605 PknotsRG: 0.586 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.43400990727e-08	+ HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.694 Pknots: 0.676 Sensitivity HotKnots: 0.705 Pknots: 0.693 Positive Predictive Value HotKnots: 0.692 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 2.81638097452e-07	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.586 Afold: 0.564 Sensitivity HotKnots: 0.630 Afold: 0.604 Positive Predictive Value HotKnots: 0.551 Afold: 0.533 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.589 ProbKnot: 0.564 Sensitivity HotKnots: 0.644 ProbKnot: 0.613 Positive Predictive Value HotKnots: 0.544 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.715 Cylofold: 0.693 Sensitivity HotKnots: 0.739 Cylofold: 0.681 Positive Predictive Value HotKnots: 0.700 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.4651262096e-08	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.631 RNAsubopt: 0.591 Sensitivity HotKnots: 0.666 RNAsubopt: 0.615 Positive Predictive Value HotKnots: 0.605 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.605 Fold: 0.557 Sensitivity HotKnots: 0.657 Fold: 0.589 Positive Predictive Value HotKnots: 0.562 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.640 RSpredict(20): 0.624 Sensitivity HotKnots: 0.663 RSpredict(20): 0.559 Positive Predictive Value HotKnots: 0.623 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08749669591e-05	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.631 Vsfold4: 0.559 Sensitivity HotKnots: 0.666 Vsfold4: 0.554 Positive Predictive Value HotKnots: 0.605 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.736 Murlet(seed): 0.571 Sensitivity HotKnots: 0.745 Murlet(seed): 0.386 Positive Predictive Value HotKnots: 0.733 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.725 Alterna: 0.647 Sensitivity HotKnots: 0.715 Alterna: 0.636 Positive Predictive Value HotKnots: 0.749 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.640 Mastr(20): 0.506 Sensitivity HotKnots: 0.663 Mastr(20): 0.337 Positive Predictive Value HotKnots: 0.623 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.631 Vsfold5: 0.518 Sensitivity HotKnots: 0.666 Vsfold5: 0.514 Positive Predictive Value HotKnots: 0.605 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.736 RDfolder: 0.549 Sensitivity HotKnots: 0.726 RDfolder: 0.487 Positive Predictive Value HotKnots: 0.758 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.667 MCFold: 0.527 Sensitivity HotKnots: 0.688 MCFold: 0.563 Positive Predictive Value HotKnots: 0.657 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.616 RSpredict(seed): 0.324 Sensitivity HotKnots: 0.657 RSpredict(seed): 0.177 Positive Predictive Value HotKnots: 0.582 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.736 Carnac(seed): 0.104 Sensitivity HotKnots: 0.745 Carnac(seed): 0.011 Positive Predictive Value HotKnots: 0.733 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.61939086268e-08	? HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.535 NanoFolder: 0.427 Sensitivity HotKnots: 0.577 NanoFolder: 0.519 Positive Predictive Value HotKnots: 0.508 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.651 CentroidHomfold‑LAST: 0.635 Sensitivity HotKnots: 0.678 CentroidHomfold‑LAST: 0.552 Positive Predictive Value HotKnots: 0.636 CentroidHomfold‑LAST: 0.743 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: 0.728 Multilign(seed): 0.629 Sensitivity HotKnots: 0.700 Multilign(seed): 0.580 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: 0.689 Multilign(20): 0.581 Sensitivity HotKnots: 0.712 Multilign(20): 0.576 Positive Predictive Value HotKnots: 0.676 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 HotKnots: 0.613 Sensitivity PETfold_pre2.0(seed): 0.619 HotKnots: 0.649 Positive Predictive Value PETfold_pre2.0(seed): 0.789 HotKnots: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.689 TurboFold(20): 0.653 Sensitivity HotKnots: 0.712 TurboFold(20): 0.606 Positive Predictive Value HotKnots: 0.676 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.651 RNAwolf: 0.436 Sensitivity HotKnots: 0.678 RNAwolf: 0.437 Positive Predictive Value HotKnots: 0.636 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs IPknot Matthews Correlation Coefficient HotKnots: 0.651 IPknot: 0.612 Sensitivity HotKnots: 0.678 IPknot: 0.579 Positive Predictive Value HotKnots: 0.636 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 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): 0.619 HotKnots: 0.609 Sensitivity PETfold_pre2.0(20): 0.570 HotKnots: 0.658 Positive Predictive Value PETfold_pre2.0(20): 0.682 HotKnots: 0.571 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.684 PPfold(seed): 0.155 Sensitivity HotKnots: 0.700 PPfold(seed): 0.047 Positive Predictive Value HotKnots: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.662 HotKnots: 0.587 Sensitivity ContextFold: 0.608 HotKnots: 0.631 Positive Predictive Value ContextFold: 0.731 HotKnots: 0.558 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.684 TurboFold(seed): 0.560 Sensitivity HotKnots: 0.700 TurboFold(seed): 0.533 Positive Predictive Value HotKnots: 0.677 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.618 CRWrnafold: 0.502 Sensitivity HotKnots: 0.654 CRWrnafold: 0.516 Positive Predictive Value HotKnots: 0.594 CRWrnafold: 0.503 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): 0.640 HotKnots: 0.639 Sensitivity RNASampler(seed): 0.554 HotKnots: 0.681 Positive Predictive Value RNASampler(seed): 0.748 HotKnots: 0.608 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.587 RNASLOpt: 0.449 Sensitivity HotKnots: 0.631 RNASLOpt: 0.438 Positive Predictive Value HotKnots: 0.558 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.715 HotKnots: 0.689 Sensitivity PPfold(20): 0.644 HotKnots: 0.712 Positive Predictive Value PPfold(20): 0.802 HotKnots: 0.676 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.616 Mastr(seed): 0.000 Sensitivity HotKnots: 0.657 Mastr(seed): 0.000 Positive Predictive Value HotKnots: 0.582 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08
RNAalifold(seed)	13 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.783 RNAalifold(seed): 0.685 Sensitivity CentroidAlifold(20): 0.667 RNAalifold(seed): 0.515 Positive Predictive Value CentroidAlifold(20): 0.923 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	16 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.753 RNAalifold(seed): 0.634 Sensitivity CentroidAlifold(seed): 0.640 RNAalifold(seed): 0.479 Positive Predictive Value CentroidAlifold(seed): 0.889 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.36983135185e-08	13 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.728 RNAalifold(seed): 0.685 Sensitivity RNAalifold(20): 0.626 RNAalifold(seed): 0.515 Positive Predictive Value RNAalifold(20): 0.851 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.19192530585e-08	16 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.681 RNAalifold(seed): 0.634 Sensitivity MXScarna(seed): 0.632 RNAalifold(seed): 0.479 Positive Predictive Value MXScarna(seed): 0.737 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.30280588002e-08	16 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.664 RNAalifold(seed): 0.634 Sensitivity CentroidFold: 0.661 RNAalifold(seed): 0.479 Positive Predictive Value CentroidFold: 0.671 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.36130997681e-08	13 RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.704 RNAalifold(seed): 0.685 Sensitivity RNASampler(20): 0.607 RNAalifold(seed): 0.515 Positive Predictive Value RNASampler(20): 0.822 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.66715895098e-08	13 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 RNAalifold(seed): 0.685 Sensitivity MXScarna(20): 0.643 RNAalifold(seed): 0.515 Positive Predictive Value MXScarna(20): 0.742 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00524908862044	16 Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.640 RNAalifold(seed): 0.634 Sensitivity Contrafold: 0.663 RNAalifold(seed): 0.479 Positive Predictive Value Contrafold: 0.622 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.000512952720519	16 Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.648 RNAalifold(seed): 0.634 Sensitivity Sfold: 0.638 RNAalifold(seed): 0.479 Positive Predictive Value Sfold: 0.664 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.9039628243e-08	15 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.623 MaxExpect: 0.601 Sensitivity RNAalifold(seed): 0.470 MaxExpect: 0.626 Positive Predictive Value RNAalifold(seed): 0.831 MaxExpect: 0.582 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.82294361511e-07	16 RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.634 HotKnots: 0.633 Sensitivity RNAalifold(seed): 0.479 HotKnots: 0.677 Positive Predictive Value RNAalifold(seed): 0.842 HotKnots: 0.597 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.00677354341424		+ RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 Murlet(20): 0.643 Sensitivity RNAalifold(seed): 0.515 Murlet(20): 0.519 Positive Predictive Value RNAalifold(seed): 0.918 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.634 UNAFold: 0.619 Sensitivity RNAalifold(seed): 0.479 UNAFold: 0.646 Positive Predictive Value RNAalifold(seed): 0.842 UNAFold: 0.599 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 6.77735941577e-06	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 Carnac(20): 0.640 Sensitivity RNAalifold(seed): 0.515 Carnac(20): 0.442 Positive Predictive Value RNAalifold(seed): 0.918 Carnac(20): 0.933 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.634 McQFold: 0.608 Sensitivity RNAalifold(seed): 0.479 McQFold: 0.638 Positive Predictive Value RNAalifold(seed): 0.842 McQFold: 0.585 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.634 RNAshapes: 0.615 Sensitivity RNAalifold(seed): 0.479 RNAshapes: 0.640 Positive Predictive Value RNAalifold(seed): 0.842 RNAshapes: 0.596 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.27752322258e-08	= RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.635 RNAalifold(seed): 0.634 Sensitivity RNAfold: 0.671 RNAalifold(seed): 0.479 Positive Predictive Value RNAfold: 0.606 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.241510530594	- PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.654 RNAalifold(seed): 0.634 Sensitivity PknotsRG: 0.697 RNAalifold(seed): 0.479 Positive Predictive Value PknotsRG: 0.618 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.1022514496e-08	+ RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.706 Pknots: 0.695 Sensitivity RNAalifold(seed): 0.564 Pknots: 0.712 Positive Predictive Value RNAalifold(seed): 0.892 Pknots: 0.686 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.000375209661743	- Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.567 RNAalifold(seed): 0.558 Sensitivity Afold: 0.617 RNAalifold(seed): 0.406 Positive Predictive Value Afold: 0.526 RNAalifold(seed): 0.772 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000382312754694	+ RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.589 ProbKnot: 0.542 Sensitivity RNAalifold(seed): 0.427 ProbKnot: 0.593 Positive Predictive Value RNAalifold(seed): 0.816 ProbKnot: 0.501 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.53777893337e-08	? Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.723 RNAalifold(seed): 0.670 Sensitivity Cylofold: 0.703 RNAalifold(seed): 0.530 Positive Predictive Value Cylofold: 0.751 RNAalifold(seed): 0.856 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.634 RNAsubopt: 0.601 Sensitivity RNAalifold(seed): 0.479 RNAsubopt: 0.634 Positive Predictive Value RNAalifold(seed): 0.842 RNAsubopt: 0.575 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.589 Fold: 0.532 Sensitivity RNAalifold(seed): 0.427 Fold: 0.570 Positive Predictive Value RNAalifold(seed): 0.816 Fold: 0.502 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 RSpredict(20): 0.590 Sensitivity RNAalifold(seed): 0.515 RSpredict(20): 0.524 Positive Predictive Value RNAalifold(seed): 0.918 RSpredict(20): 0.671 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.634 Vsfold4: 0.516 Sensitivity RNAalifold(seed): 0.479 Vsfold4: 0.517 Positive Predictive Value RNAalifold(seed): 0.842 Vsfold4: 0.522 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.706 Murlet(seed): 0.571 Sensitivity RNAalifold(seed): 0.564 Murlet(seed): 0.386 Positive Predictive Value RNAalifold(seed): 0.892 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.27752322258e-08	? Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.729 RNAalifold(seed): 0.686 Sensitivity Alterna: 0.701 RNAalifold(seed): 0.593 Positive Predictive Value Alterna: 0.770 RNAalifold(seed): 0.808 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 Mastr(20): 0.453 Sensitivity RNAalifold(seed): 0.515 Mastr(20): 0.284 Positive Predictive Value RNAalifold(seed): 0.918 Mastr(20): 0.731 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.634 Vsfold5: 0.479 Sensitivity RNAalifold(seed): 0.479 Vsfold5: 0.477 Positive Predictive Value RNAalifold(seed): 0.842 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.698 RDfolder: 0.586 Sensitivity RNAalifold(seed): 0.585 RDfolder: 0.513 Positive Predictive Value RNAalifold(seed): 0.847 RDfolder: 0.688 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.69265863073e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.684 MCFold: 0.567 Sensitivity RNAalifold(seed): 0.545 MCFold: 0.599 Positive Predictive Value RNAalifold(seed): 0.867 MCFold: 0.547 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.634 RSpredict(seed): 0.340 Sensitivity RNAalifold(seed): 0.479 RSpredict(seed): 0.192 Positive Predictive Value RNAalifold(seed): 0.842 RSpredict(seed): 0.613 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.706 Carnac(seed): 0.104 Sensitivity RNAalifold(seed): 0.564 Carnac(seed): 0.011 Positive Predictive Value RNAalifold(seed): 0.892 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.529 NanoFolder: 0.336 Sensitivity RNAalifold(seed): 0.390 NanoFolder: 0.415 Positive Predictive Value RNAalifold(seed): 0.727 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RNAalifold(seed): 0.610 Sensitivity CentroidHomfold‑LAST: 0.567 RNAalifold(seed): 0.473 Positive Predictive Value CentroidHomfold‑LAST: 0.746 RNAalifold(seed): 0.798 Number of pairs reference - predicted secondary structure: 7 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): 0.629 Multilign(seed): 0.629 Sensitivity RNAalifold(seed): 0.540 Multilign(seed): 0.580 Positive Predictive Value RNAalifold(seed): 0.750 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): 0.701 Multilign(20): 0.581 Sensitivity RNAalifold(seed): 0.538 Multilign(20): 0.576 Positive Predictive Value RNAalifold(seed): 0.922 Multilign(20): 0.598 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): 0.695 RNAalifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.619 RNAalifold(seed): 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAalifold(seed): 0.760 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): 0.701 TurboFold(20): 0.653 Sensitivity RNAalifold(seed): 0.538 TurboFold(20): 0.606 Positive Predictive Value RNAalifold(seed): 0.922 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNAwolf: 0.451 Sensitivity RNAalifold(seed): 0.473 RNAwolf: 0.447 Positive Predictive Value RNAalifold(seed): 0.798 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.610 IPknot: 0.601 Sensitivity RNAalifold(seed): 0.473 IPknot: 0.560 Positive Predictive Value RNAalifold(seed): 0.798 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 7 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): 0.691 PETfold_pre2.0(20): 0.619 Sensitivity RNAalifold(seed): 0.481 PETfold_pre2.0(20): 0.570 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 PPfold(seed): 0.155 Sensitivity RNAalifold(seed): 0.473 PPfold(seed): 0.047 Positive Predictive Value RNAalifold(seed): 0.798 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.570 RNAalifold(seed): 0.542 Sensitivity ContextFold: 0.515 RNAalifold(seed): 0.392 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.760 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 TurboFold(seed): 0.560 Sensitivity RNAalifold(seed): 0.473 TurboFold(seed): 0.533 Positive Predictive Value RNAalifold(seed): 0.798 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.582 CRWrnafold: 0.513 Sensitivity RNAalifold(seed): 0.437 CRWrnafold: 0.524 Positive Predictive Value RNAalifold(seed): 0.786 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 RNAalifold(seed): 0.612 Sensitivity RNASampler(seed): 0.554 RNAalifold(seed): 0.482 Positive Predictive Value RNASampler(seed): 0.748 RNAalifold(seed): 0.784 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.542 RNASLOpt: 0.461 Sensitivity RNAalifold(seed): 0.392 RNASLOpt: 0.443 Positive Predictive Value RNAalifold(seed): 0.760 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.715 RNAalifold(seed): 0.701 Sensitivity PPfold(20): 0.644 RNAalifold(seed): 0.538 Positive Predictive Value PPfold(20): 0.802 RNAalifold(seed): 0.922 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): 0.634 Mastr(seed): 0.000 Sensitivity RNAalifold(seed): 0.479 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.842 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.84361416392e-08
Murlet(20)	15 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Murlet(20): 0.666 Sensitivity CentroidAlifold(20): 0.694 Murlet(20): 0.548 Positive Predictive Value CentroidAlifold(20): 0.932 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	15 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 Murlet(20): 0.666 Sensitivity CentroidAlifold(seed): 0.623 Murlet(20): 0.548 Positive Predictive Value CentroidAlifold(seed): 0.934 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	15 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 Murlet(20): 0.666 Sensitivity RNAalifold(20): 0.656 Murlet(20): 0.548 Positive Predictive Value RNAalifold(20): 0.869 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 Murlet(20): 0.666 Sensitivity MXScarna(seed): 0.692 Murlet(20): 0.548 Positive Predictive Value MXScarna(seed): 0.820 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	15 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.716 Murlet(20): 0.666 Sensitivity CentroidFold: 0.687 Murlet(20): 0.548 Positive Predictive Value CentroidFold: 0.750 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	15 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.732 Murlet(20): 0.666 Sensitivity RNASampler(20): 0.639 Murlet(20): 0.548 Positive Predictive Value RNASampler(20): 0.843 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.72523032126e-08	15 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.703 Murlet(20): 0.666 Sensitivity MXScarna(20): 0.659 Murlet(20): 0.548 Positive Predictive Value MXScarna(20): 0.755 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.66715895098e-08	15 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.666 Contrafold: 0.650 Sensitivity Murlet(20): 0.548 Contrafold: 0.652 Positive Predictive Value Murlet(20): 0.814 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.42587965167e-05	15 Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.666 Sfold: 0.665 Sensitivity Murlet(20): 0.548 Sfold: 0.628 Positive Predictive Value Murlet(20): 0.814 Sfold: 0.711 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.402525058148	15 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.674 Murlet(20): 0.666 Sensitivity MaxExpect: 0.670 Murlet(20): 0.548 Positive Predictive Value MaxExpect: 0.683 Murlet(20): 0.814 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00189913880948	15 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.666 HotKnots: 0.640 Sensitivity Murlet(20): 0.548 HotKnots: 0.663 Positive Predictive Value Murlet(20): 0.814 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.40910484167e-08	13 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 Murlet(20): 0.643 Sensitivity RNAalifold(seed): 0.515 Murlet(20): 0.519 Positive Predictive Value RNAalifold(seed): 0.918 Murlet(20): 0.801 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08		+ Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.666 UNAFold: 0.662 Sensitivity Murlet(20): 0.548 UNAFold: 0.663 Positive Predictive Value Murlet(20): 0.814 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000336430132841	= Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.666 Carnac(20): 0.662 Sensitivity Murlet(20): 0.548 Carnac(20): 0.469 Positive Predictive Value Murlet(20): 0.814 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00367102518342	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.666 McQFold: 0.644 Sensitivity Murlet(20): 0.548 McQFold: 0.643 Positive Predictive Value Murlet(20): 0.814 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.30067511844e-06	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.666 RNAshapes: 0.637 Sensitivity Murlet(20): 0.548 RNAshapes: 0.637 Positive Predictive Value Murlet(20): 0.814 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.56330076937e-08	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.666 RNAfold: 0.643 Sensitivity Murlet(20): 0.548 RNAfold: 0.656 Positive Predictive Value Murlet(20): 0.814 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.99165002974e-07	= Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.666 PknotsRG: 0.664 Sensitivity Murlet(20): 0.548 PknotsRG: 0.685 Positive Predictive Value Murlet(20): 0.814 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0719792426829	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.712 Pknots: 0.670 Sensitivity Murlet(20): 0.607 Pknots: 0.691 Positive Predictive Value Murlet(20): 0.842 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86826635779e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.596 Afold: 0.565 Sensitivity Murlet(20): 0.479 Afold: 0.591 Positive Predictive Value Murlet(20): 0.747 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24852078119e-08	- ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.630 Murlet(20): 0.614 Sensitivity ProbKnot: 0.664 Murlet(20): 0.500 Positive Predictive Value ProbKnot: 0.603 Murlet(20): 0.760 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.0482910291e-08	? Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.739 Cylofold: 0.731 Sensitivity Murlet(20): 0.630 Cylofold: 0.712 Positive Predictive Value Murlet(20): 0.872 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.666 RNAsubopt: 0.620 Sensitivity Murlet(20): 0.548 RNAsubopt: 0.632 Positive Predictive Value Murlet(20): 0.814 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.21671975982e-08	= Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.621 Murlet(20): 0.614 Sensitivity Fold: 0.637 Murlet(20): 0.500 Positive Predictive Value Fold: 0.611 Murlet(20): 0.760 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00173322773106	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.666 RSpredict(20): 0.624 Sensitivity Murlet(20): 0.548 RSpredict(20): 0.559 Positive Predictive Value Murlet(20): 0.814 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.666 Vsfold4: 0.545 Sensitivity Murlet(20): 0.548 Vsfold4: 0.526 Positive Predictive Value Murlet(20): 0.814 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.690 Murlet(seed): 0.607 Sensitivity Murlet(20): 0.577 Murlet(seed): 0.407 Positive Predictive Value Murlet(20): 0.832 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.30295446166e-08	? Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.808 Alterna: 0.593 Sensitivity Murlet(20): 0.708 Alterna: 0.596 Positive Predictive Value Murlet(20): 0.931 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.666 Mastr(20): 0.506 Sensitivity Murlet(20): 0.548 Mastr(20): 0.337 Positive Predictive Value Murlet(20): 0.814 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.666 Vsfold5: 0.495 Sensitivity Murlet(20): 0.548 Vsfold5: 0.480 Positive Predictive Value Murlet(20): 0.814 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.786 RDfolder: 0.613 Sensitivity Murlet(20): 0.661 RDfolder: 0.552 Positive Predictive Value Murlet(20): 0.944 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.704 MCFold: 0.506 Sensitivity Murlet(20): 0.614 MCFold: 0.546 Positive Predictive Value Murlet(20): 0.814 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.666 RSpredict(seed): 0.350 Sensitivity Murlet(20): 0.548 RSpredict(seed): 0.181 Positive Predictive Value Murlet(20): 0.814 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.690 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.577 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.832 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 7.21563533328e-09	? Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.551 NanoFolder: 0.285 Sensitivity Murlet(20): 0.500 NanoFolder: 0.359 Positive Predictive Value Murlet(20): 0.615 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Murlet(20): 0.654 Sensitivity CentroidHomfold‑LAST: 0.644 Murlet(20): 0.576 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 6 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): 0.833 Multilign(seed): 0.755 Sensitivity Murlet(20): 0.756 Multilign(seed): 0.707 Positive Predictive Value Murlet(20): 0.925 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): 0.654 Multilign(20): 0.581 Sensitivity Murlet(20): 0.576 Multilign(20): 0.576 Positive Predictive Value Murlet(20): 0.752 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 Murlet(20): 0.537 Sensitivity PETfold_pre2.0(seed): 0.684 Murlet(20): 0.456 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs TurboFold(20) Matthews Correlation Coefficient Murlet(20): 0.654 TurboFold(20): 0.653 Sensitivity Murlet(20): 0.576 TurboFold(20): 0.606 Positive Predictive Value Murlet(20): 0.752 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.654 RNAwolf: 0.442 Sensitivity Murlet(20): 0.576 RNAwolf: 0.439 Positive Predictive Value Murlet(20): 0.752 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.654 IPknot: 0.623 Sensitivity Murlet(20): 0.576 IPknot: 0.591 Positive Predictive Value Murlet(20): 0.752 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 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): 0.619 Murlet(20): 0.537 Sensitivity PETfold_pre2.0(20): 0.570 Murlet(20): 0.456 Positive Predictive Value PETfold_pre2.0(20): 0.682 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.654 PPfold(seed): 0.036 Sensitivity Murlet(20): 0.576 PPfold(seed): 0.008 Positive Predictive Value Murlet(20): 0.752 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.567 Murlet(20): 0.537 Sensitivity ContextFold: 0.506 Murlet(20): 0.456 Positive Predictive Value ContextFold: 0.645 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs TurboFold(seed) Matthews Correlation Coefficient Murlet(20): 0.654 TurboFold(seed): 0.636 Sensitivity Murlet(20): 0.576 TurboFold(seed): 0.606 Positive Predictive Value Murlet(20): 0.752 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.622 CRWrnafold: 0.592 Sensitivity Murlet(20): 0.556 CRWrnafold: 0.611 Positive Predictive Value Murlet(20): 0.706 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 Murlet(20): 0.610 Sensitivity RNASampler(seed): 0.627 Murlet(20): 0.568 Positive Predictive Value RNASampler(seed): 0.779 Murlet(20): 0.663 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.537 RNASLOpt: 0.459 Sensitivity Murlet(20): 0.456 RNASLOpt: 0.456 Positive Predictive Value Murlet(20): 0.643 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.715 Murlet(20): 0.654 Sensitivity PPfold(20): 0.644 Murlet(20): 0.576 Positive Predictive Value PPfold(20): 0.802 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.666 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.548 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.814 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08
UNAFold	15 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 UNAFold: 0.662 Sensitivity CentroidAlifold(20): 0.694 UNAFold: 0.663 Positive Predictive Value CentroidAlifold(20): 0.932 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.18141491686e-08	19 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 UNAFold: 0.613 Sensitivity CentroidAlifold(seed): 0.598 UNAFold: 0.638 Positive Predictive Value CentroidAlifold(seed): 0.894 UNAFold: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	15 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.753 UNAFold: 0.662 Sensitivity RNAalifold(20): 0.656 UNAFold: 0.663 Positive Predictive Value RNAalifold(20): 0.869 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	19 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.711 UNAFold: 0.613 Sensitivity MXScarna(seed): 0.663 UNAFold: 0.638 Positive Predictive Value MXScarna(seed): 0.768 UNAFold: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.63594052159e-08	27 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.641 UNAFold: 0.509 Sensitivity CentroidFold: 0.639 UNAFold: 0.554 Positive Predictive Value CentroidFold: 0.644 UNAFold: 0.467 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.732 UNAFold: 0.662 Sensitivity RNASampler(20): 0.639 UNAFold: 0.663 Positive Predictive Value RNASampler(20): 0.843 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	15 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.703 UNAFold: 0.662 Sensitivity MXScarna(20): 0.659 UNAFold: 0.663 Positive Predictive Value MXScarna(20): 0.755 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	31 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.638 UNAFold: 0.502 Sensitivity Contrafold: 0.665 UNAFold: 0.539 Positive Predictive Value Contrafold: 0.613 UNAFold: 0.469 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.530 UNAFold: 0.502 Sensitivity Sfold: 0.530 UNAFold: 0.539 Positive Predictive Value Sfold: 0.529 UNAFold: 0.469 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.648 UNAFold: 0.554 Sensitivity MaxExpect: 0.660 UNAFold: 0.575 Positive Predictive Value MaxExpect: 0.637 UNAFold: 0.535 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.633 HotKnots: 0.631 Sensitivity UNAFold: 0.655 HotKnots: 0.666 Positive Predictive Value UNAFold: 0.619 HotKnots: 0.605 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.193426068958	16 RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.634 UNAFold: 0.619 Sensitivity RNAalifold(seed): 0.479 UNAFold: 0.646 Positive Predictive Value RNAalifold(seed): 0.842 UNAFold: 0.599 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 6.77735941577e-06	15 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.666 UNAFold: 0.662 Sensitivity Murlet(20): 0.548 UNAFold: 0.663 Positive Predictive Value Murlet(20): 0.814 UNAFold: 0.667 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000336430132841		= UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.662 Carnac(20): 0.662 Sensitivity UNAFold: 0.663 Carnac(20): 0.469 Positive Predictive Value UNAFold: 0.667 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0862804870082	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.502 McQFold: 0.415 Sensitivity UNAFold: 0.539 McQFold: 0.382 Positive Predictive Value UNAFold: 0.469 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.633 RNAshapes: 0.610 Sensitivity UNAFold: 0.655 RNAshapes: 0.625 Positive Predictive Value UNAFold: 0.619 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.502 RNAfold: 0.498 Sensitivity UNAFold: 0.539 RNAfold: 0.540 Positive Predictive Value UNAFold: 0.469 RNAfold: 0.460 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.502 PknotsRG: 0.486 Sensitivity UNAFold: 0.539 PknotsRG: 0.529 Positive Predictive Value UNAFold: 0.469 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.694 Pknots: 0.676 Sensitivity UNAFold: 0.692 Pknots: 0.693 Positive Predictive Value UNAFold: 0.706 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.35631047551e-06	- Afold vs UNAFold Matthews Correlation Coefficient Afold: 0.493 UNAFold: 0.485 Sensitivity Afold: 0.537 UNAFold: 0.524 Positive Predictive Value Afold: 0.453 UNAFold: 0.450 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.12827206146e-07	+ UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.573 ProbKnot: 0.564 Sensitivity UNAFold: 0.610 ProbKnot: 0.613 Positive Predictive Value UNAFold: 0.544 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	- Cylofold vs UNAFold Matthews Correlation Coefficient Cylofold: 0.693 UNAFold: 0.687 Sensitivity Cylofold: 0.681 UNAFold: 0.687 Positive Predictive Value Cylofold: 0.715 UNAFold: 0.696 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000113973846536	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.633 RNAsubopt: 0.591 Sensitivity UNAFold: 0.655 RNAsubopt: 0.615 Positive Predictive Value UNAFold: 0.619 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.590 Fold: 0.557 Sensitivity UNAFold: 0.626 Fold: 0.589 Positive Predictive Value UNAFold: 0.562 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.662 RSpredict(20): 0.624 Sensitivity UNAFold: 0.663 RSpredict(20): 0.559 Positive Predictive Value UNAFold: 0.667 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.01438538033e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.633 Vsfold4: 0.559 Sensitivity UNAFold: 0.655 Vsfold4: 0.554 Positive Predictive Value UNAFold: 0.619 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.712 Murlet(seed): 0.571 Sensitivity UNAFold: 0.701 Murlet(seed): 0.386 Positive Predictive Value UNAFold: 0.731 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.38194587311e-08	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.720 Alterna: 0.647 Sensitivity UNAFold: 0.706 Alterna: 0.636 Positive Predictive Value UNAFold: 0.746 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.662 Mastr(20): 0.506 Sensitivity UNAFold: 0.663 Mastr(20): 0.337 Positive Predictive Value UNAFold: 0.667 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.633 Vsfold5: 0.518 Sensitivity UNAFold: 0.655 Vsfold5: 0.514 Positive Predictive Value UNAFold: 0.619 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.704 RDfolder: 0.549 Sensitivity UNAFold: 0.685 RDfolder: 0.487 Positive Predictive Value UNAFold: 0.737 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.667 MCFold: 0.527 Sensitivity UNAFold: 0.671 MCFold: 0.563 Positive Predictive Value UNAFold: 0.672 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.613 RSpredict(seed): 0.324 Sensitivity UNAFold: 0.638 RSpredict(seed): 0.177 Positive Predictive Value UNAFold: 0.594 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.712 Carnac(seed): 0.104 Sensitivity UNAFold: 0.701 Carnac(seed): 0.011 Positive Predictive Value UNAFold: 0.731 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.10032755566e-08	? NanoFolder vs UNAFold Matthews Correlation Coefficient NanoFolder: 0.427 UNAFold: 0.353 Sensitivity NanoFolder: 0.519 UNAFold: 0.375 Positive Predictive Value NanoFolder: 0.365 UNAFold: 0.348 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 UNAFold: 0.531 Sensitivity CentroidHomfold‑LAST: 0.552 UNAFold: 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.743 UNAFold: 0.535 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): 0.629 UNAFold: 0.614 Sensitivity Multilign(seed): 0.580 UNAFold: 0.590 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: 0.605 Multilign(20): 0.581 Sensitivity UNAFold: 0.606 Multilign(20): 0.576 Positive Predictive Value UNAFold: 0.615 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 UNAFold: 0.384 Sensitivity PETfold_pre2.0(seed): 0.619 UNAFold: 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 UNAFold: 0.392 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.653 UNAFold: 0.605 Sensitivity TurboFold(20): 0.606 UNAFold: 0.606 Positive Predictive Value TurboFold(20): 0.714 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.531 RNAwolf: 0.436 Sensitivity UNAFold: 0.541 RNAwolf: 0.437 Positive Predictive Value UNAFold: 0.535 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.612 UNAFold: 0.531 Sensitivity IPknot: 0.579 UNAFold: 0.541 Positive Predictive Value IPknot: 0.658 UNAFold: 0.535 Number of pairs reference - predicted secondary structure: 9 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): 0.619 UNAFold: 0.466 Sensitivity PETfold_pre2.0(20): 0.570 UNAFold: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 UNAFold: 0.463 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.536 PPfold(seed): 0.155 Sensitivity UNAFold: 0.533 PPfold(seed): 0.047 Positive Predictive Value UNAFold: 0.552 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.662 UNAFold: 0.419 Sensitivity ContextFold: 0.608 UNAFold: 0.438 Positive Predictive Value ContextFold: 0.731 UNAFold: 0.416 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.560 UNAFold: 0.536 Sensitivity TurboFold(seed): 0.533 UNAFold: 0.533 Positive Predictive Value TurboFold(seed): 0.602 UNAFold: 0.552 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.502 UNAFold: 0.480 Sensitivity CRWrnafold: 0.516 UNAFold: 0.497 Positive Predictive Value CRWrnafold: 0.503 UNAFold: 0.479 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): 0.640 UNAFold: 0.613 Sensitivity RNASampler(seed): 0.554 UNAFold: 0.633 Positive Predictive Value RNASampler(seed): 0.748 UNAFold: 0.603 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs UNAFold Matthews Correlation Coefficient RNASLOpt: 0.449 UNAFold: 0.419 Sensitivity RNASLOpt: 0.438 UNAFold: 0.438 Positive Predictive Value RNASLOpt: 0.475 UNAFold: 0.416 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.715 UNAFold: 0.605 Sensitivity PPfold(20): 0.644 UNAFold: 0.606 Positive Predictive Value PPfold(20): 0.802 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.613 Mastr(seed): 0.000 Sensitivity UNAFold: 0.638 Mastr(seed): 0.000 Positive Predictive Value UNAFold: 0.594 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08
Carnac(20)	15 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Carnac(20): 0.662 Sensitivity CentroidAlifold(20): 0.694 Carnac(20): 0.469 Positive Predictive Value CentroidAlifold(20): 0.932 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	15 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 Carnac(20): 0.662 Sensitivity CentroidAlifold(seed): 0.623 Carnac(20): 0.469 Positive Predictive Value CentroidAlifold(seed): 0.934 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 Carnac(20): 0.662 Sensitivity RNAalifold(20): 0.656 Carnac(20): 0.469 Positive Predictive Value RNAalifold(20): 0.869 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 Carnac(20): 0.662 Sensitivity MXScarna(seed): 0.692 Carnac(20): 0.469 Positive Predictive Value MXScarna(seed): 0.820 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.13392142882e-08	15 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.716 Carnac(20): 0.662 Sensitivity CentroidFold: 0.687 Carnac(20): 0.469 Positive Predictive Value CentroidFold: 0.750 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.16131455263e-08	15 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.732 Carnac(20): 0.662 Sensitivity RNASampler(20): 0.639 Carnac(20): 0.469 Positive Predictive Value RNASampler(20): 0.843 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	15 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.703 Carnac(20): 0.662 Sensitivity MXScarna(20): 0.659 Carnac(20): 0.469 Positive Predictive Value MXScarna(20): 0.755 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.662 Contrafold: 0.650 Sensitivity Carnac(20): 0.469 Contrafold: 0.652 Positive Predictive Value Carnac(20): 0.938 Contrafold: 0.655 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000793683551711	15 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.665 Carnac(20): 0.662 Sensitivity Sfold: 0.628 Carnac(20): 0.469 Positive Predictive Value Sfold: 0.711 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0255587090362	15 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.674 Carnac(20): 0.662 Sensitivity MaxExpect: 0.670 Carnac(20): 0.469 Positive Predictive Value MaxExpect: 0.683 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000120909053629	15 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.662 HotKnots: 0.640 Sensitivity Carnac(20): 0.469 HotKnots: 0.663 Positive Predictive Value Carnac(20): 0.938 HotKnots: 0.623 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.03796748738e-07	13 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 Carnac(20): 0.640 Sensitivity RNAalifold(seed): 0.515 Carnac(20): 0.442 Positive Predictive Value RNAalifold(seed): 0.918 Carnac(20): 0.933 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	15 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.666 Carnac(20): 0.662 Sensitivity Murlet(20): 0.548 Carnac(20): 0.469 Positive Predictive Value Murlet(20): 0.814 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00367102518342	15 UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.662 Carnac(20): 0.662 Sensitivity UNAFold: 0.663 Carnac(20): 0.469 Positive Predictive Value UNAFold: 0.667 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0862804870082		= Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.662 McQFold: 0.644 Sensitivity Carnac(20): 0.469 McQFold: 0.643 Positive Predictive Value Carnac(20): 0.938 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00205533278294	+ Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.662 RNAshapes: 0.637 Sensitivity Carnac(20): 0.469 RNAshapes: 0.637 Positive Predictive Value Carnac(20): 0.938 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.78495854732e-07	+ Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.662 RNAfold: 0.643 Sensitivity Carnac(20): 0.469 RNAfold: 0.656 Positive Predictive Value Carnac(20): 0.938 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.72263550878e-05	= PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.664 Carnac(20): 0.662 Sensitivity PknotsRG: 0.685 Carnac(20): 0.469 Positive Predictive Value PknotsRG: 0.649 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0376522112878	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.695 Pknots: 0.670 Sensitivity Carnac(20): 0.513 Pknots: 0.691 Positive Predictive Value Carnac(20): 0.948 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.16482497632e-07	+ Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.664 Afold: 0.565 Sensitivity Carnac(20): 0.465 Afold: 0.591 Positive Predictive Value Carnac(20): 0.953 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.64686604905e-09	- ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.630 Carnac(20): 0.589 Sensitivity ProbKnot: 0.664 Carnac(20): 0.384 Positive Predictive Value ProbKnot: 0.603 Carnac(20): 0.908 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	? Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.731 Carnac(20): 0.659 Sensitivity Cylofold: 0.712 Carnac(20): 0.473 Positive Predictive Value Cylofold: 0.757 Carnac(20): 0.926 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.662 RNAsubopt: 0.620 Sensitivity Carnac(20): 0.469 RNAsubopt: 0.632 Positive Predictive Value Carnac(20): 0.938 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	- Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.621 Carnac(20): 0.589 Sensitivity Fold: 0.637 Carnac(20): 0.384 Positive Predictive Value Fold: 0.611 Carnac(20): 0.908 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.84540901819e-09	+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.662 RSpredict(20): 0.624 Sensitivity Carnac(20): 0.469 RSpredict(20): 0.559 Positive Predictive Value Carnac(20): 0.938 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.662 Vsfold4: 0.545 Sensitivity Carnac(20): 0.469 Vsfold4: 0.526 Positive Predictive Value Carnac(20): 0.938 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.673 Murlet(seed): 0.607 Sensitivity Carnac(20): 0.483 Murlet(seed): 0.407 Positive Predictive Value Carnac(20): 0.944 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	? Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.828 Alterna: 0.593 Sensitivity Carnac(20): 0.702 Alterna: 0.596 Positive Predictive Value Carnac(20): 0.984 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.662 Mastr(20): 0.506 Sensitivity Carnac(20): 0.469 Mastr(20): 0.337 Positive Predictive Value Carnac(20): 0.938 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.662 Vsfold5: 0.495 Sensitivity Carnac(20): 0.469 Vsfold5: 0.480 Positive Predictive Value Carnac(20): 0.938 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.740 RDfolder: 0.613 Sensitivity Carnac(20): 0.583 RDfolder: 0.552 Positive Predictive Value Carnac(20): 0.950 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.730 MCFold: 0.506 Sensitivity Carnac(20): 0.553 MCFold: 0.546 Positive Predictive Value Carnac(20): 0.970 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.662 RSpredict(seed): 0.350 Sensitivity Carnac(20): 0.469 RSpredict(seed): 0.181 Positive Predictive Value Carnac(20): 0.938 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.673 Carnac(seed): 0.000 Sensitivity Carnac(20): 0.483 Carnac(seed): 0.000 Positive Predictive Value Carnac(20): 0.944 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.03576421863e-08	? Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.463 NanoFolder: 0.285 Sensitivity Carnac(20): 0.297 NanoFolder: 0.359 Positive Predictive Value Carnac(20): 0.731 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Carnac(20): 0.600 Sensitivity CentroidHomfold‑LAST: 0.644 Carnac(20): 0.417 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 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): 0.755 Carnac(20): 0.733 Sensitivity Multilign(seed): 0.707 Carnac(20): 0.610 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): 0.600 Multilign(20): 0.581 Sensitivity Carnac(20): 0.417 Multilign(20): 0.576 Positive Predictive Value Carnac(20): 0.873 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 Carnac(20): 0.416 Sensitivity PETfold_pre2.0(seed): 0.684 Carnac(20): 0.241 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.653 Carnac(20): 0.600 Sensitivity TurboFold(20): 0.606 Carnac(20): 0.417 Positive Predictive Value TurboFold(20): 0.714 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.600 RNAwolf: 0.442 Sensitivity Carnac(20): 0.417 RNAwolf: 0.439 Positive Predictive Value Carnac(20): 0.873 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.623 Carnac(20): 0.600 Sensitivity IPknot: 0.591 Carnac(20): 0.417 Positive Predictive Value IPknot: 0.667 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 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): 0.619 Carnac(20): 0.416 Sensitivity PETfold_pre2.0(20): 0.570 Carnac(20): 0.241 Positive Predictive Value PETfold_pre2.0(20): 0.682 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.600 PPfold(seed): 0.036 Sensitivity Carnac(20): 0.417 PPfold(seed): 0.008 Positive Predictive Value Carnac(20): 0.873 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.567 Carnac(20): 0.416 Sensitivity ContextFold: 0.506 Carnac(20): 0.241 Positive Predictive Value ContextFold: 0.645 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 Carnac(20): 0.600 Sensitivity TurboFold(seed): 0.606 Carnac(20): 0.417 Positive Predictive Value TurboFold(seed): 0.678 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.592 Carnac(20): 0.510 Sensitivity CRWrnafold: 0.611 Carnac(20): 0.324 Positive Predictive Value CRWrnafold: 0.584 Carnac(20): 0.814 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNASampler(seed) Matthews Correlation Coefficient Carnac(20): 0.741 RNASampler(seed): 0.696 Sensitivity Carnac(20): 0.576 RNASampler(seed): 0.627 Positive Predictive Value Carnac(20): 0.958 RNASampler(seed): 0.779 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.459 Carnac(20): 0.416 Sensitivity RNASLOpt: 0.456 Carnac(20): 0.241 Positive Predictive Value RNASLOpt: 0.474 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.715 Carnac(20): 0.600 Sensitivity PPfold(20): 0.644 Carnac(20): 0.417 Positive Predictive Value PPfold(20): 0.802 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.662 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.469 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.938 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08
McQFold	15 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 McQFold: 0.644 Sensitivity CentroidAlifold(20): 0.694 McQFold: 0.643 Positive Predictive Value CentroidAlifold(20): 0.932 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.54914456376e-08	19 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 McQFold: 0.613 Sensitivity CentroidAlifold(seed): 0.598 McQFold: 0.640 Positive Predictive Value CentroidAlifold(seed): 0.894 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.94377603181e-08	15 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.753 McQFold: 0.644 Sensitivity RNAalifold(20): 0.656 McQFold: 0.643 Positive Predictive Value RNAalifold(20): 0.869 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	19 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.711 McQFold: 0.613 Sensitivity MXScarna(seed): 0.663 McQFold: 0.640 Positive Predictive Value MXScarna(seed): 0.768 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.60448791174e-08	27 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.641 McQFold: 0.433 Sensitivity CentroidFold: 0.639 McQFold: 0.383 Positive Predictive Value CentroidFold: 0.644 McQFold: 0.491 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.732 McQFold: 0.644 Sensitivity RNASampler(20): 0.639 McQFold: 0.643 Positive Predictive Value RNASampler(20): 0.843 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	15 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.703 McQFold: 0.644 Sensitivity MXScarna(20): 0.659 McQFold: 0.643 Positive Predictive Value MXScarna(20): 0.755 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	31 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.638 McQFold: 0.415 Sensitivity Contrafold: 0.665 McQFold: 0.382 Positive Predictive Value Contrafold: 0.613 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	31 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.530 McQFold: 0.415 Sensitivity Sfold: 0.530 McQFold: 0.382 Positive Predictive Value Sfold: 0.529 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	24 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.648 McQFold: 0.482 Sensitivity MaxExpect: 0.660 McQFold: 0.490 Positive Predictive Value MaxExpect: 0.637 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.631 McQFold: 0.624 Sensitivity HotKnots: 0.666 McQFold: 0.641 Positive Predictive Value HotKnots: 0.605 McQFold: 0.614 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000493106477465	16 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.634 McQFold: 0.608 Sensitivity RNAalifold(seed): 0.479 McQFold: 0.638 Positive Predictive Value RNAalifold(seed): 0.842 McQFold: 0.585 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	15 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.666 McQFold: 0.644 Sensitivity Murlet(20): 0.548 McQFold: 0.643 Positive Predictive Value Murlet(20): 0.814 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.30067511844e-06	31 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.502 McQFold: 0.415 Sensitivity UNAFold: 0.539 McQFold: 0.382 Positive Predictive Value UNAFold: 0.469 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.662 McQFold: 0.644 Sensitivity Carnac(20): 0.469 McQFold: 0.643 Positive Predictive Value Carnac(20): 0.938 McQFold: 0.650 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00205533278294		+ McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.624 RNAshapes: 0.610 Sensitivity McQFold: 0.641 RNAshapes: 0.625 Positive Predictive Value McQFold: 0.614 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.62644058675e-08	- RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.498 McQFold: 0.415 Sensitivity RNAfold: 0.540 McQFold: 0.382 Positive Predictive Value RNAfold: 0.460 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.486 McQFold: 0.415 Sensitivity PknotsRG: 0.529 McQFold: 0.382 Positive Predictive Value PknotsRG: 0.448 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.706 Pknots: 0.676 Sensitivity McQFold: 0.698 Pknots: 0.693 Positive Predictive Value McQFold: 0.723 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 6.38150542963e-08	- Afold vs McQFold Matthews Correlation Coefficient Afold: 0.493 McQFold: 0.392 Sensitivity Afold: 0.537 McQFold: 0.360 Positive Predictive Value Afold: 0.453 McQFold: 0.429 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ McQFold vs ProbKnot Matthews Correlation Coefficient McQFold: 0.572 ProbKnot: 0.564 Sensitivity McQFold: 0.606 ProbKnot: 0.613 Positive Predictive Value McQFold: 0.545 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 4.35504921354e-07	+ McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.738 Cylofold: 0.693 Sensitivity McQFold: 0.735 Cylofold: 0.681 Positive Predictive Value McQFold: 0.748 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ McQFold vs RNAsubopt Matthews Correlation Coefficient McQFold: 0.624 RNAsubopt: 0.591 Sensitivity McQFold: 0.641 RNAsubopt: 0.615 Positive Predictive Value McQFold: 0.614 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ McQFold vs Fold Matthews Correlation Coefficient McQFold: 0.597 Fold: 0.557 Sensitivity McQFold: 0.630 Fold: 0.589 Positive Predictive Value McQFold: 0.571 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.644 RSpredict(20): 0.624 Sensitivity McQFold: 0.643 RSpredict(20): 0.559 Positive Predictive Value McQFold: 0.650 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.09795090663e-05	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.624 Vsfold4: 0.559 Sensitivity McQFold: 0.641 Vsfold4: 0.554 Positive Predictive Value McQFold: 0.614 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.732 Murlet(seed): 0.571 Sensitivity McQFold: 0.729 Murlet(seed): 0.386 Positive Predictive Value McQFold: 0.743 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.717 Alterna: 0.647 Sensitivity McQFold: 0.689 Alterna: 0.636 Positive Predictive Value McQFold: 0.758 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.644 Mastr(20): 0.506 Sensitivity McQFold: 0.643 Mastr(20): 0.337 Positive Predictive Value McQFold: 0.650 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.624 Vsfold5: 0.518 Sensitivity McQFold: 0.641 Vsfold5: 0.514 Positive Predictive Value McQFold: 0.614 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.85839946686e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.722 RDfolder: 0.549 Sensitivity McQFold: 0.697 RDfolder: 0.487 Positive Predictive Value McQFold: 0.760 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.683 MCFold: 0.527 Sensitivity McQFold: 0.677 MCFold: 0.563 Positive Predictive Value McQFold: 0.698 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.613 RSpredict(seed): 0.324 Sensitivity McQFold: 0.640 RSpredict(seed): 0.177 Positive Predictive Value McQFold: 0.593 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.732 Carnac(seed): 0.104 Sensitivity McQFold: 0.729 Carnac(seed): 0.011 Positive Predictive Value McQFold: 0.743 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	? McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.603 NanoFolder: 0.427 Sensitivity McQFold: 0.625 NanoFolder: 0.519 Positive Predictive Value McQFold: 0.591 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? McQFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient McQFold: 0.687 CentroidHomfold‑LAST: 0.635 Sensitivity McQFold: 0.689 CentroidHomfold‑LAST: 0.552 Positive Predictive Value McQFold: 0.696 CentroidHomfold‑LAST: 0.743 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: 0.717 Multilign(seed): 0.629 Sensitivity McQFold: 0.690 Multilign(seed): 0.580 Positive Predictive Value McQFold: 0.758 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.685 Multilign(20): 0.581 Sensitivity McQFold: 0.705 Multilign(20): 0.576 Positive Predictive Value McQFold: 0.674 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 McQFold: 0.589 Sensitivity PETfold_pre2.0(seed): 0.619 McQFold: 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.789 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? McQFold vs TurboFold(20) Matthews Correlation Coefficient McQFold: 0.685 TurboFold(20): 0.653 Sensitivity McQFold: 0.705 TurboFold(20): 0.606 Positive Predictive Value McQFold: 0.674 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.687 RNAwolf: 0.436 Sensitivity McQFold: 0.689 RNAwolf: 0.437 Positive Predictive Value McQFold: 0.696 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? McQFold vs IPknot Matthews Correlation Coefficient McQFold: 0.687 IPknot: 0.612 Sensitivity McQFold: 0.689 IPknot: 0.579 Positive Predictive Value McQFold: 0.696 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 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): 0.619 McQFold: 0.579 Sensitivity PETfold_pre2.0(20): 0.570 McQFold: 0.620 Positive Predictive Value PETfold_pre2.0(20): 0.682 McQFold: 0.551 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.679 PPfold(seed): 0.155 Sensitivity McQFold: 0.693 PPfold(seed): 0.047 Positive Predictive Value McQFold: 0.675 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.662 McQFold: 0.621 Sensitivity ContextFold: 0.608 McQFold: 0.631 Positive Predictive Value ContextFold: 0.731 McQFold: 0.621 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? McQFold vs TurboFold(seed) Matthews Correlation Coefficient McQFold: 0.679 TurboFold(seed): 0.560 Sensitivity McQFold: 0.693 TurboFold(seed): 0.533 Positive Predictive Value McQFold: 0.675 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.657 CRWrnafold: 0.502 Sensitivity McQFold: 0.667 CRWrnafold: 0.516 Positive Predictive Value McQFold: 0.658 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.669 RNASampler(seed): 0.640 Sensitivity McQFold: 0.693 RNASampler(seed): 0.554 Positive Predictive Value McQFold: 0.653 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.621 RNASLOpt: 0.449 Sensitivity McQFold: 0.631 RNASLOpt: 0.438 Positive Predictive Value McQFold: 0.621 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.715 McQFold: 0.685 Sensitivity PPfold(20): 0.644 McQFold: 0.705 Positive Predictive Value PPfold(20): 0.802 McQFold: 0.674 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.613 Mastr(seed): 0.000 Sensitivity McQFold: 0.640 Mastr(seed): 0.000 Positive Predictive Value McQFold: 0.593 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.84041289224e-08
RNAshapes	15 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAshapes: 0.637 Sensitivity CentroidAlifold(20): 0.694 RNAshapes: 0.637 Positive Predictive Value CentroidAlifold(20): 0.932 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	19 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNAshapes: 0.594 Sensitivity CentroidAlifold(seed): 0.598 RNAshapes: 0.617 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAshapes: 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	15 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.753 RNAshapes: 0.637 Sensitivity RNAalifold(20): 0.656 RNAshapes: 0.637 Positive Predictive Value RNAalifold(20): 0.869 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	19 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.711 RNAshapes: 0.594 Sensitivity MXScarna(seed): 0.663 RNAshapes: 0.617 Positive Predictive Value MXScarna(seed): 0.768 RNAshapes: 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	25 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.704 RNAshapes: 0.613 Sensitivity CentroidFold: 0.698 RNAshapes: 0.630 Positive Predictive Value CentroidFold: 0.715 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.732 RNAshapes: 0.637 Sensitivity RNASampler(20): 0.639 RNAshapes: 0.637 Positive Predictive Value RNASampler(20): 0.843 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.52299983238e-08	15 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.703 RNAshapes: 0.637 Sensitivity MXScarna(20): 0.659 RNAshapes: 0.637 Positive Predictive Value MXScarna(20): 0.755 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.16042554876e-08	28 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.663 RNAshapes: 0.610 Sensitivity Contrafold: 0.678 RNAshapes: 0.625 Positive Predictive Value Contrafold: 0.654 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.638 RNAshapes: 0.610 Sensitivity Sfold: 0.629 RNAshapes: 0.625 Positive Predictive Value Sfold: 0.653 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.623 RNAshapes: 0.598 Sensitivity MaxExpect: 0.640 RNAshapes: 0.618 Positive Predictive Value MaxExpect: 0.612 RNAshapes: 0.586 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.631 RNAshapes: 0.610 Sensitivity HotKnots: 0.666 RNAshapes: 0.625 Positive Predictive Value HotKnots: 0.605 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	16 RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.634 RNAshapes: 0.615 Sensitivity RNAalifold(seed): 0.479 RNAshapes: 0.640 Positive Predictive Value RNAalifold(seed): 0.842 RNAshapes: 0.596 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.27752322258e-08	15 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.666 RNAshapes: 0.637 Sensitivity Murlet(20): 0.548 RNAshapes: 0.637 Positive Predictive Value Murlet(20): 0.814 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.56330076937e-08	28 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.633 RNAshapes: 0.610 Sensitivity UNAFold: 0.655 RNAshapes: 0.625 Positive Predictive Value UNAFold: 0.619 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	15 Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.662 RNAshapes: 0.637 Sensitivity Carnac(20): 0.469 RNAshapes: 0.637 Positive Predictive Value Carnac(20): 0.938 RNAshapes: 0.644 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.78495854732e-07	28 McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.624 RNAshapes: 0.610 Sensitivity McQFold: 0.641 RNAshapes: 0.625 Positive Predictive Value McQFold: 0.614 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.62644058675e-08		+ RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.610 RNAfold: 0.607 Sensitivity RNAshapes: 0.625 RNAfold: 0.633 Positive Predictive Value RNAshapes: 0.602 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 8.2028705344e-05	= PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.612 RNAshapes: 0.610 Sensitivity PknotsRG: 0.645 RNAshapes: 0.625 Positive Predictive Value PknotsRG: 0.586 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.800829089439	= Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.676 RNAshapes: 0.672 Sensitivity Pknots: 0.693 RNAshapes: 0.663 Positive Predictive Value Pknots: 0.668 RNAshapes: 0.692 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0709819156009	+ RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.573 Afold: 0.564 Sensitivity RNAshapes: 0.597 Afold: 0.604 Positive Predictive Value RNAshapes: 0.556 Afold: 0.533 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 2.81638097452e-07	+ RNAshapes vs ProbKnot Matthews Correlation Coefficient RNAshapes: 0.566 ProbKnot: 0.564 Sensitivity RNAshapes: 0.598 ProbKnot: 0.613 Positive Predictive Value RNAshapes: 0.542 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.000640523715075	- Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.693 RNAshapes: 0.677 Sensitivity Cylofold: 0.681 RNAshapes: 0.671 Positive Predictive Value Cylofold: 0.715 RNAshapes: 0.693 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.34783000218e-05	+ RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.610 RNAsubopt: 0.591 Sensitivity RNAshapes: 0.625 RNAsubopt: 0.615 Positive Predictive Value RNAshapes: 0.602 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAshapes vs Fold Matthews Correlation Coefficient RNAshapes: 0.575 Fold: 0.557 Sensitivity RNAshapes: 0.604 Fold: 0.589 Positive Predictive Value RNAshapes: 0.553 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.57076602694e-08	+ RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.637 RSpredict(20): 0.624 Sensitivity RNAshapes: 0.637 RSpredict(20): 0.559 Positive Predictive Value RNAshapes: 0.644 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000485451965192	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.610 Vsfold4: 0.559 Sensitivity RNAshapes: 0.625 Vsfold4: 0.554 Positive Predictive Value RNAshapes: 0.602 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.718 Murlet(seed): 0.571 Sensitivity RNAshapes: 0.707 Murlet(seed): 0.386 Positive Predictive Value RNAshapes: 0.737 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.705 Alterna: 0.647 Sensitivity RNAshapes: 0.678 Alterna: 0.636 Positive Predictive Value RNAshapes: 0.745 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.637 Mastr(20): 0.506 Sensitivity RNAshapes: 0.637 Mastr(20): 0.337 Positive Predictive Value RNAshapes: 0.644 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.610 Vsfold5: 0.518 Sensitivity RNAshapes: 0.625 Vsfold5: 0.514 Positive Predictive Value RNAshapes: 0.602 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.691 RDfolder: 0.549 Sensitivity RNAshapes: 0.661 RDfolder: 0.487 Positive Predictive Value RNAshapes: 0.736 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.651 MCFold: 0.527 Sensitivity RNAshapes: 0.647 MCFold: 0.563 Positive Predictive Value RNAshapes: 0.664 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.594 RSpredict(seed): 0.324 Sensitivity RNAshapes: 0.617 RSpredict(seed): 0.177 Positive Predictive Value RNAshapes: 0.578 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.718 Carnac(seed): 0.104 Sensitivity RNAshapes: 0.707 Carnac(seed): 0.011 Positive Predictive Value RNAshapes: 0.737 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	? RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.456 NanoFolder: 0.427 Sensitivity RNAshapes: 0.481 NanoFolder: 0.519 Positive Predictive Value RNAshapes: 0.446 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAshapes: 0.572 Sensitivity CentroidHomfold‑LAST: 0.552 RNAshapes: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAshapes: 0.583 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: 0.728 Multilign(seed): 0.629 Sensitivity RNAshapes: 0.700 Multilign(seed): 0.580 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: 0.608 Multilign(20): 0.581 Sensitivity RNAshapes: 0.606 Multilign(20): 0.576 Positive Predictive Value RNAshapes: 0.620 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAshapes: 0.499 Sensitivity PETfold_pre2.0(seed): 0.619 RNAshapes: 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAshapes: 0.505 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.653 RNAshapes: 0.608 Sensitivity TurboFold(20): 0.606 RNAshapes: 0.606 Positive Predictive Value TurboFold(20): 0.714 RNAshapes: 0.620 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.572 RNAwolf: 0.436 Sensitivity RNAshapes: 0.574 RNAwolf: 0.437 Positive Predictive Value RNAshapes: 0.583 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.612 RNAshapes: 0.572 Sensitivity IPknot: 0.579 RNAshapes: 0.574 Positive Predictive Value IPknot: 0.658 RNAshapes: 0.583 Number of pairs reference - predicted secondary structure: 9 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): 0.619 RNAshapes: 0.469 Sensitivity PETfold_pre2.0(20): 0.570 RNAshapes: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAshapes: 0.469 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.611 PPfold(seed): 0.155 Sensitivity RNAshapes: 0.607 PPfold(seed): 0.047 Positive Predictive Value RNAshapes: 0.628 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.662 RNAshapes: 0.473 Sensitivity ContextFold: 0.608 RNAshapes: 0.485 Positive Predictive Value ContextFold: 0.731 RNAshapes: 0.477 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.611 TurboFold(seed): 0.560 Sensitivity RNAshapes: 0.607 TurboFold(seed): 0.533 Positive Predictive Value RNAshapes: 0.628 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.526 CRWrnafold: 0.502 Sensitivity RNAshapes: 0.535 CRWrnafold: 0.516 Positive Predictive Value RNAshapes: 0.531 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.655 RNASampler(seed): 0.640 Sensitivity RNAshapes: 0.675 RNASampler(seed): 0.554 Positive Predictive Value RNAshapes: 0.644 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.473 RNASLOpt: 0.449 Sensitivity RNAshapes: 0.485 RNASLOpt: 0.438 Positive Predictive Value RNAshapes: 0.477 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.715 RNAshapes: 0.608 Sensitivity PPfold(20): 0.644 RNAshapes: 0.606 Positive Predictive Value PPfold(20): 0.802 RNAshapes: 0.620 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.594 Mastr(seed): 0.000 Sensitivity RNAshapes: 0.617 Mastr(seed): 0.000 Positive Predictive Value RNAshapes: 0.578 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08
RNAfold	15 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAfold: 0.643 Sensitivity CentroidAlifold(20): 0.694 RNAfold: 0.656 Positive Predictive Value CentroidAlifold(20): 0.932 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	19 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNAfold: 0.618 Sensitivity CentroidAlifold(seed): 0.598 RNAfold: 0.652 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAfold: 0.591 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	15 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.753 RNAfold: 0.643 Sensitivity RNAalifold(20): 0.656 RNAfold: 0.656 Positive Predictive Value RNAalifold(20): 0.869 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.10198558684e-08	19 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.711 RNAfold: 0.618 Sensitivity MXScarna(seed): 0.663 RNAfold: 0.652 Positive Predictive Value MXScarna(seed): 0.768 RNAfold: 0.591 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.18846395401e-08	27 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.641 RNAfold: 0.499 Sensitivity CentroidFold: 0.639 RNAfold: 0.550 Positive Predictive Value CentroidFold: 0.644 RNAfold: 0.454 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	15 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.732 RNAfold: 0.643 Sensitivity RNASampler(20): 0.639 RNAfold: 0.656 Positive Predictive Value RNASampler(20): 0.843 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.13260312532e-08	15 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.703 RNAfold: 0.643 Sensitivity MXScarna(20): 0.659 RNAfold: 0.656 Positive Predictive Value MXScarna(20): 0.755 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.52609899389e-08	31 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.638 RNAfold: 0.498 Sensitivity Contrafold: 0.665 RNAfold: 0.540 Positive Predictive Value Contrafold: 0.613 RNAfold: 0.460 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.530 RNAfold: 0.498 Sensitivity Sfold: 0.530 RNAfold: 0.540 Positive Predictive Value Sfold: 0.529 RNAfold: 0.460 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.648 RNAfold: 0.540 Sensitivity MaxExpect: 0.660 RNAfold: 0.567 Positive Predictive Value MaxExpect: 0.637 RNAfold: 0.516 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.631 RNAfold: 0.607 Sensitivity HotKnots: 0.666 RNAfold: 0.633 Positive Predictive Value HotKnots: 0.605 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	16 RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.635 RNAalifold(seed): 0.634 Sensitivity RNAfold: 0.671 RNAalifold(seed): 0.479 Positive Predictive Value RNAfold: 0.606 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.241510530594	15 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.666 RNAfold: 0.643 Sensitivity Murlet(20): 0.548 RNAfold: 0.656 Positive Predictive Value Murlet(20): 0.814 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.99165002974e-07	31 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.502 RNAfold: 0.498 Sensitivity UNAFold: 0.539 RNAfold: 0.540 Positive Predictive Value UNAFold: 0.469 RNAfold: 0.460 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 4.48494289621e-08	15 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.662 RNAfold: 0.643 Sensitivity Carnac(20): 0.469 RNAfold: 0.656 Positive Predictive Value Carnac(20): 0.938 RNAfold: 0.637 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.72263550878e-05	31 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.498 McQFold: 0.415 Sensitivity RNAfold: 0.540 McQFold: 0.382 Positive Predictive Value RNAfold: 0.460 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.610 RNAfold: 0.607 Sensitivity RNAshapes: 0.625 RNAfold: 0.633 Positive Predictive Value RNAshapes: 0.602 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 8.2028705344e-05		+ RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.498 PknotsRG: 0.486 Sensitivity RNAfold: 0.540 PknotsRG: 0.529 Positive Predictive Value RNAfold: 0.460 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.676 RNAfold: 0.664 Sensitivity Pknots: 0.693 RNAfold: 0.664 Positive Predictive Value Pknots: 0.668 RNAfold: 0.674 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 7.75145471427e-06	- Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.493 RNAfold: 0.483 Sensitivity Afold: 0.537 RNAfold: 0.527 Positive Predictive Value Afold: 0.453 RNAfold: 0.442 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAfold vs ProbKnot Matthews Correlation Coefficient RNAfold: 0.583 ProbKnot: 0.564 Sensitivity RNAfold: 0.627 ProbKnot: 0.613 Positive Predictive Value RNAfold: 0.548 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 6.84390417318e-09	- Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.693 RNAfold: 0.652 Sensitivity Cylofold: 0.681 RNAfold: 0.652 Positive Predictive Value Cylofold: 0.715 RNAfold: 0.662 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.51039672358e-08	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.607 RNAsubopt: 0.591 Sensitivity RNAfold: 0.633 RNAsubopt: 0.615 Positive Predictive Value RNAfold: 0.588 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.01188337103e-07	+ RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.570 Fold: 0.557 Sensitivity RNAfold: 0.610 Fold: 0.589 Positive Predictive Value RNAfold: 0.538 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45802991547e-07	+ RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.643 RSpredict(20): 0.624 Sensitivity RNAfold: 0.656 RSpredict(20): 0.559 Positive Predictive Value RNAfold: 0.637 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.1187875805e-05	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.607 Vsfold4: 0.559 Sensitivity RNAfold: 0.633 Vsfold4: 0.554 Positive Predictive Value RNAfold: 0.588 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.743 Murlet(seed): 0.571 Sensitivity RNAfold: 0.737 Murlet(seed): 0.386 Positive Predictive Value RNAfold: 0.756 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.668 Alterna: 0.647 Sensitivity RNAfold: 0.655 Alterna: 0.636 Positive Predictive Value RNAfold: 0.695 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.643 Mastr(20): 0.506 Sensitivity RNAfold: 0.656 Mastr(20): 0.337 Positive Predictive Value RNAfold: 0.637 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.607 Vsfold5: 0.518 Sensitivity RNAfold: 0.633 Vsfold5: 0.514 Positive Predictive Value RNAfold: 0.588 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.659 RDfolder: 0.549 Sensitivity RNAfold: 0.642 RDfolder: 0.487 Positive Predictive Value RNAfold: 0.692 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.659 MCFold: 0.527 Sensitivity RNAfold: 0.665 MCFold: 0.563 Positive Predictive Value RNAfold: 0.665 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.618 RSpredict(seed): 0.324 Sensitivity RNAfold: 0.652 RSpredict(seed): 0.177 Positive Predictive Value RNAfold: 0.591 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.743 Carnac(seed): 0.104 Sensitivity RNAfold: 0.737 Carnac(seed): 0.011 Positive Predictive Value RNAfold: 0.756 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	? RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.452 NanoFolder: 0.427 Sensitivity RNAfold: 0.481 NanoFolder: 0.519 Positive Predictive Value RNAfold: 0.439 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAfold: 0.569 Sensitivity CentroidHomfold‑LAST: 0.552 RNAfold: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAfold: 0.577 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: 0.728 Multilign(seed): 0.629 Sensitivity RNAfold: 0.700 Multilign(seed): 0.580 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: 0.603 Multilign(20): 0.581 Sensitivity RNAfold: 0.606 Multilign(20): 0.576 Positive Predictive Value RNAfold: 0.611 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAfold: 0.493 Sensitivity PETfold_pre2.0(seed): 0.619 RNAfold: 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.653 RNAfold: 0.603 Sensitivity TurboFold(20): 0.606 RNAfold: 0.606 Positive Predictive Value TurboFold(20): 0.714 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.569 RNAwolf: 0.436 Sensitivity RNAfold: 0.574 RNAwolf: 0.437 Positive Predictive Value RNAfold: 0.577 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.612 RNAfold: 0.569 Sensitivity IPknot: 0.579 RNAfold: 0.574 Positive Predictive Value IPknot: 0.658 RNAfold: 0.577 Number of pairs reference - predicted secondary structure: 9 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): 0.619 RNAfold: 0.463 Sensitivity PETfold_pre2.0(20): 0.570 RNAfold: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAfold: 0.458 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.607 PPfold(seed): 0.155 Sensitivity RNAfold: 0.607 PPfold(seed): 0.047 Positive Predictive Value RNAfold: 0.619 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.662 RNAfold: 0.470 Sensitivity ContextFold: 0.608 RNAfold: 0.485 Positive Predictive Value ContextFold: 0.731 RNAfold: 0.470 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.607 TurboFold(seed): 0.560 Sensitivity RNAfold: 0.607 TurboFold(seed): 0.533 Positive Predictive Value RNAfold: 0.619 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.522 CRWrnafold: 0.502 Sensitivity RNAfold: 0.535 CRWrnafold: 0.516 Positive Predictive Value RNAfold: 0.525 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.673 RNASampler(seed): 0.640 Sensitivity RNAfold: 0.699 RNASampler(seed): 0.554 Positive Predictive Value RNAfold: 0.655 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.470 RNASLOpt: 0.449 Sensitivity RNAfold: 0.485 RNASLOpt: 0.438 Positive Predictive Value RNAfold: 0.470 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.715 RNAfold: 0.603 Sensitivity PPfold(20): 0.644 RNAfold: 0.606 Positive Predictive Value PPfold(20): 0.802 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.618 Mastr(seed): 0.000 Sensitivity RNAfold: 0.652 Mastr(seed): 0.000 Positive Predictive Value RNAfold: 0.591 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08
PknotsRG	15 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.803 PknotsRG: 0.664 Sensitivity CentroidAlifold(20): 0.694 PknotsRG: 0.685 Positive Predictive Value CentroidAlifold(20): 0.932 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	19 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 PknotsRG: 0.634 Sensitivity CentroidAlifold(seed): 0.598 PknotsRG: 0.675 Positive Predictive Value CentroidAlifold(seed): 0.894 PknotsRG: 0.602 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.91763127434e-08	15 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.753 PknotsRG: 0.664 Sensitivity RNAalifold(20): 0.656 PknotsRG: 0.685 Positive Predictive Value RNAalifold(20): 0.869 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	19 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.711 PknotsRG: 0.634 Sensitivity MXScarna(seed): 0.663 PknotsRG: 0.675 Positive Predictive Value MXScarna(seed): 0.768 PknotsRG: 0.602 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.20167918023e-08	27 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.641 PknotsRG: 0.489 Sensitivity CentroidFold: 0.639 PknotsRG: 0.539 Positive Predictive Value CentroidFold: 0.644 PknotsRG: 0.443 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	15 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.732 PknotsRG: 0.664 Sensitivity RNASampler(20): 0.639 PknotsRG: 0.685 Positive Predictive Value RNASampler(20): 0.843 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	15 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.703 PknotsRG: 0.664 Sensitivity MXScarna(20): 0.659 PknotsRG: 0.685 Positive Predictive Value MXScarna(20): 0.755 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.83658036805e-08	31 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.638 PknotsRG: 0.486 Sensitivity Contrafold: 0.665 PknotsRG: 0.529 Positive Predictive Value Contrafold: 0.613 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.530 PknotsRG: 0.486 Sensitivity Sfold: 0.530 PknotsRG: 0.529 Positive Predictive Value Sfold: 0.529 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.648 PknotsRG: 0.524 Sensitivity MaxExpect: 0.660 PknotsRG: 0.552 Positive Predictive Value MaxExpect: 0.637 PknotsRG: 0.498 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.631 PknotsRG: 0.612 Sensitivity HotKnots: 0.666 PknotsRG: 0.645 Positive Predictive Value HotKnots: 0.605 PknotsRG: 0.586 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.43400990727e-08	16 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.654 RNAalifold(seed): 0.634 Sensitivity PknotsRG: 0.697 RNAalifold(seed): 0.479 Positive Predictive Value PknotsRG: 0.618 RNAalifold(seed): 0.842 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.1022514496e-08	15 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.666 PknotsRG: 0.664 Sensitivity Murlet(20): 0.548 PknotsRG: 0.685 Positive Predictive Value Murlet(20): 0.814 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0719792426829	31 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.502 PknotsRG: 0.486 Sensitivity UNAFold: 0.539 PknotsRG: 0.529 Positive Predictive Value UNAFold: 0.469 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.664 Carnac(20): 0.662 Sensitivity PknotsRG: 0.685 Carnac(20): 0.469 Positive Predictive Value PknotsRG: 0.649 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.0376522112878	31 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.486 McQFold: 0.415 Sensitivity PknotsRG: 0.529 McQFold: 0.382 Positive Predictive Value PknotsRG: 0.448 McQFold: 0.451 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.612 RNAshapes: 0.610 Sensitivity PknotsRG: 0.645 RNAshapes: 0.625 Positive Predictive Value PknotsRG: 0.586 RNAshapes: 0.602 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.800829089439	31 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.498 PknotsRG: 0.486 Sensitivity RNAfold: 0.540 PknotsRG: 0.529 Positive Predictive Value RNAfold: 0.460 PknotsRG: 0.448 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08		= Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.676 PknotsRG: 0.669 Sensitivity Pknots: 0.693 PknotsRG: 0.680 Positive Predictive Value Pknots: 0.668 PknotsRG: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0890053463623	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.493 PknotsRG: 0.468 Sensitivity Afold: 0.537 PknotsRG: 0.512 Positive Predictive Value Afold: 0.453 PknotsRG: 0.428 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.602 ProbKnot: 0.564 Sensitivity PknotsRG: 0.654 ProbKnot: 0.613 Positive Predictive Value PknotsRG: 0.560 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.91763127434e-08	- Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.693 PknotsRG: 0.682 Sensitivity Cylofold: 0.681 PknotsRG: 0.694 Positive Predictive Value Cylofold: 0.715 PknotsRG: 0.680 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.73294613682e-07	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.612 RNAsubopt: 0.591 Sensitivity PknotsRG: 0.645 RNAsubopt: 0.615 Positive Predictive Value PknotsRG: 0.586 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.07491858776e-08	+ PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.588 Fold: 0.557 Sensitivity PknotsRG: 0.635 Fold: 0.589 Positive Predictive Value PknotsRG: 0.549 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.664 RSpredict(20): 0.624 Sensitivity PknotsRG: 0.685 RSpredict(20): 0.559 Positive Predictive Value PknotsRG: 0.649 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.86050763602e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.612 Vsfold4: 0.559 Sensitivity PknotsRG: 0.645 Vsfold4: 0.554 Positive Predictive Value PknotsRG: 0.586 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.768 Murlet(seed): 0.571 Sensitivity PknotsRG: 0.773 Murlet(seed): 0.386 Positive Predictive Value PknotsRG: 0.770 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	= PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.648 Alterna: 0.647 Sensitivity PknotsRG: 0.641 Alterna: 0.636 Positive Predictive Value PknotsRG: 0.670 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00235582146837	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.664 Mastr(20): 0.506 Sensitivity PknotsRG: 0.685 Mastr(20): 0.337 Positive Predictive Value PknotsRG: 0.649 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.612 Vsfold5: 0.518 Sensitivity PknotsRG: 0.645 Vsfold5: 0.514 Positive Predictive Value PknotsRG: 0.586 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.669 RDfolder: 0.549 Sensitivity PknotsRG: 0.663 RDfolder: 0.487 Positive Predictive Value PknotsRG: 0.690 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.667 MCFold: 0.527 Sensitivity PknotsRG: 0.684 MCFold: 0.563 Positive Predictive Value PknotsRG: 0.661 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.634 RSpredict(seed): 0.324 Sensitivity PknotsRG: 0.675 RSpredict(seed): 0.177 Positive Predictive Value PknotsRG: 0.602 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.768 Carnac(seed): 0.104 Sensitivity PknotsRG: 0.773 Carnac(seed): 0.011 Positive Predictive Value PknotsRG: 0.770 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	? PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.531 NanoFolder: 0.427 Sensitivity PknotsRG: 0.577 NanoFolder: 0.519 Positive Predictive Value PknotsRG: 0.500 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 PknotsRG: 0.623 Sensitivity CentroidHomfold‑LAST: 0.552 PknotsRG: 0.645 Positive Predictive Value CentroidHomfold‑LAST: 0.743 PknotsRG: 0.615 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: 0.721 Multilign(seed): 0.629 Sensitivity PknotsRG: 0.690 Multilign(seed): 0.580 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: 0.675 Multilign(20): 0.581 Sensitivity PknotsRG: 0.705 Multilign(20): 0.576 Positive Predictive Value PknotsRG: 0.655 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 PknotsRG: 0.607 Sensitivity PETfold_pre2.0(seed): 0.619 PknotsRG: 0.649 Positive Predictive Value PETfold_pre2.0(seed): 0.789 PknotsRG: 0.578 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.675 TurboFold(20): 0.653 Sensitivity PknotsRG: 0.705 TurboFold(20): 0.606 Positive Predictive Value PknotsRG: 0.655 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.623 RNAwolf: 0.436 Sensitivity PknotsRG: 0.645 RNAwolf: 0.437 Positive Predictive Value PknotsRG: 0.615 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs IPknot Matthews Correlation Coefficient PknotsRG: 0.623 IPknot: 0.612 Sensitivity PknotsRG: 0.645 IPknot: 0.579 Positive Predictive Value PknotsRG: 0.615 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 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): 0.619 PknotsRG: 0.598 Sensitivity PETfold_pre2.0(20): 0.570 PknotsRG: 0.658 Positive Predictive Value PETfold_pre2.0(20): 0.682 PknotsRG: 0.553 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.673 PPfold(seed): 0.155 Sensitivity PknotsRG: 0.693 PPfold(seed): 0.047 Positive Predictive Value PknotsRG: 0.662 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.662 PknotsRG: 0.556 Sensitivity ContextFold: 0.608 PknotsRG: 0.592 Positive Predictive Value ContextFold: 0.731 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.673 TurboFold(seed): 0.560 Sensitivity PknotsRG: 0.693 TurboFold(seed): 0.533 Positive Predictive Value PknotsRG: 0.662 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.586 CRWrnafold: 0.502 Sensitivity PknotsRG: 0.616 CRWrnafold: 0.516 Positive Predictive Value PknotsRG: 0.570 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.665 RNASampler(seed): 0.640 Sensitivity PknotsRG: 0.693 RNASampler(seed): 0.554 Positive Predictive Value PknotsRG: 0.646 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.556 RNASLOpt: 0.449 Sensitivity PknotsRG: 0.592 RNASLOpt: 0.438 Positive Predictive Value PknotsRG: 0.535 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.715 PknotsRG: 0.675 Sensitivity PPfold(20): 0.644 PknotsRG: 0.705 Positive Predictive Value PPfold(20): 0.802 PknotsRG: 0.655 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.634 Mastr(seed): 0.000 Sensitivity PknotsRG: 0.675 Mastr(seed): 0.000 Positive Predictive Value PknotsRG: 0.602 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08
Pknots	14 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.834 Pknots: 0.670 Sensitivity CentroidAlifold(20): 0.741 Pknots: 0.691 Positive Predictive Value CentroidAlifold(20): 0.943 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.77512146924e-08	17 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.787 Pknots: 0.710 Sensitivity CentroidAlifold(seed): 0.641 Pknots: 0.727 Positive Predictive Value CentroidAlifold(seed): 0.972 Pknots: 0.701 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	14 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.778 Pknots: 0.670 Sensitivity RNAalifold(20): 0.702 Pknots: 0.691 Positive Predictive Value RNAalifold(20): 0.869 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.54914456376e-08	17 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.746 Pknots: 0.710 Sensitivity MXScarna(seed): 0.690 Pknots: 0.727 Positive Predictive Value MXScarna(seed): 0.813 Pknots: 0.701 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	23 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.778 Pknots: 0.682 Sensitivity CentroidFold: 0.747 Pknots: 0.697 Positive Predictive Value CentroidFold: 0.818 Pknots: 0.676 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	14 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.784 Pknots: 0.670 Sensitivity RNASampler(20): 0.699 Pknots: 0.691 Positive Predictive Value RNASampler(20): 0.884 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	14 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.734 Pknots: 0.670 Sensitivity MXScarna(20): 0.691 Pknots: 0.691 Positive Predictive Value MXScarna(20): 0.787 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.66062906821e-08	26 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.729 Pknots: 0.676 Sensitivity Contrafold: 0.719 Pknots: 0.693 Positive Predictive Value Contrafold: 0.747 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.695 Pknots: 0.676 Sensitivity Sfold: 0.666 Pknots: 0.693 Positive Predictive Value Sfold: 0.735 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 8.58720925105e-07	21 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.682 Pknots: 0.655 Sensitivity MaxExpect: 0.676 Pknots: 0.673 Positive Predictive Value MaxExpect: 0.697 Pknots: 0.647 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 3.32276783474e-07	26 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.694 Pknots: 0.676 Sensitivity HotKnots: 0.705 Pknots: 0.693 Positive Predictive Value HotKnots: 0.692 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 2.81638097452e-07	14 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.706 Pknots: 0.695 Sensitivity RNAalifold(seed): 0.564 Pknots: 0.712 Positive Predictive Value RNAalifold(seed): 0.892 Pknots: 0.686 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.000375209661743	14 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.712 Pknots: 0.670 Sensitivity Murlet(20): 0.607 Pknots: 0.691 Positive Predictive Value Murlet(20): 0.842 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.86826635779e-08	26 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.694 Pknots: 0.676 Sensitivity UNAFold: 0.692 Pknots: 0.693 Positive Predictive Value UNAFold: 0.706 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.35631047551e-06	14 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.695 Pknots: 0.670 Sensitivity Carnac(20): 0.513 Pknots: 0.691 Positive Predictive Value Carnac(20): 0.948 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 3.16482497632e-07	26 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.706 Pknots: 0.676 Sensitivity McQFold: 0.698 Pknots: 0.693 Positive Predictive Value McQFold: 0.723 Pknots: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 6.38150542963e-08	26 Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.676 RNAshapes: 0.672 Sensitivity Pknots: 0.693 RNAshapes: 0.663 Positive Predictive Value Pknots: 0.668 RNAshapes: 0.692 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0709819156009	26 Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.676 RNAfold: 0.664 Sensitivity Pknots: 0.693 RNAfold: 0.664 Positive Predictive Value Pknots: 0.668 RNAfold: 0.674 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 7.75145471427e-06	26 Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.676 PknotsRG: 0.669 Sensitivity Pknots: 0.693 PknotsRG: 0.680 Positive Predictive Value Pknots: 0.668 PknotsRG: 0.668 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.0890053463623		+ Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.705 Afold: 0.637 Sensitivity Pknots: 0.729 Afold: 0.647 Positive Predictive Value Pknots: 0.691 Afold: 0.639 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08	= Pknots vs ProbKnot Matthews Correlation Coefficient Pknots: 0.623 ProbKnot: 0.622 Sensitivity Pknots: 0.653 ProbKnot: 0.656 Positive Predictive Value Pknots: 0.604 ProbKnot: 0.600 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.111384766941	- Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.693 Pknots: 0.657 Sensitivity Cylofold: 0.681 Pknots: 0.684 Positive Predictive Value Cylofold: 0.715 Pknots: 0.640 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: 0.676 RNAsubopt: 0.635 Sensitivity Pknots: 0.693 RNAsubopt: 0.637 Positive Predictive Value Pknots: 0.668 RNAsubopt: 0.644 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Pknots vs Fold Matthews Correlation Coefficient Pknots: 0.654 Fold: 0.609 Sensitivity Pknots: 0.681 Fold: 0.619 Positive Predictive Value Pknots: 0.636 Fold: 0.610 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ Pknots vs RSpredict(20) Matthews Correlation Coefficient Pknots: 0.670 RSpredict(20): 0.625 Sensitivity Pknots: 0.691 RSpredict(20): 0.557 Positive Predictive Value Pknots: 0.658 RSpredict(20): 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.676 Vsfold4: 0.625 Sensitivity Pknots: 0.693 Vsfold4: 0.598 Positive Predictive Value Pknots: 0.668 Vsfold4: 0.665 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.695 Murlet(seed): 0.571 Sensitivity Pknots: 0.712 Murlet(seed): 0.386 Positive Predictive Value Pknots: 0.686 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.748 Alterna: 0.647 Sensitivity Pknots: 0.746 Alterna: 0.636 Positive Predictive Value Pknots: 0.761 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ Pknots vs Mastr(20) Matthews Correlation Coefficient Pknots: 0.670 Mastr(20): 0.568 Sensitivity Pknots: 0.691 Mastr(20): 0.426 Positive Predictive Value Pknots: 0.658 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.676 Vsfold5: 0.576 Sensitivity Pknots: 0.693 Vsfold5: 0.560 Positive Predictive Value Pknots: 0.668 Vsfold5: 0.605 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.727 RDfolder: 0.549 Sensitivity Pknots: 0.726 RDfolder: 0.487 Positive Predictive Value Pknots: 0.739 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.665 MCFold: 0.527 Sensitivity Pknots: 0.688 MCFold: 0.563 Positive Predictive Value Pknots: 0.653 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.710 RSpredict(seed): 0.357 Sensitivity Pknots: 0.727 RSpredict(seed): 0.203 Positive Predictive Value Pknots: 0.701 RSpredict(seed): 0.644 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.695 Carnac(seed): 0.104 Sensitivity Pknots: 0.712 Carnac(seed): 0.011 Positive Predictive Value Pknots: 0.686 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08	? Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.468 NanoFolder: 0.427 Sensitivity Pknots: 0.500 NanoFolder: 0.519 Positive Predictive Value Pknots: 0.452 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Pknots: 0.605 Sensitivity CentroidHomfold‑LAST: 0.552 Pknots: 0.623 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Pknots: 0.600 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: 0.649 Multilign(seed): 0.629 Sensitivity Pknots: 0.640 Multilign(seed): 0.580 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	? Pknots vs Multilign(20) Matthews Correlation Coefficient Pknots: 0.644 Multilign(20): 0.581 Sensitivity Pknots: 0.659 Multilign(20): 0.576 Positive Predictive Value Pknots: 0.640 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Pknots: 0.579 Sensitivity PETfold_pre2.0(seed): 0.619 Pknots: 0.608 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Pknots: 0.562 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.653 Pknots: 0.644 Sensitivity TurboFold(20): 0.606 Pknots: 0.659 Positive Predictive Value TurboFold(20): 0.714 Pknots: 0.640 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.605 RNAwolf: 0.436 Sensitivity Pknots: 0.623 RNAwolf: 0.437 Positive Predictive Value Pknots: 0.600 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.612 Pknots: 0.605 Sensitivity IPknot: 0.579 Pknots: 0.623 Positive Predictive Value IPknot: 0.658 Pknots: 0.600 Number of pairs reference - predicted secondary structure: 9 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): 0.619 Pknots: 0.525 Sensitivity PETfold_pre2.0(20): 0.570 Pknots: 0.557 Positive Predictive Value PETfold_pre2.0(20): 0.682 Pknots: 0.506 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.666 PPfold(seed): 0.155 Sensitivity Pknots: 0.680 PPfold(seed): 0.047 Positive Predictive Value Pknots: 0.662 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.662 Pknots: 0.517 Sensitivity ContextFold: 0.608 Pknots: 0.546 Positive Predictive Value ContextFold: 0.731 Pknots: 0.504 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Pknots vs TurboFold(seed) Matthews Correlation Coefficient Pknots: 0.666 TurboFold(seed): 0.560 Sensitivity Pknots: 0.680 TurboFold(seed): 0.533 Positive Predictive Value Pknots: 0.662 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: 0.562 CRWrnafold: 0.502 Sensitivity Pknots: 0.585 CRWrnafold: 0.516 Positive Predictive Value Pknots: 0.554 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.702 RNASampler(seed): 0.640 Sensitivity Pknots: 0.747 RNASampler(seed): 0.554 Positive Predictive Value Pknots: 0.667 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: 0.517 RNASLOpt: 0.449 Sensitivity Pknots: 0.546 RNASLOpt: 0.438 Positive Predictive Value Pknots: 0.504 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.715 Pknots: 0.644 Sensitivity PPfold(20): 0.644 Pknots: 0.659 Positive Predictive Value PPfold(20): 0.802 Pknots: 0.640 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.710 Mastr(seed): 0.000 Sensitivity Pknots: 0.727 Mastr(seed): 0.000 Positive Predictive Value Pknots: 0.701 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08
Afold	10 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.762 Afold: 0.565 Sensitivity CentroidAlifold(20): 0.640 Afold: 0.591 Positive Predictive Value CentroidAlifold(20): 0.911 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.45489855545e-09	14 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.668 Afold: 0.551 Sensitivity CentroidAlifold(seed): 0.526 Afold: 0.597 Positive Predictive Value CentroidAlifold(seed): 0.851 Afold: 0.514 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	10 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.694 Afold: 0.565 Sensitivity RNAalifold(20): 0.587 Afold: 0.591 Positive Predictive Value RNAalifold(20): 0.824 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	14 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.688 Afold: 0.551 Sensitivity MXScarna(seed): 0.627 Afold: 0.597 Positive Predictive Value MXScarna(seed): 0.758 Afold: 0.514 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.89169006118e-08	20 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.628 Afold: 0.484 Sensitivity CentroidFold: 0.629 Afold: 0.539 Positive Predictive Value CentroidFold: 0.627 Afold: 0.435 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	10 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.689 Afold: 0.565 Sensitivity RNASampler(20): 0.601 Afold: 0.591 Positive Predictive Value RNASampler(20): 0.795 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	10 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.667 Afold: 0.565 Sensitivity MXScarna(20): 0.617 Afold: 0.591 Positive Predictive Value MXScarna(20): 0.725 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.35199149577e-09	24 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.630 Afold: 0.493 Sensitivity Contrafold: 0.658 Afold: 0.537 Positive Predictive Value Contrafold: 0.602 Afold: 0.453 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	24 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.514 Afold: 0.493 Sensitivity Sfold: 0.517 Afold: 0.537 Positive Predictive Value Sfold: 0.512 Afold: 0.453 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.98172311752e-08	17 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.632 Afold: 0.534 Sensitivity MaxExpect: 0.648 Afold: 0.563 Positive Predictive Value MaxExpect: 0.616 Afold: 0.507 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	21 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.586 Afold: 0.564 Sensitivity HotKnots: 0.630 Afold: 0.604 Positive Predictive Value HotKnots: 0.551 Afold: 0.533 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	11 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.567 RNAalifold(seed): 0.558 Sensitivity Afold: 0.617 RNAalifold(seed): 0.406 Positive Predictive Value Afold: 0.526 RNAalifold(seed): 0.772 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000382312754694	10 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.596 Afold: 0.565 Sensitivity Murlet(20): 0.479 Afold: 0.591 Positive Predictive Value Murlet(20): 0.747 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24852078119e-08	24 Afold vs UNAFold Matthews Correlation Coefficient Afold: 0.493 UNAFold: 0.485 Sensitivity Afold: 0.537 UNAFold: 0.524 Positive Predictive Value Afold: 0.453 UNAFold: 0.450 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.12827206146e-07	10 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.664 Afold: 0.565 Sensitivity Carnac(20): 0.465 Afold: 0.591 Positive Predictive Value Carnac(20): 0.953 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.64686604905e-09	24 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.493 McQFold: 0.392 Sensitivity Afold: 0.537 McQFold: 0.360 Positive Predictive Value Afold: 0.453 McQFold: 0.429 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.573 Afold: 0.564 Sensitivity RNAshapes: 0.597 Afold: 0.604 Positive Predictive Value RNAshapes: 0.556 Afold: 0.533 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 2.81638097452e-07	24 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.493 RNAfold: 0.483 Sensitivity Afold: 0.537 RNAfold: 0.527 Positive Predictive Value Afold: 0.453 RNAfold: 0.442 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.02343278931e-08	24 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.493 PknotsRG: 0.468 Sensitivity Afold: 0.537 PknotsRG: 0.512 Positive Predictive Value Afold: 0.453 PknotsRG: 0.428 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	19 Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.705 Afold: 0.637 Sensitivity Pknots: 0.729 Afold: 0.647 Positive Predictive Value Pknots: 0.691 Afold: 0.639 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.9966815982e-08		+ Afold vs ProbKnot Matthews Correlation Coefficient Afold: 0.502 ProbKnot: 0.490 Sensitivity Afold: 0.563 ProbKnot: 0.545 Positive Predictive Value Afold: 0.452 ProbKnot: 0.446 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.98587013887e-06	? Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.679 Cylofold: 0.673 Sensitivity Afold: 0.699 Cylofold: 0.680 Positive Predictive Value Afold: 0.669 Cylofold: 0.675 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	= RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.567 Afold: 0.564 Sensitivity RNAsubopt: 0.600 Afold: 0.604 Positive Predictive Value RNAsubopt: 0.542 Afold: 0.533 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.00183945888045	+ Afold vs Fold Matthews Correlation Coefficient Afold: 0.530 Fold: 0.496 Sensitivity Afold: 0.590 Fold: 0.539 Positive Predictive Value Afold: 0.482 Fold: 0.462 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08	- RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.620 Afold: 0.565 Sensitivity RSpredict(20): 0.581 Afold: 0.591 Positive Predictive Value RSpredict(20): 0.667 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.19853615606e-08	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.564 Vsfold4: 0.554 Sensitivity Afold: 0.604 Vsfold4: 0.557 Positive Predictive Value Afold: 0.533 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 1.35125075749e-05	? Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.712 Murlet(seed): 0.546 Sensitivity Afold: 0.706 Murlet(seed): 0.383 Positive Predictive Value Afold: 0.726 Murlet(seed): 0.788 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	= Afold vs Alterna Matthews Correlation Coefficient Afold: 0.685 Alterna: 0.682 Sensitivity Afold: 0.678 Alterna: 0.668 Positive Predictive Value Afold: 0.705 Alterna: 0.710 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0342527507493	= Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.565 Mastr(20): 0.538 Sensitivity Afold: 0.591 Mastr(20): 0.350 Positive Predictive Value Afold: 0.547 Mastr(20): 0.835 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0286195353294	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.564 Vsfold5: 0.514 Sensitivity Afold: 0.604 Vsfold5: 0.515 Positive Predictive Value Afold: 0.533 Vsfold5: 0.521 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 9.26661638959e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.691 RDfolder: 0.592 Sensitivity Afold: 0.681 RDfolder: 0.535 Positive Predictive Value Afold: 0.714 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.600 MCFold: 0.514 Sensitivity Afold: 0.617 MCFold: 0.557 Positive Predictive Value Afold: 0.594 MCFold: 0.489 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.551 RSpredict(seed): 0.351 Sensitivity Afold: 0.597 RSpredict(seed): 0.205 Positive Predictive Value Afold: 0.514 RSpredict(seed): 0.608 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	? Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.712 Carnac(seed): 0.136 Sensitivity Afold: 0.706 Carnac(seed): 0.019 Positive Predictive Value Afold: 0.726 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.411 NanoFolder: 0.395 Sensitivity Afold: 0.467 NanoFolder: 0.517 Positive Predictive Value Afold: 0.373 NanoFolder: 0.313 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Afold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Afold: 0.567 CentroidHomfold‑LAST: 0.557 Sensitivity Afold: 0.596 CentroidHomfold‑LAST: 0.505 Positive Predictive Value Afold: 0.551 CentroidHomfold‑LAST: 0.625 Number of pairs reference - predicted secondary structure: 5 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: 0.792 Multilign(seed): 0.534 Sensitivity Afold: 0.738 Multilign(seed): 0.476 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: 0.577 Multilign(20): 0.503 Sensitivity Afold: 0.610 Multilign(20): 0.525 Positive Predictive Value Afold: 0.554 Multilign(20): 0.492 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): 0.627 Afold: 0.469 Sensitivity PETfold_pre2.0(seed): 0.547 Afold: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.725 Afold: 0.443 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): 0.604 Afold: 0.577 Sensitivity TurboFold(20): 0.576 Afold: 0.610 Positive Predictive Value TurboFold(20): 0.642 Afold: 0.554 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.567 RNAwolf: 0.491 Sensitivity Afold: 0.596 RNAwolf: 0.495 Positive Predictive Value Afold: 0.551 RNAwolf: 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.664 Afold: 0.567 Sensitivity IPknot: 0.626 Afold: 0.596 Positive Predictive Value IPknot: 0.713 Afold: 0.551 Number of pairs reference - predicted secondary structure: 5 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): 0.404 Afold: 0.398 Sensitivity PETfold_pre2.0(20): 0.371 Afold: 0.457 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.356 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.590 PPfold(seed): 0.218 Sensitivity Afold: 0.610 PPfold(seed): 0.091 Positive Predictive Value Afold: 0.580 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.646 Afold: 0.477 Sensitivity ContextFold: 0.600 Afold: 0.520 Positive Predictive Value ContextFold: 0.703 Afold: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.590 TurboFold(seed): 0.444 Sensitivity Afold: 0.610 TurboFold(seed): 0.442 Positive Predictive Value Afold: 0.580 TurboFold(seed): 0.459 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.477 CRWrnafold: 0.343 Sensitivity Afold: 0.520 CRWrnafold: 0.373 Positive Predictive Value Afold: 0.448 CRWrnafold: 0.329 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.647 RNASampler(seed): 0.627 Sensitivity Afold: 0.672 RNASampler(seed): 0.555 Positive Predictive Value Afold: 0.630 RNASampler(seed): 0.717 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Afold Matthews Correlation Coefficient RNASLOpt: 0.479 Afold: 0.477 Sensitivity RNASLOpt: 0.507 Afold: 0.520 Positive Predictive Value RNASLOpt: 0.463 Afold: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.598 Afold: 0.577 Sensitivity PPfold(20): 0.525 Afold: 0.610 Positive Predictive Value PPfold(20): 0.689 Afold: 0.554 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.551 Mastr(seed): 0.000 Sensitivity Afold: 0.597 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.514 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08
ProbKnot	10 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.758 ProbKnot: 0.630 Sensitivity CentroidAlifold(20): 0.631 ProbKnot: 0.664 Positive Predictive Value CentroidAlifold(20): 0.914 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	12 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 ProbKnot: 0.542 Sensitivity CentroidAlifold(seed): 0.585 ProbKnot: 0.593 Positive Predictive Value CentroidAlifold(seed): 0.862 ProbKnot: 0.501 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.14531876181e-08	10 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.690 ProbKnot: 0.630 Sensitivity RNAalifold(20): 0.586 ProbKnot: 0.664 Positive Predictive Value RNAalifold(20): 0.817 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.26710183075e-09	12 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.650 ProbKnot: 0.542 Sensitivity MXScarna(seed): 0.607 ProbKnot: 0.593 Positive Predictive Value MXScarna(seed): 0.699 ProbKnot: 0.501 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	16 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.620 ProbKnot: 0.564 Sensitivity CentroidFold: 0.623 ProbKnot: 0.613 Positive Predictive Value CentroidFold: 0.623 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.89169006118e-08	10 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.659 ProbKnot: 0.630 Sensitivity RNASampler(20): 0.563 ProbKnot: 0.664 Positive Predictive Value RNASampler(20): 0.778 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.45186852942e-09	10 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.657 ProbKnot: 0.630 Sensitivity MXScarna(20): 0.613 ProbKnot: 0.664 Positive Predictive Value MXScarna(20): 0.708 ProbKnot: 0.603 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.02533530638e-08	16 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.599 ProbKnot: 0.564 Sensitivity Contrafold: 0.629 ProbKnot: 0.613 Positive Predictive Value Contrafold: 0.575 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.13260312532e-08	16 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.600 ProbKnot: 0.564 Sensitivity Sfold: 0.602 ProbKnot: 0.613 Positive Predictive Value Sfold: 0.603 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	16 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.569 ProbKnot: 0.564 Sensitivity MaxExpect: 0.598 ProbKnot: 0.613 Positive Predictive Value MaxExpect: 0.548 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	16 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.589 ProbKnot: 0.564 Sensitivity HotKnots: 0.644 ProbKnot: 0.613 Positive Predictive Value HotKnots: 0.544 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	12 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.589 ProbKnot: 0.542 Sensitivity RNAalifold(seed): 0.427 ProbKnot: 0.593 Positive Predictive Value RNAalifold(seed): 0.816 ProbKnot: 0.501 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.53777893337e-08	10 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.630 Murlet(20): 0.614 Sensitivity ProbKnot: 0.664 Murlet(20): 0.500 Positive Predictive Value ProbKnot: 0.603 Murlet(20): 0.760 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.0482910291e-08	16 UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.573 ProbKnot: 0.564 Sensitivity UNAFold: 0.610 ProbKnot: 0.613 Positive Predictive Value UNAFold: 0.544 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	10 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.630 Carnac(20): 0.589 Sensitivity ProbKnot: 0.664 Carnac(20): 0.384 Positive Predictive Value ProbKnot: 0.603 Carnac(20): 0.908 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	16 McQFold vs ProbKnot Matthews Correlation Coefficient McQFold: 0.572 ProbKnot: 0.564 Sensitivity McQFold: 0.606 ProbKnot: 0.613 Positive Predictive Value McQFold: 0.545 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 4.35504921354e-07	16 RNAshapes vs ProbKnot Matthews Correlation Coefficient RNAshapes: 0.566 ProbKnot: 0.564 Sensitivity RNAshapes: 0.598 ProbKnot: 0.613 Positive Predictive Value RNAshapes: 0.542 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.000640523715075	16 RNAfold vs ProbKnot Matthews Correlation Coefficient RNAfold: 0.583 ProbKnot: 0.564 Sensitivity RNAfold: 0.627 ProbKnot: 0.613 Positive Predictive Value RNAfold: 0.548 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 6.84390417318e-09	16 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.602 ProbKnot: 0.564 Sensitivity PknotsRG: 0.654 ProbKnot: 0.613 Positive Predictive Value PknotsRG: 0.560 ProbKnot: 0.525 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.91763127434e-08	14 Pknots vs ProbKnot Matthews Correlation Coefficient Pknots: 0.623 ProbKnot: 0.622 Sensitivity Pknots: 0.653 ProbKnot: 0.656 Positive Predictive Value Pknots: 0.604 ProbKnot: 0.600 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.111384766941	10 Afold vs ProbKnot Matthews Correlation Coefficient Afold: 0.502 ProbKnot: 0.490 Sensitivity Afold: 0.563 ProbKnot: 0.545 Positive Predictive Value Afold: 0.452 ProbKnot: 0.446 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.98587013887e-06		- Cylofold vs ProbKnot Matthews Correlation Coefficient Cylofold: 0.676 ProbKnot: 0.649 Sensitivity Cylofold: 0.664 ProbKnot: 0.675 Positive Predictive Value Cylofold: 0.697 ProbKnot: 0.634 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.00909278955e-07	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.564 RNAsubopt: 0.553 Sensitivity ProbKnot: 0.613 RNAsubopt: 0.594 Positive Predictive Value ProbKnot: 0.525 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.69265863073e-08	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.564 Fold: 0.538 Sensitivity ProbKnot: 0.613 Fold: 0.571 Positive Predictive Value ProbKnot: 0.525 Fold: 0.513 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.630 RSpredict(20): 0.558 Sensitivity ProbKnot: 0.664 RSpredict(20): 0.506 Positive Predictive Value ProbKnot: 0.603 RSpredict(20): 0.623 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.01499922709e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.564 Vsfold4: 0.470 Sensitivity ProbKnot: 0.613 Vsfold4: 0.479 Positive Predictive Value ProbKnot: 0.525 Vsfold4: 0.467 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.603 Murlet(seed): 0.534 Sensitivity ProbKnot: 0.637 Murlet(seed): 0.344 Positive Predictive Value ProbKnot: 0.581 Murlet(seed): 0.840 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.48548913747e-08	? ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.594 Alterna: 0.536 Sensitivity ProbKnot: 0.604 Alterna: 0.525 Positive Predictive Value ProbKnot: 0.604 Alterna: 0.570 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.630 Mastr(20): 0.365 Sensitivity ProbKnot: 0.664 Mastr(20): 0.199 Positive Predictive Value ProbKnot: 0.603 Mastr(20): 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.564 Vsfold5: 0.469 Sensitivity ProbKnot: 0.613 Vsfold5: 0.481 Positive Predictive Value ProbKnot: 0.525 Vsfold5: 0.463 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.36983135185e-08	? ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.606 RDfolder: 0.424 Sensitivity ProbKnot: 0.606 RDfolder: 0.363 Positive Predictive Value ProbKnot: 0.626 RDfolder: 0.523 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.585 MCFold: 0.544 Sensitivity ProbKnot: 0.633 MCFold: 0.588 Positive Predictive Value ProbKnot: 0.552 MCFold: 0.514 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.97952969696e-09	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.542 RSpredict(seed): 0.231 Sensitivity ProbKnot: 0.593 RSpredict(seed): 0.119 Positive Predictive Value ProbKnot: 0.501 RSpredict(seed): 0.457 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.603 Carnac(seed): 0.124 Sensitivity ProbKnot: 0.637 Carnac(seed): 0.015 Positive Predictive Value ProbKnot: 0.581 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.87872347734e-08	? NanoFolder vs ProbKnot Matthews Correlation Coefficient NanoFolder: 0.427 ProbKnot: 0.380 Sensitivity NanoFolder: 0.519 ProbKnot: 0.413 Positive Predictive Value NanoFolder: 0.365 ProbKnot: 0.364 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 ProbKnot: 0.527 Sensitivity CentroidHomfold‑LAST: 0.552 ProbKnot: 0.552 Positive Predictive Value CentroidHomfold‑LAST: 0.743 ProbKnot: 0.518 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): 0.629 ProbKnot: 0.575 Sensitivity Multilign(seed): 0.580 ProbKnot: 0.570 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	? Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.581 ProbKnot: 0.577 Sensitivity Multilign(20): 0.576 ProbKnot: 0.614 Positive Predictive Value Multilign(20): 0.598 ProbKnot: 0.555 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 ProbKnot: 0.392 Sensitivity PETfold_pre2.0(seed): 0.619 ProbKnot: 0.423 Positive Predictive Value PETfold_pre2.0(seed): 0.789 ProbKnot: 0.380 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.653 ProbKnot: 0.577 Sensitivity TurboFold(20): 0.606 ProbKnot: 0.614 Positive Predictive Value TurboFold(20): 0.714 ProbKnot: 0.555 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.527 RNAwolf: 0.436 Sensitivity ProbKnot: 0.552 RNAwolf: 0.437 Positive Predictive Value ProbKnot: 0.518 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.612 ProbKnot: 0.527 Sensitivity IPknot: 0.579 ProbKnot: 0.552 Positive Predictive Value IPknot: 0.658 ProbKnot: 0.518 Number of pairs reference - predicted secondary structure: 9 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): 0.619 ProbKnot: 0.472 Sensitivity PETfold_pre2.0(20): 0.570 ProbKnot: 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.682 ProbKnot: 0.441 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.514 PPfold(seed): 0.155 Sensitivity ProbKnot: 0.540 PPfold(seed): 0.047 Positive Predictive Value ProbKnot: 0.503 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.662 ProbKnot: 0.441 Sensitivity ContextFold: 0.608 ProbKnot: 0.469 Positive Predictive Value ContextFold: 0.731 ProbKnot: 0.430 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.560 ProbKnot: 0.514 Sensitivity TurboFold(seed): 0.533 ProbKnot: 0.540 Positive Predictive Value TurboFold(seed): 0.602 ProbKnot: 0.503 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.502 ProbKnot: 0.480 Sensitivity CRWrnafold: 0.516 ProbKnot: 0.509 Positive Predictive Value CRWrnafold: 0.503 ProbKnot: 0.468 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): 0.554 ProbKnot: 0.432 Sensitivity RNASampler(seed): 0.487 ProbKnot: 0.496 Positive Predictive Value RNASampler(seed): 0.640 ProbKnot: 0.386 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs ProbKnot Matthews Correlation Coefficient RNASLOpt: 0.449 ProbKnot: 0.441 Sensitivity RNASLOpt: 0.438 ProbKnot: 0.469 Positive Predictive Value RNASLOpt: 0.475 ProbKnot: 0.430 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.715 ProbKnot: 0.577 Sensitivity PPfold(20): 0.644 ProbKnot: 0.614 Positive Predictive Value PPfold(20): 0.802 ProbKnot: 0.555 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.542 Mastr(seed): 0.000 Sensitivity ProbKnot: 0.593 Mastr(seed): 0.000 Positive Predictive Value ProbKnot: 0.501 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.00627773251e-08
Cylofold	7 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.836 Cylofold: 0.731 Sensitivity CentroidAlifold(20): 0.728 Cylofold: 0.712 Positive Predictive Value CentroidAlifold(20): 0.964 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 Cylofold: 0.723 Sensitivity CentroidAlifold(seed): 0.673 Cylofold: 0.703 Positive Predictive Value CentroidAlifold(seed): 0.978 Cylofold: 0.751 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.774 Cylofold: 0.731 Sensitivity RNAalifold(20): 0.679 Cylofold: 0.712 Positive Predictive Value RNAalifold(20): 0.887 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.723 MXScarna(seed): 0.675 Sensitivity Cylofold: 0.703 MXScarna(seed): 0.629 Positive Predictive Value Cylofold: 0.751 MXScarna(seed): 0.734 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	13 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.755 Cylofold: 0.693 Sensitivity CentroidFold: 0.713 Cylofold: 0.681 Positive Predictive Value CentroidFold: 0.807 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.87872347734e-08	7 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.767 Cylofold: 0.731 Sensitivity RNASampler(20): 0.674 Cylofold: 0.712 Positive Predictive Value RNASampler(20): 0.879 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs MXScarna(20) Matthews Correlation Coefficient Cylofold: 0.731 MXScarna(20): 0.730 Sensitivity Cylofold: 0.712 MXScarna(20): 0.668 Positive Predictive Value Cylofold: 0.757 MXScarna(20): 0.804 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	13 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.727 Cylofold: 0.693 Sensitivity Contrafold: 0.719 Cylofold: 0.681 Positive Predictive Value Contrafold: 0.743 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	13 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.700 Cylofold: 0.693 Sensitivity Sfold: 0.665 Cylofold: 0.681 Positive Predictive Value Sfold: 0.746 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000109045993861	13 Cylofold vs MaxExpect Matthews Correlation Coefficient Cylofold: 0.693 MaxExpect: 0.679 Sensitivity Cylofold: 0.681 MaxExpect: 0.671 Positive Predictive Value Cylofold: 0.715 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.06154098047e-05	13 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.715 Cylofold: 0.693 Sensitivity HotKnots: 0.739 Cylofold: 0.681 Positive Predictive Value HotKnots: 0.700 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.4651262096e-08	8 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.723 RNAalifold(seed): 0.670 Sensitivity Cylofold: 0.703 RNAalifold(seed): 0.530 Positive Predictive Value Cylofold: 0.751 RNAalifold(seed): 0.856 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.739 Cylofold: 0.731 Sensitivity Murlet(20): 0.630 Cylofold: 0.712 Positive Predictive Value Murlet(20): 0.872 Cylofold: 0.757 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	13 Cylofold vs UNAFold Matthews Correlation Coefficient Cylofold: 0.693 UNAFold: 0.687 Sensitivity Cylofold: 0.681 UNAFold: 0.687 Positive Predictive Value Cylofold: 0.715 UNAFold: 0.696 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000113973846536	7 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.731 Carnac(20): 0.659 Sensitivity Cylofold: 0.712 Carnac(20): 0.473 Positive Predictive Value Cylofold: 0.757 Carnac(20): 0.926 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	13 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.738 Cylofold: 0.693 Sensitivity McQFold: 0.735 Cylofold: 0.681 Positive Predictive Value McQFold: 0.748 Cylofold: 0.715 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.45096400029e-08	13 Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.693 RNAshapes: 0.677 Sensitivity Cylofold: 0.681 RNAshapes: 0.671 Positive Predictive Value Cylofold: 0.715 RNAshapes: 0.693 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.34783000218e-05	13 Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.693 RNAfold: 0.652 Sensitivity Cylofold: 0.681 RNAfold: 0.652 Positive Predictive Value Cylofold: 0.715 RNAfold: 0.662 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.51039672358e-08	13 Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.693 PknotsRG: 0.682 Sensitivity Cylofold: 0.681 PknotsRG: 0.694 Positive Predictive Value Cylofold: 0.715 PknotsRG: 0.680 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.73294613682e-07	13 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.693 Pknots: 0.657 Sensitivity Cylofold: 0.681 Pknots: 0.684 Positive Predictive Value Cylofold: 0.715 Pknots: 0.640 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.41358941668e-08	7 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.679 Cylofold: 0.673 Sensitivity Afold: 0.699 Cylofold: 0.680 Positive Predictive Value Afold: 0.669 Cylofold: 0.675 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	12 Cylofold vs ProbKnot Matthews Correlation Coefficient Cylofold: 0.676 ProbKnot: 0.649 Sensitivity Cylofold: 0.664 ProbKnot: 0.675 Positive Predictive Value Cylofold: 0.697 ProbKnot: 0.634 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.00909278955e-07		+ Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.693 RNAsubopt: 0.663 Sensitivity Cylofold: 0.681 RNAsubopt: 0.665 Positive Predictive Value Cylofold: 0.715 RNAsubopt: 0.671 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.85564755195e-08	+ Cylofold vs Fold Matthews Correlation Coefficient Cylofold: 0.693 Fold: 0.629 Sensitivity Cylofold: 0.681 Fold: 0.629 Positive Predictive Value Cylofold: 0.715 Fold: 0.639 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	? Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.731 RSpredict(20): 0.643 Sensitivity Cylofold: 0.712 RSpredict(20): 0.598 Positive Predictive Value Cylofold: 0.757 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.693 Vsfold4: 0.582 Sensitivity Cylofold: 0.681 Vsfold4: 0.565 Positive Predictive Value Cylofold: 0.715 Vsfold4: 0.612 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	? Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.723 Murlet(seed): 0.520 Sensitivity Cylofold: 0.703 Murlet(seed): 0.342 Positive Predictive Value Cylofold: 0.751 Murlet(seed): 0.802 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.690 Alterna: 0.560 Sensitivity Cylofold: 0.657 Alterna: 0.552 Positive Predictive Value Cylofold: 0.739 Alterna: 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.731 Mastr(20): 0.483 Sensitivity Cylofold: 0.712 Mastr(20): 0.304 Positive Predictive Value Cylofold: 0.757 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.693 Vsfold5: 0.570 Sensitivity Cylofold: 0.681 Vsfold5: 0.565 Positive Predictive Value Cylofold: 0.715 Vsfold5: 0.587 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	? Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.699 RDfolder: 0.435 Sensitivity Cylofold: 0.668 RDfolder: 0.378 Positive Predictive Value Cylofold: 0.746 RDfolder: 0.525 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.688 MCFold: 0.587 Sensitivity Cylofold: 0.680 MCFold: 0.618 Positive Predictive Value Cylofold: 0.705 MCFold: 0.570 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.94879201882e-09	? Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.723 RSpredict(seed): 0.290 Sensitivity Cylofold: 0.703 RSpredict(seed): 0.163 Positive Predictive Value Cylofold: 0.751 RSpredict(seed): 0.532 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.723 Carnac(seed): 0.140 Sensitivity Cylofold: 0.703 Carnac(seed): 0.020 Positive Predictive Value Cylofold: 0.751 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.585 NanoFolder: 0.576 Sensitivity Cylofold: 0.583 NanoFolder: 0.643 Positive Predictive Value Cylofold: 0.605 NanoFolder: 0.535 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.696 Cylofold: 0.664 Sensitivity CentroidHomfold‑LAST: 0.589 Cylofold: 0.650 Positive Predictive Value CentroidHomfold‑LAST: 0.835 Cylofold: 0.693 Number of pairs reference - predicted secondary structure: 8 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: 0.661 Multilign(seed): 0.629 Sensitivity Cylofold: 0.620 Multilign(seed): 0.580 Positive Predictive Value Cylofold: 0.721 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: 0.756 Multilign(20): 0.678 Sensitivity Cylofold: 0.723 Multilign(20): 0.634 Positive Predictive Value Cylofold: 0.802 Multilign(20): 0.740 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: 0.701 PETfold_pre2.0(seed): 0.666 Sensitivity Cylofold: 0.675 PETfold_pre2.0(seed): 0.584 Positive Predictive Value Cylofold: 0.743 PETfold_pre2.0(seed): 0.776 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.756 TurboFold(20): 0.750 Sensitivity Cylofold: 0.723 TurboFold(20): 0.670 Positive Predictive Value Cylofold: 0.802 TurboFold(20): 0.852 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.664 RNAwolf: 0.484 Sensitivity Cylofold: 0.650 RNAwolf: 0.472 Positive Predictive Value Cylofold: 0.693 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.666 Cylofold: 0.664 Sensitivity IPknot: 0.620 Cylofold: 0.650 Positive Predictive Value IPknot: 0.732 Cylofold: 0.693 Number of pairs reference - predicted secondary structure: 8 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): 0.763 Cylofold: 0.720 Sensitivity PETfold_pre2.0(20): 0.678 Cylofold: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.870 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.740 PPfold(seed): 0.182 Sensitivity Cylofold: 0.708 PPfold(seed): 0.046 Positive Predictive Value Cylofold: 0.786 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.738 Cylofold: 0.602 Sensitivity ContextFold: 0.673 Cylofold: 0.600 Positive Predictive Value ContextFold: 0.822 Cylofold: 0.623 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.740 TurboFold(seed): 0.641 Sensitivity Cylofold: 0.708 TurboFold(seed): 0.577 Positive Predictive Value Cylofold: 0.786 TurboFold(seed): 0.728 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.624 CRWrnafold: 0.563 Sensitivity Cylofold: 0.619 CRWrnafold: 0.554 Positive Predictive Value Cylofold: 0.647 CRWrnafold: 0.592 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.659 RNASampler(seed): 0.596 Sensitivity Cylofold: 0.667 RNASampler(seed): 0.505 Positive Predictive Value Cylofold: 0.660 RNASampler(seed): 0.712 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.602 RNASLOpt: 0.493 Sensitivity Cylofold: 0.600 RNASLOpt: 0.445 Positive Predictive Value Cylofold: 0.623 RNASLOpt: 0.570 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.797 Cylofold: 0.756 Sensitivity PPfold(20): 0.714 Cylofold: 0.723 Positive Predictive Value PPfold(20): 0.899 Cylofold: 0.802 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.723 Mastr(seed): 0.000 Sensitivity Cylofold: 0.703 Mastr(seed): 0.000 Positive Predictive Value Cylofold: 0.751 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
RNAsubopt	15 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RNAsubopt: 0.620 Sensitivity CentroidAlifold(20): 0.694 RNAsubopt: 0.632 Positive Predictive Value CentroidAlifold(20): 0.932 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	19 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RNAsubopt: 0.573 Sensitivity CentroidAlifold(seed): 0.598 RNAsubopt: 0.603 Positive Predictive Value CentroidAlifold(seed): 0.894 RNAsubopt: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	15 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.753 RNAsubopt: 0.620 Sensitivity RNAalifold(20): 0.656 RNAsubopt: 0.632 Positive Predictive Value RNAalifold(20): 0.869 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	19 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.711 RNAsubopt: 0.573 Sensitivity MXScarna(seed): 0.663 RNAsubopt: 0.603 Positive Predictive Value MXScarna(seed): 0.768 RNAsubopt: 0.550 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	25 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.704 RNAsubopt: 0.593 Sensitivity CentroidFold: 0.698 RNAsubopt: 0.620 Positive Predictive Value CentroidFold: 0.715 RNAsubopt: 0.573 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.732 RNAsubopt: 0.620 Sensitivity RNASampler(20): 0.639 RNAsubopt: 0.632 Positive Predictive Value RNASampler(20): 0.843 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	15 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.703 RNAsubopt: 0.620 Sensitivity MXScarna(20): 0.659 RNAsubopt: 0.632 Positive Predictive Value MXScarna(20): 0.755 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	28 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.663 RNAsubopt: 0.591 Sensitivity Contrafold: 0.678 RNAsubopt: 0.615 Positive Predictive Value Contrafold: 0.654 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.638 RNAsubopt: 0.591 Sensitivity Sfold: 0.629 RNAsubopt: 0.615 Positive Predictive Value Sfold: 0.653 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.623 RNAsubopt: 0.579 Sensitivity MaxExpect: 0.640 RNAsubopt: 0.608 Positive Predictive Value MaxExpect: 0.612 RNAsubopt: 0.558 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.631 RNAsubopt: 0.591 Sensitivity HotKnots: 0.666 RNAsubopt: 0.615 Positive Predictive Value HotKnots: 0.605 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	16 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.634 RNAsubopt: 0.601 Sensitivity RNAalifold(seed): 0.479 RNAsubopt: 0.634 Positive Predictive Value RNAalifold(seed): 0.842 RNAsubopt: 0.575 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.89649746203e-08	15 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.666 RNAsubopt: 0.620 Sensitivity Murlet(20): 0.548 RNAsubopt: 0.632 Positive Predictive Value Murlet(20): 0.814 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.21671975982e-08	28 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.633 RNAsubopt: 0.591 Sensitivity UNAFold: 0.655 RNAsubopt: 0.615 Positive Predictive Value UNAFold: 0.619 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.662 RNAsubopt: 0.620 Sensitivity Carnac(20): 0.469 RNAsubopt: 0.632 Positive Predictive Value Carnac(20): 0.938 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.8150742666e-08	28 McQFold vs RNAsubopt Matthews Correlation Coefficient McQFold: 0.624 RNAsubopt: 0.591 Sensitivity McQFold: 0.641 RNAsubopt: 0.615 Positive Predictive Value McQFold: 0.614 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.610 RNAsubopt: 0.591 Sensitivity RNAshapes: 0.625 RNAsubopt: 0.615 Positive Predictive Value RNAshapes: 0.602 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	28 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.607 RNAsubopt: 0.591 Sensitivity RNAfold: 0.633 RNAsubopt: 0.615 Positive Predictive Value RNAfold: 0.588 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.01188337103e-07	28 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.612 RNAsubopt: 0.591 Sensitivity PknotsRG: 0.645 RNAsubopt: 0.615 Positive Predictive Value PknotsRG: 0.586 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 6.07491858776e-08	26 Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: 0.676 RNAsubopt: 0.635 Sensitivity Pknots: 0.693 RNAsubopt: 0.637 Positive Predictive Value Pknots: 0.668 RNAsubopt: 0.644 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	21 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.567 Afold: 0.564 Sensitivity RNAsubopt: 0.600 Afold: 0.604 Positive Predictive Value RNAsubopt: 0.542 Afold: 0.533 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.00183945888045	16 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.564 RNAsubopt: 0.553 Sensitivity ProbKnot: 0.613 RNAsubopt: 0.594 Positive Predictive Value ProbKnot: 0.525 RNAsubopt: 0.521 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.69265863073e-08	13 Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.693 RNAsubopt: 0.663 Sensitivity Cylofold: 0.681 RNAsubopt: 0.665 Positive Predictive Value Cylofold: 0.715 RNAsubopt: 0.671 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.85564755195e-08		+ RNAsubopt vs Fold Matthews Correlation Coefficient RNAsubopt: 0.579 Fold: 0.557 Sensitivity RNAsubopt: 0.618 Fold: 0.589 Positive Predictive Value RNAsubopt: 0.547 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	= RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.624 RNAsubopt: 0.620 Sensitivity RSpredict(20): 0.559 RNAsubopt: 0.632 Positive Predictive Value RSpredict(20): 0.702 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.127313587452	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.591 Vsfold4: 0.559 Sensitivity RNAsubopt: 0.615 Vsfold4: 0.554 Positive Predictive Value RNAsubopt: 0.574 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.679 Murlet(seed): 0.571 Sensitivity RNAsubopt: 0.677 Murlet(seed): 0.386 Positive Predictive Value RNAsubopt: 0.690 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.16131455263e-08	= Alterna vs RNAsubopt Matthews Correlation Coefficient Alterna: 0.647 RNAsubopt: 0.645 Sensitivity Alterna: 0.636 RNAsubopt: 0.633 Positive Predictive Value Alterna: 0.674 RNAsubopt: 0.673 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0286720377294	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.620 Mastr(20): 0.506 Sensitivity RNAsubopt: 0.632 Mastr(20): 0.337 Positive Predictive Value RNAsubopt: 0.615 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.591 Vsfold5: 0.518 Sensitivity RNAsubopt: 0.615 Vsfold5: 0.514 Positive Predictive Value RNAsubopt: 0.574 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.640 RDfolder: 0.549 Sensitivity RNAsubopt: 0.625 RDfolder: 0.487 Positive Predictive Value RNAsubopt: 0.672 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.597 MCFold: 0.527 Sensitivity RNAsubopt: 0.604 MCFold: 0.563 Positive Predictive Value RNAsubopt: 0.602 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.573 RSpredict(seed): 0.324 Sensitivity RNAsubopt: 0.603 RSpredict(seed): 0.177 Positive Predictive Value RNAsubopt: 0.550 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.679 Carnac(seed): 0.104 Sensitivity RNAsubopt: 0.677 Carnac(seed): 0.011 Positive Predictive Value RNAsubopt: 0.690 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	? NanoFolder vs RNAsubopt Matthews Correlation Coefficient NanoFolder: 0.427 RNAsubopt: 0.356 Sensitivity NanoFolder: 0.519 RNAsubopt: 0.385 Positive Predictive Value NanoFolder: 0.365 RNAsubopt: 0.345 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAsubopt: 0.513 Sensitivity CentroidHomfold‑LAST: 0.552 RNAsubopt: 0.525 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAsubopt: 0.516 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): 0.629 RNAsubopt: 0.610 Sensitivity Multilign(seed): 0.580 RNAsubopt: 0.590 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: 0.596 Multilign(20): 0.581 Sensitivity RNAsubopt: 0.606 Multilign(20): 0.576 Positive Predictive Value RNAsubopt: 0.597 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAsubopt: 0.386 Sensitivity PETfold_pre2.0(seed): 0.619 RNAsubopt: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAsubopt: 0.386 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.653 RNAsubopt: 0.596 Sensitivity TurboFold(20): 0.606 RNAsubopt: 0.606 Positive Predictive Value TurboFold(20): 0.714 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.513 RNAwolf: 0.436 Sensitivity RNAsubopt: 0.525 RNAwolf: 0.437 Positive Predictive Value RNAsubopt: 0.516 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.612 RNAsubopt: 0.513 Sensitivity IPknot: 0.579 RNAsubopt: 0.525 Positive Predictive Value IPknot: 0.658 RNAsubopt: 0.516 Number of pairs reference - predicted secondary structure: 9 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): 0.619 RNAsubopt: 0.467 Sensitivity PETfold_pre2.0(20): 0.570 RNAsubopt: 0.494 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAsubopt: 0.453 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.528 PPfold(seed): 0.155 Sensitivity RNAsubopt: 0.533 PPfold(seed): 0.047 Positive Predictive Value RNAsubopt: 0.537 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.662 RNAsubopt: 0.402 Sensitivity ContextFold: 0.608 RNAsubopt: 0.423 Positive Predictive Value ContextFold: 0.731 RNAsubopt: 0.399 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.560 RNAsubopt: 0.528 Sensitivity TurboFold(seed): 0.533 RNAsubopt: 0.533 Positive Predictive Value TurboFold(seed): 0.602 RNAsubopt: 0.537 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.502 RNAsubopt: 0.460 Sensitivity CRWrnafold: 0.516 RNAsubopt: 0.478 Positive Predictive Value CRWrnafold: 0.503 RNAsubopt: 0.458 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): 0.640 RNAsubopt: 0.598 Sensitivity RNASampler(seed): 0.554 RNAsubopt: 0.620 Positive Predictive Value RNASampler(seed): 0.748 RNAsubopt: 0.585 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.449 RNAsubopt: 0.402 Sensitivity RNASLOpt: 0.438 RNAsubopt: 0.423 Positive Predictive Value RNASLOpt: 0.475 RNAsubopt: 0.399 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.715 RNAsubopt: 0.596 Sensitivity PPfold(20): 0.644 RNAsubopt: 0.606 Positive Predictive Value PPfold(20): 0.802 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.573 Mastr(seed): 0.000 Sensitivity RNAsubopt: 0.603 Mastr(seed): 0.000 Positive Predictive Value RNAsubopt: 0.550 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.42071836373e-08
Fold	10 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.758 Fold: 0.621 Sensitivity CentroidAlifold(20): 0.631 Fold: 0.637 Positive Predictive Value CentroidAlifold(20): 0.914 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.09700314043e-09	12 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Fold: 0.532 Sensitivity CentroidAlifold(seed): 0.585 Fold: 0.570 Positive Predictive Value CentroidAlifold(seed): 0.862 Fold: 0.502 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.95070920198e-08	10 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.690 Fold: 0.621 Sensitivity RNAalifold(20): 0.586 Fold: 0.637 Positive Predictive Value RNAalifold(20): 0.817 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1568170475e-08	12 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.650 Fold: 0.532 Sensitivity MXScarna(seed): 0.607 Fold: 0.570 Positive Predictive Value MXScarna(seed): 0.699 Fold: 0.502 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.84361416392e-08	17 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.643 Fold: 0.557 Sensitivity CentroidFold: 0.645 Fold: 0.589 Positive Predictive Value CentroidFold: 0.646 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	10 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.659 Fold: 0.621 Sensitivity RNASampler(20): 0.563 Fold: 0.637 Positive Predictive Value RNASampler(20): 0.778 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	10 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.657 Fold: 0.621 Sensitivity MXScarna(20): 0.613 Fold: 0.637 Positive Predictive Value MXScarna(20): 0.708 Fold: 0.611 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.45186852942e-09	17 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.622 Fold: 0.557 Sensitivity Contrafold: 0.651 Fold: 0.589 Positive Predictive Value Contrafold: 0.600 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.63594052159e-08	17 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.605 Fold: 0.557 Sensitivity Sfold: 0.604 Fold: 0.589 Positive Predictive Value Sfold: 0.610 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	17 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.587 Fold: 0.557 Sensitivity MaxExpect: 0.614 Fold: 0.589 Positive Predictive Value MaxExpect: 0.567 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	17 HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.605 Fold: 0.557 Sensitivity HotKnots: 0.657 Fold: 0.589 Positive Predictive Value HotKnots: 0.562 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.70887622364e-08	12 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.589 Fold: 0.532 Sensitivity RNAalifold(seed): 0.427 Fold: 0.570 Positive Predictive Value RNAalifold(seed): 0.816 Fold: 0.502 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	10 Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.621 Murlet(20): 0.614 Sensitivity Fold: 0.637 Murlet(20): 0.500 Positive Predictive Value Fold: 0.611 Murlet(20): 0.760 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.00173322773106	17 UNAFold vs Fold Matthews Correlation Coefficient UNAFold: 0.590 Fold: 0.557 Sensitivity UNAFold: 0.626 Fold: 0.589 Positive Predictive Value UNAFold: 0.562 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	10 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.621 Carnac(20): 0.589 Sensitivity Fold: 0.637 Carnac(20): 0.384 Positive Predictive Value Fold: 0.611 Carnac(20): 0.908 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.84540901819e-09	17 McQFold vs Fold Matthews Correlation Coefficient McQFold: 0.597 Fold: 0.557 Sensitivity McQFold: 0.630 Fold: 0.589 Positive Predictive Value McQFold: 0.571 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.62913390836e-08	17 RNAshapes vs Fold Matthews Correlation Coefficient RNAshapes: 0.575 Fold: 0.557 Sensitivity RNAshapes: 0.604 Fold: 0.589 Positive Predictive Value RNAshapes: 0.553 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.57076602694e-08	17 RNAfold vs Fold Matthews Correlation Coefficient RNAfold: 0.570 Fold: 0.557 Sensitivity RNAfold: 0.610 Fold: 0.589 Positive Predictive Value RNAfold: 0.538 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45802991547e-07	17 PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.588 Fold: 0.557 Sensitivity PknotsRG: 0.635 Fold: 0.589 Positive Predictive Value PknotsRG: 0.549 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.64481516727e-08	15 Pknots vs Fold Matthews Correlation Coefficient Pknots: 0.654 Fold: 0.609 Sensitivity Pknots: 0.681 Fold: 0.619 Positive Predictive Value Pknots: 0.636 Fold: 0.610 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	11 Afold vs Fold Matthews Correlation Coefficient Afold: 0.530 Fold: 0.496 Sensitivity Afold: 0.590 Fold: 0.539 Positive Predictive Value Afold: 0.482 Fold: 0.462 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08	16 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.564 Fold: 0.538 Sensitivity ProbKnot: 0.613 Fold: 0.571 Positive Predictive Value ProbKnot: 0.525 Fold: 0.513 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	13 Cylofold vs Fold Matthews Correlation Coefficient Cylofold: 0.693 Fold: 0.629 Sensitivity Cylofold: 0.681 Fold: 0.629 Positive Predictive Value Cylofold: 0.715 Fold: 0.639 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	17 RNAsubopt vs Fold Matthews Correlation Coefficient RNAsubopt: 0.579 Fold: 0.557 Sensitivity RNAsubopt: 0.618 Fold: 0.589 Positive Predictive Value RNAsubopt: 0.547 Fold: 0.534 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08		+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.621 RSpredict(20): 0.558 Sensitivity Fold: 0.637 RSpredict(20): 0.506 Positive Predictive Value Fold: 0.611 RSpredict(20): 0.623 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.26036189514e-09	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.557 Vsfold4: 0.499 Sensitivity Fold: 0.589 Vsfold4: 0.507 Positive Predictive Value Fold: 0.534 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.589 Murlet(seed): 0.534 Sensitivity Fold: 0.602 Murlet(seed): 0.344 Positive Predictive Value Fold: 0.586 Murlet(seed): 0.840 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.60468628729e-08	? Fold vs Alterna Matthews Correlation Coefficient Fold: 0.589 Alterna: 0.560 Sensitivity Fold: 0.582 Alterna: 0.552 Positive Predictive Value Fold: 0.614 Alterna: 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.621 Mastr(20): 0.365 Sensitivity Fold: 0.637 Mastr(20): 0.199 Positive Predictive Value Fold: 0.611 Mastr(20): 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.557 Vsfold5: 0.482 Sensitivity Fold: 0.589 Vsfold5: 0.489 Positive Predictive Value Fold: 0.534 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.60448791174e-08	? Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.558 RDfolder: 0.435 Sensitivity Fold: 0.544 RDfolder: 0.378 Positive Predictive Value Fold: 0.593 RDfolder: 0.525 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	= MCFold vs Fold Matthews Correlation Coefficient MCFold: 0.544 Fold: 0.530 Sensitivity MCFold: 0.588 Fold: 0.551 Positive Predictive Value MCFold: 0.514 Fold: 0.521 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0318548130709	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.532 RSpredict(seed): 0.231 Sensitivity Fold: 0.570 RSpredict(seed): 0.119 Positive Predictive Value Fold: 0.502 RSpredict(seed): 0.457 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.589 Carnac(seed): 0.124 Sensitivity Fold: 0.602 Carnac(seed): 0.015 Positive Predictive Value Fold: 0.586 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.34193807955e-08	? NanoFolder vs Fold Matthews Correlation Coefficient NanoFolder: 0.427 Fold: 0.366 Sensitivity NanoFolder: 0.519 Fold: 0.385 Positive Predictive Value NanoFolder: 0.365 Fold: 0.364 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Fold: 0.468 Sensitivity CentroidHomfold‑LAST: 0.552 Fold: 0.475 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Fold: 0.478 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): 0.629 Fold: 0.589 Sensitivity Multilign(seed): 0.580 Fold: 0.570 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): 0.581 Fold: 0.537 Sensitivity Multilign(20): 0.576 Fold: 0.545 Positive Predictive Value Multilign(20): 0.598 Fold: 0.541 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Fold: 0.318 Sensitivity PETfold_pre2.0(seed): 0.619 Fold: 0.330 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Fold: 0.323 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.653 Fold: 0.537 Sensitivity TurboFold(20): 0.606 Fold: 0.545 Positive Predictive Value TurboFold(20): 0.714 Fold: 0.541 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.468 RNAwolf: 0.436 Sensitivity Fold: 0.475 RNAwolf: 0.437 Positive Predictive Value Fold: 0.478 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.612 Fold: 0.468 Sensitivity IPknot: 0.579 Fold: 0.475 Positive Predictive Value IPknot: 0.658 Fold: 0.478 Number of pairs reference - predicted secondary structure: 9 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): 0.619 Fold: 0.386 Sensitivity PETfold_pre2.0(20): 0.570 Fold: 0.405 Positive Predictive Value PETfold_pre2.0(20): 0.682 Fold: 0.381 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.475 PPfold(seed): 0.155 Sensitivity Fold: 0.480 PPfold(seed): 0.047 Positive Predictive Value Fold: 0.486 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.662 Fold: 0.348 Sensitivity ContextFold: 0.608 Fold: 0.362 Positive Predictive Value ContextFold: 0.731 Fold: 0.353 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.560 Fold: 0.475 Sensitivity TurboFold(seed): 0.533 Fold: 0.480 Positive Predictive Value TurboFold(seed): 0.602 Fold: 0.486 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.502 Fold: 0.409 Sensitivity CRWrnafold: 0.516 Fold: 0.421 Positive Predictive Value CRWrnafold: 0.503 Fold: 0.414 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): 0.554 Fold: 0.450 Sensitivity RNASampler(seed): 0.487 Fold: 0.496 Positive Predictive Value RNASampler(seed): 0.640 Fold: 0.418 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Fold Matthews Correlation Coefficient RNASLOpt: 0.449 Fold: 0.348 Sensitivity RNASLOpt: 0.438 Fold: 0.362 Positive Predictive Value RNASLOpt: 0.475 Fold: 0.353 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.715 Fold: 0.537 Sensitivity PPfold(20): 0.644 Fold: 0.545 Positive Predictive Value PPfold(20): 0.802 Fold: 0.541 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.532 Mastr(seed): 0.000 Sensitivity Fold: 0.570 Mastr(seed): 0.000 Positive Predictive Value Fold: 0.502 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.00475527001e-08
RSpredict(20)	15 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RSpredict(20): 0.624 Sensitivity CentroidAlifold(20): 0.694 RSpredict(20): 0.559 Positive Predictive Value CentroidAlifold(20): 0.932 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	15 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 RSpredict(20): 0.624 Sensitivity CentroidAlifold(seed): 0.623 RSpredict(20): 0.559 Positive Predictive Value CentroidAlifold(seed): 0.934 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	15 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 RSpredict(20): 0.624 Sensitivity RNAalifold(20): 0.656 RSpredict(20): 0.559 Positive Predictive Value RNAalifold(20): 0.869 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08	15 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 RSpredict(20): 0.624 Sensitivity MXScarna(seed): 0.692 RSpredict(20): 0.559 Positive Predictive Value MXScarna(seed): 0.820 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	15 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.716 RSpredict(20): 0.624 Sensitivity CentroidFold: 0.687 RSpredict(20): 0.559 Positive Predictive Value CentroidFold: 0.750 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.97012568641e-08	15 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.732 RSpredict(20): 0.624 Sensitivity RNASampler(20): 0.639 RSpredict(20): 0.559 Positive Predictive Value RNASampler(20): 0.843 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.77512146924e-08	15 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.703 RSpredict(20): 0.624 Sensitivity MXScarna(20): 0.659 RSpredict(20): 0.559 Positive Predictive Value MXScarna(20): 0.755 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.95070920198e-08	15 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.650 RSpredict(20): 0.624 Sensitivity Contrafold: 0.652 RSpredict(20): 0.559 Positive Predictive Value Contrafold: 0.655 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.0326876712e-07	15 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.665 RSpredict(20): 0.624 Sensitivity Sfold: 0.628 RSpredict(20): 0.559 Positive Predictive Value Sfold: 0.711 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.16236719691e-08	15 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.674 RSpredict(20): 0.624 Sensitivity MaxExpect: 0.670 RSpredict(20): 0.559 Positive Predictive Value MaxExpect: 0.683 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.20167918023e-08	15 HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.640 RSpredict(20): 0.624 Sensitivity HotKnots: 0.663 RSpredict(20): 0.559 Positive Predictive Value HotKnots: 0.623 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08749669591e-05	13 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 RSpredict(20): 0.590 Sensitivity RNAalifold(seed): 0.515 RSpredict(20): 0.524 Positive Predictive Value RNAalifold(seed): 0.918 RSpredict(20): 0.671 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.75835195567e-08	15 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.666 RSpredict(20): 0.624 Sensitivity Murlet(20): 0.548 RSpredict(20): 0.559 Positive Predictive Value Murlet(20): 0.814 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	15 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.662 RSpredict(20): 0.624 Sensitivity UNAFold: 0.663 RSpredict(20): 0.559 Positive Predictive Value UNAFold: 0.667 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.01438538033e-08	15 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.662 RSpredict(20): 0.624 Sensitivity Carnac(20): 0.469 RSpredict(20): 0.559 Positive Predictive Value Carnac(20): 0.938 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	15 McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.644 RSpredict(20): 0.624 Sensitivity McQFold: 0.643 RSpredict(20): 0.559 Positive Predictive Value McQFold: 0.650 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.09795090663e-05	15 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.637 RSpredict(20): 0.624 Sensitivity RNAshapes: 0.637 RSpredict(20): 0.559 Positive Predictive Value RNAshapes: 0.644 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.000485451965192	15 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.643 RSpredict(20): 0.624 Sensitivity RNAfold: 0.656 RSpredict(20): 0.559 Positive Predictive Value RNAfold: 0.637 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 7.1187875805e-05	15 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.664 RSpredict(20): 0.624 Sensitivity PknotsRG: 0.685 RSpredict(20): 0.559 Positive Predictive Value PknotsRG: 0.649 RSpredict(20): 0.702 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 5.86050763602e-08	14 Pknots vs RSpredict(20) Matthews Correlation Coefficient Pknots: 0.670 RSpredict(20): 0.625 Sensitivity Pknots: 0.691 RSpredict(20): 0.557 Positive Predictive Value Pknots: 0.658 RSpredict(20): 0.712 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.74172190343e-08	10 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.620 Afold: 0.565 Sensitivity RSpredict(20): 0.581 Afold: 0.591 Positive Predictive Value RSpredict(20): 0.667 Afold: 0.547 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.19853615606e-08	10 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.630 RSpredict(20): 0.558 Sensitivity ProbKnot: 0.664 RSpredict(20): 0.506 Positive Predictive Value ProbKnot: 0.603 RSpredict(20): 0.623 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.01499922709e-08	7 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.731 RSpredict(20): 0.643 Sensitivity Cylofold: 0.712 RSpredict(20): 0.598 Positive Predictive Value Cylofold: 0.757 RSpredict(20): 0.701 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	15 RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.624 RNAsubopt: 0.620 Sensitivity RSpredict(20): 0.559 RNAsubopt: 0.632 Positive Predictive Value RSpredict(20): 0.702 RNAsubopt: 0.615 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.127313587452	10 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.621 RSpredict(20): 0.558 Sensitivity Fold: 0.637 RSpredict(20): 0.506 Positive Predictive Value Fold: 0.611 RSpredict(20): 0.623 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.26036189514e-09		+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.624 Vsfold4: 0.545 Sensitivity RSpredict(20): 0.559 Vsfold4: 0.526 Positive Predictive Value RSpredict(20): 0.702 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.59816551561e-08	- Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.607 RSpredict(20): 0.581 Sensitivity Murlet(seed): 0.407 RSpredict(20): 0.511 Positive Predictive Value Murlet(seed): 0.915 RSpredict(20): 0.672 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.81576394991e-06	? RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.828 Alterna: 0.593 Sensitivity RSpredict(20): 0.760 Alterna: 0.596 Positive Predictive Value RSpredict(20): 0.909 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.624 Mastr(20): 0.506 Sensitivity RSpredict(20): 0.559 Mastr(20): 0.337 Positive Predictive Value RSpredict(20): 0.702 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.624 Vsfold5: 0.495 Sensitivity RSpredict(20): 0.559 Vsfold5: 0.480 Positive Predictive Value RSpredict(20): 0.702 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.742 RDfolder: 0.613 Sensitivity RSpredict(20): 0.643 RDfolder: 0.552 Positive Predictive Value RSpredict(20): 0.865 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.26497248087e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.694 MCFold: 0.506 Sensitivity RSpredict(20): 0.662 MCFold: 0.546 Positive Predictive Value RSpredict(20): 0.735 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.624 RSpredict(seed): 0.350 Sensitivity RSpredict(20): 0.559 RSpredict(seed): 0.181 Positive Predictive Value RSpredict(20): 0.702 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.581 Carnac(seed): 0.000 Sensitivity RSpredict(20): 0.511 Carnac(seed): 0.000 Positive Predictive Value RSpredict(20): 0.672 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.87872347734e-08	? RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.316 NanoFolder: 0.285 Sensitivity RSpredict(20): 0.281 NanoFolder: 0.359 Positive Predictive Value RSpredict(20): 0.367 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 RSpredict(20): 0.573 Sensitivity CentroidHomfold‑LAST: 0.644 RSpredict(20): 0.530 Positive Predictive Value CentroidHomfold‑LAST: 0.825 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 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): 0.755 RSpredict(20): 0.707 Sensitivity Multilign(seed): 0.707 RSpredict(20): 0.634 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): 0.581 RSpredict(20): 0.573 Sensitivity Multilign(20): 0.576 RSpredict(20): 0.530 Positive Predictive Value Multilign(20): 0.598 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 RSpredict(20): 0.351 Sensitivity PETfold_pre2.0(seed): 0.684 RSpredict(20): 0.304 Positive Predictive Value PETfold_pre2.0(seed): 0.831 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.653 RSpredict(20): 0.573 Sensitivity TurboFold(20): 0.606 RSpredict(20): 0.530 Positive Predictive Value TurboFold(20): 0.714 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.573 RNAwolf: 0.442 Sensitivity RSpredict(20): 0.530 RNAwolf: 0.439 Positive Predictive Value RSpredict(20): 0.631 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.623 RSpredict(20): 0.573 Sensitivity IPknot: 0.591 RSpredict(20): 0.530 Positive Predictive Value IPknot: 0.667 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 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): 0.619 RSpredict(20): 0.351 Sensitivity PETfold_pre2.0(20): 0.570 RSpredict(20): 0.304 Positive Predictive Value PETfold_pre2.0(20): 0.682 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.573 PPfold(seed): 0.036 Sensitivity RSpredict(20): 0.530 PPfold(seed): 0.008 Positive Predictive Value RSpredict(20): 0.631 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.567 RSpredict(20): 0.351 Sensitivity ContextFold: 0.506 RSpredict(20): 0.304 Positive Predictive Value ContextFold: 0.645 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 RSpredict(20): 0.573 Sensitivity TurboFold(seed): 0.606 RSpredict(20): 0.530 Positive Predictive Value TurboFold(seed): 0.678 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.592 RSpredict(20): 0.494 Sensitivity CRWrnafold: 0.611 RSpredict(20): 0.454 Positive Predictive Value CRWrnafold: 0.584 RSpredict(20): 0.551 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 RSpredict(20): 0.640 Sensitivity RNASampler(seed): 0.627 RSpredict(20): 0.703 Positive Predictive Value RNASampler(seed): 0.779 RSpredict(20): 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.459 RSpredict(20): 0.351 Sensitivity RNASLOpt: 0.456 RSpredict(20): 0.304 Positive Predictive Value RNASLOpt: 0.474 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.715 RSpredict(20): 0.573 Sensitivity PPfold(20): 0.644 RSpredict(20): 0.530 Positive Predictive Value PPfold(20): 0.802 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.624 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.559 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.702 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.9966815982e-08
Vsfold4	15 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Vsfold4: 0.545 Sensitivity CentroidAlifold(20): 0.694 Vsfold4: 0.526 Positive Predictive Value CentroidAlifold(20): 0.932 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.26346675981e-08	19 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Vsfold4: 0.531 Sensitivity CentroidAlifold(seed): 0.598 Vsfold4: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.894 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.64318034126e-08	15 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.753 Vsfold4: 0.545 Sensitivity RNAalifold(20): 0.656 Vsfold4: 0.526 Positive Predictive Value RNAalifold(20): 0.869 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	19 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.711 Vsfold4: 0.531 Sensitivity MXScarna(seed): 0.663 Vsfold4: 0.530 Positive Predictive Value MXScarna(seed): 0.768 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	25 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.704 Vsfold4: 0.553 Sensitivity CentroidFold: 0.698 Vsfold4: 0.550 Positive Predictive Value CentroidFold: 0.715 Vsfold4: 0.563 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 4.89920829651e-08	15 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.732 Vsfold4: 0.545 Sensitivity RNASampler(20): 0.639 Vsfold4: 0.526 Positive Predictive Value RNASampler(20): 0.843 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.45805449719e-08	15 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.703 Vsfold4: 0.545 Sensitivity MXScarna(20): 0.659 Vsfold4: 0.526 Positive Predictive Value MXScarna(20): 0.755 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.43573297697e-08	28 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.663 Vsfold4: 0.559 Sensitivity Contrafold: 0.678 Vsfold4: 0.554 Positive Predictive Value Contrafold: 0.654 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.638 Vsfold4: 0.559 Sensitivity Sfold: 0.629 Vsfold4: 0.554 Positive Predictive Value Sfold: 0.653 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.89920829651e-08	23 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.623 Vsfold4: 0.522 Sensitivity MaxExpect: 0.640 Vsfold4: 0.520 Positive Predictive Value MaxExpect: 0.612 Vsfold4: 0.531 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.631 Vsfold4: 0.559 Sensitivity HotKnots: 0.666 Vsfold4: 0.554 Positive Predictive Value HotKnots: 0.605 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	16 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.634 Vsfold4: 0.516 Sensitivity RNAalifold(seed): 0.479 Vsfold4: 0.517 Positive Predictive Value RNAalifold(seed): 0.842 Vsfold4: 0.522 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.78993384543e-08	15 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.666 Vsfold4: 0.545 Sensitivity Murlet(20): 0.548 Vsfold4: 0.526 Positive Predictive Value Murlet(20): 0.814 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.06323189071e-08	28 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.633 Vsfold4: 0.559 Sensitivity UNAFold: 0.655 Vsfold4: 0.554 Positive Predictive Value UNAFold: 0.619 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.662 Vsfold4: 0.545 Sensitivity Carnac(20): 0.469 Vsfold4: 0.526 Positive Predictive Value Carnac(20): 0.938 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	28 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.624 Vsfold4: 0.559 Sensitivity McQFold: 0.641 Vsfold4: 0.554 Positive Predictive Value McQFold: 0.614 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.610 Vsfold4: 0.559 Sensitivity RNAshapes: 0.625 Vsfold4: 0.554 Positive Predictive Value RNAshapes: 0.602 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.607 Vsfold4: 0.559 Sensitivity RNAfold: 0.633 Vsfold4: 0.554 Positive Predictive Value RNAfold: 0.588 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.612 Vsfold4: 0.559 Sensitivity PknotsRG: 0.645 Vsfold4: 0.554 Positive Predictive Value PknotsRG: 0.586 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.676 Vsfold4: 0.625 Sensitivity Pknots: 0.693 Vsfold4: 0.598 Positive Predictive Value Pknots: 0.668 Vsfold4: 0.665 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.564 Vsfold4: 0.554 Sensitivity Afold: 0.604 Vsfold4: 0.557 Positive Predictive Value Afold: 0.533 Vsfold4: 0.558 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 1.35125075749e-05	16 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.564 Vsfold4: 0.470 Sensitivity ProbKnot: 0.613 Vsfold4: 0.479 Positive Predictive Value ProbKnot: 0.525 Vsfold4: 0.467 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.24270395587e-08	13 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.693 Vsfold4: 0.582 Sensitivity Cylofold: 0.681 Vsfold4: 0.565 Positive Predictive Value Cylofold: 0.715 Vsfold4: 0.612 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	28 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.591 Vsfold4: 0.559 Sensitivity RNAsubopt: 0.615 Vsfold4: 0.554 Positive Predictive Value RNAsubopt: 0.574 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.557 Vsfold4: 0.499 Sensitivity Fold: 0.589 Vsfold4: 0.507 Positive Predictive Value Fold: 0.534 Vsfold4: 0.498 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	15 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.624 Vsfold4: 0.545 Sensitivity RSpredict(20): 0.559 Vsfold4: 0.526 Positive Predictive Value RSpredict(20): 0.702 Vsfold4: 0.572 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.59816551561e-08		+ Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.603 Murlet(seed): 0.571 Sensitivity Vsfold4: 0.573 Murlet(seed): 0.386 Positive Predictive Value Vsfold4: 0.645 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.59578924681e-08	= Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.660 Alterna: 0.647 Sensitivity Vsfold4: 0.624 Alterna: 0.636 Positive Predictive Value Vsfold4: 0.713 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0214945749572	+ Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.545 Mastr(20): 0.506 Sensitivity Vsfold4: 0.526 Mastr(20): 0.337 Positive Predictive Value Vsfold4: 0.572 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.53980171438e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.559 Vsfold5: 0.518 Sensitivity Vsfold4: 0.554 Vsfold5: 0.514 Positive Predictive Value Vsfold4: 0.572 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.658 RDfolder: 0.549 Sensitivity Vsfold4: 0.617 RDfolder: 0.487 Positive Predictive Value Vsfold4: 0.716 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.596 MCFold: 0.527 Sensitivity Vsfold4: 0.572 MCFold: 0.563 Positive Predictive Value Vsfold4: 0.633 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.531 RSpredict(seed): 0.324 Sensitivity Vsfold4: 0.530 RSpredict(seed): 0.177 Positive Predictive Value Vsfold4: 0.538 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.603 Carnac(seed): 0.104 Sensitivity Vsfold4: 0.573 Carnac(seed): 0.011 Positive Predictive Value Vsfold4: 0.645 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.50323628132e-08	? NanoFolder vs Vsfold4 Matthews Correlation Coefficient NanoFolder: 0.427 Vsfold4: 0.419 Sensitivity NanoFolder: 0.519 Vsfold4: 0.413 Positive Predictive Value NanoFolder: 0.365 Vsfold4: 0.439 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Vsfold4: 0.478 Sensitivity CentroidHomfold‑LAST: 0.552 Vsfold4: 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Vsfold4: 0.509 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): 0.629 Vsfold4: 0.425 Sensitivity Multilign(seed): 0.580 Vsfold4: 0.410 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): 0.581 Vsfold4: 0.544 Sensitivity Multilign(20): 0.576 Vsfold4: 0.523 Positive Predictive Value Multilign(20): 0.598 Vsfold4: 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Vsfold4: 0.462 Sensitivity PETfold_pre2.0(seed): 0.619 Vsfold4: 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Vsfold4: 0.506 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.653 Vsfold4: 0.544 Sensitivity TurboFold(20): 0.606 Vsfold4: 0.523 Positive Predictive Value TurboFold(20): 0.714 Vsfold4: 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.478 RNAwolf: 0.436 Sensitivity Vsfold4: 0.464 RNAwolf: 0.437 Positive Predictive Value Vsfold4: 0.509 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.612 Vsfold4: 0.478 Sensitivity IPknot: 0.579 Vsfold4: 0.464 Positive Predictive Value IPknot: 0.658 Vsfold4: 0.509 Number of pairs reference - predicted secondary structure: 9 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): 0.619 Vsfold4: 0.560 Sensitivity PETfold_pre2.0(20): 0.570 Vsfold4: 0.532 Positive Predictive Value PETfold_pre2.0(20): 0.682 Vsfold4: 0.600 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.483 PPfold(seed): 0.155 Sensitivity Vsfold4: 0.460 PPfold(seed): 0.047 Positive Predictive Value Vsfold4: 0.523 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.662 Vsfold4: 0.461 Sensitivity ContextFold: 0.608 Vsfold4: 0.446 Positive Predictive Value ContextFold: 0.731 Vsfold4: 0.492 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.560 Vsfold4: 0.483 Sensitivity TurboFold(seed): 0.533 Vsfold4: 0.460 Positive Predictive Value TurboFold(seed): 0.602 Vsfold4: 0.523 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.502 Vsfold4: 0.417 Sensitivity CRWrnafold: 0.516 Vsfold4: 0.409 Positive Predictive Value CRWrnafold: 0.503 Vsfold4: 0.442 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): 0.640 Vsfold4: 0.512 Sensitivity RNASampler(seed): 0.554 Vsfold4: 0.506 Positive Predictive Value RNASampler(seed): 0.748 Vsfold4: 0.528 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs RNASLOpt Matthews Correlation Coefficient Vsfold4: 0.461 RNASLOpt: 0.449 Sensitivity Vsfold4: 0.446 RNASLOpt: 0.438 Positive Predictive Value Vsfold4: 0.492 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.715 Vsfold4: 0.544 Sensitivity PPfold(20): 0.644 Vsfold4: 0.523 Positive Predictive Value PPfold(20): 0.802 Vsfold4: 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.531 Mastr(seed): 0.000 Sensitivity Vsfold4: 0.530 Mastr(seed): 0.000 Positive Predictive Value Vsfold4: 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08
Murlet(seed)	12 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.814 Murlet(seed): 0.607 Sensitivity CentroidAlifold(20): 0.713 Murlet(seed): 0.407 Positive Predictive Value CentroidAlifold(20): 0.934 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.25253056981e-08	14 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.826 Murlet(seed): 0.571 Sensitivity CentroidAlifold(seed): 0.707 Murlet(seed): 0.386 Positive Predictive Value CentroidAlifold(seed): 0.970 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.22797000563e-08	12 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.750 Murlet(seed): 0.607 Sensitivity RNAalifold(20): 0.669 Murlet(seed): 0.407 Positive Predictive Value RNAalifold(20): 0.848 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.87872347734e-08	14 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.709 Murlet(seed): 0.571 Sensitivity MXScarna(seed): 0.652 Murlet(seed): 0.386 Positive Predictive Value MXScarna(seed): 0.778 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	14 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.762 Murlet(seed): 0.571 Sensitivity CentroidFold: 0.723 Murlet(seed): 0.386 Positive Predictive Value CentroidFold: 0.810 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.89649746203e-08	12 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.756 Murlet(seed): 0.607 Sensitivity RNASampler(20): 0.666 Murlet(seed): 0.407 Positive Predictive Value RNASampler(20): 0.865 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.50834591464e-08	12 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.720 Murlet(seed): 0.607 Sensitivity MXScarna(20): 0.675 Murlet(seed): 0.407 Positive Predictive Value MXScarna(20): 0.775 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.67657656842e-08	14 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.735 Murlet(seed): 0.571 Sensitivity Contrafold: 0.723 Murlet(seed): 0.386 Positive Predictive Value Contrafold: 0.754 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08	14 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.749 Murlet(seed): 0.571 Sensitivity Sfold: 0.701 Murlet(seed): 0.386 Positive Predictive Value Sfold: 0.808 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	13 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.681 Murlet(seed): 0.566 Sensitivity MaxExpect: 0.675 Murlet(seed): 0.385 Positive Predictive Value MaxExpect: 0.695 Murlet(seed): 0.843 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.52299983238e-08	14 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.736 Murlet(seed): 0.571 Sensitivity HotKnots: 0.745 Murlet(seed): 0.386 Positive Predictive Value HotKnots: 0.733 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.22210847902e-08	14 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.706 Murlet(seed): 0.571 Sensitivity RNAalifold(seed): 0.564 Murlet(seed): 0.386 Positive Predictive Value RNAalifold(seed): 0.892 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.27752322258e-08	12 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.690 Murlet(seed): 0.607 Sensitivity Murlet(20): 0.577 Murlet(seed): 0.407 Positive Predictive Value Murlet(20): 0.832 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.30295446166e-08	14 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.712 Murlet(seed): 0.571 Sensitivity UNAFold: 0.701 Murlet(seed): 0.386 Positive Predictive Value UNAFold: 0.731 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.38194587311e-08	12 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.673 Murlet(seed): 0.607 Sensitivity Carnac(20): 0.483 Murlet(seed): 0.407 Positive Predictive Value Carnac(20): 0.944 Murlet(seed): 0.915 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	14 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.732 Murlet(seed): 0.571 Sensitivity McQFold: 0.729 Murlet(seed): 0.386 Positive Predictive Value McQFold: 0.743 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.59578924681e-08	14 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.718 Murlet(seed): 0.571 Sensitivity RNAshapes: 0.707 Murlet(seed): 0.386 Positive Predictive Value RNAshapes: 0.737 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.08252958266e-08	14 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.743 Murlet(seed): 0.571 Sensitivity RNAfold: 0.737 Murlet(seed): 0.386 Positive Predictive Value RNAfold: 0.756 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.8150742666e-08	14 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.768 Murlet(seed): 0.571 Sensitivity PknotsRG: 0.773 Murlet(seed): 0.386 Positive Predictive Value PknotsRG: 0.770 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	14 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.695 Murlet(seed): 0.571 Sensitivity Pknots: 0.712 Murlet(seed): 0.386 Positive Predictive Value Pknots: 0.686 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	9 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.712 Murlet(seed): 0.546 Sensitivity Afold: 0.706 Murlet(seed): 0.383 Positive Predictive Value Afold: 0.726 Murlet(seed): 0.788 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.603 Murlet(seed): 0.534 Sensitivity ProbKnot: 0.637 Murlet(seed): 0.344 Positive Predictive Value ProbKnot: 0.581 Murlet(seed): 0.840 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.48548913747e-08	8 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.723 Murlet(seed): 0.520 Sensitivity Cylofold: 0.703 Murlet(seed): 0.342 Positive Predictive Value Cylofold: 0.751 Murlet(seed): 0.802 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.679 Murlet(seed): 0.571 Sensitivity RNAsubopt: 0.677 Murlet(seed): 0.386 Positive Predictive Value RNAsubopt: 0.690 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.16131455263e-08	10 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.589 Murlet(seed): 0.534 Sensitivity Fold: 0.602 Murlet(seed): 0.344 Positive Predictive Value Fold: 0.586 Murlet(seed): 0.840 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.60468628729e-08	12 Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.607 RSpredict(20): 0.581 Sensitivity Murlet(seed): 0.407 RSpredict(20): 0.511 Positive Predictive Value Murlet(seed): 0.915 RSpredict(20): 0.672 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.81576394991e-06	14 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.603 Murlet(seed): 0.571 Sensitivity Vsfold4: 0.573 Murlet(seed): 0.386 Positive Predictive Value Vsfold4: 0.645 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.59578924681e-08		? Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.729 Murlet(seed): 0.560 Sensitivity Alterna: 0.701 Murlet(seed): 0.424 Positive Predictive Value Alterna: 0.770 Murlet(seed): 0.758 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.607 Mastr(20): 0.515 Sensitivity Murlet(seed): 0.407 Mastr(20): 0.369 Positive Predictive Value Murlet(seed): 0.915 Mastr(20): 0.731 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.571 Vsfold5: 0.556 Sensitivity Murlet(seed): 0.386 Vsfold5: 0.537 Positive Predictive Value Murlet(seed): 0.855 Vsfold5: 0.589 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 9.47856437497e-05	= RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.586 Murlet(seed): 0.582 Sensitivity RDfolder: 0.513 Murlet(seed): 0.428 Positive Predictive Value RDfolder: 0.688 Murlet(seed): 0.808 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.490072995861	= MCFold vs Murlet(seed) Matthews Correlation Coefficient MCFold: 0.567 Murlet(seed): 0.558 Sensitivity MCFold: 0.599 Murlet(seed): 0.381 Positive Predictive Value MCFold: 0.547 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.206948167051	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.571 RSpredict(seed): 0.384 Sensitivity Murlet(seed): 0.386 RSpredict(seed): 0.227 Positive Predictive Value Murlet(seed): 0.855 RSpredict(seed): 0.664 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.571 Carnac(seed): 0.104 Sensitivity Murlet(seed): 0.386 Carnac(seed): 0.011 Positive Predictive Value Murlet(seed): 0.855 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.49381627234e-08	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.473 NanoFolder: 0.336 Sensitivity Murlet(seed): 0.329 NanoFolder: 0.415 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Murlet(seed): 0.531 Sensitivity CentroidHomfold‑LAST: 0.567 Murlet(seed): 0.373 Positive Predictive Value CentroidHomfold‑LAST: 0.746 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 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): 0.629 Murlet(seed): 0.496 Sensitivity Multilign(seed): 0.580 Murlet(seed): 0.370 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): 0.621 Multilign(20): 0.581 Sensitivity Murlet(seed): 0.424 Multilign(20): 0.576 Positive Predictive Value Murlet(seed): 0.918 Multilign(20): 0.598 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): 0.695 Murlet(seed): 0.495 Sensitivity PETfold_pre2.0(seed): 0.619 Murlet(seed): 0.340 Positive Predictive Value PETfold_pre2.0(seed): 0.789 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): 0.653 Murlet(seed): 0.621 Sensitivity TurboFold(20): 0.606 Murlet(seed): 0.424 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 RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.531 RNAwolf: 0.451 Sensitivity Murlet(seed): 0.373 RNAwolf: 0.447 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.601 Murlet(seed): 0.531 Sensitivity IPknot: 0.560 Murlet(seed): 0.373 Positive Predictive Value IPknot: 0.656 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 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): 0.644 PETfold_pre2.0(20): 0.619 Sensitivity Murlet(seed): 0.418 PETfold_pre2.0(20): 0.570 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.531 PPfold(seed): 0.155 Sensitivity Murlet(seed): 0.373 PPfold(seed): 0.047 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	? ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.570 Murlet(seed): 0.495 Sensitivity ContextFold: 0.515 Murlet(seed): 0.340 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	? TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.560 Murlet(seed): 0.531 Sensitivity TurboFold(seed): 0.533 Murlet(seed): 0.373 Positive Predictive Value TurboFold(seed): 0.602 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Murlet(seed): 0.510 Sensitivity CRWrnafold: 0.524 Murlet(seed): 0.349 Positive Predictive Value CRWrnafold: 0.516 Murlet(seed): 0.759 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 Murlet(seed): 0.514 Sensitivity RNASampler(seed): 0.554 Murlet(seed): 0.361 Positive Predictive Value RNASampler(seed): 0.748 Murlet(seed): 0.741 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.495 RNASLOpt: 0.461 Sensitivity Murlet(seed): 0.340 RNASLOpt: 0.443 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.715 Murlet(seed): 0.621 Sensitivity PPfold(20): 0.644 Murlet(seed): 0.424 Positive Predictive Value PPfold(20): 0.802 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): 0.571 Mastr(seed): 0.000 Sensitivity Murlet(seed): 0.386 Mastr(seed): 0.000 Positive Predictive Value Murlet(seed): 0.855 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.24019667966e-08
Alterna	7 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.900 Alterna: 0.593 Sensitivity CentroidAlifold(20): 0.836 Alterna: 0.596 Positive Predictive Value CentroidAlifold(20): 0.973 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	10 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.772 Alterna: 0.657 Sensitivity CentroidAlifold(seed): 0.618 Alterna: 0.651 Positive Predictive Value CentroidAlifold(seed): 0.974 Alterna: 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.05690340753e-08	7 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.891 Alterna: 0.593 Sensitivity RNAalifold(20): 0.836 Alterna: 0.596 Positive Predictive Value RNAalifold(20): 0.953 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	10 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.789 Alterna: 0.657 Sensitivity MXScarna(seed): 0.726 Alterna: 0.651 Positive Predictive Value MXScarna(seed): 0.866 Alterna: 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.09700314043e-09	14 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.823 Alterna: 0.638 Sensitivity CentroidFold: 0.786 Alterna: 0.633 Positive Predictive Value CentroidFold: 0.870 Alterna: 0.658 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.26346675981e-08	7 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.903 Alterna: 0.593 Sensitivity RNASampler(20): 0.825 Alterna: 0.596 Positive Predictive Value RNASampler(20): 0.993 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.819 Alterna: 0.593 Sensitivity MXScarna(20): 0.778 Alterna: 0.596 Positive Predictive Value MXScarna(20): 0.869 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.757 Alterna: 0.647 Sensitivity Contrafold: 0.737 Alterna: 0.636 Positive Predictive Value Contrafold: 0.789 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	17 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.715 Alterna: 0.647 Sensitivity Sfold: 0.681 Alterna: 0.636 Positive Predictive Value Sfold: 0.763 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	12 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.711 Alterna: 0.584 Sensitivity MaxExpect: 0.689 Alterna: 0.582 Positive Predictive Value MaxExpect: 0.745 Alterna: 0.604 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.91441904741e-08	17 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.725 Alterna: 0.647 Sensitivity HotKnots: 0.715 Alterna: 0.636 Positive Predictive Value HotKnots: 0.749 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	7 Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.729 RNAalifold(seed): 0.686 Sensitivity Alterna: 0.701 RNAalifold(seed): 0.593 Positive Predictive Value Alterna: 0.770 RNAalifold(seed): 0.808 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.808 Alterna: 0.593 Sensitivity Murlet(20): 0.708 Alterna: 0.596 Positive Predictive Value Murlet(20): 0.931 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.720 Alterna: 0.647 Sensitivity UNAFold: 0.706 Alterna: 0.636 Positive Predictive Value UNAFold: 0.746 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	7 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.828 Alterna: 0.593 Sensitivity Carnac(20): 0.702 Alterna: 0.596 Positive Predictive Value Carnac(20): 0.984 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.717 Alterna: 0.647 Sensitivity McQFold: 0.689 Alterna: 0.636 Positive Predictive Value McQFold: 0.758 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.95070920198e-08	17 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.705 Alterna: 0.647 Sensitivity RNAshapes: 0.678 Alterna: 0.636 Positive Predictive Value RNAshapes: 0.745 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	17 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.668 Alterna: 0.647 Sensitivity RNAfold: 0.655 Alterna: 0.636 Positive Predictive Value RNAfold: 0.695 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	17 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.648 Alterna: 0.647 Sensitivity PknotsRG: 0.641 Alterna: 0.636 Positive Predictive Value PknotsRG: 0.670 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00235582146837	17 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.748 Alterna: 0.647 Sensitivity Pknots: 0.746 Alterna: 0.636 Positive Predictive Value Pknots: 0.761 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	14 Afold vs Alterna Matthews Correlation Coefficient Afold: 0.685 Alterna: 0.682 Sensitivity Afold: 0.678 Alterna: 0.668 Positive Predictive Value Afold: 0.705 Alterna: 0.710 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.0342527507493	5 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.594 Alterna: 0.536 Sensitivity ProbKnot: 0.604 Alterna: 0.525 Positive Predictive Value ProbKnot: 0.604 Alterna: 0.570 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.690 Alterna: 0.560 Sensitivity Cylofold: 0.657 Alterna: 0.552 Positive Predictive Value Cylofold: 0.739 Alterna: 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	17 Alterna vs RNAsubopt Matthews Correlation Coefficient Alterna: 0.647 RNAsubopt: 0.645 Sensitivity Alterna: 0.636 RNAsubopt: 0.633 Positive Predictive Value Alterna: 0.674 RNAsubopt: 0.673 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0286720377294	6 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.589 Alterna: 0.560 Sensitivity Fold: 0.582 Alterna: 0.552 Positive Predictive Value Fold: 0.614 Alterna: 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.828 Alterna: 0.593 Sensitivity RSpredict(20): 0.760 Alterna: 0.596 Positive Predictive Value RSpredict(20): 0.909 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.660 Alterna: 0.647 Sensitivity Vsfold4: 0.624 Alterna: 0.636 Positive Predictive Value Vsfold4: 0.713 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0214945749572	7 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.729 Murlet(seed): 0.560 Sensitivity Alterna: 0.701 Murlet(seed): 0.424 Positive Predictive Value Alterna: 0.770 Murlet(seed): 0.758 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		? Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.783 Alterna: 0.593 Sensitivity Mastr(20): 0.725 Alterna: 0.596 Positive Predictive Value Mastr(20): 0.855 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.647 Vsfold5: 0.568 Sensitivity Alterna: 0.636 Vsfold5: 0.537 Positive Predictive Value Alterna: 0.674 Vsfold5: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.647 RDfolder: 0.566 Sensitivity Alterna: 0.636 RDfolder: 0.503 Positive Predictive Value Alterna: 0.674 RDfolder: 0.657 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.649 MCFold: 0.521 Sensitivity Alterna: 0.636 MCFold: 0.548 Positive Predictive Value Alterna: 0.678 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.657 RSpredict(seed): 0.464 Sensitivity Alterna: 0.651 RSpredict(seed): 0.299 Positive Predictive Value Alterna: 0.677 RSpredict(seed): 0.742 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	? Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.729 Carnac(seed): 0.149 Sensitivity Alterna: 0.701 Carnac(seed): 0.023 Positive Predictive Value Alterna: 0.770 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs Alterna Matthews Correlation Coefficient NanoFolder: 0.536 Alterna: 0.471 Sensitivity NanoFolder: 0.611 Alterna: 0.444 Positive Predictive Value NanoFolder: 0.500 Alterna: 0.533 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Alterna vs CentroidHomfold‑LAST Matthews Correlation Coefficient Alterna: 0.568 CentroidHomfold‑LAST: 0.553 Sensitivity Alterna: 0.549 CentroidHomfold‑LAST: 0.451 Positive Predictive Value Alterna: 0.608 CentroidHomfold‑LAST: 0.698 Number of pairs reference - predicted secondary structure: 4 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: 0.624 Multilign(seed): 0.589 Sensitivity Alterna: 0.606 Multilign(seed): 0.549 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): 0.784 Alterna: 0.673 Sensitivity Multilign(20): 0.774 Alterna: 0.660 Positive Predictive Value Multilign(20): 0.804 Alterna: 0.700 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Alterna vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Alterna: 0.471 PETfold_pre2.0(seed): 0.411 Sensitivity Alterna: 0.444 PETfold_pre2.0(seed): 0.333 Positive Predictive Value Alterna: 0.533 PETfold_pre2.0(seed): 0.545 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.797 Alterna: 0.673 Sensitivity TurboFold(20): 0.755 Alterna: 0.660 Positive Predictive Value TurboFold(20): 0.851 Alterna: 0.700 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.583 Alterna: 0.568 Sensitivity RNAwolf: 0.585 Alterna: 0.549 Positive Predictive Value RNAwolf: 0.600 Alterna: 0.608 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.640 Alterna: 0.568 Sensitivity IPknot: 0.585 Alterna: 0.549 Positive Predictive Value IPknot: 0.716 Alterna: 0.608 Number of pairs reference - predicted secondary structure: 4 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 PPfold(seed) Matthews Correlation Coefficient Alterna: 0.624 PPfold(seed): 0.247 Sensitivity Alterna: 0.606 PPfold(seed): 0.085 Positive Predictive Value Alterna: 0.662 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.659 Alterna: 0.362 Sensitivity ContextFold: 0.621 Alterna: 0.345 Positive Predictive Value ContextFold: 0.720 Alterna: 0.417 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.624 TurboFold(seed): 0.594 Sensitivity Alterna: 0.606 TurboFold(seed): 0.563 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 CRWrnafold Matthews Correlation Coefficient Alterna: 0.462 CRWrnafold: 0.394 Sensitivity Alterna: 0.448 CRWrnafold: 0.397 Positive Predictive Value Alterna: 0.500 CRWrnafold: 0.418 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.732 RNASampler(seed): 0.710 Sensitivity Alterna: 0.702 RNASampler(seed): 0.589 Positive Predictive Value Alterna: 0.777 RNASampler(seed): 0.869 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.379 Alterna: 0.362 Sensitivity RNASLOpt: 0.310 Alterna: 0.345 Positive Predictive Value RNASLOpt: 0.500 Alterna: 0.417 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.836 Alterna: 0.673 Sensitivity PPfold(20): 0.774 Alterna: 0.660 Positive Predictive Value PPfold(20): 0.911 Alterna: 0.700 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.657 Mastr(seed): 0.000 Sensitivity Alterna: 0.651 Mastr(seed): 0.000 Positive Predictive Value Alterna: 0.677 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.07229227445e-09
Mastr(20)	15 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Mastr(20): 0.506 Sensitivity CentroidAlifold(20): 0.694 Mastr(20): 0.337 Positive Predictive Value CentroidAlifold(20): 0.932 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	15 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 Mastr(20): 0.506 Sensitivity CentroidAlifold(seed): 0.623 Mastr(20): 0.337 Positive Predictive Value CentroidAlifold(seed): 0.934 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.66062906821e-08	15 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.753 Mastr(20): 0.506 Sensitivity RNAalifold(20): 0.656 Mastr(20): 0.337 Positive Predictive Value RNAalifold(20): 0.869 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	15 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.751 Mastr(20): 0.506 Sensitivity MXScarna(seed): 0.692 Mastr(20): 0.337 Positive Predictive Value MXScarna(seed): 0.820 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 9.35568223474e-09	15 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.716 Mastr(20): 0.506 Sensitivity CentroidFold: 0.687 Mastr(20): 0.337 Positive Predictive Value CentroidFold: 0.750 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	15 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.732 Mastr(20): 0.506 Sensitivity RNASampler(20): 0.639 Mastr(20): 0.337 Positive Predictive Value RNASampler(20): 0.843 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.12160100812e-08	15 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.703 Mastr(20): 0.506 Sensitivity MXScarna(20): 0.659 Mastr(20): 0.337 Positive Predictive Value MXScarna(20): 0.755 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	15 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.650 Mastr(20): 0.506 Sensitivity Contrafold: 0.652 Mastr(20): 0.337 Positive Predictive Value Contrafold: 0.655 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	15 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.665 Mastr(20): 0.506 Sensitivity Sfold: 0.628 Mastr(20): 0.337 Positive Predictive Value Sfold: 0.711 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	15 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.674 Mastr(20): 0.506 Sensitivity MaxExpect: 0.670 Mastr(20): 0.337 Positive Predictive Value MaxExpect: 0.683 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.59578924681e-08	15 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.640 Mastr(20): 0.506 Sensitivity HotKnots: 0.663 Mastr(20): 0.337 Positive Predictive Value HotKnots: 0.623 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	13 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.685 Mastr(20): 0.453 Sensitivity RNAalifold(seed): 0.515 Mastr(20): 0.284 Positive Predictive Value RNAalifold(seed): 0.918 Mastr(20): 0.731 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	15 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.666 Mastr(20): 0.506 Sensitivity Murlet(20): 0.548 Mastr(20): 0.337 Positive Predictive Value Murlet(20): 0.814 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-08	15 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.662 Mastr(20): 0.506 Sensitivity UNAFold: 0.663 Mastr(20): 0.337 Positive Predictive Value UNAFold: 0.667 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	15 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.662 Mastr(20): 0.506 Sensitivity Carnac(20): 0.469 Mastr(20): 0.337 Positive Predictive Value Carnac(20): 0.938 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	15 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.644 Mastr(20): 0.506 Sensitivity McQFold: 0.643 Mastr(20): 0.337 Positive Predictive Value McQFold: 0.650 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	15 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.637 Mastr(20): 0.506 Sensitivity RNAshapes: 0.637 Mastr(20): 0.337 Positive Predictive Value RNAshapes: 0.644 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.43692248862e-08	15 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.643 Mastr(20): 0.506 Sensitivity RNAfold: 0.656 Mastr(20): 0.337 Positive Predictive Value RNAfold: 0.637 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	15 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.664 Mastr(20): 0.506 Sensitivity PknotsRG: 0.685 Mastr(20): 0.337 Positive Predictive Value PknotsRG: 0.649 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.93248927742e-08	14 Pknots vs Mastr(20) Matthews Correlation Coefficient Pknots: 0.670 Mastr(20): 0.568 Sensitivity Pknots: 0.691 Mastr(20): 0.426 Positive Predictive Value Pknots: 0.658 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.79203144115e-08	10 Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.565 Mastr(20): 0.538 Sensitivity Afold: 0.591 Mastr(20): 0.350 Positive Predictive Value Afold: 0.547 Mastr(20): 0.835 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.0286195353294	10 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.630 Mastr(20): 0.365 Sensitivity ProbKnot: 0.664 Mastr(20): 0.199 Positive Predictive Value ProbKnot: 0.603 Mastr(20): 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.80908287419e-08	7 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.731 Mastr(20): 0.483 Sensitivity Cylofold: 0.712 Mastr(20): 0.304 Positive Predictive Value Cylofold: 0.757 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	15 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.620 Mastr(20): 0.506 Sensitivity RNAsubopt: 0.632 Mastr(20): 0.337 Positive Predictive Value RNAsubopt: 0.615 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	10 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.621 Mastr(20): 0.365 Sensitivity Fold: 0.637 Mastr(20): 0.199 Positive Predictive Value Fold: 0.611 Mastr(20): 0.677 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	15 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.624 Mastr(20): 0.506 Sensitivity RSpredict(20): 0.559 Mastr(20): 0.337 Positive Predictive Value RSpredict(20): 0.702 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	15 Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.545 Mastr(20): 0.506 Sensitivity Vsfold4: 0.526 Mastr(20): 0.337 Positive Predictive Value Vsfold4: 0.572 Mastr(20): 0.769 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.53980171438e-08	12 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.607 Mastr(20): 0.515 Sensitivity Murlet(seed): 0.407 Mastr(20): 0.369 Positive Predictive Value Murlet(seed): 0.915 Mastr(20): 0.731 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	7 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.783 Alterna: 0.593 Sensitivity Mastr(20): 0.725 Alterna: 0.596 Positive Predictive Value Mastr(20): 0.855 Alterna: 0.607 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		= Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.506 Vsfold5: 0.495 Sensitivity Mastr(20): 0.337 Vsfold5: 0.480 Positive Predictive Value Mastr(20): 0.769 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.155505742079	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.709 RDfolder: 0.613 Sensitivity Mastr(20): 0.617 RDfolder: 0.552 Positive Predictive Value Mastr(20): 0.826 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.36051213211e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.620 MCFold: 0.506 Sensitivity Mastr(20): 0.451 MCFold: 0.546 Positive Predictive Value Mastr(20): 0.863 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.506 RSpredict(seed): 0.350 Sensitivity Mastr(20): 0.337 RSpredict(seed): 0.181 Positive Predictive Value Mastr(20): 0.769 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.515 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.369 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.731 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	? Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.379 NanoFolder: 0.285 Sensitivity Mastr(20): 0.234 NanoFolder: 0.359 Positive Predictive Value Mastr(20): 0.625 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Mastr(20): 0.570 Sensitivity CentroidHomfold‑LAST: 0.644 Mastr(20): 0.424 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 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): 0.755 Mastr(20): 0.656 Sensitivity Multilign(seed): 0.707 Mastr(20): 0.585 Positive Predictive Value Multilign(seed): 0.817 Mastr(20): 0.750 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.581 Mastr(20): 0.570 Sensitivity Multilign(20): 0.576 Mastr(20): 0.424 Positive Predictive Value Multilign(20): 0.598 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 Mastr(20): 0.386 Sensitivity PETfold_pre2.0(seed): 0.684 Mastr(20): 0.228 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.653 Mastr(20): 0.570 Sensitivity TurboFold(20): 0.606 Mastr(20): 0.424 Positive Predictive Value TurboFold(20): 0.714 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.570 RNAwolf: 0.442 Sensitivity Mastr(20): 0.424 RNAwolf: 0.439 Positive Predictive Value Mastr(20): 0.778 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.623 Mastr(20): 0.570 Sensitivity IPknot: 0.591 Mastr(20): 0.424 Positive Predictive Value IPknot: 0.667 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 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): 0.619 Mastr(20): 0.386 Sensitivity PETfold_pre2.0(20): 0.570 Mastr(20): 0.228 Positive Predictive Value PETfold_pre2.0(20): 0.682 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.570 PPfold(seed): 0.036 Sensitivity Mastr(20): 0.424 PPfold(seed): 0.008 Positive Predictive Value Mastr(20): 0.778 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.567 Mastr(20): 0.386 Sensitivity ContextFold: 0.506 Mastr(20): 0.228 Positive Predictive Value ContextFold: 0.645 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 Mastr(20): 0.570 Sensitivity TurboFold(seed): 0.606 Mastr(20): 0.424 Positive Predictive Value TurboFold(seed): 0.678 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.592 Mastr(20): 0.502 Sensitivity CRWrnafold: 0.611 Mastr(20): 0.361 Positive Predictive Value CRWrnafold: 0.584 Mastr(20): 0.709 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 Mastr(20): 0.644 Sensitivity RNASampler(seed): 0.627 Mastr(20): 0.483 Positive Predictive Value RNASampler(seed): 0.779 Mastr(20): 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.459 Mastr(20): 0.386 Sensitivity RNASLOpt: 0.456 Mastr(20): 0.228 Positive Predictive Value RNASLOpt: 0.474 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.715 Mastr(20): 0.570 Sensitivity PPfold(20): 0.644 Mastr(20): 0.424 Positive Predictive Value PPfold(20): 0.802 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.506 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.337 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.769 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08
Vsfold5	15 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Vsfold5: 0.495 Sensitivity CentroidAlifold(20): 0.694 Vsfold5: 0.480 Positive Predictive Value CentroidAlifold(20): 0.932 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	19 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Vsfold5: 0.498 Sensitivity CentroidAlifold(seed): 0.598 Vsfold5: 0.496 Positive Predictive Value CentroidAlifold(seed): 0.894 Vsfold5: 0.508 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	15 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.753 Vsfold5: 0.495 Sensitivity RNAalifold(20): 0.656 Vsfold5: 0.480 Positive Predictive Value RNAalifold(20): 0.869 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.07760058607e-08	19 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.711 Vsfold5: 0.498 Sensitivity MXScarna(seed): 0.663 Vsfold5: 0.496 Positive Predictive Value MXScarna(seed): 0.768 Vsfold5: 0.508 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	25 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.704 Vsfold5: 0.510 Sensitivity CentroidFold: 0.698 Vsfold5: 0.506 Positive Predictive Value CentroidFold: 0.715 Vsfold5: 0.521 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.06544643719e-08	15 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.732 Vsfold5: 0.495 Sensitivity RNASampler(20): 0.639 Vsfold5: 0.480 Positive Predictive Value RNASampler(20): 0.843 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.84361416392e-08	15 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.703 Vsfold5: 0.495 Sensitivity MXScarna(20): 0.659 Vsfold5: 0.480 Positive Predictive Value MXScarna(20): 0.755 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	28 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.663 Vsfold5: 0.518 Sensitivity Contrafold: 0.678 Vsfold5: 0.514 Positive Predictive Value Contrafold: 0.654 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	28 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.638 Vsfold5: 0.518 Sensitivity Sfold: 0.629 Vsfold5: 0.514 Positive Predictive Value Sfold: 0.653 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.623 Vsfold5: 0.476 Sensitivity MaxExpect: 0.640 Vsfold5: 0.473 Positive Predictive Value MaxExpect: 0.612 Vsfold5: 0.486 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	28 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.631 Vsfold5: 0.518 Sensitivity HotKnots: 0.666 Vsfold5: 0.514 Positive Predictive Value HotKnots: 0.605 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	16 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.634 Vsfold5: 0.479 Sensitivity RNAalifold(seed): 0.479 Vsfold5: 0.477 Positive Predictive Value RNAalifold(seed): 0.842 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.30549897711e-08	15 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.666 Vsfold5: 0.495 Sensitivity Murlet(20): 0.548 Vsfold5: 0.480 Positive Predictive Value Murlet(20): 0.814 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	28 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.633 Vsfold5: 0.518 Sensitivity UNAFold: 0.655 Vsfold5: 0.514 Positive Predictive Value UNAFold: 0.619 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.662 Vsfold5: 0.495 Sensitivity Carnac(20): 0.469 Vsfold5: 0.480 Positive Predictive Value Carnac(20): 0.938 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	28 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.624 Vsfold5: 0.518 Sensitivity McQFold: 0.641 Vsfold5: 0.514 Positive Predictive Value McQFold: 0.614 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.85839946686e-08	28 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.610 Vsfold5: 0.518 Sensitivity RNAshapes: 0.625 Vsfold5: 0.514 Positive Predictive Value RNAshapes: 0.602 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.02343278931e-08	28 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.607 Vsfold5: 0.518 Sensitivity RNAfold: 0.633 Vsfold5: 0.514 Positive Predictive Value RNAfold: 0.588 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.612 Vsfold5: 0.518 Sensitivity PknotsRG: 0.645 Vsfold5: 0.514 Positive Predictive Value PknotsRG: 0.586 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	26 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.676 Vsfold5: 0.576 Sensitivity Pknots: 0.693 Vsfold5: 0.560 Positive Predictive Value Pknots: 0.668 Vsfold5: 0.605 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	21 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.564 Vsfold5: 0.514 Sensitivity Afold: 0.604 Vsfold5: 0.515 Positive Predictive Value Afold: 0.533 Vsfold5: 0.521 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 9.26661638959e-08	16 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.564 Vsfold5: 0.469 Sensitivity ProbKnot: 0.613 Vsfold5: 0.481 Positive Predictive Value ProbKnot: 0.525 Vsfold5: 0.463 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.36983135185e-08	13 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.693 Vsfold5: 0.570 Sensitivity Cylofold: 0.681 Vsfold5: 0.565 Positive Predictive Value Cylofold: 0.715 Vsfold5: 0.587 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	28 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.591 Vsfold5: 0.518 Sensitivity RNAsubopt: 0.615 Vsfold5: 0.514 Positive Predictive Value RNAsubopt: 0.574 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	17 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.557 Vsfold5: 0.482 Sensitivity Fold: 0.589 Vsfold5: 0.489 Positive Predictive Value Fold: 0.534 Vsfold5: 0.481 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.60448791174e-08	15 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.624 Vsfold5: 0.495 Sensitivity RSpredict(20): 0.559 Vsfold5: 0.480 Positive Predictive Value RSpredict(20): 0.702 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.02344513449e-08	28 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.559 Vsfold5: 0.518 Sensitivity Vsfold4: 0.554 Vsfold5: 0.514 Positive Predictive Value Vsfold4: 0.572 Vsfold5: 0.530 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	14 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.571 Vsfold5: 0.556 Sensitivity Murlet(seed): 0.386 Vsfold5: 0.537 Positive Predictive Value Murlet(seed): 0.855 Vsfold5: 0.589 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 9.47856437497e-05	17 Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.647 Vsfold5: 0.568 Sensitivity Alterna: 0.636 Vsfold5: 0.537 Positive Predictive Value Alterna: 0.674 Vsfold5: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	15 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.506 Vsfold5: 0.495 Sensitivity Mastr(20): 0.337 Vsfold5: 0.480 Positive Predictive Value Mastr(20): 0.769 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.155505742079		+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.576 RDfolder: 0.549 Sensitivity Vsfold5: 0.547 RDfolder: 0.487 Positive Predictive Value Vsfold5: 0.626 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.17906639633e-07	+ Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.579 MCFold: 0.527 Sensitivity Vsfold5: 0.570 MCFold: 0.563 Positive Predictive Value Vsfold5: 0.601 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.498 RSpredict(seed): 0.324 Sensitivity Vsfold5: 0.496 RSpredict(seed): 0.177 Positive Predictive Value Vsfold5: 0.508 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.556 Carnac(seed): 0.104 Sensitivity Vsfold5: 0.537 Carnac(seed): 0.011 Positive Predictive Value Vsfold5: 0.589 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	? NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.427 Vsfold5: 0.379 Sensitivity NanoFolder: 0.519 Vsfold5: 0.394 Positive Predictive Value NanoFolder: 0.365 Vsfold5: 0.380 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Vsfold5: 0.461 Sensitivity CentroidHomfold‑LAST: 0.552 Vsfold5: 0.470 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Vsfold5: 0.470 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): 0.629 Vsfold5: 0.327 Sensitivity Multilign(seed): 0.580 Vsfold5: 0.320 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): 0.581 Vsfold5: 0.518 Sensitivity Multilign(20): 0.576 Vsfold5: 0.530 Positive Predictive Value Multilign(20): 0.598 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Vsfold5: 0.446 Sensitivity PETfold_pre2.0(seed): 0.619 Vsfold5: 0.454 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Vsfold5: 0.454 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.653 Vsfold5: 0.518 Sensitivity TurboFold(20): 0.606 Vsfold5: 0.530 Positive Predictive Value TurboFold(20): 0.714 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs RNAwolf Matthews Correlation Coefficient Vsfold5: 0.461 RNAwolf: 0.436 Sensitivity Vsfold5: 0.470 RNAwolf: 0.437 Positive Predictive Value Vsfold5: 0.470 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.612 Vsfold5: 0.461 Sensitivity IPknot: 0.579 Vsfold5: 0.470 Positive Predictive Value IPknot: 0.658 Vsfold5: 0.470 Number of pairs reference - predicted secondary structure: 9 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): 0.619 Vsfold5: 0.535 Sensitivity PETfold_pre2.0(20): 0.570 Vsfold5: 0.557 Positive Predictive Value PETfold_pre2.0(20): 0.682 Vsfold5: 0.524 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.462 PPfold(seed): 0.155 Sensitivity Vsfold5: 0.467 PPfold(seed): 0.047 Positive Predictive Value Vsfold5: 0.473 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.662 Vsfold5: 0.450 Sensitivity ContextFold: 0.608 Vsfold5: 0.462 Positive Predictive Value ContextFold: 0.731 Vsfold5: 0.455 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.560 Vsfold5: 0.462 Sensitivity TurboFold(seed): 0.533 Vsfold5: 0.467 Positive Predictive Value TurboFold(seed): 0.602 Vsfold5: 0.473 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.502 Vsfold5: 0.395 Sensitivity CRWrnafold: 0.516 Vsfold5: 0.403 Positive Predictive Value CRWrnafold: 0.503 Vsfold5: 0.405 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): 0.640 Vsfold5: 0.547 Sensitivity RNASampler(seed): 0.554 Vsfold5: 0.554 Positive Predictive Value RNASampler(seed): 0.748 Vsfold5: 0.551 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs RNASLOpt Matthews Correlation Coefficient Vsfold5: 0.450 RNASLOpt: 0.449 Sensitivity Vsfold5: 0.462 RNASLOpt: 0.438 Positive Predictive Value Vsfold5: 0.455 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.715 Vsfold5: 0.518 Sensitivity PPfold(20): 0.644 Vsfold5: 0.530 Positive Predictive Value PPfold(20): 0.802 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.498 Mastr(seed): 0.000 Sensitivity Vsfold5: 0.496 Mastr(seed): 0.000 Positive Predictive Value Vsfold5: 0.508 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.34821445183e-08
RDfolder	10 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.878 RDfolder: 0.613 Sensitivity CentroidAlifold(20): 0.791 RDfolder: 0.552 Positive Predictive Value CentroidAlifold(20): 0.978 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.34193807955e-08	13 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.780 RDfolder: 0.600 Sensitivity CentroidAlifold(seed): 0.627 RDfolder: 0.543 Positive Predictive Value CentroidAlifold(seed): 0.979 RDfolder: 0.679 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.19192530585e-08	10 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.850 RDfolder: 0.613 Sensitivity RNAalifold(20): 0.757 RDfolder: 0.552 Positive Predictive Value RNAalifold(20): 0.961 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.58287649515e-08	13 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.756 RDfolder: 0.600 Sensitivity MXScarna(seed): 0.690 RDfolder: 0.543 Positive Predictive Value MXScarna(seed): 0.838 RDfolder: 0.679 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.40919803867e-08	17 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.801 RDfolder: 0.535 Sensitivity CentroidFold: 0.760 RDfolder: 0.476 Positive Predictive Value CentroidFold: 0.853 RDfolder: 0.622 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	10 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.862 RDfolder: 0.613 Sensitivity RNASampler(20): 0.765 RDfolder: 0.552 Positive Predictive Value RNASampler(20): 0.978 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.50834591464e-08	10 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.766 RDfolder: 0.613 Sensitivity MXScarna(20): 0.704 RDfolder: 0.552 Positive Predictive Value MXScarna(20): 0.844 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.69265863073e-08	20 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.747 RDfolder: 0.549 Sensitivity Contrafold: 0.722 RDfolder: 0.487 Positive Predictive Value Contrafold: 0.784 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.06544643719e-08	20 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.705 RDfolder: 0.549 Sensitivity Sfold: 0.663 RDfolder: 0.487 Positive Predictive Value Sfold: 0.763 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.692 RDfolder: 0.501 Sensitivity MaxExpect: 0.667 RDfolder: 0.442 Positive Predictive Value MaxExpect: 0.731 RDfolder: 0.588 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.67657656842e-08	20 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.736 RDfolder: 0.549 Sensitivity HotKnots: 0.726 RDfolder: 0.487 Positive Predictive Value HotKnots: 0.758 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	10 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.698 RDfolder: 0.586 Sensitivity RNAalifold(seed): 0.585 RDfolder: 0.513 Positive Predictive Value RNAalifold(seed): 0.847 RDfolder: 0.688 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.69265863073e-08	10 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.786 RDfolder: 0.613 Sensitivity Murlet(20): 0.661 RDfolder: 0.552 Positive Predictive Value Murlet(20): 0.944 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	20 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.704 RDfolder: 0.549 Sensitivity UNAFold: 0.685 RDfolder: 0.487 Positive Predictive Value UNAFold: 0.737 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	10 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.740 RDfolder: 0.613 Sensitivity Carnac(20): 0.583 RDfolder: 0.552 Positive Predictive Value Carnac(20): 0.950 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	20 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.722 RDfolder: 0.549 Sensitivity McQFold: 0.697 RDfolder: 0.487 Positive Predictive Value McQFold: 0.760 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	20 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.691 RDfolder: 0.549 Sensitivity RNAshapes: 0.661 RDfolder: 0.487 Positive Predictive Value RNAshapes: 0.736 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.02343278931e-08	20 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.659 RDfolder: 0.549 Sensitivity RNAfold: 0.642 RDfolder: 0.487 Positive Predictive Value RNAfold: 0.692 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	20 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.669 RDfolder: 0.549 Sensitivity PknotsRG: 0.663 RDfolder: 0.487 Positive Predictive Value PknotsRG: 0.690 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	20 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.727 RDfolder: 0.549 Sensitivity Pknots: 0.726 RDfolder: 0.487 Positive Predictive Value Pknots: 0.739 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.98172311752e-08	15 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.691 RDfolder: 0.592 Sensitivity Afold: 0.681 RDfolder: 0.535 Positive Predictive Value Afold: 0.714 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	8 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.606 RDfolder: 0.424 Sensitivity ProbKnot: 0.606 RDfolder: 0.363 Positive Predictive Value ProbKnot: 0.626 RDfolder: 0.523 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.699 RDfolder: 0.435 Sensitivity Cylofold: 0.668 RDfolder: 0.378 Positive Predictive Value Cylofold: 0.746 RDfolder: 0.525 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	20 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.640 RDfolder: 0.549 Sensitivity RNAsubopt: 0.625 RDfolder: 0.487 Positive Predictive Value RNAsubopt: 0.672 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.1503931209e-08	9 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.558 RDfolder: 0.435 Sensitivity Fold: 0.544 RDfolder: 0.378 Positive Predictive Value Fold: 0.593 RDfolder: 0.525 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.742 RDfolder: 0.613 Sensitivity RSpredict(20): 0.643 RDfolder: 0.552 Positive Predictive Value RSpredict(20): 0.865 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.26497248087e-08	20 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.658 RDfolder: 0.549 Sensitivity Vsfold4: 0.617 RDfolder: 0.487 Positive Predictive Value Vsfold4: 0.716 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.10776592382e-08	10 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.586 Murlet(seed): 0.582 Sensitivity RDfolder: 0.513 Murlet(seed): 0.428 Positive Predictive Value RDfolder: 0.688 Murlet(seed): 0.808 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.490072995861	17 Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.647 RDfolder: 0.566 Sensitivity Alterna: 0.636 RDfolder: 0.503 Positive Predictive Value Alterna: 0.674 RDfolder: 0.657 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.34821445183e-08	10 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.709 RDfolder: 0.613 Sensitivity Mastr(20): 0.617 RDfolder: 0.552 Positive Predictive Value Mastr(20): 0.826 RDfolder: 0.698 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.36051213211e-08	20 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.576 RDfolder: 0.549 Sensitivity Vsfold5: 0.547 RDfolder: 0.487 Positive Predictive Value Vsfold5: 0.626 RDfolder: 0.640 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.17906639633e-07		+ RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.567 MCFold: 0.524 Sensitivity RDfolder: 0.499 MCFold: 0.547 Positive Predictive Value RDfolder: 0.665 MCFold: 0.523 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.600 RSpredict(seed): 0.447 Sensitivity RDfolder: 0.543 RSpredict(seed): 0.280 Positive Predictive Value RDfolder: 0.679 RSpredict(seed): 0.737 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.586 Carnac(seed): 0.129 Sensitivity RDfolder: 0.513 Carnac(seed): 0.017 Positive Predictive Value RDfolder: 0.688 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	? NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.499 RDfolder: 0.300 Sensitivity NanoFolder: 0.548 RDfolder: 0.274 Positive Predictive Value NanoFolder: 0.479 RDfolder: 0.362 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.681 RDfolder: 0.423 Sensitivity CentroidHomfold‑LAST: 0.567 RDfolder: 0.355 Positive Predictive Value CentroidHomfold‑LAST: 0.833 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 7 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): 0.629 RDfolder: 0.444 Sensitivity Multilign(seed): 0.580 RDfolder: 0.380 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): 0.678 RDfolder: 0.533 Sensitivity Multilign(20): 0.634 RDfolder: 0.446 Positive Predictive Value Multilign(20): 0.740 RDfolder: 0.658 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.666 RDfolder: 0.332 Sensitivity PETfold_pre2.0(seed): 0.584 RDfolder: 0.299 Positive Predictive Value PETfold_pre2.0(seed): 0.776 RDfolder: 0.404 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.750 RDfolder: 0.533 Sensitivity TurboFold(20): 0.670 RDfolder: 0.446 Positive Predictive Value TurboFold(20): 0.852 RDfolder: 0.658 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.481 RDfolder: 0.423 Sensitivity RNAwolf: 0.468 RDfolder: 0.355 Positive Predictive Value RNAwolf: 0.520 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.625 RDfolder: 0.423 Sensitivity IPknot: 0.574 RDfolder: 0.355 Positive Predictive Value IPknot: 0.698 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 7 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): 0.763 RDfolder: 0.445 Sensitivity PETfold_pre2.0(20): 0.678 RDfolder: 0.390 Positive Predictive Value PETfold_pre2.0(20): 0.870 RDfolder: 0.535 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.451 PPfold(seed): 0.182 Sensitivity RDfolder: 0.385 PPfold(seed): 0.046 Positive Predictive Value RDfolder: 0.556 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.673 RDfolder: 0.299 Sensitivity ContextFold: 0.602 RDfolder: 0.261 Positive Predictive Value ContextFold: 0.768 RDfolder: 0.377 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.641 RDfolder: 0.451 Sensitivity TurboFold(seed): 0.577 RDfolder: 0.385 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	? CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.580 RDfolder: 0.310 Sensitivity CRWrnafold: 0.556 RDfolder: 0.256 Positive Predictive Value CRWrnafold: 0.625 RDfolder: 0.405 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): 0.710 RDfolder: 0.579 Sensitivity RNASampler(seed): 0.589 RDfolder: 0.492 Positive Predictive Value RNASampler(seed): 0.869 RDfolder: 0.701 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.499 RDfolder: 0.299 Sensitivity RNASLOpt: 0.420 RDfolder: 0.261 Positive Predictive Value RNASLOpt: 0.617 RDfolder: 0.377 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.797 RDfolder: 0.533 Sensitivity PPfold(20): 0.714 RDfolder: 0.446 Positive Predictive Value PPfold(20): 0.899 RDfolder: 0.658 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.600 Mastr(seed): 0.000 Sensitivity RDfolder: 0.543 Mastr(seed): 0.000 Positive Predictive Value RDfolder: 0.679 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.66062906821e-08
MCFold	12 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.836 MCFold: 0.506 Sensitivity CentroidAlifold(20): 0.747 MCFold: 0.546 Positive Predictive Value CentroidAlifold(20): 0.940 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.26346675981e-08	15 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.778 MCFold: 0.551 Sensitivity CentroidAlifold(seed): 0.628 MCFold: 0.587 Positive Predictive Value CentroidAlifold(seed): 0.970 MCFold: 0.530 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.71568867205e-08	12 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.776 MCFold: 0.506 Sensitivity RNAalifold(20): 0.717 MCFold: 0.546 Positive Predictive Value RNAalifold(20): 0.847 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.59816551561e-08	15 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.747 MCFold: 0.551 Sensitivity MXScarna(seed): 0.689 MCFold: 0.587 Positive Predictive Value MXScarna(seed): 0.817 MCFold: 0.530 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.02510705504e-08	19 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.766 MCFold: 0.533 Sensitivity CentroidFold: 0.734 MCFold: 0.569 Positive Predictive Value CentroidFold: 0.806 MCFold: 0.513 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	12 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.796 MCFold: 0.506 Sensitivity RNASampler(20): 0.727 MCFold: 0.546 Positive Predictive Value RNASampler(20): 0.877 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.96907987703e-08	12 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.735 MCFold: 0.506 Sensitivity MXScarna(20): 0.686 MCFold: 0.546 Positive Predictive Value MXScarna(20): 0.794 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	22 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.704 MCFold: 0.527 Sensitivity Contrafold: 0.697 MCFold: 0.563 Positive Predictive Value Contrafold: 0.720 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	22 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.680 MCFold: 0.527 Sensitivity Sfold: 0.654 MCFold: 0.563 Positive Predictive Value Sfold: 0.717 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.652 MCFold: 0.493 Sensitivity MaxExpect: 0.652 MCFold: 0.529 Positive Predictive Value MaxExpect: 0.662 MCFold: 0.473 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	22 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.667 MCFold: 0.527 Sensitivity HotKnots: 0.688 MCFold: 0.563 Positive Predictive Value HotKnots: 0.657 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	12 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.684 MCFold: 0.567 Sensitivity RNAalifold(seed): 0.545 MCFold: 0.599 Positive Predictive Value RNAalifold(seed): 0.867 MCFold: 0.547 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.06323189071e-08	12 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.704 MCFold: 0.506 Sensitivity Murlet(20): 0.614 MCFold: 0.546 Positive Predictive Value Murlet(20): 0.814 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	22 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.667 MCFold: 0.527 Sensitivity UNAFold: 0.671 MCFold: 0.563 Positive Predictive Value UNAFold: 0.672 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.10776592382e-08	12 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.730 MCFold: 0.506 Sensitivity Carnac(20): 0.553 MCFold: 0.546 Positive Predictive Value Carnac(20): 0.970 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.67657656842e-08	22 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.683 MCFold: 0.527 Sensitivity McQFold: 0.677 MCFold: 0.563 Positive Predictive Value McQFold: 0.698 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	22 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.651 MCFold: 0.527 Sensitivity RNAshapes: 0.647 MCFold: 0.563 Positive Predictive Value RNAshapes: 0.664 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	22 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.659 MCFold: 0.527 Sensitivity RNAfold: 0.665 MCFold: 0.563 Positive Predictive Value RNAfold: 0.665 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	22 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.667 MCFold: 0.527 Sensitivity PknotsRG: 0.684 MCFold: 0.563 Positive Predictive Value PknotsRG: 0.661 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	22 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.665 MCFold: 0.527 Sensitivity Pknots: 0.688 MCFold: 0.563 Positive Predictive Value Pknots: 0.653 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.02343278931e-08	17 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.600 MCFold: 0.514 Sensitivity Afold: 0.617 MCFold: 0.557 Positive Predictive Value Afold: 0.594 MCFold: 0.489 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	11 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.585 MCFold: 0.544 Sensitivity ProbKnot: 0.633 MCFold: 0.588 Positive Predictive Value ProbKnot: 0.552 MCFold: 0.514 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.97952969696e-09	10 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.688 MCFold: 0.587 Sensitivity Cylofold: 0.680 MCFold: 0.618 Positive Predictive Value Cylofold: 0.705 MCFold: 0.570 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.94879201882e-09	22 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.597 MCFold: 0.527 Sensitivity RNAsubopt: 0.604 MCFold: 0.563 Positive Predictive Value RNAsubopt: 0.602 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	11 MCFold vs Fold Matthews Correlation Coefficient MCFold: 0.544 Fold: 0.530 Sensitivity MCFold: 0.588 Fold: 0.551 Positive Predictive Value MCFold: 0.514 Fold: 0.521 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0318548130709	12 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.694 MCFold: 0.506 Sensitivity RSpredict(20): 0.662 MCFold: 0.546 Positive Predictive Value RSpredict(20): 0.735 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.02510705504e-08	22 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.596 MCFold: 0.527 Sensitivity Vsfold4: 0.572 MCFold: 0.563 Positive Predictive Value Vsfold4: 0.633 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	12 MCFold vs Murlet(seed) Matthews Correlation Coefficient MCFold: 0.567 Murlet(seed): 0.558 Sensitivity MCFold: 0.599 Murlet(seed): 0.381 Positive Predictive Value MCFold: 0.547 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.206948167051	16 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.649 MCFold: 0.521 Sensitivity Alterna: 0.636 MCFold: 0.548 Positive Predictive Value Alterna: 0.678 MCFold: 0.516 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.78993384543e-08	12 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.620 MCFold: 0.506 Sensitivity Mastr(20): 0.451 MCFold: 0.546 Positive Predictive Value Mastr(20): 0.863 MCFold: 0.482 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.86109605532e-08	22 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.579 MCFold: 0.527 Sensitivity Vsfold5: 0.570 MCFold: 0.563 Positive Predictive Value Vsfold5: 0.601 MCFold: 0.508 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	18 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.567 MCFold: 0.524 Sensitivity RDfolder: 0.499 MCFold: 0.547 Positive Predictive Value RDfolder: 0.665 MCFold: 0.523 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08		+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.551 RSpredict(seed): 0.377 Sensitivity MCFold: 0.587 RSpredict(seed): 0.223 Positive Predictive Value MCFold: 0.530 RSpredict(seed): 0.653 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.567 Carnac(seed): 0.115 Sensitivity MCFold: 0.599 Carnac(seed): 0.013 Positive Predictive Value MCFold: 0.547 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 7.68522644707e-09	? NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: 0.441 MCFold: 0.419 Sensitivity NanoFolder: 0.560 MCFold: 0.467 Positive Predictive Value NanoFolder: 0.359 MCFold: 0.389 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.596 MCFold: 0.500 Sensitivity CentroidHomfold‑LAST: 0.519 MCFold: 0.532 Positive Predictive Value CentroidHomfold‑LAST: 0.696 MCFold: 0.485 Number of pairs reference - predicted secondary structure: 8 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): 0.589 MCFold: 0.586 Sensitivity Multilign(seed): 0.549 MCFold: 0.592 Positive Predictive Value Multilign(seed): 0.650 MCFold: 0.600 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): 0.580 MCFold: 0.498 Sensitivity Multilign(20): 0.583 MCFold: 0.534 Positive Predictive Value Multilign(20): 0.588 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.625 MCFold: 0.388 Sensitivity PETfold_pre2.0(seed): 0.544 MCFold: 0.426 Positive Predictive Value PETfold_pre2.0(seed): 0.725 MCFold: 0.367 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.650 MCFold: 0.498 Sensitivity TurboFold(20): 0.612 MCFold: 0.534 Positive Predictive Value TurboFold(20): 0.700 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.500 RNAwolf: 0.466 Sensitivity MCFold: 0.532 RNAwolf: 0.474 Positive Predictive Value MCFold: 0.485 RNAwolf: 0.474 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.633 MCFold: 0.500 Sensitivity IPknot: 0.597 MCFold: 0.532 Positive Predictive Value IPknot: 0.681 MCFold: 0.485 Number of pairs reference - predicted secondary structure: 8 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): 0.465 MCFold: 0.371 Sensitivity PETfold_pre2.0(20): 0.420 MCFold: 0.420 Positive Predictive Value PETfold_pre2.0(20): 0.525 MCFold: 0.339 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.491 PPfold(seed): 0.173 Sensitivity MCFold: 0.521 PPfold(seed): 0.058 Positive Predictive Value MCFold: 0.477 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.673 MCFold: 0.436 Sensitivity ContextFold: 0.614 MCFold: 0.475 Positive Predictive Value ContextFold: 0.747 MCFold: 0.414 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.537 MCFold: 0.491 Sensitivity TurboFold(seed): 0.521 MCFold: 0.521 Positive Predictive Value TurboFold(seed): 0.568 MCFold: 0.477 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.459 MCFold: 0.434 Sensitivity CRWrnafold: 0.477 MCFold: 0.469 Positive Predictive Value CRWrnafold: 0.456 MCFold: 0.418 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): 0.640 MCFold: 0.521 Sensitivity RNASampler(seed): 0.554 MCFold: 0.572 Positive Predictive Value RNASampler(seed): 0.748 MCFold: 0.485 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.483 MCFold: 0.436 Sensitivity RNASLOpt: 0.485 MCFold: 0.475 Positive Predictive Value RNASLOpt: 0.495 MCFold: 0.414 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.668 MCFold: 0.498 Sensitivity PPfold(20): 0.592 MCFold: 0.534 Positive Predictive Value PPfold(20): 0.763 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.551 Mastr(seed): 0.000 Sensitivity MCFold: 0.587 Mastr(seed): 0.000 Positive Predictive Value MCFold: 0.530 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08
RSpredict(seed)	15 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 RSpredict(seed): 0.350 Sensitivity CentroidAlifold(20): 0.694 RSpredict(seed): 0.181 Positive Predictive Value CentroidAlifold(20): 0.932 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.07760058607e-08	19 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 RSpredict(seed): 0.324 Sensitivity CentroidAlifold(seed): 0.598 RSpredict(seed): 0.177 Positive Predictive Value CentroidAlifold(seed): 0.894 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	15 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.753 RSpredict(seed): 0.350 Sensitivity RNAalifold(20): 0.656 RSpredict(seed): 0.181 Positive Predictive Value RNAalifold(20): 0.869 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	19 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.711 RSpredict(seed): 0.324 Sensitivity MXScarna(seed): 0.663 RSpredict(seed): 0.177 Positive Predictive Value MXScarna(seed): 0.768 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	19 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.675 RSpredict(seed): 0.324 Sensitivity CentroidFold: 0.675 RSpredict(seed): 0.177 Positive Predictive Value CentroidFold: 0.681 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	15 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.732 RSpredict(seed): 0.350 Sensitivity RNASampler(20): 0.639 RSpredict(seed): 0.181 Positive Predictive Value RNASampler(20): 0.843 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.703 RSpredict(seed): 0.350 Sensitivity MXScarna(20): 0.659 RSpredict(seed): 0.181 Positive Predictive Value MXScarna(20): 0.755 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	19 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.623 RSpredict(seed): 0.324 Sensitivity Contrafold: 0.647 RSpredict(seed): 0.177 Positive Predictive Value Contrafold: 0.606 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	19 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.632 RSpredict(seed): 0.324 Sensitivity Sfold: 0.623 RSpredict(seed): 0.177 Positive Predictive Value Sfold: 0.646 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.07760058607e-08	17 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.591 RSpredict(seed): 0.307 Sensitivity MaxExpect: 0.614 RSpredict(seed): 0.166 Positive Predictive Value MaxExpect: 0.575 RSpredict(seed): 0.576 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	19 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.616 RSpredict(seed): 0.324 Sensitivity HotKnots: 0.657 RSpredict(seed): 0.177 Positive Predictive Value HotKnots: 0.582 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	16 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.634 RSpredict(seed): 0.340 Sensitivity RNAalifold(seed): 0.479 RSpredict(seed): 0.192 Positive Predictive Value RNAalifold(seed): 0.842 RSpredict(seed): 0.613 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.54914456376e-08	15 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.666 RSpredict(seed): 0.350 Sensitivity Murlet(20): 0.548 RSpredict(seed): 0.181 Positive Predictive Value Murlet(20): 0.814 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.74172190343e-08	19 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.613 RSpredict(seed): 0.324 Sensitivity UNAFold: 0.638 RSpredict(seed): 0.177 Positive Predictive Value UNAFold: 0.594 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	15 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.662 RSpredict(seed): 0.350 Sensitivity Carnac(20): 0.469 RSpredict(seed): 0.181 Positive Predictive Value Carnac(20): 0.938 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	19 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.613 RSpredict(seed): 0.324 Sensitivity McQFold: 0.640 RSpredict(seed): 0.177 Positive Predictive Value McQFold: 0.593 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	19 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.594 RSpredict(seed): 0.324 Sensitivity RNAshapes: 0.617 RSpredict(seed): 0.177 Positive Predictive Value RNAshapes: 0.578 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	19 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.618 RSpredict(seed): 0.324 Sensitivity RNAfold: 0.652 RSpredict(seed): 0.177 Positive Predictive Value RNAfold: 0.591 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	19 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.634 RSpredict(seed): 0.324 Sensitivity PknotsRG: 0.675 RSpredict(seed): 0.177 Positive Predictive Value PknotsRG: 0.602 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.61939086268e-08	17 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.710 RSpredict(seed): 0.357 Sensitivity Pknots: 0.727 RSpredict(seed): 0.203 Positive Predictive Value Pknots: 0.701 RSpredict(seed): 0.644 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	14 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.551 RSpredict(seed): 0.351 Sensitivity Afold: 0.597 RSpredict(seed): 0.205 Positive Predictive Value Afold: 0.514 RSpredict(seed): 0.608 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.12160100812e-08	12 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.542 RSpredict(seed): 0.231 Sensitivity ProbKnot: 0.593 RSpredict(seed): 0.119 Positive Predictive Value ProbKnot: 0.501 RSpredict(seed): 0.457 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.72523032126e-08	8 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.723 RSpredict(seed): 0.290 Sensitivity Cylofold: 0.703 RSpredict(seed): 0.163 Positive Predictive Value Cylofold: 0.751 RSpredict(seed): 0.532 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	19 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.573 RSpredict(seed): 0.324 Sensitivity RNAsubopt: 0.603 RSpredict(seed): 0.177 Positive Predictive Value RNAsubopt: 0.550 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	12 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.532 RSpredict(seed): 0.231 Sensitivity Fold: 0.570 RSpredict(seed): 0.119 Positive Predictive Value Fold: 0.502 RSpredict(seed): 0.457 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.41358941668e-08	15 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.624 RSpredict(seed): 0.350 Sensitivity RSpredict(20): 0.559 RSpredict(seed): 0.181 Positive Predictive Value RSpredict(20): 0.702 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.76499031155e-08	19 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.531 RSpredict(seed): 0.324 Sensitivity Vsfold4: 0.530 RSpredict(seed): 0.177 Positive Predictive Value Vsfold4: 0.538 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.54229534325e-08	14 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.571 RSpredict(seed): 0.384 Sensitivity Murlet(seed): 0.386 RSpredict(seed): 0.227 Positive Predictive Value Murlet(seed): 0.855 RSpredict(seed): 0.664 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.93248927742e-08	10 Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.657 RSpredict(seed): 0.464 Sensitivity Alterna: 0.651 RSpredict(seed): 0.299 Positive Predictive Value Alterna: 0.677 RSpredict(seed): 0.742 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.24019667966e-08	15 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.506 RSpredict(seed): 0.350 Sensitivity Mastr(20): 0.337 RSpredict(seed): 0.181 Positive Predictive Value Mastr(20): 0.769 RSpredict(seed): 0.689 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.08252958266e-08	19 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.498 RSpredict(seed): 0.324 Sensitivity Vsfold5: 0.496 RSpredict(seed): 0.177 Positive Predictive Value Vsfold5: 0.508 RSpredict(seed): 0.600 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.89649746203e-08	13 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.600 RSpredict(seed): 0.447 Sensitivity RDfolder: 0.543 RSpredict(seed): 0.280 Positive Predictive Value RDfolder: 0.679 RSpredict(seed): 0.737 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	15 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.551 RSpredict(seed): 0.377 Sensitivity MCFold: 0.587 RSpredict(seed): 0.223 Positive Predictive Value MCFold: 0.530 RSpredict(seed): 0.653 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08		+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.384 Carnac(seed): 0.104 Sensitivity RSpredict(seed): 0.227 Carnac(seed): 0.011 Positive Predictive Value RSpredict(seed): 0.664 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	? NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.336 RSpredict(seed): 0.179 Sensitivity NanoFolder: 0.415 RSpredict(seed): 0.110 Positive Predictive Value NanoFolder: 0.288 RSpredict(seed): 0.310 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RSpredict(seed): 0.331 Sensitivity CentroidHomfold‑LAST: 0.567 RSpredict(seed): 0.200 Positive Predictive Value CentroidHomfold‑LAST: 0.746 RSpredict(seed): 0.566 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): 0.629 RSpredict(seed): 0.376 Sensitivity Multilign(seed): 0.580 RSpredict(seed): 0.240 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): 0.581 RSpredict(seed): 0.409 Sensitivity Multilign(20): 0.576 RSpredict(seed): 0.227 Positive Predictive Value Multilign(20): 0.598 RSpredict(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RSpredict(seed): 0.203 Sensitivity PETfold_pre2.0(seed): 0.619 RSpredict(seed): 0.124 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RSpredict(seed): 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 RSpredict(seed): 0.409 Sensitivity TurboFold(20): 0.606 RSpredict(seed): 0.227 Positive Predictive Value TurboFold(20): 0.714 RSpredict(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.451 RSpredict(seed): 0.331 Sensitivity RNAwolf: 0.447 RSpredict(seed): 0.200 Positive Predictive Value RNAwolf: 0.472 RSpredict(seed): 0.566 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.601 RSpredict(seed): 0.331 Sensitivity IPknot: 0.560 RSpredict(seed): 0.200 Positive Predictive Value IPknot: 0.656 RSpredict(seed): 0.566 Number of pairs reference - predicted secondary structure: 7 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): 0.619 RSpredict(seed): 0.291 Sensitivity PETfold_pre2.0(20): 0.570 RSpredict(seed): 0.152 Positive Predictive Value PETfold_pre2.0(20): 0.682 RSpredict(seed): 0.571 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.331 PPfold(seed): 0.155 Sensitivity RSpredict(seed): 0.200 PPfold(seed): 0.047 Positive Predictive Value RSpredict(seed): 0.566 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.570 RSpredict(seed): 0.203 Sensitivity ContextFold: 0.515 RSpredict(seed): 0.124 Positive Predictive Value ContextFold: 0.641 RSpredict(seed): 0.353 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): 0.560 RSpredict(seed): 0.331 Sensitivity TurboFold(seed): 0.533 RSpredict(seed): 0.200 Positive Predictive Value TurboFold(seed): 0.602 RSpredict(seed): 0.566 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 RSpredict(seed): 0.178 Sensitivity CRWrnafold: 0.524 RSpredict(seed): 0.095 Positive Predictive Value CRWrnafold: 0.516 RSpredict(seed): 0.353 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 RSpredict(seed): 0.435 Sensitivity RNASampler(seed): 0.554 RSpredict(seed): 0.289 Positive Predictive Value RNASampler(seed): 0.748 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 RSpredict(seed): 0.203 Sensitivity RNASLOpt: 0.443 RSpredict(seed): 0.124 Positive Predictive Value RNASLOpt: 0.494 RSpredict(seed): 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.715 RSpredict(seed): 0.409 Sensitivity PPfold(20): 0.644 RSpredict(seed): 0.227 Positive Predictive Value PPfold(20): 0.802 RSpredict(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.324 Mastr(seed): 0.000 Sensitivity RSpredict(seed): 0.177 Mastr(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.600 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08
Carnac(seed)	12 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.814 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.713 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.934 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.70887622364e-08	14 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.826 Carnac(seed): 0.104 Sensitivity CentroidAlifold(seed): 0.707 Carnac(seed): 0.011 Positive Predictive Value CentroidAlifold(seed): 0.970 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.57237423209e-08	12 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.750 Carnac(seed): 0.000 Sensitivity RNAalifold(20): 0.669 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.848 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.91441904741e-08	14 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.709 Carnac(seed): 0.104 Sensitivity MXScarna(seed): 0.652 Carnac(seed): 0.011 Positive Predictive Value MXScarna(seed): 0.778 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.1413769576e-08	14 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.762 Carnac(seed): 0.104 Sensitivity CentroidFold: 0.723 Carnac(seed): 0.011 Positive Predictive Value CentroidFold: 0.810 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.02510705504e-08	12 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.756 Carnac(seed): 0.000 Sensitivity RNASampler(20): 0.666 Carnac(seed): 0.000 Positive Predictive Value RNASampler(20): 0.865 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 6.84390417318e-09	12 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.720 Carnac(seed): 0.000 Sensitivity MXScarna(20): 0.675 Carnac(seed): 0.000 Positive Predictive Value MXScarna(20): 0.775 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	14 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.735 Carnac(seed): 0.104 Sensitivity Contrafold: 0.723 Carnac(seed): 0.011 Positive Predictive Value Contrafold: 0.754 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.78993384543e-08	14 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.749 Carnac(seed): 0.104 Sensitivity Sfold: 0.701 Carnac(seed): 0.011 Positive Predictive Value Sfold: 0.808 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.18141491686e-08	13 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.681 Carnac(seed): 0.109 Sensitivity MaxExpect: 0.675 Carnac(seed): 0.012 Positive Predictive Value MaxExpect: 0.695 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	14 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.736 Carnac(seed): 0.104 Sensitivity HotKnots: 0.745 Carnac(seed): 0.011 Positive Predictive Value HotKnots: 0.733 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.61939086268e-08	14 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.706 Carnac(seed): 0.104 Sensitivity RNAalifold(seed): 0.564 Carnac(seed): 0.011 Positive Predictive Value RNAalifold(seed): 0.892 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.69132796717e-08	12 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.690 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.577 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.832 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 7.21563533328e-09	14 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.712 Carnac(seed): 0.104 Sensitivity UNAFold: 0.701 Carnac(seed): 0.011 Positive Predictive Value UNAFold: 0.731 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.10032755566e-08	12 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.673 Carnac(seed): 0.000 Sensitivity Carnac(20): 0.483 Carnac(seed): 0.000 Positive Predictive Value Carnac(20): 0.944 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.03576421863e-08	14 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.732 Carnac(seed): 0.104 Sensitivity McQFold: 0.729 Carnac(seed): 0.011 Positive Predictive Value McQFold: 0.743 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	14 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.718 Carnac(seed): 0.104 Sensitivity RNAshapes: 0.707 Carnac(seed): 0.011 Positive Predictive Value RNAshapes: 0.737 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.64318034126e-08	14 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.743 Carnac(seed): 0.104 Sensitivity RNAfold: 0.737 Carnac(seed): 0.011 Positive Predictive Value RNAfold: 0.756 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.04409141234e-08	14 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.768 Carnac(seed): 0.104 Sensitivity PknotsRG: 0.773 Carnac(seed): 0.011 Positive Predictive Value PknotsRG: 0.770 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	14 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.695 Carnac(seed): 0.104 Sensitivity Pknots: 0.712 Carnac(seed): 0.011 Positive Predictive Value Pknots: 0.686 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.96907987703e-08	9 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.712 Carnac(seed): 0.136 Sensitivity Afold: 0.706 Carnac(seed): 0.019 Positive Predictive Value Afold: 0.726 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.603 Carnac(seed): 0.124 Sensitivity ProbKnot: 0.637 Carnac(seed): 0.015 Positive Predictive Value ProbKnot: 0.581 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.87872347734e-08	8 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.723 Carnac(seed): 0.140 Sensitivity Cylofold: 0.703 Carnac(seed): 0.020 Positive Predictive Value Cylofold: 0.751 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	14 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.679 Carnac(seed): 0.104 Sensitivity RNAsubopt: 0.677 Carnac(seed): 0.011 Positive Predictive Value RNAsubopt: 0.690 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	10 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.589 Carnac(seed): 0.124 Sensitivity Fold: 0.602 Carnac(seed): 0.015 Positive Predictive Value Fold: 0.586 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.34193807955e-08	12 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.581 Carnac(seed): 0.000 Sensitivity RSpredict(20): 0.511 Carnac(seed): 0.000 Positive Predictive Value RSpredict(20): 0.672 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.87872347734e-08	14 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.603 Carnac(seed): 0.104 Sensitivity Vsfold4: 0.573 Carnac(seed): 0.011 Positive Predictive Value Vsfold4: 0.645 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.50323628132e-08	14 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.571 Carnac(seed): 0.104 Sensitivity Murlet(seed): 0.386 Carnac(seed): 0.011 Positive Predictive Value Murlet(seed): 0.855 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.49381627234e-08	7 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.729 Carnac(seed): 0.149 Sensitivity Alterna: 0.701 Carnac(seed): 0.023 Positive Predictive Value Alterna: 0.770 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	12 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.515 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.369 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.731 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	14 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.556 Carnac(seed): 0.104 Sensitivity Vsfold5: 0.537 Carnac(seed): 0.011 Positive Predictive Value Vsfold5: 0.589 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	10 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.586 Carnac(seed): 0.129 Sensitivity RDfolder: 0.513 Carnac(seed): 0.017 Positive Predictive Value RDfolder: 0.688 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	12 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.567 Carnac(seed): 0.115 Sensitivity MCFold: 0.599 Carnac(seed): 0.013 Positive Predictive Value MCFold: 0.547 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 7.68522644707e-09	14 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.384 Carnac(seed): 0.104 Sensitivity RSpredict(seed): 0.227 Carnac(seed): 0.011 Positive Predictive Value RSpredict(seed): 0.664 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08		? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.336 Carnac(seed): 0.220 Sensitivity NanoFolder: 0.415 Carnac(seed): 0.049 Positive Predictive Value NanoFolder: 0.288 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Carnac(seed): 0.162 Sensitivity CentroidHomfold‑LAST: 0.567 Carnac(seed): 0.027 Positive Predictive Value CentroidHomfold‑LAST: 0.746 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 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): 0.629 Carnac(seed): 0.198 Sensitivity Multilign(seed): 0.580 Carnac(seed): 0.040 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): 0.581 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.576 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.598 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Carnac(seed): 0.202 Sensitivity PETfold_pre2.0(seed): 0.619 Carnac(seed): 0.041 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.606 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.714 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.451 Carnac(seed): 0.162 Sensitivity RNAwolf: 0.447 Carnac(seed): 0.027 Positive Predictive Value RNAwolf: 0.472 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.601 Carnac(seed): 0.162 Sensitivity IPknot: 0.560 Carnac(seed): 0.027 Positive Predictive Value IPknot: 0.656 Carnac(seed): 1.000 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): 0.619 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.570 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.682 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.162 PPfold(seed): 0.155 Sensitivity Carnac(seed): 0.027 PPfold(seed): 0.047 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.570 Carnac(seed): 0.202 Sensitivity ContextFold: 0.515 Carnac(seed): 0.041 Positive Predictive Value ContextFold: 0.641 Carnac(seed): 1.000 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): 0.560 Carnac(seed): 0.162 Sensitivity TurboFold(seed): 0.533 Carnac(seed): 0.027 Positive Predictive Value TurboFold(seed): 0.602 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Carnac(seed): 0.177 Sensitivity CRWrnafold: 0.524 Carnac(seed): 0.032 Positive Predictive Value CRWrnafold: 0.516 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 Carnac(seed): 0.154 Sensitivity RNASampler(seed): 0.554 Carnac(seed): 0.024 Positive Predictive Value RNASampler(seed): 0.748 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 Carnac(seed): 0.202 Sensitivity RNASLOpt: 0.443 Carnac(seed): 0.041 Positive Predictive Value RNASLOpt: 0.494 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.715 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.644 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.802 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.104 Mastr(seed): 0.000 Sensitivity Carnac(seed): 0.011 Mastr(seed): 0.000 Positive Predictive Value Carnac(seed): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.95923378787e-08
NanoFolder	3 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.681 NanoFolder: 0.285 Sensitivity CentroidAlifold(20): 0.547 NanoFolder: 0.359 Positive Predictive Value CentroidAlifold(20): 0.854 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.679 NanoFolder: 0.336 Sensitivity CentroidAlifold(seed): 0.476 NanoFolder: 0.415 Positive Predictive Value CentroidAlifold(seed): 0.975 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.545 NanoFolder: 0.285 Sensitivity RNAalifold(20): 0.500 NanoFolder: 0.359 Positive Predictive Value RNAalifold(20): 0.604 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.468 NanoFolder: 0.336 Sensitivity MXScarna(seed): 0.415 NanoFolder: 0.415 Positive Predictive Value MXScarna(seed): 0.540 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.544 NanoFolder: 0.427 Sensitivity CentroidFold: 0.519 NanoFolder: 0.519 Positive Predictive Value CentroidFold: 0.581 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.568 NanoFolder: 0.285 Sensitivity RNASampler(20): 0.516 NanoFolder: 0.359 Positive Predictive Value RNASampler(20): 0.635 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.512 NanoFolder: 0.285 Sensitivity MXScarna(20): 0.500 NanoFolder: 0.359 Positive Predictive Value MXScarna(20): 0.533 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.542 NanoFolder: 0.427 Sensitivity Contrafold: 0.529 NanoFolder: 0.519 Positive Predictive Value Contrafold: 0.567 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.451 NanoFolder: 0.427 Sensitivity Sfold: 0.442 NanoFolder: 0.519 Positive Predictive Value Sfold: 0.474 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs MaxExpect Matthews Correlation Coefficient NanoFolder: 0.427 MaxExpect: 0.369 Sensitivity NanoFolder: 0.519 MaxExpect: 0.385 Positive Predictive Value NanoFolder: 0.365 MaxExpect: 0.370 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.535 NanoFolder: 0.427 Sensitivity HotKnots: 0.577 NanoFolder: 0.519 Positive Predictive Value HotKnots: 0.508 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.529 NanoFolder: 0.336 Sensitivity RNAalifold(seed): 0.390 NanoFolder: 0.415 Positive Predictive Value RNAalifold(seed): 0.727 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.551 NanoFolder: 0.285 Sensitivity Murlet(20): 0.500 NanoFolder: 0.359 Positive Predictive Value Murlet(20): 0.615 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs UNAFold Matthews Correlation Coefficient NanoFolder: 0.427 UNAFold: 0.353 Sensitivity NanoFolder: 0.519 UNAFold: 0.375 Positive Predictive Value NanoFolder: 0.365 UNAFold: 0.348 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.463 NanoFolder: 0.285 Sensitivity Carnac(20): 0.297 NanoFolder: 0.359 Positive Predictive Value Carnac(20): 0.731 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.603 NanoFolder: 0.427 Sensitivity McQFold: 0.625 NanoFolder: 0.519 Positive Predictive Value McQFold: 0.591 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.456 NanoFolder: 0.427 Sensitivity RNAshapes: 0.481 NanoFolder: 0.519 Positive Predictive Value RNAshapes: 0.446 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.452 NanoFolder: 0.427 Sensitivity RNAfold: 0.481 NanoFolder: 0.519 Positive Predictive Value RNAfold: 0.439 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.531 NanoFolder: 0.427 Sensitivity PknotsRG: 0.577 NanoFolder: 0.519 Positive Predictive Value PknotsRG: 0.500 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.468 NanoFolder: 0.427 Sensitivity Pknots: 0.500 NanoFolder: 0.519 Positive Predictive Value Pknots: 0.452 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.411 NanoFolder: 0.395 Sensitivity Afold: 0.467 NanoFolder: 0.517 Positive Predictive Value Afold: 0.373 NanoFolder: 0.313 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs ProbKnot Matthews Correlation Coefficient NanoFolder: 0.427 ProbKnot: 0.380 Sensitivity NanoFolder: 0.519 ProbKnot: 0.413 Positive Predictive Value NanoFolder: 0.365 ProbKnot: 0.364 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.585 NanoFolder: 0.576 Sensitivity Cylofold: 0.583 NanoFolder: 0.643 Positive Predictive Value Cylofold: 0.605 NanoFolder: 0.535 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs RNAsubopt Matthews Correlation Coefficient NanoFolder: 0.427 RNAsubopt: 0.356 Sensitivity NanoFolder: 0.519 RNAsubopt: 0.385 Positive Predictive Value NanoFolder: 0.365 RNAsubopt: 0.345 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs Fold Matthews Correlation Coefficient NanoFolder: 0.427 Fold: 0.366 Sensitivity NanoFolder: 0.519 Fold: 0.385 Positive Predictive Value NanoFolder: 0.365 Fold: 0.364 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.316 NanoFolder: 0.285 Sensitivity RSpredict(20): 0.281 NanoFolder: 0.359 Positive Predictive Value RSpredict(20): 0.367 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs Vsfold4 Matthews Correlation Coefficient NanoFolder: 0.427 Vsfold4: 0.419 Sensitivity NanoFolder: 0.519 Vsfold4: 0.413 Positive Predictive Value NanoFolder: 0.365 Vsfold4: 0.439 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.473 NanoFolder: 0.336 Sensitivity Murlet(seed): 0.329 NanoFolder: 0.415 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	1 NanoFolder vs Alterna Matthews Correlation Coefficient NanoFolder: 0.536 Alterna: 0.471 Sensitivity NanoFolder: 0.611 Alterna: 0.444 Positive Predictive Value NanoFolder: 0.500 Alterna: 0.533 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	3 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.379 NanoFolder: 0.285 Sensitivity Mastr(20): 0.234 NanoFolder: 0.359 Positive Predictive Value Mastr(20): 0.625 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.427 Vsfold5: 0.379 Sensitivity NanoFolder: 0.519 Vsfold5: 0.394 Positive Predictive Value NanoFolder: 0.365 Vsfold5: 0.380 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.499 RDfolder: 0.300 Sensitivity NanoFolder: 0.548 RDfolder: 0.274 Positive Predictive Value NanoFolder: 0.479 RDfolder: 0.362 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: 0.441 MCFold: 0.419 Sensitivity NanoFolder: 0.560 MCFold: 0.467 Positive Predictive Value NanoFolder: 0.359 MCFold: 0.389 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.336 RSpredict(seed): 0.179 Sensitivity NanoFolder: 0.415 RSpredict(seed): 0.110 Positive Predictive Value NanoFolder: 0.288 RSpredict(seed): 0.310 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.336 Carnac(seed): 0.220 Sensitivity NanoFolder: 0.415 Carnac(seed): 0.049 Positive Predictive Value NanoFolder: 0.288 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.566 NanoFolder: 0.427 Sensitivity CentroidHomfold‑LAST: 0.510 NanoFolder: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.639 NanoFolder: 0.365 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): 0.458 NanoFolder: 0.447 Sensitivity Multilign(seed): 0.404 NanoFolder: 0.489 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): 0.456 NanoFolder: 0.285 Sensitivity Multilign(20): 0.469 NanoFolder: 0.359 Positive Predictive Value Multilign(20): 0.455 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.709 NanoFolder: 0.336 Sensitivity PETfold_pre2.0(seed): 0.634 NanoFolder: 0.415 Positive Predictive Value PETfold_pre2.0(seed): 0.800 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.513 NanoFolder: 0.285 Sensitivity TurboFold(20): 0.484 NanoFolder: 0.359 Positive Predictive Value TurboFold(20): 0.554 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs RNAwolf Matthews Correlation Coefficient NanoFolder: 0.427 RNAwolf: 0.332 Sensitivity NanoFolder: 0.519 RNAwolf: 0.337 Positive Predictive Value NanoFolder: 0.365 RNAwolf: 0.343 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.530 NanoFolder: 0.427 Sensitivity IPknot: 0.510 NanoFolder: 0.519 Positive Predictive Value IPknot: 0.564 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 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): 0.609 NanoFolder: 0.285 Sensitivity PETfold_pre2.0(20): 0.578 NanoFolder: 0.359 Positive Predictive Value PETfold_pre2.0(20): 0.649 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.336 PPfold(seed): 0.211 Sensitivity NanoFolder: 0.415 PPfold(seed): 0.085 Positive Predictive Value NanoFolder: 0.288 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.637 NanoFolder: 0.427 Sensitivity ContextFold: 0.596 NanoFolder: 0.519 Positive Predictive Value ContextFold: 0.689 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.383 NanoFolder: 0.336 Sensitivity TurboFold(seed): 0.378 NanoFolder: 0.415 Positive Predictive Value TurboFold(seed): 0.403 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.437 NanoFolder: 0.427 Sensitivity CRWrnafold: 0.462 NanoFolder: 0.519 Positive Predictive Value CRWrnafold: 0.429 NanoFolder: 0.365 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): 0.232 NanoFolder: 0.207 Sensitivity RNASampler(seed): 0.211 NanoFolder: 0.289 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.159 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs RNASLOpt Matthews Correlation Coefficient NanoFolder: 0.427 RNASLOpt: 0.420 Sensitivity NanoFolder: 0.519 RNASLOpt: 0.423 Positive Predictive Value NanoFolder: 0.365 RNASLOpt: 0.431 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.632 NanoFolder: 0.285 Sensitivity PPfold(20): 0.578 NanoFolder: 0.359 Positive Predictive Value PPfold(20): 0.698 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.336 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.415 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.288 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0
CentroidHomfold‑LAST	6 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.764 CentroidHomfold‑LAST: 0.726 Sensitivity CentroidAlifold(20): 0.636 CentroidHomfold‑LAST: 0.644 Positive Predictive Value CentroidAlifold(20): 0.923 CentroidHomfold‑LAST: 0.825 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 CentroidHomfold‑LAST: 0.645 Sensitivity CentroidAlifold(seed): 0.593 CentroidHomfold‑LAST: 0.567 Positive Predictive Value CentroidAlifold(seed): 0.978 CentroidHomfold‑LAST: 0.746 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 RNAalifold(20): 0.658 Sensitivity CentroidHomfold‑LAST: 0.644 RNAalifold(20): 0.591 Positive Predictive Value CentroidHomfold‑LAST: 0.825 RNAalifold(20): 0.743 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 MXScarna(seed): 0.593 Sensitivity CentroidHomfold‑LAST: 0.567 MXScarna(seed): 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.746 MXScarna(seed): 0.672 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 CentroidFold: 0.632 Sensitivity CentroidHomfold‑LAST: 0.552 CentroidFold: 0.596 Positive Predictive Value CentroidHomfold‑LAST: 0.743 CentroidFold: 0.681 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 RNASampler(20): 0.693 Sensitivity CentroidHomfold‑LAST: 0.644 RNASampler(20): 0.606 Positive Predictive Value CentroidHomfold‑LAST: 0.825 RNASampler(20): 0.800 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 MXScarna(20): 0.606 Sensitivity CentroidHomfold‑LAST: 0.644 MXScarna(20): 0.561 Positive Predictive Value CentroidHomfold‑LAST: 0.825 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Contrafold: 0.629 Sensitivity CentroidHomfold‑LAST: 0.552 Contrafold: 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Contrafold: 0.659 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Sfold: 0.595 Sensitivity CentroidHomfold‑LAST: 0.552 Sfold: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Sfold: 0.629 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 MaxExpect: 0.522 Sensitivity CentroidHomfold‑LAST: 0.552 MaxExpect: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.743 MaxExpect: 0.540 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.651 CentroidHomfold‑LAST: 0.635 Sensitivity HotKnots: 0.678 CentroidHomfold‑LAST: 0.552 Positive Predictive Value HotKnots: 0.636 CentroidHomfold‑LAST: 0.743 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RNAalifold(seed): 0.610 Sensitivity CentroidHomfold‑LAST: 0.567 RNAalifold(seed): 0.473 Positive Predictive Value CentroidHomfold‑LAST: 0.746 RNAalifold(seed): 0.798 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Murlet(20): 0.654 Sensitivity CentroidHomfold‑LAST: 0.644 Murlet(20): 0.576 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 UNAFold: 0.531 Sensitivity CentroidHomfold‑LAST: 0.552 UNAFold: 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.743 UNAFold: 0.535 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Carnac(20): 0.600 Sensitivity CentroidHomfold‑LAST: 0.644 Carnac(20): 0.417 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 McQFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient McQFold: 0.687 CentroidHomfold‑LAST: 0.635 Sensitivity McQFold: 0.689 CentroidHomfold‑LAST: 0.552 Positive Predictive Value McQFold: 0.696 CentroidHomfold‑LAST: 0.743 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAshapes: 0.572 Sensitivity CentroidHomfold‑LAST: 0.552 RNAshapes: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAshapes: 0.583 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAfold: 0.569 Sensitivity CentroidHomfold‑LAST: 0.552 RNAfold: 0.574 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAfold: 0.577 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 PknotsRG: 0.623 Sensitivity CentroidHomfold‑LAST: 0.552 PknotsRG: 0.645 Positive Predictive Value CentroidHomfold‑LAST: 0.743 PknotsRG: 0.615 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Pknots: 0.605 Sensitivity CentroidHomfold‑LAST: 0.552 Pknots: 0.623 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Pknots: 0.600 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 Afold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Afold: 0.567 CentroidHomfold‑LAST: 0.557 Sensitivity Afold: 0.596 CentroidHomfold‑LAST: 0.505 Positive Predictive Value Afold: 0.551 CentroidHomfold‑LAST: 0.625 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 ProbKnot: 0.527 Sensitivity CentroidHomfold‑LAST: 0.552 ProbKnot: 0.552 Positive Predictive Value CentroidHomfold‑LAST: 0.743 ProbKnot: 0.518 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.696 Cylofold: 0.664 Sensitivity CentroidHomfold‑LAST: 0.589 Cylofold: 0.650 Positive Predictive Value CentroidHomfold‑LAST: 0.835 Cylofold: 0.693 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAsubopt: 0.513 Sensitivity CentroidHomfold‑LAST: 0.552 RNAsubopt: 0.525 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAsubopt: 0.516 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Fold: 0.468 Sensitivity CentroidHomfold‑LAST: 0.552 Fold: 0.475 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Fold: 0.478 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 RSpredict(20): 0.573 Sensitivity CentroidHomfold‑LAST: 0.644 RSpredict(20): 0.530 Positive Predictive Value CentroidHomfold‑LAST: 0.825 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Vsfold4: 0.478 Sensitivity CentroidHomfold‑LAST: 0.552 Vsfold4: 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Vsfold4: 0.509 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Murlet(seed): 0.531 Sensitivity CentroidHomfold‑LAST: 0.567 Murlet(seed): 0.373 Positive Predictive Value CentroidHomfold‑LAST: 0.746 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 Alterna vs CentroidHomfold‑LAST Matthews Correlation Coefficient Alterna: 0.568 CentroidHomfold‑LAST: 0.553 Sensitivity Alterna: 0.549 CentroidHomfold‑LAST: 0.451 Positive Predictive Value Alterna: 0.608 CentroidHomfold‑LAST: 0.698 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Mastr(20): 0.570 Sensitivity CentroidHomfold‑LAST: 0.644 Mastr(20): 0.424 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 Vsfold5: 0.461 Sensitivity CentroidHomfold‑LAST: 0.552 Vsfold5: 0.470 Positive Predictive Value CentroidHomfold‑LAST: 0.743 Vsfold5: 0.470 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.681 RDfolder: 0.423 Sensitivity CentroidHomfold‑LAST: 0.567 RDfolder: 0.355 Positive Predictive Value CentroidHomfold‑LAST: 0.833 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.596 MCFold: 0.500 Sensitivity CentroidHomfold‑LAST: 0.519 MCFold: 0.532 Positive Predictive Value CentroidHomfold‑LAST: 0.696 MCFold: 0.485 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RSpredict(seed): 0.331 Sensitivity CentroidHomfold‑LAST: 0.567 RSpredict(seed): 0.200 Positive Predictive Value CentroidHomfold‑LAST: 0.746 RSpredict(seed): 0.566 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Carnac(seed): 0.162 Sensitivity CentroidHomfold‑LAST: 0.567 Carnac(seed): 0.027 Positive Predictive Value CentroidHomfold‑LAST: 0.746 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.566 NanoFolder: 0.427 Sensitivity CentroidHomfold‑LAST: 0.510 NanoFolder: 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.639 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 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: 0.682 Multilign(seed): 0.629 Sensitivity CentroidHomfold‑LAST: 0.580 Multilign(seed): 0.580 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: 0.726 Multilign(20): 0.581 Sensitivity CentroidHomfold‑LAST: 0.644 Multilign(20): 0.576 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CentroidHomfold‑LAST: 0.558 Sensitivity PETfold_pre2.0(seed): 0.619 CentroidHomfold‑LAST: 0.495 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CentroidHomfold‑LAST: 0.640 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 TurboFold(20): 0.653 Sensitivity CentroidHomfold‑LAST: 0.644 TurboFold(20): 0.606 Positive Predictive Value CentroidHomfold‑LAST: 0.825 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAwolf: 0.436 Sensitivity CentroidHomfold‑LAST: 0.552 RNAwolf: 0.437 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 IPknot: 0.612 Sensitivity CentroidHomfold‑LAST: 0.552 IPknot: 0.579 Positive Predictive Value CentroidHomfold‑LAST: 0.743 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 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	? CentroidHomfold‑LAST vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.672 PETfold_pre2.0(20): 0.619 Sensitivity CentroidHomfold‑LAST: 0.608 PETfold_pre2.0(20): 0.570 Positive Predictive Value CentroidHomfold‑LAST: 0.750 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 PPfold(seed): 0.155 Sensitivity CentroidHomfold‑LAST: 0.567 PPfold(seed): 0.047 Positive Predictive Value CentroidHomfold‑LAST: 0.746 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.662 CentroidHomfold‑LAST: 0.565 Sensitivity ContextFold: 0.608 CentroidHomfold‑LAST: 0.492 Positive Predictive Value ContextFold: 0.731 CentroidHomfold‑LAST: 0.660 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 TurboFold(seed): 0.560 Sensitivity CentroidHomfold‑LAST: 0.567 TurboFold(seed): 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.746 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.601 CRWrnafold: 0.502 Sensitivity CentroidHomfold‑LAST: 0.522 CRWrnafold: 0.516 Positive Predictive Value CentroidHomfold‑LAST: 0.703 CRWrnafold: 0.503 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): 0.559 CentroidHomfold‑LAST: 0.517 Sensitivity RNASampler(seed): 0.484 CentroidHomfold‑LAST: 0.462 Positive Predictive Value RNASampler(seed): 0.657 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.565 RNASLOpt: 0.449 Sensitivity CentroidHomfold‑LAST: 0.492 RNASLOpt: 0.438 Positive Predictive Value CentroidHomfold‑LAST: 0.660 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 PPfold(20): 0.715 Sensitivity CentroidHomfold‑LAST: 0.644 PPfold(20): 0.644 Positive Predictive Value CentroidHomfold‑LAST: 0.825 PPfold(20): 0.802 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.567 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.746 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 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 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 RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 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 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 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 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs 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 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 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 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 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs 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 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 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 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 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 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 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 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 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 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	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		? 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 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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)	3 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.867 Multilign(seed): 0.755 Sensitivity CentroidAlifold(20): 0.768 Multilign(seed): 0.707 Positive Predictive Value CentroidAlifold(20): 0.984 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): 0.797 Multilign(seed): 0.629 Sensitivity CentroidAlifold(seed): 0.650 Multilign(seed): 0.580 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	3 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.834 Multilign(seed): 0.755 Sensitivity RNAalifold(20): 0.768 Multilign(seed): 0.707 Positive Predictive Value RNAalifold(20): 0.913 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(seed): 0.643 Multilign(seed): 0.629 Sensitivity MXScarna(seed): 0.600 Multilign(seed): 0.580 Positive Predictive Value MXScarna(seed): 0.706 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.659 Multilign(seed): 0.629 Sensitivity CentroidFold: 0.610 Multilign(seed): 0.580 Positive Predictive Value CentroidFold: 0.726 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.802 Multilign(seed): 0.755 Sensitivity RNASampler(20): 0.695 Multilign(seed): 0.707 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	3 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.755 MXScarna(20): 0.750 Sensitivity Multilign(seed): 0.707 MXScarna(20): 0.732 Positive Predictive Value Multilign(seed): 0.817 MXScarna(20): 0.779 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.646 Multilign(seed): 0.629 Sensitivity Contrafold: 0.620 Multilign(seed): 0.580 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: 0.703 Multilign(seed): 0.629 Sensitivity Sfold: 0.650 Multilign(seed): 0.580 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): 0.629 MaxExpect: 0.592 Sensitivity Multilign(seed): 0.580 MaxExpect: 0.570 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 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.728 Multilign(seed): 0.629 Sensitivity HotKnots: 0.700 Multilign(seed): 0.580 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	4 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.629 Multilign(seed): 0.629 Sensitivity RNAalifold(seed): 0.540 Multilign(seed): 0.580 Positive Predictive Value RNAalifold(seed): 0.750 Multilign(seed): 0.699 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): 0.833 Multilign(seed): 0.755 Sensitivity Murlet(20): 0.756 Multilign(seed): 0.707 Positive Predictive Value Murlet(20): 0.925 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): 0.629 UNAFold: 0.614 Sensitivity Multilign(seed): 0.580 UNAFold: 0.590 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	3 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.755 Carnac(20): 0.733 Sensitivity Multilign(seed): 0.707 Carnac(20): 0.610 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	4 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.717 Multilign(seed): 0.629 Sensitivity McQFold: 0.690 Multilign(seed): 0.580 Positive Predictive Value McQFold: 0.758 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: 0.728 Multilign(seed): 0.629 Sensitivity RNAshapes: 0.700 Multilign(seed): 0.580 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	4 RNAfold vs Multilign(seed) Matthews Correlation Coefficient RNAfold: 0.728 Multilign(seed): 0.629 Sensitivity RNAfold: 0.700 Multilign(seed): 0.580 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: 0.721 Multilign(seed): 0.629 Sensitivity PknotsRG: 0.690 Multilign(seed): 0.580 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 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.649 Multilign(seed): 0.629 Sensitivity Pknots: 0.640 Multilign(seed): 0.580 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	2 Afold vs Multilign(seed) Matthews Correlation Coefficient Afold: 0.792 Multilign(seed): 0.534 Sensitivity Afold: 0.738 Multilign(seed): 0.476 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 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.629 ProbKnot: 0.575 Sensitivity Multilign(seed): 0.580 ProbKnot: 0.570 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	4 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.661 Multilign(seed): 0.629 Sensitivity Cylofold: 0.620 Multilign(seed): 0.580 Positive Predictive Value Cylofold: 0.721 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): 0.629 RNAsubopt: 0.610 Sensitivity Multilign(seed): 0.580 RNAsubopt: 0.590 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	4 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.629 Fold: 0.589 Sensitivity Multilign(seed): 0.580 Fold: 0.570 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	3 Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.755 RSpredict(20): 0.707 Sensitivity Multilign(seed): 0.707 RSpredict(20): 0.634 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	4 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.629 Vsfold4: 0.425 Sensitivity Multilign(seed): 0.580 Vsfold4: 0.410 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	4 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.629 Murlet(seed): 0.496 Sensitivity Multilign(seed): 0.580 Murlet(seed): 0.370 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	3 Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.624 Multilign(seed): 0.589 Sensitivity Alterna: 0.606 Multilign(seed): 0.549 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	3 Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.755 Mastr(20): 0.656 Sensitivity Multilign(seed): 0.707 Mastr(20): 0.585 Positive Predictive Value Multilign(seed): 0.817 Mastr(20): 0.750 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.629 Vsfold5: 0.327 Sensitivity Multilign(seed): 0.580 Vsfold5: 0.320 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 RDfolder Matthews Correlation Coefficient Multilign(seed): 0.629 RDfolder: 0.444 Sensitivity Multilign(seed): 0.580 RDfolder: 0.380 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): 0.589 MCFold: 0.586 Sensitivity Multilign(seed): 0.549 MCFold: 0.592 Positive Predictive Value Multilign(seed): 0.650 MCFold: 0.600 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): 0.629 RSpredict(seed): 0.376 Sensitivity Multilign(seed): 0.580 RSpredict(seed): 0.240 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 Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.629 Carnac(seed): 0.198 Sensitivity Multilign(seed): 0.580 Carnac(seed): 0.040 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): 0.458 NanoFolder: 0.447 Sensitivity Multilign(seed): 0.404 NanoFolder: 0.489 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	4 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.682 Multilign(seed): 0.629 Sensitivity CentroidHomfold‑LAST: 0.580 Multilign(seed): 0.580 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	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): 0.755 Multilign(20): 0.716 Sensitivity Multilign(seed): 0.707 Multilign(20): 0.695 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): 0.699 Multilign(seed): 0.458 Sensitivity PETfold_pre2.0(seed): 0.617 Multilign(seed): 0.404 Positive Predictive Value PETfold_pre2.0(seed): 0.806 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): 0.755 TurboFold(20): 0.753 Sensitivity Multilign(seed): 0.707 TurboFold(20): 0.695 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 RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.629 RNAwolf: 0.552 Sensitivity Multilign(seed): 0.580 RNAwolf: 0.530 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.596 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.656 Multilign(seed): 0.629 Sensitivity IPknot: 0.600 Multilign(seed): 0.580 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	? 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): 0.872 Multilign(seed): 0.731 Sensitivity PETfold_pre2.0(20): 0.828 Multilign(seed): 0.655 Positive Predictive Value PETfold_pre2.0(20): 0.923 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.629 PPfold(seed): 0.208 Sensitivity Multilign(seed): 0.580 PPfold(seed): 0.060 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	? ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.606 Multilign(seed): 0.458 Sensitivity ContextFold: 0.574 Multilign(seed): 0.404 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	? Multilign(seed) vs TurboFold(seed) Matthews Correlation Coefficient Multilign(seed): 0.629 TurboFold(seed): 0.614 Sensitivity Multilign(seed): 0.580 TurboFold(seed): 0.570 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	? Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.540 CRWrnafold: 0.513 Sensitivity Multilign(seed): 0.500 CRWrnafold: 0.513 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	? RNASampler(seed) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(seed): 0.616 Multilign(seed): 0.589 Sensitivity RNASampler(seed): 0.507 Multilign(seed): 0.549 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	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.458 RNASLOpt: 0.375 Sensitivity Multilign(seed): 0.404 RNASLOpt: 0.319 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	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.849 Multilign(seed): 0.755 Sensitivity PPfold(20): 0.793 Multilign(seed): 0.707 Positive Predictive Value PPfold(20): 0.915 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): 0.629 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.580 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)	6 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 Multilign(20): 0.581 Sensitivity CentroidAlifold(20): 0.636 Multilign(20): 0.576 Positive Predictive Value CentroidAlifold(20): 0.923 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 Multilign(20): 0.581 Sensitivity CentroidAlifold(seed): 0.674 Multilign(20): 0.576 Positive Predictive Value CentroidAlifold(seed): 0.978 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.658 Multilign(20): 0.581 Sensitivity RNAalifold(20): 0.591 Multilign(20): 0.576 Positive Predictive Value RNAalifold(20): 0.743 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.663 Multilign(20): 0.581 Sensitivity MXScarna(seed): 0.606 Multilign(20): 0.576 Positive Predictive Value MXScarna(seed): 0.734 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.633 Multilign(20): 0.581 Sensitivity CentroidFold: 0.614 Multilign(20): 0.576 Positive Predictive Value CentroidFold: 0.664 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.693 Multilign(20): 0.581 Sensitivity RNASampler(20): 0.606 Multilign(20): 0.576 Positive Predictive Value RNASampler(20): 0.800 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.606 Multilign(20): 0.581 Sensitivity MXScarna(20): 0.561 Multilign(20): 0.576 Positive Predictive Value MXScarna(20): 0.667 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.628 Multilign(20): 0.581 Sensitivity Contrafold: 0.621 Multilign(20): 0.576 Positive Predictive Value Contrafold: 0.646 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.636 Multilign(20): 0.581 Sensitivity Sfold: 0.598 Multilign(20): 0.576 Positive Predictive Value Sfold: 0.687 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 MaxExpect vs Multilign(20) Matthews Correlation Coefficient MaxExpect: 0.590 Multilign(20): 0.581 Sensitivity MaxExpect: 0.591 Multilign(20): 0.576 Positive Predictive Value MaxExpect: 0.600 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.689 Multilign(20): 0.581 Sensitivity HotKnots: 0.712 Multilign(20): 0.576 Positive Predictive Value HotKnots: 0.676 Multilign(20): 0.598 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): 0.701 Multilign(20): 0.581 Sensitivity RNAalifold(seed): 0.538 Multilign(20): 0.576 Positive Predictive Value RNAalifold(seed): 0.922 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.654 Multilign(20): 0.581 Sensitivity Murlet(20): 0.576 Multilign(20): 0.576 Positive Predictive Value Murlet(20): 0.752 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.605 Multilign(20): 0.581 Sensitivity UNAFold: 0.606 Multilign(20): 0.576 Positive Predictive Value UNAFold: 0.615 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Carnac(20) vs Multilign(20) Matthews Correlation Coefficient Carnac(20): 0.600 Multilign(20): 0.581 Sensitivity Carnac(20): 0.417 Multilign(20): 0.576 Positive Predictive Value Carnac(20): 0.873 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 McQFold vs Multilign(20) Matthews Correlation Coefficient McQFold: 0.685 Multilign(20): 0.581 Sensitivity McQFold: 0.705 Multilign(20): 0.576 Positive Predictive Value McQFold: 0.674 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.608 Multilign(20): 0.581 Sensitivity RNAshapes: 0.606 Multilign(20): 0.576 Positive Predictive Value RNAshapes: 0.620 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.603 Multilign(20): 0.581 Sensitivity RNAfold: 0.606 Multilign(20): 0.576 Positive Predictive Value RNAfold: 0.611 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.675 Multilign(20): 0.581 Sensitivity PknotsRG: 0.705 Multilign(20): 0.576 Positive Predictive Value PknotsRG: 0.655 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Pknots vs Multilign(20) Matthews Correlation Coefficient Pknots: 0.644 Multilign(20): 0.581 Sensitivity Pknots: 0.659 Multilign(20): 0.576 Positive Predictive Value Pknots: 0.640 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.577 Multilign(20): 0.503 Sensitivity Afold: 0.610 Multilign(20): 0.525 Positive Predictive Value Afold: 0.554 Multilign(20): 0.492 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.581 ProbKnot: 0.577 Sensitivity Multilign(20): 0.576 ProbKnot: 0.614 Positive Predictive Value Multilign(20): 0.598 ProbKnot: 0.555 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.756 Multilign(20): 0.678 Sensitivity Cylofold: 0.723 Multilign(20): 0.634 Positive Predictive Value Cylofold: 0.802 Multilign(20): 0.740 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.596 Multilign(20): 0.581 Sensitivity RNAsubopt: 0.606 Multilign(20): 0.576 Positive Predictive Value RNAsubopt: 0.597 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.581 Fold: 0.537 Sensitivity Multilign(20): 0.576 Fold: 0.545 Positive Predictive Value Multilign(20): 0.598 Fold: 0.541 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.581 RSpredict(20): 0.573 Sensitivity Multilign(20): 0.576 RSpredict(20): 0.530 Positive Predictive Value Multilign(20): 0.598 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.581 Vsfold4: 0.544 Sensitivity Multilign(20): 0.576 Vsfold4: 0.523 Positive Predictive Value Multilign(20): 0.598 Vsfold4: 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.621 Multilign(20): 0.581 Sensitivity Murlet(seed): 0.424 Multilign(20): 0.576 Positive Predictive Value Murlet(seed): 0.918 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	2 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.784 Alterna: 0.673 Sensitivity Multilign(20): 0.774 Alterna: 0.660 Positive Predictive Value Multilign(20): 0.804 Alterna: 0.700 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.581 Mastr(20): 0.570 Sensitivity Multilign(20): 0.576 Mastr(20): 0.424 Positive Predictive Value Multilign(20): 0.598 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.581 Vsfold5: 0.518 Sensitivity Multilign(20): 0.576 Vsfold5: 0.530 Positive Predictive Value Multilign(20): 0.598 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.678 RDfolder: 0.533 Sensitivity Multilign(20): 0.634 RDfolder: 0.446 Positive Predictive Value Multilign(20): 0.740 RDfolder: 0.658 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.580 MCFold: 0.498 Sensitivity Multilign(20): 0.583 MCFold: 0.534 Positive Predictive Value Multilign(20): 0.588 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.581 RSpredict(seed): 0.409 Sensitivity Multilign(20): 0.576 RSpredict(seed): 0.227 Positive Predictive Value Multilign(20): 0.598 RSpredict(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.581 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.576 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.598 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.456 NanoFolder: 0.285 Sensitivity Multilign(20): 0.469 NanoFolder: 0.359 Positive Predictive Value Multilign(20): 0.455 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Multilign(20): 0.581 Sensitivity CentroidHomfold‑LAST: 0.644 Multilign(20): 0.576 Positive Predictive Value CentroidHomfold‑LAST: 0.825 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 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): 0.755 Multilign(20): 0.716 Sensitivity Multilign(seed): 0.707 Multilign(20): 0.695 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): 0.751 Multilign(20): 0.446 Sensitivity PETfold_pre2.0(seed): 0.684 Multilign(20): 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Multilign(20): 0.461 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.653 Multilign(20): 0.581 Sensitivity TurboFold(20): 0.606 Multilign(20): 0.576 Positive Predictive Value TurboFold(20): 0.714 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.581 RNAwolf: 0.442 Sensitivity Multilign(20): 0.576 RNAwolf: 0.439 Positive Predictive Value Multilign(20): 0.598 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.623 Multilign(20): 0.581 Sensitivity IPknot: 0.591 Multilign(20): 0.576 Positive Predictive Value IPknot: 0.667 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 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): 0.619 Multilign(20): 0.446 Sensitivity PETfold_pre2.0(20): 0.570 Multilign(20): 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.682 Multilign(20): 0.461 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): 0.581 PPfold(seed): 0.036 Sensitivity Multilign(20): 0.576 PPfold(seed): 0.008 Positive Predictive Value Multilign(20): 0.598 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.567 Multilign(20): 0.446 Sensitivity ContextFold: 0.506 Multilign(20): 0.443 Positive Predictive Value ContextFold: 0.645 Multilign(20): 0.461 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 Multilign(20): 0.581 Sensitivity TurboFold(seed): 0.606 Multilign(20): 0.576 Positive Predictive Value TurboFold(seed): 0.678 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.592 Multilign(20): 0.510 Sensitivity CRWrnafold: 0.611 Multilign(20): 0.509 Positive Predictive Value CRWrnafold: 0.584 Multilign(20): 0.524 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.679 Multilign(20): 0.590 Sensitivity RNASampler(seed): 0.603 Multilign(20): 0.630 Positive Predictive Value RNASampler(seed): 0.772 Multilign(20): 0.561 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Multilign(20) Matthews Correlation Coefficient RNASLOpt: 0.459 Multilign(20): 0.446 Sensitivity RNASLOpt: 0.456 Multilign(20): 0.443 Positive Predictive Value RNASLOpt: 0.474 Multilign(20): 0.461 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.715 Multilign(20): 0.581 Sensitivity PPfold(20): 0.644 Multilign(20): 0.576 Positive Predictive Value PPfold(20): 0.802 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.581 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.576 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.598 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
PETfold_pre2.0(seed)	4 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 CentroidAlifold(20): 0.698 Sensitivity PETfold_pre2.0(seed): 0.684 CentroidAlifold(20): 0.557 Positive Predictive Value PETfold_pre2.0(seed): 0.831 CentroidAlifold(20): 0.880 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CentroidAlifold(seed): 0.686 Sensitivity PETfold_pre2.0(seed): 0.619 CentroidAlifold(seed): 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CentroidAlifold(seed): 0.979 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 RNAalifold(20): 0.532 Sensitivity PETfold_pre2.0(seed): 0.684 RNAalifold(20): 0.456 Positive Predictive Value PETfold_pre2.0(seed): 0.831 RNAalifold(20): 0.632 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 MXScarna(seed): 0.476 Sensitivity PETfold_pre2.0(seed): 0.619 MXScarna(seed): 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 MXScarna(seed): 0.563 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CentroidFold: 0.526 Sensitivity PETfold_pre2.0(seed): 0.619 CentroidFold: 0.495 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CentroidFold: 0.571 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 RNASampler(20): 0.582 Sensitivity PETfold_pre2.0(seed): 0.684 RNASampler(20): 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.831 RNASampler(20): 0.678 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 MXScarna(20): 0.477 Sensitivity PETfold_pre2.0(seed): 0.684 MXScarna(20): 0.430 Positive Predictive Value PETfold_pre2.0(seed): 0.831 MXScarna(20): 0.540 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Contrafold: 0.525 Sensitivity PETfold_pre2.0(seed): 0.619 Contrafold: 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Contrafold: 0.557 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Sfold: 0.499 Sensitivity PETfold_pre2.0(seed): 0.619 Sfold: 0.464 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Sfold: 0.549 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 MaxExpect: 0.384 Sensitivity PETfold_pre2.0(seed): 0.619 MaxExpect: 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 MaxExpect: 0.392 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 HotKnots: 0.613 Sensitivity PETfold_pre2.0(seed): 0.619 HotKnots: 0.649 Positive Predictive Value PETfold_pre2.0(seed): 0.789 HotKnots: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAalifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.619 RNAalifold(seed): 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAalifold(seed): 0.760 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 Murlet(20): 0.537 Sensitivity PETfold_pre2.0(seed): 0.684 Murlet(20): 0.456 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 UNAFold: 0.384 Sensitivity PETfold_pre2.0(seed): 0.619 UNAFold: 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 UNAFold: 0.392 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 Carnac(20): 0.416 Sensitivity PETfold_pre2.0(seed): 0.684 Carnac(20): 0.241 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 McQFold: 0.589 Sensitivity PETfold_pre2.0(seed): 0.619 McQFold: 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.789 McQFold: 0.571 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAshapes: 0.499 Sensitivity PETfold_pre2.0(seed): 0.619 RNAshapes: 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAshapes: 0.505 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAfold: 0.493 Sensitivity PETfold_pre2.0(seed): 0.619 RNAfold: 0.505 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 PknotsRG: 0.607 Sensitivity PETfold_pre2.0(seed): 0.619 PknotsRG: 0.649 Positive Predictive Value PETfold_pre2.0(seed): 0.789 PknotsRG: 0.578 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Pknots: 0.579 Sensitivity PETfold_pre2.0(seed): 0.619 Pknots: 0.608 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Pknots: 0.562 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.627 Afold: 0.469 Sensitivity PETfold_pre2.0(seed): 0.547 Afold: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.725 Afold: 0.443 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 ProbKnot: 0.392 Sensitivity PETfold_pre2.0(seed): 0.619 ProbKnot: 0.423 Positive Predictive Value PETfold_pre2.0(seed): 0.789 ProbKnot: 0.380 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: 0.701 PETfold_pre2.0(seed): 0.666 Sensitivity Cylofold: 0.675 PETfold_pre2.0(seed): 0.584 Positive Predictive Value Cylofold: 0.743 PETfold_pre2.0(seed): 0.776 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAsubopt: 0.386 Sensitivity PETfold_pre2.0(seed): 0.619 RNAsubopt: 0.402 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAsubopt: 0.386 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Fold: 0.318 Sensitivity PETfold_pre2.0(seed): 0.619 Fold: 0.330 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Fold: 0.323 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 RSpredict(20): 0.351 Sensitivity PETfold_pre2.0(seed): 0.684 RSpredict(20): 0.304 Positive Predictive Value PETfold_pre2.0(seed): 0.831 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Vsfold4: 0.462 Sensitivity PETfold_pre2.0(seed): 0.619 Vsfold4: 0.433 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Vsfold4: 0.506 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Murlet(seed): 0.495 Sensitivity PETfold_pre2.0(seed): 0.619 Murlet(seed): 0.340 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	1 Alterna vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Alterna: 0.471 PETfold_pre2.0(seed): 0.411 Sensitivity Alterna: 0.444 PETfold_pre2.0(seed): 0.333 Positive Predictive Value Alterna: 0.533 PETfold_pre2.0(seed): 0.545 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 Mastr(20): 0.386 Sensitivity PETfold_pre2.0(seed): 0.684 Mastr(20): 0.228 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Vsfold5: 0.446 Sensitivity PETfold_pre2.0(seed): 0.619 Vsfold5: 0.454 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Vsfold5: 0.454 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.666 RDfolder: 0.332 Sensitivity PETfold_pre2.0(seed): 0.584 RDfolder: 0.299 Positive Predictive Value PETfold_pre2.0(seed): 0.776 RDfolder: 0.404 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.625 MCFold: 0.388 Sensitivity PETfold_pre2.0(seed): 0.544 MCFold: 0.426 Positive Predictive Value PETfold_pre2.0(seed): 0.725 MCFold: 0.367 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RSpredict(seed): 0.203 Sensitivity PETfold_pre2.0(seed): 0.619 RSpredict(seed): 0.124 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RSpredict(seed): 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Carnac(seed): 0.202 Sensitivity PETfold_pre2.0(seed): 0.619 Carnac(seed): 0.041 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.709 NanoFolder: 0.336 Sensitivity PETfold_pre2.0(seed): 0.634 NanoFolder: 0.415 Positive Predictive Value PETfold_pre2.0(seed): 0.800 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CentroidHomfold‑LAST: 0.558 Sensitivity PETfold_pre2.0(seed): 0.619 CentroidHomfold‑LAST: 0.495 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CentroidHomfold‑LAST: 0.640 Number of pairs reference - predicted secondary structure: 5 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): 0.699 Multilign(seed): 0.458 Sensitivity PETfold_pre2.0(seed): 0.617 Multilign(seed): 0.404 Positive Predictive Value PETfold_pre2.0(seed): 0.806 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 Multilign(20): 0.446 Sensitivity PETfold_pre2.0(seed): 0.684 Multilign(20): 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.831 Multilign(20): 0.461 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 TurboFold(20): 0.554 Sensitivity PETfold_pre2.0(seed): 0.684 TurboFold(20): 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.831 TurboFold(20): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAwolf: 0.309 Sensitivity PETfold_pre2.0(seed): 0.619 RNAwolf: 0.309 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 IPknot: 0.484 Sensitivity PETfold_pre2.0(seed): 0.619 IPknot: 0.454 Positive Predictive Value PETfold_pre2.0(seed): 0.789 IPknot: 0.530 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): 0.751 PETfold_pre2.0(20): 0.619 Sensitivity PETfold_pre2.0(seed): 0.684 PETfold_pre2.0(20): 0.570 Positive Predictive Value PETfold_pre2.0(seed): 0.831 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 PPfold(seed): 0.194 Sensitivity PETfold_pre2.0(seed): 0.619 PPfold(seed): 0.072 Positive Predictive Value PETfold_pre2.0(seed): 0.789 PPfold(seed): 0.538 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): 0.695 ContextFold: 0.570 Sensitivity PETfold_pre2.0(seed): 0.619 ContextFold: 0.515 Positive Predictive Value PETfold_pre2.0(seed): 0.789 ContextFold: 0.641 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): 0.695 TurboFold(seed): 0.431 Sensitivity PETfold_pre2.0(seed): 0.619 TurboFold(seed): 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 TurboFold(seed): 0.465 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CRWrnafold: 0.478 Sensitivity PETfold_pre2.0(seed): 0.619 CRWrnafold: 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CRWrnafold: 0.485 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.630 RNASampler(seed): 0.232 Sensitivity PETfold_pre2.0(seed): 0.553 RNASampler(seed): 0.211 Positive Predictive Value PETfold_pre2.0(seed): 0.724 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 RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNASLOpt: 0.461 Sensitivity PETfold_pre2.0(seed): 0.619 RNASLOpt: 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 PPfold(20): 0.630 Sensitivity PETfold_pre2.0(seed): 0.684 PPfold(20): 0.557 Positive Predictive Value PETfold_pre2.0(seed): 0.831 PPfold(20): 0.721 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.619 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
TurboFold(20)	6 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 TurboFold(20): 0.653 Sensitivity CentroidAlifold(20): 0.636 TurboFold(20): 0.606 Positive Predictive Value CentroidAlifold(20): 0.923 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 TurboFold(20): 0.653 Sensitivity CentroidAlifold(seed): 0.674 TurboFold(20): 0.606 Positive Predictive Value CentroidAlifold(seed): 0.978 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(20) vs TurboFold(20) Matthews Correlation Coefficient RNAalifold(20): 0.658 TurboFold(20): 0.653 Sensitivity RNAalifold(20): 0.591 TurboFold(20): 0.606 Positive Predictive Value RNAalifold(20): 0.743 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 MXScarna(seed) vs TurboFold(20) Matthews Correlation Coefficient MXScarna(seed): 0.663 TurboFold(20): 0.653 Sensitivity MXScarna(seed): 0.606 TurboFold(20): 0.606 Positive Predictive Value MXScarna(seed): 0.734 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.653 CentroidFold: 0.633 Sensitivity TurboFold(20): 0.606 CentroidFold: 0.614 Positive Predictive Value TurboFold(20): 0.714 CentroidFold: 0.664 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.693 TurboFold(20): 0.653 Sensitivity RNASampler(20): 0.606 TurboFold(20): 0.606 Positive Predictive Value RNASampler(20): 0.800 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.653 MXScarna(20): 0.606 Sensitivity TurboFold(20): 0.606 MXScarna(20): 0.561 Positive Predictive Value TurboFold(20): 0.714 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.653 Contrafold: 0.628 Sensitivity TurboFold(20): 0.606 Contrafold: 0.621 Positive Predictive Value TurboFold(20): 0.714 Contrafold: 0.646 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.653 Sfold: 0.636 Sensitivity TurboFold(20): 0.606 Sfold: 0.598 Positive Predictive Value TurboFold(20): 0.714 Sfold: 0.687 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.653 MaxExpect: 0.590 Sensitivity TurboFold(20): 0.606 MaxExpect: 0.591 Positive Predictive Value TurboFold(20): 0.714 MaxExpect: 0.600 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.689 TurboFold(20): 0.653 Sensitivity HotKnots: 0.712 TurboFold(20): 0.606 Positive Predictive Value HotKnots: 0.676 TurboFold(20): 0.714 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): 0.701 TurboFold(20): 0.653 Sensitivity RNAalifold(seed): 0.538 TurboFold(20): 0.606 Positive Predictive Value RNAalifold(seed): 0.922 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 Murlet(20) vs TurboFold(20) Matthews Correlation Coefficient Murlet(20): 0.654 TurboFold(20): 0.653 Sensitivity Murlet(20): 0.576 TurboFold(20): 0.606 Positive Predictive Value Murlet(20): 0.752 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.653 UNAFold: 0.605 Sensitivity TurboFold(20): 0.606 UNAFold: 0.606 Positive Predictive Value TurboFold(20): 0.714 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.653 Carnac(20): 0.600 Sensitivity TurboFold(20): 0.606 Carnac(20): 0.417 Positive Predictive Value TurboFold(20): 0.714 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 McQFold vs TurboFold(20) Matthews Correlation Coefficient McQFold: 0.685 TurboFold(20): 0.653 Sensitivity McQFold: 0.705 TurboFold(20): 0.606 Positive Predictive Value McQFold: 0.674 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.653 RNAshapes: 0.608 Sensitivity TurboFold(20): 0.606 RNAshapes: 0.606 Positive Predictive Value TurboFold(20): 0.714 RNAshapes: 0.620 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.653 RNAfold: 0.603 Sensitivity TurboFold(20): 0.606 RNAfold: 0.606 Positive Predictive Value TurboFold(20): 0.714 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.675 TurboFold(20): 0.653 Sensitivity PknotsRG: 0.705 TurboFold(20): 0.606 Positive Predictive Value PknotsRG: 0.655 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.653 Pknots: 0.644 Sensitivity TurboFold(20): 0.606 Pknots: 0.659 Positive Predictive Value TurboFold(20): 0.714 Pknots: 0.640 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.604 Afold: 0.577 Sensitivity TurboFold(20): 0.576 Afold: 0.610 Positive Predictive Value TurboFold(20): 0.642 Afold: 0.554 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.653 ProbKnot: 0.577 Sensitivity TurboFold(20): 0.606 ProbKnot: 0.614 Positive Predictive Value TurboFold(20): 0.714 ProbKnot: 0.555 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.756 TurboFold(20): 0.750 Sensitivity Cylofold: 0.723 TurboFold(20): 0.670 Positive Predictive Value Cylofold: 0.802 TurboFold(20): 0.852 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.653 RNAsubopt: 0.596 Sensitivity TurboFold(20): 0.606 RNAsubopt: 0.606 Positive Predictive Value TurboFold(20): 0.714 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.653 Fold: 0.537 Sensitivity TurboFold(20): 0.606 Fold: 0.545 Positive Predictive Value TurboFold(20): 0.714 Fold: 0.541 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.653 RSpredict(20): 0.573 Sensitivity TurboFold(20): 0.606 RSpredict(20): 0.530 Positive Predictive Value TurboFold(20): 0.714 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.653 Vsfold4: 0.544 Sensitivity TurboFold(20): 0.606 Vsfold4: 0.523 Positive Predictive Value TurboFold(20): 0.714 Vsfold4: 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 Murlet(seed): 0.621 Sensitivity TurboFold(20): 0.606 Murlet(seed): 0.424 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	2 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.797 Alterna: 0.673 Sensitivity TurboFold(20): 0.755 Alterna: 0.660 Positive Predictive Value TurboFold(20): 0.851 Alterna: 0.700 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.653 Mastr(20): 0.570 Sensitivity TurboFold(20): 0.606 Mastr(20): 0.424 Positive Predictive Value TurboFold(20): 0.714 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.653 Vsfold5: 0.518 Sensitivity TurboFold(20): 0.606 Vsfold5: 0.530 Positive Predictive Value TurboFold(20): 0.714 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.750 RDfolder: 0.533 Sensitivity TurboFold(20): 0.670 RDfolder: 0.446 Positive Predictive Value TurboFold(20): 0.852 RDfolder: 0.658 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.650 MCFold: 0.498 Sensitivity TurboFold(20): 0.612 MCFold: 0.534 Positive Predictive Value TurboFold(20): 0.700 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 RSpredict(seed): 0.409 Sensitivity TurboFold(20): 0.606 RSpredict(seed): 0.227 Positive Predictive Value TurboFold(20): 0.714 RSpredict(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.606 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.714 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.513 NanoFolder: 0.285 Sensitivity TurboFold(20): 0.484 NanoFolder: 0.359 Positive Predictive Value TurboFold(20): 0.554 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 TurboFold(20): 0.653 Sensitivity CentroidHomfold‑LAST: 0.644 TurboFold(20): 0.606 Positive Predictive Value CentroidHomfold‑LAST: 0.825 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 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): 0.755 TurboFold(20): 0.753 Sensitivity Multilign(seed): 0.707 TurboFold(20): 0.695 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	6 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.653 Multilign(20): 0.581 Sensitivity TurboFold(20): 0.606 Multilign(20): 0.576 Positive Predictive Value TurboFold(20): 0.714 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 TurboFold(20): 0.554 Sensitivity PETfold_pre2.0(seed): 0.684 TurboFold(20): 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.831 TurboFold(20): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.653 RNAwolf: 0.442 Sensitivity TurboFold(20): 0.606 RNAwolf: 0.439 Positive Predictive Value TurboFold(20): 0.714 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.653 IPknot: 0.623 Sensitivity TurboFold(20): 0.606 IPknot: 0.591 Positive Predictive Value TurboFold(20): 0.714 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 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): 0.619 TurboFold(20): 0.554 Sensitivity PETfold_pre2.0(20): 0.570 TurboFold(20): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 TurboFold(20): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 PPfold(seed): 0.036 Sensitivity TurboFold(20): 0.606 PPfold(seed): 0.008 Positive Predictive Value TurboFold(20): 0.714 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.567 TurboFold(20): 0.554 Sensitivity ContextFold: 0.506 TurboFold(20): 0.506 Positive Predictive Value ContextFold: 0.645 TurboFold(20): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 TurboFold(seed): 0.636 Sensitivity TurboFold(20): 0.606 TurboFold(seed): 0.606 Positive Predictive Value TurboFold(20): 0.714 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.597 CRWrnafold: 0.592 Sensitivity TurboFold(20): 0.556 CRWrnafold: 0.611 Positive Predictive Value TurboFold(20): 0.652 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): 0.679 TurboFold(20): 0.621 Sensitivity RNASampler(seed): 0.603 TurboFold(20): 0.616 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	? TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.554 RNASLOpt: 0.459 Sensitivity TurboFold(20): 0.506 RNASLOpt: 0.456 Positive Predictive Value TurboFold(20): 0.615 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.715 TurboFold(20): 0.653 Sensitivity PPfold(20): 0.644 TurboFold(20): 0.606 Positive Predictive Value PPfold(20): 0.802 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.606 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.714 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
RNAwolf	6 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.764 RNAwolf: 0.442 Sensitivity CentroidAlifold(20): 0.636 RNAwolf: 0.439 Positive Predictive Value CentroidAlifold(20): 0.923 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 RNAwolf: 0.451 Sensitivity CentroidAlifold(seed): 0.593 RNAwolf: 0.447 Positive Predictive Value CentroidAlifold(seed): 0.978 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.658 RNAwolf: 0.442 Sensitivity RNAalifold(20): 0.591 RNAwolf: 0.439 Positive Predictive Value RNAalifold(20): 0.743 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.593 RNAwolf: 0.451 Sensitivity MXScarna(seed): 0.533 RNAwolf: 0.447 Positive Predictive Value MXScarna(seed): 0.672 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.632 RNAwolf: 0.436 Sensitivity CentroidFold: 0.596 RNAwolf: 0.437 Positive Predictive Value CentroidFold: 0.681 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.693 RNAwolf: 0.442 Sensitivity RNASampler(20): 0.606 RNAwolf: 0.439 Positive Predictive Value RNASampler(20): 0.800 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.606 RNAwolf: 0.442 Sensitivity MXScarna(20): 0.561 RNAwolf: 0.439 Positive Predictive Value MXScarna(20): 0.667 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.629 RNAwolf: 0.436 Sensitivity Contrafold: 0.612 RNAwolf: 0.437 Positive Predictive Value Contrafold: 0.659 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.595 RNAwolf: 0.436 Sensitivity Sfold: 0.574 RNAwolf: 0.437 Positive Predictive Value Sfold: 0.629 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.522 RNAwolf: 0.436 Sensitivity MaxExpect: 0.519 RNAwolf: 0.437 Positive Predictive Value MaxExpect: 0.540 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.651 RNAwolf: 0.436 Sensitivity HotKnots: 0.678 RNAwolf: 0.437 Positive Predictive Value HotKnots: 0.636 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNAwolf: 0.451 Sensitivity RNAalifold(seed): 0.473 RNAwolf: 0.447 Positive Predictive Value RNAalifold(seed): 0.798 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.654 RNAwolf: 0.442 Sensitivity Murlet(20): 0.576 RNAwolf: 0.439 Positive Predictive Value Murlet(20): 0.752 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.531 RNAwolf: 0.436 Sensitivity UNAFold: 0.541 RNAwolf: 0.437 Positive Predictive Value UNAFold: 0.535 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.600 RNAwolf: 0.442 Sensitivity Carnac(20): 0.417 RNAwolf: 0.439 Positive Predictive Value Carnac(20): 0.873 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.687 RNAwolf: 0.436 Sensitivity McQFold: 0.689 RNAwolf: 0.437 Positive Predictive Value McQFold: 0.696 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.572 RNAwolf: 0.436 Sensitivity RNAshapes: 0.574 RNAwolf: 0.437 Positive Predictive Value RNAshapes: 0.583 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.569 RNAwolf: 0.436 Sensitivity RNAfold: 0.574 RNAwolf: 0.437 Positive Predictive Value RNAfold: 0.577 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.623 RNAwolf: 0.436 Sensitivity PknotsRG: 0.645 RNAwolf: 0.437 Positive Predictive Value PknotsRG: 0.615 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.605 RNAwolf: 0.436 Sensitivity Pknots: 0.623 RNAwolf: 0.437 Positive Predictive Value Pknots: 0.600 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.567 RNAwolf: 0.491 Sensitivity Afold: 0.596 RNAwolf: 0.495 Positive Predictive Value Afold: 0.551 RNAwolf: 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.527 RNAwolf: 0.436 Sensitivity ProbKnot: 0.552 RNAwolf: 0.437 Positive Predictive Value ProbKnot: 0.518 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.664 RNAwolf: 0.484 Sensitivity Cylofold: 0.650 RNAwolf: 0.472 Positive Predictive Value Cylofold: 0.693 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.513 RNAwolf: 0.436 Sensitivity RNAsubopt: 0.525 RNAwolf: 0.437 Positive Predictive Value RNAsubopt: 0.516 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.468 RNAwolf: 0.436 Sensitivity Fold: 0.475 RNAwolf: 0.437 Positive Predictive Value Fold: 0.478 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.573 RNAwolf: 0.442 Sensitivity RSpredict(20): 0.530 RNAwolf: 0.439 Positive Predictive Value RSpredict(20): 0.631 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.478 RNAwolf: 0.436 Sensitivity Vsfold4: 0.464 RNAwolf: 0.437 Positive Predictive Value Vsfold4: 0.509 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.531 RNAwolf: 0.451 Sensitivity Murlet(seed): 0.373 RNAwolf: 0.447 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.583 Alterna: 0.568 Sensitivity RNAwolf: 0.585 Alterna: 0.549 Positive Predictive Value RNAwolf: 0.600 Alterna: 0.608 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.570 RNAwolf: 0.442 Sensitivity Mastr(20): 0.424 RNAwolf: 0.439 Positive Predictive Value Mastr(20): 0.778 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 Vsfold5 vs RNAwolf Matthews Correlation Coefficient Vsfold5: 0.461 RNAwolf: 0.436 Sensitivity Vsfold5: 0.470 RNAwolf: 0.437 Positive Predictive Value Vsfold5: 0.470 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.481 RDfolder: 0.423 Sensitivity RNAwolf: 0.468 RDfolder: 0.355 Positive Predictive Value RNAwolf: 0.520 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.500 RNAwolf: 0.466 Sensitivity MCFold: 0.532 RNAwolf: 0.474 Positive Predictive Value MCFold: 0.485 RNAwolf: 0.474 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.451 RSpredict(seed): 0.331 Sensitivity RNAwolf: 0.447 RSpredict(seed): 0.200 Positive Predictive Value RNAwolf: 0.472 RSpredict(seed): 0.566 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.451 Carnac(seed): 0.162 Sensitivity RNAwolf: 0.447 Carnac(seed): 0.027 Positive Predictive Value RNAwolf: 0.472 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs RNAwolf Matthews Correlation Coefficient NanoFolder: 0.427 RNAwolf: 0.332 Sensitivity NanoFolder: 0.519 RNAwolf: 0.337 Positive Predictive Value NanoFolder: 0.365 RNAwolf: 0.343 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 RNAwolf: 0.436 Sensitivity CentroidHomfold‑LAST: 0.552 RNAwolf: 0.437 Positive Predictive Value CentroidHomfold‑LAST: 0.743 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	4 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.629 RNAwolf: 0.552 Sensitivity Multilign(seed): 0.580 RNAwolf: 0.530 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.596 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.581 RNAwolf: 0.442 Sensitivity Multilign(20): 0.576 RNAwolf: 0.439 Positive Predictive Value Multilign(20): 0.598 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAwolf: 0.309 Sensitivity PETfold_pre2.0(seed): 0.619 RNAwolf: 0.309 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.653 RNAwolf: 0.442 Sensitivity TurboFold(20): 0.606 RNAwolf: 0.439 Positive Predictive Value TurboFold(20): 0.714 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0		? IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.612 RNAwolf: 0.436 Sensitivity IPknot: 0.579 RNAwolf: 0.437 Positive Predictive Value IPknot: 0.658 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 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): 0.619 RNAwolf: 0.263 Sensitivity PETfold_pre2.0(20): 0.570 RNAwolf: 0.266 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAwolf: 0.276 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.451 PPfold(seed): 0.155 Sensitivity RNAwolf: 0.447 PPfold(seed): 0.047 Positive Predictive Value RNAwolf: 0.472 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.662 RNAwolf: 0.325 Sensitivity ContextFold: 0.608 RNAwolf: 0.331 Positive Predictive Value ContextFold: 0.731 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.560 RNAwolf: 0.451 Sensitivity TurboFold(seed): 0.533 RNAwolf: 0.447 Positive Predictive Value TurboFold(seed): 0.602 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.502 RNAwolf: 0.372 Sensitivity CRWrnafold: 0.516 RNAwolf: 0.377 Positive Predictive Value CRWrnafold: 0.503 RNAwolf: 0.385 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): 0.559 RNAwolf: 0.521 Sensitivity RNASampler(seed): 0.484 RNAwolf: 0.538 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.516 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.449 RNAwolf: 0.325 Sensitivity RNASLOpt: 0.438 RNAwolf: 0.331 Positive Predictive Value RNASLOpt: 0.475 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.715 RNAwolf: 0.442 Sensitivity PPfold(20): 0.644 RNAwolf: 0.439 Positive Predictive Value PPfold(20): 0.802 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.451 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.447 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.472 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
IPknot	6 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.764 IPknot: 0.623 Sensitivity CentroidAlifold(20): 0.636 IPknot: 0.591 Positive Predictive Value CentroidAlifold(20): 0.923 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 IPknot: 0.601 Sensitivity CentroidAlifold(seed): 0.593 IPknot: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.978 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.658 IPknot: 0.623 Sensitivity RNAalifold(20): 0.591 IPknot: 0.591 Positive Predictive Value RNAalifold(20): 0.743 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.601 MXScarna(seed): 0.593 Sensitivity IPknot: 0.560 MXScarna(seed): 0.533 Positive Predictive Value IPknot: 0.656 MXScarna(seed): 0.672 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 CentroidFold vs IPknot Matthews Correlation Coefficient CentroidFold: 0.632 IPknot: 0.612 Sensitivity CentroidFold: 0.596 IPknot: 0.579 Positive Predictive Value CentroidFold: 0.681 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.693 IPknot: 0.623 Sensitivity RNASampler(20): 0.606 IPknot: 0.591 Positive Predictive Value RNASampler(20): 0.800 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.623 MXScarna(20): 0.606 Sensitivity IPknot: 0.591 MXScarna(20): 0.561 Positive Predictive Value IPknot: 0.667 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 Contrafold vs IPknot Matthews Correlation Coefficient Contrafold: 0.629 IPknot: 0.612 Sensitivity Contrafold: 0.612 IPknot: 0.579 Positive Predictive Value Contrafold: 0.659 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.612 Sfold: 0.595 Sensitivity IPknot: 0.579 Sfold: 0.574 Positive Predictive Value IPknot: 0.658 Sfold: 0.629 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.612 MaxExpect: 0.522 Sensitivity IPknot: 0.579 MaxExpect: 0.519 Positive Predictive Value IPknot: 0.658 MaxExpect: 0.540 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs IPknot Matthews Correlation Coefficient HotKnots: 0.651 IPknot: 0.612 Sensitivity HotKnots: 0.678 IPknot: 0.579 Positive Predictive Value HotKnots: 0.636 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.610 IPknot: 0.601 Sensitivity RNAalifold(seed): 0.473 IPknot: 0.560 Positive Predictive Value RNAalifold(seed): 0.798 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.654 IPknot: 0.623 Sensitivity Murlet(20): 0.576 IPknot: 0.591 Positive Predictive Value Murlet(20): 0.752 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.612 UNAFold: 0.531 Sensitivity IPknot: 0.579 UNAFold: 0.541 Positive Predictive Value IPknot: 0.658 UNAFold: 0.535 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.623 Carnac(20): 0.600 Sensitivity IPknot: 0.591 Carnac(20): 0.417 Positive Predictive Value IPknot: 0.667 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 McQFold vs IPknot Matthews Correlation Coefficient McQFold: 0.687 IPknot: 0.612 Sensitivity McQFold: 0.689 IPknot: 0.579 Positive Predictive Value McQFold: 0.696 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.612 RNAshapes: 0.572 Sensitivity IPknot: 0.579 RNAshapes: 0.574 Positive Predictive Value IPknot: 0.658 RNAshapes: 0.583 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.612 RNAfold: 0.569 Sensitivity IPknot: 0.579 RNAfold: 0.574 Positive Predictive Value IPknot: 0.658 RNAfold: 0.577 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs IPknot Matthews Correlation Coefficient PknotsRG: 0.623 IPknot: 0.612 Sensitivity PknotsRG: 0.645 IPknot: 0.579 Positive Predictive Value PknotsRG: 0.615 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.612 Pknots: 0.605 Sensitivity IPknot: 0.579 Pknots: 0.623 Positive Predictive Value IPknot: 0.658 Pknots: 0.600 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.664 Afold: 0.567 Sensitivity IPknot: 0.626 Afold: 0.596 Positive Predictive Value IPknot: 0.713 Afold: 0.551 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.612 ProbKnot: 0.527 Sensitivity IPknot: 0.579 ProbKnot: 0.552 Positive Predictive Value IPknot: 0.658 ProbKnot: 0.518 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.666 Cylofold: 0.664 Sensitivity IPknot: 0.620 Cylofold: 0.650 Positive Predictive Value IPknot: 0.732 Cylofold: 0.693 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.612 RNAsubopt: 0.513 Sensitivity IPknot: 0.579 RNAsubopt: 0.525 Positive Predictive Value IPknot: 0.658 RNAsubopt: 0.516 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.612 Fold: 0.468 Sensitivity IPknot: 0.579 Fold: 0.475 Positive Predictive Value IPknot: 0.658 Fold: 0.478 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	6 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.623 RSpredict(20): 0.573 Sensitivity IPknot: 0.591 RSpredict(20): 0.530 Positive Predictive Value IPknot: 0.667 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.612 Vsfold4: 0.478 Sensitivity IPknot: 0.579 Vsfold4: 0.464 Positive Predictive Value IPknot: 0.658 Vsfold4: 0.509 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.601 Murlet(seed): 0.531 Sensitivity IPknot: 0.560 Murlet(seed): 0.373 Positive Predictive Value IPknot: 0.656 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.640 Alterna: 0.568 Sensitivity IPknot: 0.585 Alterna: 0.549 Positive Predictive Value IPknot: 0.716 Alterna: 0.608 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.623 Mastr(20): 0.570 Sensitivity IPknot: 0.591 Mastr(20): 0.424 Positive Predictive Value IPknot: 0.667 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.612 Vsfold5: 0.461 Sensitivity IPknot: 0.579 Vsfold5: 0.470 Positive Predictive Value IPknot: 0.658 Vsfold5: 0.470 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.625 RDfolder: 0.423 Sensitivity IPknot: 0.574 RDfolder: 0.355 Positive Predictive Value IPknot: 0.698 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.633 MCFold: 0.500 Sensitivity IPknot: 0.597 MCFold: 0.532 Positive Predictive Value IPknot: 0.681 MCFold: 0.485 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.601 RSpredict(seed): 0.331 Sensitivity IPknot: 0.560 RSpredict(seed): 0.200 Positive Predictive Value IPknot: 0.656 RSpredict(seed): 0.566 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.601 Carnac(seed): 0.162 Sensitivity IPknot: 0.560 Carnac(seed): 0.027 Positive Predictive Value IPknot: 0.656 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.530 NanoFolder: 0.427 Sensitivity IPknot: 0.510 NanoFolder: 0.519 Positive Predictive Value IPknot: 0.564 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.635 IPknot: 0.612 Sensitivity CentroidHomfold‑LAST: 0.552 IPknot: 0.579 Positive Predictive Value CentroidHomfold‑LAST: 0.743 IPknot: 0.658 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	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	4 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.656 Multilign(seed): 0.629 Sensitivity IPknot: 0.600 Multilign(seed): 0.580 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	6 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.623 Multilign(20): 0.581 Sensitivity IPknot: 0.591 Multilign(20): 0.576 Positive Predictive Value IPknot: 0.667 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 IPknot: 0.484 Sensitivity PETfold_pre2.0(seed): 0.619 IPknot: 0.454 Positive Predictive Value PETfold_pre2.0(seed): 0.789 IPknot: 0.530 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.653 IPknot: 0.623 Sensitivity TurboFold(20): 0.606 IPknot: 0.591 Positive Predictive Value TurboFold(20): 0.714 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.612 RNAwolf: 0.436 Sensitivity IPknot: 0.579 RNAwolf: 0.437 Positive Predictive Value IPknot: 0.658 RNAwolf: 0.452 Number of pairs reference - predicted secondary structure: 9 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): 0.619 IPknot: 0.498 Sensitivity PETfold_pre2.0(20): 0.570 IPknot: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 IPknot: 0.528 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.601 PPfold(seed): 0.155 Sensitivity IPknot: 0.560 PPfold(seed): 0.047 Positive Predictive Value IPknot: 0.656 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.662 IPknot: 0.531 Sensitivity ContextFold: 0.608 IPknot: 0.508 Positive Predictive Value ContextFold: 0.731 IPknot: 0.569 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.601 TurboFold(seed): 0.560 Sensitivity IPknot: 0.560 TurboFold(seed): 0.533 Positive Predictive Value IPknot: 0.656 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.568 CRWrnafold: 0.502 Sensitivity IPknot: 0.541 CRWrnafold: 0.516 Positive Predictive Value IPknot: 0.610 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.597 RNASampler(seed): 0.559 Sensitivity IPknot: 0.560 RNASampler(seed): 0.484 Positive Predictive Value IPknot: 0.646 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.531 RNASLOpt: 0.449 Sensitivity IPknot: 0.508 RNASLOpt: 0.438 Positive Predictive Value IPknot: 0.569 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.715 IPknot: 0.623 Sensitivity PPfold(20): 0.644 IPknot: 0.591 Positive Predictive Value PPfold(20): 0.802 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.601 Mastr(seed): 0.000 Sensitivity IPknot: 0.560 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.656 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
CMfinder(20)	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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	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 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 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	? 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	? 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	? 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	? 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	? 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	? 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	? 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)	4 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.698 PETfold_pre2.0(20): 0.619 Sensitivity CentroidAlifold(20): 0.557 PETfold_pre2.0(20): 0.570 Positive Predictive Value CentroidAlifold(20): 0.880 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.761 PETfold_pre2.0(20): 0.619 Sensitivity CentroidAlifold(seed): 0.595 PETfold_pre2.0(20): 0.570 Positive Predictive Value CentroidAlifold(seed): 0.979 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNAalifold(20): 0.532 Sensitivity PETfold_pre2.0(20): 0.570 RNAalifold(20): 0.456 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAalifold(20): 0.632 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 MXScarna(seed): 0.572 Sensitivity PETfold_pre2.0(20): 0.570 MXScarna(seed): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 MXScarna(seed): 0.656 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 CentroidFold: 0.531 Sensitivity PETfold_pre2.0(20): 0.570 CentroidFold: 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.682 CentroidFold: 0.554 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNASampler(20): 0.582 Sensitivity PETfold_pre2.0(20): 0.570 RNASampler(20): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNASampler(20): 0.678 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 MXScarna(20): 0.477 Sensitivity PETfold_pre2.0(20): 0.570 MXScarna(20): 0.430 Positive Predictive Value PETfold_pre2.0(20): 0.682 MXScarna(20): 0.540 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Contrafold: 0.537 Sensitivity PETfold_pre2.0(20): 0.570 Contrafold: 0.532 Positive Predictive Value PETfold_pre2.0(20): 0.682 Contrafold: 0.553 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Sfold: 0.506 Sensitivity PETfold_pre2.0(20): 0.570 Sfold: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 Sfold: 0.543 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 MaxExpect: 0.466 Sensitivity PETfold_pre2.0(20): 0.570 MaxExpect: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 MaxExpect: 0.463 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 HotKnots: 0.609 Sensitivity PETfold_pre2.0(20): 0.570 HotKnots: 0.658 Positive Predictive Value PETfold_pre2.0(20): 0.682 HotKnots: 0.571 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.691 PETfold_pre2.0(20): 0.619 Sensitivity RNAalifold(seed): 0.481 PETfold_pre2.0(20): 0.570 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Murlet(20): 0.537 Sensitivity PETfold_pre2.0(20): 0.570 Murlet(20): 0.456 Positive Predictive Value PETfold_pre2.0(20): 0.682 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 UNAFold: 0.466 Sensitivity PETfold_pre2.0(20): 0.570 UNAFold: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 UNAFold: 0.463 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Carnac(20): 0.416 Sensitivity PETfold_pre2.0(20): 0.570 Carnac(20): 0.241 Positive Predictive Value PETfold_pre2.0(20): 0.682 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 McQFold: 0.579 Sensitivity PETfold_pre2.0(20): 0.570 McQFold: 0.620 Positive Predictive Value PETfold_pre2.0(20): 0.682 McQFold: 0.551 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNAshapes: 0.469 Sensitivity PETfold_pre2.0(20): 0.570 RNAshapes: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAshapes: 0.469 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNAfold: 0.463 Sensitivity PETfold_pre2.0(20): 0.570 RNAfold: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAfold: 0.458 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 PknotsRG: 0.598 Sensitivity PETfold_pre2.0(20): 0.570 PknotsRG: 0.658 Positive Predictive Value PETfold_pre2.0(20): 0.682 PknotsRG: 0.553 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Pknots: 0.525 Sensitivity PETfold_pre2.0(20): 0.570 Pknots: 0.557 Positive Predictive Value PETfold_pre2.0(20): 0.682 Pknots: 0.506 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.404 Afold: 0.398 Sensitivity PETfold_pre2.0(20): 0.371 Afold: 0.457 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.356 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 ProbKnot: 0.472 Sensitivity PETfold_pre2.0(20): 0.570 ProbKnot: 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.682 ProbKnot: 0.441 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.763 Cylofold: 0.720 Sensitivity PETfold_pre2.0(20): 0.678 Cylofold: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.870 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNAsubopt: 0.467 Sensitivity PETfold_pre2.0(20): 0.570 RNAsubopt: 0.494 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAsubopt: 0.453 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Fold: 0.386 Sensitivity PETfold_pre2.0(20): 0.570 Fold: 0.405 Positive Predictive Value PETfold_pre2.0(20): 0.682 Fold: 0.381 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RSpredict(20): 0.351 Sensitivity PETfold_pre2.0(20): 0.570 RSpredict(20): 0.304 Positive Predictive Value PETfold_pre2.0(20): 0.682 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Vsfold4: 0.560 Sensitivity PETfold_pre2.0(20): 0.570 Vsfold4: 0.532 Positive Predictive Value PETfold_pre2.0(20): 0.682 Vsfold4: 0.600 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Murlet(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Murlet(seed): 0.644 PETfold_pre2.0(20): 0.619 Sensitivity Murlet(seed): 0.418 PETfold_pre2.0(20): 0.570 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 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	4 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Mastr(20): 0.386 Sensitivity PETfold_pre2.0(20): 0.570 Mastr(20): 0.228 Positive Predictive Value PETfold_pre2.0(20): 0.682 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Vsfold5: 0.535 Sensitivity PETfold_pre2.0(20): 0.570 Vsfold5: 0.557 Positive Predictive Value PETfold_pre2.0(20): 0.682 Vsfold5: 0.524 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.763 RDfolder: 0.445 Sensitivity PETfold_pre2.0(20): 0.678 RDfolder: 0.390 Positive Predictive Value PETfold_pre2.0(20): 0.870 RDfolder: 0.535 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.465 MCFold: 0.371 Sensitivity PETfold_pre2.0(20): 0.420 MCFold: 0.420 Positive Predictive Value PETfold_pre2.0(20): 0.525 MCFold: 0.339 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RSpredict(seed): 0.291 Sensitivity PETfold_pre2.0(20): 0.570 RSpredict(seed): 0.152 Positive Predictive Value PETfold_pre2.0(20): 0.682 RSpredict(seed): 0.571 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.570 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.682 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.609 NanoFolder: 0.285 Sensitivity PETfold_pre2.0(20): 0.578 NanoFolder: 0.359 Positive Predictive Value PETfold_pre2.0(20): 0.649 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	4 CentroidHomfold‑LAST vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.672 PETfold_pre2.0(20): 0.619 Sensitivity CentroidHomfold‑LAST: 0.608 PETfold_pre2.0(20): 0.570 Positive Predictive Value CentroidHomfold‑LAST: 0.750 PETfold_pre2.0(20): 0.682 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): 0.872 Multilign(seed): 0.731 Sensitivity PETfold_pre2.0(20): 0.828 Multilign(seed): 0.655 Positive Predictive Value PETfold_pre2.0(20): 0.923 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Multilign(20): 0.446 Sensitivity PETfold_pre2.0(20): 0.570 Multilign(20): 0.443 Positive Predictive Value PETfold_pre2.0(20): 0.682 Multilign(20): 0.461 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 PETfold_pre2.0(20): 0.619 Sensitivity PETfold_pre2.0(seed): 0.684 PETfold_pre2.0(20): 0.570 Positive Predictive Value PETfold_pre2.0(seed): 0.831 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 TurboFold(20): 0.554 Sensitivity PETfold_pre2.0(20): 0.570 TurboFold(20): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 TurboFold(20): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNAwolf: 0.263 Sensitivity PETfold_pre2.0(20): 0.570 RNAwolf: 0.266 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNAwolf: 0.276 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 IPknot: 0.498 Sensitivity PETfold_pre2.0(20): 0.570 IPknot: 0.481 Positive Predictive Value PETfold_pre2.0(20): 0.682 IPknot: 0.528 Number of pairs reference - predicted secondary structure: 4 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 PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 PPfold(seed): 0.048 Sensitivity PETfold_pre2.0(20): 0.570 PPfold(seed): 0.013 Positive Predictive Value PETfold_pre2.0(20): 0.682 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 ContextFold: 0.567 Sensitivity PETfold_pre2.0(20): 0.570 ContextFold: 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 TurboFold(seed): 0.529 Sensitivity PETfold_pre2.0(20): 0.570 TurboFold(seed): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 CRWrnafold: 0.579 Sensitivity PETfold_pre2.0(20): 0.570 CRWrnafold: 0.595 Positive Predictive Value PETfold_pre2.0(20): 0.682 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.397 PETfold_pre2.0(20): 0.247 Sensitivity RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 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 RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNASLOpt: 0.459 Sensitivity PETfold_pre2.0(20): 0.570 RNASLOpt: 0.456 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(20): 0.630 PETfold_pre2.0(20): 0.619 Sensitivity PPfold(20): 0.557 PETfold_pre2.0(20): 0.570 Positive Predictive Value PPfold(20): 0.721 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.570 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.682 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0
PPfold(seed)	6 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 PPfold(seed): 0.036 Sensitivity CentroidAlifold(20): 0.636 PPfold(seed): 0.008 Positive Predictive Value CentroidAlifold(20): 0.923 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 PPfold(seed): 0.155 Sensitivity CentroidAlifold(seed): 0.593 PPfold(seed): 0.047 Positive Predictive Value CentroidAlifold(seed): 0.978 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.658 PPfold(seed): 0.036 Sensitivity RNAalifold(20): 0.591 PPfold(seed): 0.008 Positive Predictive Value RNAalifold(20): 0.743 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.593 PPfold(seed): 0.155 Sensitivity MXScarna(seed): 0.533 PPfold(seed): 0.047 Positive Predictive Value MXScarna(seed): 0.672 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.620 PPfold(seed): 0.155 Sensitivity CentroidFold: 0.587 PPfold(seed): 0.047 Positive Predictive Value CentroidFold: 0.667 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.693 PPfold(seed): 0.036 Sensitivity RNASampler(20): 0.606 PPfold(seed): 0.008 Positive Predictive Value RNASampler(20): 0.800 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.606 PPfold(seed): 0.036 Sensitivity MXScarna(20): 0.561 PPfold(seed): 0.008 Positive Predictive Value MXScarna(20): 0.667 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.611 PPfold(seed): 0.155 Sensitivity Contrafold: 0.593 PPfold(seed): 0.047 Positive Predictive Value Contrafold: 0.640 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.618 PPfold(seed): 0.155 Sensitivity Sfold: 0.573 PPfold(seed): 0.047 Positive Predictive Value Sfold: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.522 PPfold(seed): 0.155 Sensitivity MaxExpect: 0.520 PPfold(seed): 0.047 Positive Predictive Value MaxExpect: 0.538 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.684 PPfold(seed): 0.155 Sensitivity HotKnots: 0.700 PPfold(seed): 0.047 Positive Predictive Value HotKnots: 0.677 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 PPfold(seed): 0.155 Sensitivity RNAalifold(seed): 0.473 PPfold(seed): 0.047 Positive Predictive Value RNAalifold(seed): 0.798 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.654 PPfold(seed): 0.036 Sensitivity Murlet(20): 0.576 PPfold(seed): 0.008 Positive Predictive Value Murlet(20): 0.752 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.536 PPfold(seed): 0.155 Sensitivity UNAFold: 0.533 PPfold(seed): 0.047 Positive Predictive Value UNAFold: 0.552 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.600 PPfold(seed): 0.036 Sensitivity Carnac(20): 0.417 PPfold(seed): 0.008 Positive Predictive Value Carnac(20): 0.873 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.679 PPfold(seed): 0.155 Sensitivity McQFold: 0.693 PPfold(seed): 0.047 Positive Predictive Value McQFold: 0.675 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.611 PPfold(seed): 0.155 Sensitivity RNAshapes: 0.607 PPfold(seed): 0.047 Positive Predictive Value RNAshapes: 0.628 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.607 PPfold(seed): 0.155 Sensitivity RNAfold: 0.607 PPfold(seed): 0.047 Positive Predictive Value RNAfold: 0.619 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.673 PPfold(seed): 0.155 Sensitivity PknotsRG: 0.693 PPfold(seed): 0.047 Positive Predictive Value PknotsRG: 0.662 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.666 PPfold(seed): 0.155 Sensitivity Pknots: 0.680 PPfold(seed): 0.047 Positive Predictive Value Pknots: 0.662 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.590 PPfold(seed): 0.218 Sensitivity Afold: 0.610 PPfold(seed): 0.091 Positive Predictive Value Afold: 0.580 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.514 PPfold(seed): 0.155 Sensitivity ProbKnot: 0.540 PPfold(seed): 0.047 Positive Predictive Value ProbKnot: 0.503 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.740 PPfold(seed): 0.182 Sensitivity Cylofold: 0.708 PPfold(seed): 0.046 Positive Predictive Value Cylofold: 0.786 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.528 PPfold(seed): 0.155 Sensitivity RNAsubopt: 0.533 PPfold(seed): 0.047 Positive Predictive Value RNAsubopt: 0.537 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.475 PPfold(seed): 0.155 Sensitivity Fold: 0.480 PPfold(seed): 0.047 Positive Predictive Value Fold: 0.486 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.573 PPfold(seed): 0.036 Sensitivity RSpredict(20): 0.530 PPfold(seed): 0.008 Positive Predictive Value RSpredict(20): 0.631 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.483 PPfold(seed): 0.155 Sensitivity Vsfold4: 0.460 PPfold(seed): 0.047 Positive Predictive Value Vsfold4: 0.523 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.531 PPfold(seed): 0.155 Sensitivity Murlet(seed): 0.373 PPfold(seed): 0.047 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	3 Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.624 PPfold(seed): 0.247 Sensitivity Alterna: 0.606 PPfold(seed): 0.085 Positive Predictive Value Alterna: 0.662 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.570 PPfold(seed): 0.036 Sensitivity Mastr(20): 0.424 PPfold(seed): 0.008 Positive Predictive Value Mastr(20): 0.778 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.462 PPfold(seed): 0.155 Sensitivity Vsfold5: 0.467 PPfold(seed): 0.047 Positive Predictive Value Vsfold5: 0.473 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.451 PPfold(seed): 0.182 Sensitivity RDfolder: 0.385 PPfold(seed): 0.046 Positive Predictive Value RDfolder: 0.556 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.491 PPfold(seed): 0.173 Sensitivity MCFold: 0.521 PPfold(seed): 0.058 Positive Predictive Value MCFold: 0.477 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.331 PPfold(seed): 0.155 Sensitivity RSpredict(seed): 0.200 PPfold(seed): 0.047 Positive Predictive Value RSpredict(seed): 0.566 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.162 PPfold(seed): 0.155 Sensitivity Carnac(seed): 0.027 PPfold(seed): 0.047 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.336 PPfold(seed): 0.211 Sensitivity NanoFolder: 0.415 PPfold(seed): 0.085 Positive Predictive Value NanoFolder: 0.288 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 PPfold(seed): 0.155 Sensitivity CentroidHomfold‑LAST: 0.567 PPfold(seed): 0.047 Positive Predictive Value CentroidHomfold‑LAST: 0.746 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	4 Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.629 PPfold(seed): 0.208 Sensitivity Multilign(seed): 0.580 PPfold(seed): 0.060 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	6 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.581 PPfold(seed): 0.036 Sensitivity Multilign(20): 0.576 PPfold(seed): 0.008 Positive Predictive Value Multilign(20): 0.598 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 PPfold(seed): 0.194 Sensitivity PETfold_pre2.0(seed): 0.619 PPfold(seed): 0.072 Positive Predictive Value PETfold_pre2.0(seed): 0.789 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 PPfold(seed): 0.036 Sensitivity TurboFold(20): 0.606 PPfold(seed): 0.008 Positive Predictive Value TurboFold(20): 0.714 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.451 PPfold(seed): 0.155 Sensitivity RNAwolf: 0.447 PPfold(seed): 0.047 Positive Predictive Value RNAwolf: 0.472 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.601 PPfold(seed): 0.155 Sensitivity IPknot: 0.560 PPfold(seed): 0.047 Positive Predictive Value IPknot: 0.656 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	4 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 PPfold(seed): 0.048 Sensitivity PETfold_pre2.0(20): 0.570 PPfold(seed): 0.013 Positive Predictive Value PETfold_pre2.0(20): 0.682 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.570 PPfold(seed): 0.194 Sensitivity ContextFold: 0.515 PPfold(seed): 0.072 Positive Predictive Value ContextFold: 0.641 PPfold(seed): 0.538 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): 0.560 PPfold(seed): 0.155 Sensitivity TurboFold(seed): 0.533 PPfold(seed): 0.047 Positive Predictive Value TurboFold(seed): 0.602 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 PPfold(seed): 0.170 Sensitivity CRWrnafold: 0.524 PPfold(seed): 0.056 Positive Predictive Value CRWrnafold: 0.516 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.559 PPfold(seed): 0.200 Sensitivity RNASampler(seed): 0.484 PPfold(seed): 0.077 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	? RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 PPfold(seed): 0.194 Sensitivity RNASLOpt: 0.443 PPfold(seed): 0.072 Positive Predictive Value RNASLOpt: 0.494 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.715 PPfold(seed): 0.036 Sensitivity PPfold(20): 0.644 PPfold(seed): 0.008 Positive Predictive Value PPfold(20): 0.802 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.155 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.047 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
ContextFold	4 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.698 ContextFold: 0.567 Sensitivity CentroidAlifold(20): 0.557 ContextFold: 0.506 Positive Predictive Value CentroidAlifold(20): 0.880 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(seed) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 ContextFold: 0.570 Sensitivity CentroidAlifold(seed): 0.485 ContextFold: 0.515 Positive Predictive Value CentroidAlifold(seed): 0.979 ContextFold: 0.641 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.567 RNAalifold(20): 0.532 Sensitivity ContextFold: 0.506 RNAalifold(20): 0.456 Positive Predictive Value ContextFold: 0.645 RNAalifold(20): 0.632 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.570 MXScarna(seed): 0.476 Sensitivity ContextFold: 0.515 MXScarna(seed): 0.412 Positive Predictive Value ContextFold: 0.641 MXScarna(seed): 0.563 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.662 CentroidFold: 0.566 Sensitivity ContextFold: 0.608 CentroidFold: 0.531 Positive Predictive Value ContextFold: 0.731 CentroidFold: 0.616 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs ContextFold Matthews Correlation Coefficient RNASampler(20): 0.582 ContextFold: 0.567 Sensitivity RNASampler(20): 0.506 ContextFold: 0.506 Positive Predictive Value RNASampler(20): 0.678 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.567 MXScarna(20): 0.477 Sensitivity ContextFold: 0.506 MXScarna(20): 0.430 Positive Predictive Value ContextFold: 0.645 MXScarna(20): 0.540 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.662 Contrafold: 0.573 Sensitivity ContextFold: 0.608 Contrafold: 0.554 Positive Predictive Value ContextFold: 0.731 Contrafold: 0.605 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.662 Sfold: 0.501 Sensitivity ContextFold: 0.608 Sfold: 0.492 Positive Predictive Value ContextFold: 0.731 Sfold: 0.525 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.662 MaxExpect: 0.418 Sensitivity ContextFold: 0.608 MaxExpect: 0.423 Positive Predictive Value ContextFold: 0.731 MaxExpect: 0.430 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.662 HotKnots: 0.587 Sensitivity ContextFold: 0.608 HotKnots: 0.631 Positive Predictive Value ContextFold: 0.731 HotKnots: 0.558 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.570 RNAalifold(seed): 0.542 Sensitivity ContextFold: 0.515 RNAalifold(seed): 0.392 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.760 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.567 Murlet(20): 0.537 Sensitivity ContextFold: 0.506 Murlet(20): 0.456 Positive Predictive Value ContextFold: 0.645 Murlet(20): 0.643 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.662 UNAFold: 0.419 Sensitivity ContextFold: 0.608 UNAFold: 0.438 Positive Predictive Value ContextFold: 0.731 UNAFold: 0.416 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.567 Carnac(20): 0.416 Sensitivity ContextFold: 0.506 Carnac(20): 0.241 Positive Predictive Value ContextFold: 0.645 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.662 McQFold: 0.621 Sensitivity ContextFold: 0.608 McQFold: 0.631 Positive Predictive Value ContextFold: 0.731 McQFold: 0.621 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.662 RNAshapes: 0.473 Sensitivity ContextFold: 0.608 RNAshapes: 0.485 Positive Predictive Value ContextFold: 0.731 RNAshapes: 0.477 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.662 RNAfold: 0.470 Sensitivity ContextFold: 0.608 RNAfold: 0.485 Positive Predictive Value ContextFold: 0.731 RNAfold: 0.470 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.662 PknotsRG: 0.556 Sensitivity ContextFold: 0.608 PknotsRG: 0.592 Positive Predictive Value ContextFold: 0.731 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.662 Pknots: 0.517 Sensitivity ContextFold: 0.608 Pknots: 0.546 Positive Predictive Value ContextFold: 0.731 Pknots: 0.504 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.646 Afold: 0.477 Sensitivity ContextFold: 0.600 Afold: 0.520 Positive Predictive Value ContextFold: 0.703 Afold: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.662 ProbKnot: 0.441 Sensitivity ContextFold: 0.608 ProbKnot: 0.469 Positive Predictive Value ContextFold: 0.731 ProbKnot: 0.430 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.738 Cylofold: 0.602 Sensitivity ContextFold: 0.673 Cylofold: 0.600 Positive Predictive Value ContextFold: 0.822 Cylofold: 0.623 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.662 RNAsubopt: 0.402 Sensitivity ContextFold: 0.608 RNAsubopt: 0.423 Positive Predictive Value ContextFold: 0.731 RNAsubopt: 0.399 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.662 Fold: 0.348 Sensitivity ContextFold: 0.608 Fold: 0.362 Positive Predictive Value ContextFold: 0.731 Fold: 0.353 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.567 RSpredict(20): 0.351 Sensitivity ContextFold: 0.506 RSpredict(20): 0.304 Positive Predictive Value ContextFold: 0.645 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.662 Vsfold4: 0.461 Sensitivity ContextFold: 0.608 Vsfold4: 0.446 Positive Predictive Value ContextFold: 0.731 Vsfold4: 0.492 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.570 Murlet(seed): 0.495 Sensitivity ContextFold: 0.515 Murlet(seed): 0.340 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	2 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.659 Alterna: 0.362 Sensitivity ContextFold: 0.621 Alterna: 0.345 Positive Predictive Value ContextFold: 0.720 Alterna: 0.417 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.567 Mastr(20): 0.386 Sensitivity ContextFold: 0.506 Mastr(20): 0.228 Positive Predictive Value ContextFold: 0.645 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.662 Vsfold5: 0.450 Sensitivity ContextFold: 0.608 Vsfold5: 0.462 Positive Predictive Value ContextFold: 0.731 Vsfold5: 0.455 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.673 RDfolder: 0.299 Sensitivity ContextFold: 0.602 RDfolder: 0.261 Positive Predictive Value ContextFold: 0.768 RDfolder: 0.377 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.673 MCFold: 0.436 Sensitivity ContextFold: 0.614 MCFold: 0.475 Positive Predictive Value ContextFold: 0.747 MCFold: 0.414 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.570 RSpredict(seed): 0.203 Sensitivity ContextFold: 0.515 RSpredict(seed): 0.124 Positive Predictive Value ContextFold: 0.641 RSpredict(seed): 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.570 Carnac(seed): 0.202 Sensitivity ContextFold: 0.515 Carnac(seed): 0.041 Positive Predictive Value ContextFold: 0.641 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.637 NanoFolder: 0.427 Sensitivity ContextFold: 0.596 NanoFolder: 0.519 Positive Predictive Value ContextFold: 0.689 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.662 CentroidHomfold‑LAST: 0.565 Sensitivity ContextFold: 0.608 CentroidHomfold‑LAST: 0.492 Positive Predictive Value ContextFold: 0.731 CentroidHomfold‑LAST: 0.660 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	2 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.606 Multilign(seed): 0.458 Sensitivity ContextFold: 0.574 Multilign(seed): 0.404 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 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.567 Multilign(20): 0.446 Sensitivity ContextFold: 0.506 Multilign(20): 0.443 Positive Predictive Value ContextFold: 0.645 Multilign(20): 0.461 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 ContextFold: 0.570 Sensitivity PETfold_pre2.0(seed): 0.619 ContextFold: 0.515 Positive Predictive Value PETfold_pre2.0(seed): 0.789 ContextFold: 0.641 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.567 TurboFold(20): 0.554 Sensitivity ContextFold: 0.506 TurboFold(20): 0.506 Positive Predictive Value ContextFold: 0.645 TurboFold(20): 0.615 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.662 RNAwolf: 0.325 Sensitivity ContextFold: 0.608 RNAwolf: 0.331 Positive Predictive Value ContextFold: 0.731 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.662 IPknot: 0.531 Sensitivity ContextFold: 0.608 IPknot: 0.508 Positive Predictive Value ContextFold: 0.731 IPknot: 0.569 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	4 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 ContextFold: 0.567 Sensitivity PETfold_pre2.0(20): 0.570 ContextFold: 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.570 PPfold(seed): 0.194 Sensitivity ContextFold: 0.515 PPfold(seed): 0.072 Positive Predictive Value ContextFold: 0.641 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.570 TurboFold(seed): 0.431 Sensitivity ContextFold: 0.515 TurboFold(seed): 0.412 Positive Predictive Value ContextFold: 0.641 TurboFold(seed): 0.465 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.662 CRWrnafold: 0.473 Sensitivity ContextFold: 0.608 CRWrnafold: 0.485 Positive Predictive Value ContextFold: 0.731 CRWrnafold: 0.477 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.413 RNASampler(seed): 0.232 Sensitivity ContextFold: 0.395 RNASampler(seed): 0.211 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	? ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.662 RNASLOpt: 0.449 Sensitivity ContextFold: 0.608 RNASLOpt: 0.438 Positive Predictive Value ContextFold: 0.731 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.630 ContextFold: 0.567 Sensitivity PPfold(20): 0.557 ContextFold: 0.506 Positive Predictive Value PPfold(20): 0.721 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.570 Mastr(seed): 0.000 Sensitivity ContextFold: 0.515 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.641 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
TurboFold(seed)	6 CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 TurboFold(seed): 0.636 Sensitivity CentroidAlifold(20): 0.636 TurboFold(seed): 0.606 Positive Predictive Value CentroidAlifold(20): 0.923 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.759 TurboFold(seed): 0.560 Sensitivity CentroidAlifold(seed): 0.593 TurboFold(seed): 0.533 Positive Predictive Value CentroidAlifold(seed): 0.978 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(20) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.658 TurboFold(seed): 0.636 Sensitivity RNAalifold(20): 0.591 TurboFold(seed): 0.606 Positive Predictive Value RNAalifold(20): 0.743 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.593 TurboFold(seed): 0.560 Sensitivity MXScarna(seed): 0.533 TurboFold(seed): 0.533 Positive Predictive Value MXScarna(seed): 0.672 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.620 TurboFold(seed): 0.560 Sensitivity CentroidFold: 0.587 TurboFold(seed): 0.533 Positive Predictive Value CentroidFold: 0.667 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.693 TurboFold(seed): 0.636 Sensitivity RNASampler(20): 0.606 TurboFold(seed): 0.606 Positive Predictive Value RNASampler(20): 0.800 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 MXScarna(20): 0.606 Sensitivity TurboFold(seed): 0.606 MXScarna(20): 0.561 Positive Predictive Value TurboFold(seed): 0.678 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.611 TurboFold(seed): 0.560 Sensitivity Contrafold: 0.593 TurboFold(seed): 0.533 Positive Predictive Value Contrafold: 0.640 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.618 TurboFold(seed): 0.560 Sensitivity Sfold: 0.573 TurboFold(seed): 0.533 Positive Predictive Value Sfold: 0.677 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.560 MaxExpect: 0.522 Sensitivity TurboFold(seed): 0.533 MaxExpect: 0.520 Positive Predictive Value TurboFold(seed): 0.602 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.684 TurboFold(seed): 0.560 Sensitivity HotKnots: 0.700 TurboFold(seed): 0.533 Positive Predictive Value HotKnots: 0.677 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 TurboFold(seed): 0.560 Sensitivity RNAalifold(seed): 0.473 TurboFold(seed): 0.533 Positive Predictive Value RNAalifold(seed): 0.798 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Murlet(20) vs TurboFold(seed) Matthews Correlation Coefficient Murlet(20): 0.654 TurboFold(seed): 0.636 Sensitivity Murlet(20): 0.576 TurboFold(seed): 0.606 Positive Predictive Value Murlet(20): 0.752 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.560 UNAFold: 0.536 Sensitivity TurboFold(seed): 0.533 UNAFold: 0.533 Positive Predictive Value TurboFold(seed): 0.602 UNAFold: 0.552 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 Carnac(20): 0.600 Sensitivity TurboFold(seed): 0.606 Carnac(20): 0.417 Positive Predictive Value TurboFold(seed): 0.678 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 McQFold vs TurboFold(seed) Matthews Correlation Coefficient McQFold: 0.679 TurboFold(seed): 0.560 Sensitivity McQFold: 0.693 TurboFold(seed): 0.533 Positive Predictive Value McQFold: 0.675 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.611 TurboFold(seed): 0.560 Sensitivity RNAshapes: 0.607 TurboFold(seed): 0.533 Positive Predictive Value RNAshapes: 0.628 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.607 TurboFold(seed): 0.560 Sensitivity RNAfold: 0.607 TurboFold(seed): 0.533 Positive Predictive Value RNAfold: 0.619 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.673 TurboFold(seed): 0.560 Sensitivity PknotsRG: 0.693 TurboFold(seed): 0.533 Positive Predictive Value PknotsRG: 0.662 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Pknots vs TurboFold(seed) Matthews Correlation Coefficient Pknots: 0.666 TurboFold(seed): 0.560 Sensitivity Pknots: 0.680 TurboFold(seed): 0.533 Positive Predictive Value Pknots: 0.662 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.590 TurboFold(seed): 0.444 Sensitivity Afold: 0.610 TurboFold(seed): 0.442 Positive Predictive Value Afold: 0.580 TurboFold(seed): 0.459 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.560 ProbKnot: 0.514 Sensitivity TurboFold(seed): 0.533 ProbKnot: 0.540 Positive Predictive Value TurboFold(seed): 0.602 ProbKnot: 0.503 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.740 TurboFold(seed): 0.641 Sensitivity Cylofold: 0.708 TurboFold(seed): 0.577 Positive Predictive Value Cylofold: 0.786 TurboFold(seed): 0.728 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.560 RNAsubopt: 0.528 Sensitivity TurboFold(seed): 0.533 RNAsubopt: 0.533 Positive Predictive Value TurboFold(seed): 0.602 RNAsubopt: 0.537 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.560 Fold: 0.475 Sensitivity TurboFold(seed): 0.533 Fold: 0.480 Positive Predictive Value TurboFold(seed): 0.602 Fold: 0.486 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 RSpredict(20): 0.573 Sensitivity TurboFold(seed): 0.606 RSpredict(20): 0.530 Positive Predictive Value TurboFold(seed): 0.678 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.560 Vsfold4: 0.483 Sensitivity TurboFold(seed): 0.533 Vsfold4: 0.460 Positive Predictive Value TurboFold(seed): 0.602 Vsfold4: 0.523 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.560 Murlet(seed): 0.531 Sensitivity TurboFold(seed): 0.533 Murlet(seed): 0.373 Positive Predictive Value TurboFold(seed): 0.602 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	3 Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.624 TurboFold(seed): 0.594 Sensitivity Alterna: 0.606 TurboFold(seed): 0.563 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 Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 Mastr(20): 0.570 Sensitivity TurboFold(seed): 0.606 Mastr(20): 0.424 Positive Predictive Value TurboFold(seed): 0.678 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.560 Vsfold5: 0.462 Sensitivity TurboFold(seed): 0.533 Vsfold5: 0.467 Positive Predictive Value TurboFold(seed): 0.602 Vsfold5: 0.473 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.641 RDfolder: 0.451 Sensitivity TurboFold(seed): 0.577 RDfolder: 0.385 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	6 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.537 MCFold: 0.491 Sensitivity TurboFold(seed): 0.521 MCFold: 0.521 Positive Predictive Value TurboFold(seed): 0.568 MCFold: 0.477 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.560 RSpredict(seed): 0.331 Sensitivity TurboFold(seed): 0.533 RSpredict(seed): 0.200 Positive Predictive Value TurboFold(seed): 0.602 RSpredict(seed): 0.566 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.560 Carnac(seed): 0.162 Sensitivity TurboFold(seed): 0.533 Carnac(seed): 0.027 Positive Predictive Value TurboFold(seed): 0.602 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.383 NanoFolder: 0.336 Sensitivity TurboFold(seed): 0.378 NanoFolder: 0.415 Positive Predictive Value TurboFold(seed): 0.403 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 TurboFold(seed): 0.560 Sensitivity CentroidHomfold‑LAST: 0.567 TurboFold(seed): 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.746 TurboFold(seed): 0.602 Number of pairs reference - predicted secondary structure: 7 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): 0.629 TurboFold(seed): 0.614 Sensitivity Multilign(seed): 0.580 TurboFold(seed): 0.570 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	6 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.636 Multilign(20): 0.581 Sensitivity TurboFold(seed): 0.606 Multilign(20): 0.576 Positive Predictive Value TurboFold(seed): 0.678 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 TurboFold(seed): 0.431 Sensitivity PETfold_pre2.0(seed): 0.619 TurboFold(seed): 0.412 Positive Predictive Value PETfold_pre2.0(seed): 0.789 TurboFold(seed): 0.465 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 TurboFold(seed): 0.636 Sensitivity TurboFold(20): 0.606 TurboFold(seed): 0.606 Positive Predictive Value TurboFold(20): 0.714 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.560 RNAwolf: 0.451 Sensitivity TurboFold(seed): 0.533 RNAwolf: 0.447 Positive Predictive Value TurboFold(seed): 0.602 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.601 TurboFold(seed): 0.560 Sensitivity IPknot: 0.560 TurboFold(seed): 0.533 Positive Predictive Value IPknot: 0.656 TurboFold(seed): 0.602 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	4 PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 TurboFold(seed): 0.529 Sensitivity PETfold_pre2.0(20): 0.570 TurboFold(seed): 0.506 Positive Predictive Value PETfold_pre2.0(20): 0.682 TurboFold(seed): 0.563 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.560 PPfold(seed): 0.155 Sensitivity TurboFold(seed): 0.533 PPfold(seed): 0.047 Positive Predictive Value TurboFold(seed): 0.602 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.570 TurboFold(seed): 0.431 Sensitivity ContextFold: 0.515 TurboFold(seed): 0.412 Positive Predictive Value ContextFold: 0.641 TurboFold(seed): 0.465 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 TurboFold(seed): 0.496 Sensitivity CRWrnafold: 0.524 TurboFold(seed): 0.476 Positive Predictive Value CRWrnafold: 0.516 TurboFold(seed): 0.531 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.559 TurboFold(seed): 0.486 Sensitivity RNASampler(seed): 0.484 TurboFold(seed): 0.495 Positive Predictive Value RNASampler(seed): 0.657 TurboFold(seed): 0.489 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs TurboFold(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 TurboFold(seed): 0.431 Sensitivity RNASLOpt: 0.443 TurboFold(seed): 0.412 Positive Predictive Value RNASLOpt: 0.494 TurboFold(seed): 0.465 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.715 TurboFold(seed): 0.636 Sensitivity PPfold(20): 0.644 TurboFold(seed): 0.606 Positive Predictive Value PPfold(20): 0.802 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.560 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.533 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.602 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
CRWrnafold	5 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.741 CRWrnafold: 0.592 Sensitivity CentroidAlifold(20): 0.611 CRWrnafold: 0.611 Positive Predictive Value CentroidAlifold(20): 0.904 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.727 CRWrnafold: 0.513 Sensitivity CentroidAlifold(seed): 0.548 CRWrnafold: 0.524 Positive Predictive Value CentroidAlifold(seed): 0.972 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.625 CRWrnafold: 0.592 Sensitivity RNAalifold(20): 0.565 CRWrnafold: 0.611 Positive Predictive Value RNAalifold(20): 0.701 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.544 CRWrnafold: 0.513 Sensitivity MXScarna(seed): 0.492 CRWrnafold: 0.524 Positive Predictive Value MXScarna(seed): 0.614 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.591 CRWrnafold: 0.502 Sensitivity CentroidFold: 0.560 CRWrnafold: 0.516 Positive Predictive Value CentroidFold: 0.636 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.642 CRWrnafold: 0.592 Sensitivity RNASampler(20): 0.556 CRWrnafold: 0.611 Positive Predictive Value RNASampler(20): 0.750 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs MXScarna(20) Matthews Correlation Coefficient CRWrnafold: 0.592 MXScarna(20): 0.554 Sensitivity CRWrnafold: 0.611 MXScarna(20): 0.519 Positive Predictive Value CRWrnafold: 0.584 MXScarna(20): 0.602 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.594 CRWrnafold: 0.502 Sensitivity Contrafold: 0.579 CRWrnafold: 0.516 Positive Predictive Value Contrafold: 0.622 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.550 CRWrnafold: 0.502 Sensitivity Sfold: 0.535 CRWrnafold: 0.516 Positive Predictive Value Sfold: 0.578 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.502 MaxExpect: 0.468 Sensitivity CRWrnafold: 0.516 MaxExpect: 0.472 Positive Predictive Value CRWrnafold: 0.503 MaxExpect: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.618 CRWrnafold: 0.502 Sensitivity HotKnots: 0.654 CRWrnafold: 0.516 Positive Predictive Value HotKnots: 0.594 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.582 CRWrnafold: 0.513 Sensitivity RNAalifold(seed): 0.437 CRWrnafold: 0.524 Positive Predictive Value RNAalifold(seed): 0.786 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.622 CRWrnafold: 0.592 Sensitivity Murlet(20): 0.556 CRWrnafold: 0.611 Positive Predictive Value Murlet(20): 0.706 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.502 UNAFold: 0.480 Sensitivity CRWrnafold: 0.516 UNAFold: 0.497 Positive Predictive Value CRWrnafold: 0.503 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.592 Carnac(20): 0.510 Sensitivity CRWrnafold: 0.611 Carnac(20): 0.324 Positive Predictive Value CRWrnafold: 0.584 Carnac(20): 0.814 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.657 CRWrnafold: 0.502 Sensitivity McQFold: 0.667 CRWrnafold: 0.516 Positive Predictive Value McQFold: 0.658 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.526 CRWrnafold: 0.502 Sensitivity RNAshapes: 0.535 CRWrnafold: 0.516 Positive Predictive Value RNAshapes: 0.531 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.522 CRWrnafold: 0.502 Sensitivity RNAfold: 0.535 CRWrnafold: 0.516 Positive Predictive Value RNAfold: 0.525 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.586 CRWrnafold: 0.502 Sensitivity PknotsRG: 0.616 CRWrnafold: 0.516 Positive Predictive Value PknotsRG: 0.570 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: 0.562 CRWrnafold: 0.502 Sensitivity Pknots: 0.585 CRWrnafold: 0.516 Positive Predictive Value Pknots: 0.554 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	4 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.477 CRWrnafold: 0.343 Sensitivity Afold: 0.520 CRWrnafold: 0.373 Positive Predictive Value Afold: 0.448 CRWrnafold: 0.329 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.502 ProbKnot: 0.480 Sensitivity CRWrnafold: 0.516 ProbKnot: 0.509 Positive Predictive Value CRWrnafold: 0.503 ProbKnot: 0.468 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.624 CRWrnafold: 0.563 Sensitivity Cylofold: 0.619 CRWrnafold: 0.554 Positive Predictive Value Cylofold: 0.647 CRWrnafold: 0.592 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.502 RNAsubopt: 0.460 Sensitivity CRWrnafold: 0.516 RNAsubopt: 0.478 Positive Predictive Value CRWrnafold: 0.503 RNAsubopt: 0.458 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.502 Fold: 0.409 Sensitivity CRWrnafold: 0.516 Fold: 0.421 Positive Predictive Value CRWrnafold: 0.503 Fold: 0.414 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.592 RSpredict(20): 0.494 Sensitivity CRWrnafold: 0.611 RSpredict(20): 0.454 Positive Predictive Value CRWrnafold: 0.584 RSpredict(20): 0.551 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.502 Vsfold4: 0.417 Sensitivity CRWrnafold: 0.516 Vsfold4: 0.409 Positive Predictive Value CRWrnafold: 0.503 Vsfold4: 0.442 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Murlet(seed): 0.510 Sensitivity CRWrnafold: 0.524 Murlet(seed): 0.349 Positive Predictive Value CRWrnafold: 0.516 Murlet(seed): 0.759 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 Alterna vs CRWrnafold Matthews Correlation Coefficient Alterna: 0.462 CRWrnafold: 0.394 Sensitivity Alterna: 0.448 CRWrnafold: 0.397 Positive Predictive Value Alterna: 0.500 CRWrnafold: 0.418 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.592 Mastr(20): 0.502 Sensitivity CRWrnafold: 0.611 Mastr(20): 0.361 Positive Predictive Value CRWrnafold: 0.584 Mastr(20): 0.709 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.502 Vsfold5: 0.395 Sensitivity CRWrnafold: 0.516 Vsfold5: 0.403 Positive Predictive Value CRWrnafold: 0.503 Vsfold5: 0.405 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.580 RDfolder: 0.310 Sensitivity CRWrnafold: 0.556 RDfolder: 0.256 Positive Predictive Value CRWrnafold: 0.625 RDfolder: 0.405 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.459 MCFold: 0.434 Sensitivity CRWrnafold: 0.477 MCFold: 0.469 Positive Predictive Value CRWrnafold: 0.456 MCFold: 0.418 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 RSpredict(seed): 0.178 Sensitivity CRWrnafold: 0.524 RSpredict(seed): 0.095 Positive Predictive Value CRWrnafold: 0.516 RSpredict(seed): 0.353 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Carnac(seed): 0.177 Sensitivity CRWrnafold: 0.524 Carnac(seed): 0.032 Positive Predictive Value CRWrnafold: 0.516 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.437 NanoFolder: 0.427 Sensitivity CRWrnafold: 0.462 NanoFolder: 0.519 Positive Predictive Value CRWrnafold: 0.429 NanoFolder: 0.365 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.601 CRWrnafold: 0.502 Sensitivity CentroidHomfold‑LAST: 0.522 CRWrnafold: 0.516 Positive Predictive Value CentroidHomfold‑LAST: 0.703 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	3 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.540 CRWrnafold: 0.513 Sensitivity Multilign(seed): 0.500 CRWrnafold: 0.513 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	5 CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.592 Multilign(20): 0.510 Sensitivity CRWrnafold: 0.611 Multilign(20): 0.509 Positive Predictive Value CRWrnafold: 0.584 Multilign(20): 0.524 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 CRWrnafold: 0.478 Sensitivity PETfold_pre2.0(seed): 0.619 CRWrnafold: 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.789 CRWrnafold: 0.485 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.597 CRWrnafold: 0.592 Sensitivity TurboFold(20): 0.556 CRWrnafold: 0.611 Positive Predictive Value TurboFold(20): 0.652 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.502 RNAwolf: 0.372 Sensitivity CRWrnafold: 0.516 RNAwolf: 0.377 Positive Predictive Value CRWrnafold: 0.503 RNAwolf: 0.385 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.568 CRWrnafold: 0.502 Sensitivity IPknot: 0.541 CRWrnafold: 0.516 Positive Predictive Value IPknot: 0.610 CRWrnafold: 0.503 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	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	4 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 CRWrnafold: 0.579 Sensitivity PETfold_pre2.0(20): 0.570 CRWrnafold: 0.595 Positive Predictive Value PETfold_pre2.0(20): 0.682 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 PPfold(seed): 0.170 Sensitivity CRWrnafold: 0.524 PPfold(seed): 0.056 Positive Predictive Value CRWrnafold: 0.516 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.662 CRWrnafold: 0.473 Sensitivity ContextFold: 0.608 CRWrnafold: 0.485 Positive Predictive Value ContextFold: 0.731 CRWrnafold: 0.477 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 TurboFold(seed): 0.496 Sensitivity CRWrnafold: 0.524 TurboFold(seed): 0.476 Positive Predictive Value CRWrnafold: 0.516 TurboFold(seed): 0.531 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0		? RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.423 CRWrnafold: 0.322 Sensitivity RNASampler(seed): 0.358 CRWrnafold: 0.358 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.304 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.473 RNASLOpt: 0.449 Sensitivity CRWrnafold: 0.485 RNASLOpt: 0.438 Positive Predictive Value CRWrnafold: 0.477 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.681 CRWrnafold: 0.592 Sensitivity PPfold(20): 0.611 CRWrnafold: 0.611 Positive Predictive Value PPfold(20): 0.767 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.524 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.516 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
RNASampler(seed)	5 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.741 RNASampler(seed): 0.696 Sensitivity CentroidAlifold(20): 0.627 RNASampler(seed): 0.627 Positive Predictive Value CentroidAlifold(20): 0.881 RNASampler(seed): 0.779 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.783 RNASampler(seed): 0.640 Sensitivity CentroidAlifold(seed): 0.645 RNASampler(seed): 0.554 Positive Predictive Value CentroidAlifold(seed): 0.955 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 RNAalifold(20): 0.640 Sensitivity RNASampler(seed): 0.627 RNAalifold(20): 0.619 Positive Predictive Value RNASampler(seed): 0.779 RNAalifold(20): 0.670 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 MXScarna(seed): 0.636 Sensitivity RNASampler(seed): 0.554 MXScarna(seed): 0.572 Positive Predictive Value RNASampler(seed): 0.748 MXScarna(seed): 0.714 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.681 RNASampler(seed): 0.640 Sensitivity CentroidFold: 0.651 RNASampler(seed): 0.554 Positive Predictive Value CentroidFold: 0.720 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs RNASampler(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 RNASampler(20): 0.681 Sensitivity RNASampler(seed): 0.627 RNASampler(20): 0.636 Positive Predictive Value RNASampler(seed): 0.779 RNASampler(20): 0.735 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 MXScarna(20): 0.652 Sensitivity RNASampler(seed): 0.627 MXScarna(20): 0.636 Positive Predictive Value RNASampler(seed): 0.779 MXScarna(20): 0.676 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.642 RNASampler(seed): 0.640 Sensitivity Contrafold: 0.645 RNASampler(seed): 0.554 Positive Predictive Value Contrafold: 0.648 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.695 RNASampler(seed): 0.640 Sensitivity Sfold: 0.669 RNASampler(seed): 0.554 Positive Predictive Value Sfold: 0.730 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.616 MaxExpect: 0.525 Sensitivity RNASampler(seed): 0.544 MaxExpect: 0.551 Positive Predictive Value RNASampler(seed): 0.705 MaxExpect: 0.510 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.640 HotKnots: 0.639 Sensitivity RNASampler(seed): 0.554 HotKnots: 0.681 Positive Predictive Value RNASampler(seed): 0.748 HotKnots: 0.608 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 RNAalifold(seed): 0.612 Sensitivity RNASampler(seed): 0.554 RNAalifold(seed): 0.482 Positive Predictive Value RNASampler(seed): 0.748 RNAalifold(seed): 0.784 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 Murlet(20): 0.610 Sensitivity RNASampler(seed): 0.627 Murlet(20): 0.568 Positive Predictive Value RNASampler(seed): 0.779 Murlet(20): 0.663 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.640 UNAFold: 0.613 Sensitivity RNASampler(seed): 0.554 UNAFold: 0.633 Positive Predictive Value RNASampler(seed): 0.748 UNAFold: 0.603 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RNASampler(seed) Matthews Correlation Coefficient Carnac(20): 0.741 RNASampler(seed): 0.696 Sensitivity Carnac(20): 0.576 RNASampler(seed): 0.627 Positive Predictive Value Carnac(20): 0.958 RNASampler(seed): 0.779 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.669 RNASampler(seed): 0.640 Sensitivity McQFold: 0.693 RNASampler(seed): 0.554 Positive Predictive Value McQFold: 0.653 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.655 RNASampler(seed): 0.640 Sensitivity RNAshapes: 0.675 RNASampler(seed): 0.554 Positive Predictive Value RNAshapes: 0.644 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.673 RNASampler(seed): 0.640 Sensitivity RNAfold: 0.699 RNASampler(seed): 0.554 Positive Predictive Value RNAfold: 0.655 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.665 RNASampler(seed): 0.640 Sensitivity PknotsRG: 0.693 RNASampler(seed): 0.554 Positive Predictive Value PknotsRG: 0.646 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.702 RNASampler(seed): 0.640 Sensitivity Pknots: 0.747 RNASampler(seed): 0.554 Positive Predictive Value Pknots: 0.667 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.647 RNASampler(seed): 0.627 Sensitivity Afold: 0.672 RNASampler(seed): 0.555 Positive Predictive Value Afold: 0.630 RNASampler(seed): 0.717 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.554 ProbKnot: 0.432 Sensitivity RNASampler(seed): 0.487 ProbKnot: 0.496 Positive Predictive Value RNASampler(seed): 0.640 ProbKnot: 0.386 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.659 RNASampler(seed): 0.596 Sensitivity Cylofold: 0.667 RNASampler(seed): 0.505 Positive Predictive Value Cylofold: 0.660 RNASampler(seed): 0.712 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.640 RNAsubopt: 0.598 Sensitivity RNASampler(seed): 0.554 RNAsubopt: 0.620 Positive Predictive Value RNASampler(seed): 0.748 RNAsubopt: 0.585 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.554 Fold: 0.450 Sensitivity RNASampler(seed): 0.487 Fold: 0.496 Positive Predictive Value RNASampler(seed): 0.640 Fold: 0.418 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 RSpredict(20): 0.640 Sensitivity RNASampler(seed): 0.627 RSpredict(20): 0.703 Positive Predictive Value RNASampler(seed): 0.779 RSpredict(20): 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.640 Vsfold4: 0.512 Sensitivity RNASampler(seed): 0.554 Vsfold4: 0.506 Positive Predictive Value RNASampler(seed): 0.748 Vsfold4: 0.528 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 Murlet(seed): 0.514 Sensitivity RNASampler(seed): 0.554 Murlet(seed): 0.361 Positive Predictive Value RNASampler(seed): 0.748 Murlet(seed): 0.741 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.732 RNASampler(seed): 0.710 Sensitivity Alterna: 0.702 RNASampler(seed): 0.589 Positive Predictive Value Alterna: 0.777 RNASampler(seed): 0.869 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.696 Mastr(20): 0.644 Sensitivity RNASampler(seed): 0.627 Mastr(20): 0.483 Positive Predictive Value RNASampler(seed): 0.779 Mastr(20): 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.640 Vsfold5: 0.547 Sensitivity RNASampler(seed): 0.554 Vsfold5: 0.554 Positive Predictive Value RNASampler(seed): 0.748 Vsfold5: 0.551 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.710 RDfolder: 0.579 Sensitivity RNASampler(seed): 0.589 RDfolder: 0.492 Positive Predictive Value RNASampler(seed): 0.869 RDfolder: 0.701 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.640 MCFold: 0.521 Sensitivity RNASampler(seed): 0.554 MCFold: 0.572 Positive Predictive Value RNASampler(seed): 0.748 MCFold: 0.485 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 RSpredict(seed): 0.435 Sensitivity RNASampler(seed): 0.554 RSpredict(seed): 0.289 Positive Predictive Value RNASampler(seed): 0.748 RSpredict(seed): 0.667 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 Carnac(seed): 0.154 Sensitivity RNASampler(seed): 0.554 Carnac(seed): 0.024 Positive Predictive Value RNASampler(seed): 0.748 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	2 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.232 NanoFolder: 0.207 Sensitivity RNASampler(seed): 0.211 NanoFolder: 0.289 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.159 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.559 CentroidHomfold‑LAST: 0.517 Sensitivity RNASampler(seed): 0.484 CentroidHomfold‑LAST: 0.462 Positive Predictive Value RNASampler(seed): 0.657 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 4 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): 0.616 Multilign(seed): 0.589 Sensitivity RNASampler(seed): 0.507 Multilign(seed): 0.549 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): 0.679 Multilign(20): 0.590 Sensitivity RNASampler(seed): 0.603 Multilign(20): 0.630 Positive Predictive Value RNASampler(seed): 0.772 Multilign(20): 0.561 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): 0.630 RNASampler(seed): 0.232 Sensitivity PETfold_pre2.0(seed): 0.553 RNASampler(seed): 0.211 Positive Predictive Value PETfold_pre2.0(seed): 0.724 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): 0.679 TurboFold(20): 0.621 Sensitivity RNASampler(seed): 0.603 TurboFold(20): 0.616 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	4 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.559 RNAwolf: 0.521 Sensitivity RNASampler(seed): 0.484 RNAwolf: 0.538 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.516 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.597 RNASampler(seed): 0.559 Sensitivity IPknot: 0.560 RNASampler(seed): 0.484 Positive Predictive Value IPknot: 0.646 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 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): 0.397 PETfold_pre2.0(20): 0.247 Sensitivity RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 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 PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.559 PPfold(seed): 0.200 Sensitivity RNASampler(seed): 0.484 PPfold(seed): 0.077 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	2 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.413 RNASampler(seed): 0.232 Sensitivity ContextFold: 0.395 RNASampler(seed): 0.211 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	4 RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.559 TurboFold(seed): 0.486 Sensitivity RNASampler(seed): 0.484 TurboFold(seed): 0.495 Positive Predictive Value RNASampler(seed): 0.657 TurboFold(seed): 0.489 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.423 CRWrnafold: 0.322 Sensitivity RNASampler(seed): 0.358 CRWrnafold: 0.358 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.304 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0		? RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.358 RNASampler(seed): 0.232 Sensitivity RNASLOpt: 0.395 RNASampler(seed): 0.211 Positive Predictive Value RNASLOpt: 0.333 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.681 RNASampler(seed): 0.679 Sensitivity PPfold(20): 0.630 RNASampler(seed): 0.603 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): 0.640 Mastr(seed): 0.000 Sensitivity RNASampler(seed): 0.554 Mastr(seed): 0.000 Positive Predictive Value RNASampler(seed): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
RNASLOpt	4 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.698 RNASLOpt: 0.459 Sensitivity CentroidAlifold(20): 0.557 RNASLOpt: 0.456 Positive Predictive Value CentroidAlifold(20): 0.880 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.686 RNASLOpt: 0.461 Sensitivity CentroidAlifold(seed): 0.485 RNASLOpt: 0.443 Positive Predictive Value CentroidAlifold(seed): 0.979 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.532 RNASLOpt: 0.459 Sensitivity RNAalifold(20): 0.456 RNASLOpt: 0.456 Positive Predictive Value RNAalifold(20): 0.632 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.476 RNASLOpt: 0.461 Sensitivity MXScarna(seed): 0.412 RNASLOpt: 0.443 Positive Predictive Value MXScarna(seed): 0.563 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.566 RNASLOpt: 0.449 Sensitivity CentroidFold: 0.531 RNASLOpt: 0.438 Positive Predictive Value CentroidFold: 0.616 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.582 RNASLOpt: 0.459 Sensitivity RNASampler(20): 0.506 RNASLOpt: 0.456 Positive Predictive Value RNASampler(20): 0.678 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.477 RNASLOpt: 0.459 Sensitivity MXScarna(20): 0.430 RNASLOpt: 0.456 Positive Predictive Value MXScarna(20): 0.540 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.573 RNASLOpt: 0.449 Sensitivity Contrafold: 0.554 RNASLOpt: 0.438 Positive Predictive Value Contrafold: 0.605 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.501 RNASLOpt: 0.449 Sensitivity Sfold: 0.492 RNASLOpt: 0.438 Positive Predictive Value Sfold: 0.525 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASLOpt vs MaxExpect Matthews Correlation Coefficient RNASLOpt: 0.449 MaxExpect: 0.418 Sensitivity RNASLOpt: 0.438 MaxExpect: 0.423 Positive Predictive Value RNASLOpt: 0.475 MaxExpect: 0.430 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.587 RNASLOpt: 0.449 Sensitivity HotKnots: 0.631 RNASLOpt: 0.438 Positive Predictive Value HotKnots: 0.558 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.542 RNASLOpt: 0.461 Sensitivity RNAalifold(seed): 0.392 RNASLOpt: 0.443 Positive Predictive Value RNAalifold(seed): 0.760 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.537 RNASLOpt: 0.459 Sensitivity Murlet(20): 0.456 RNASLOpt: 0.456 Positive Predictive Value Murlet(20): 0.643 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 RNASLOpt vs UNAFold Matthews Correlation Coefficient RNASLOpt: 0.449 UNAFold: 0.419 Sensitivity RNASLOpt: 0.438 UNAFold: 0.438 Positive Predictive Value RNASLOpt: 0.475 UNAFold: 0.416 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.459 Carnac(20): 0.416 Sensitivity RNASLOpt: 0.456 Carnac(20): 0.241 Positive Predictive Value RNASLOpt: 0.474 Carnac(20): 0.731 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.621 RNASLOpt: 0.449 Sensitivity McQFold: 0.631 RNASLOpt: 0.438 Positive Predictive Value McQFold: 0.621 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.473 RNASLOpt: 0.449 Sensitivity RNAshapes: 0.485 RNASLOpt: 0.438 Positive Predictive Value RNAshapes: 0.477 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.470 RNASLOpt: 0.449 Sensitivity RNAfold: 0.485 RNASLOpt: 0.438 Positive Predictive Value RNAfold: 0.470 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.556 RNASLOpt: 0.449 Sensitivity PknotsRG: 0.592 RNASLOpt: 0.438 Positive Predictive Value PknotsRG: 0.535 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: 0.517 RNASLOpt: 0.449 Sensitivity Pknots: 0.546 RNASLOpt: 0.438 Positive Predictive Value Pknots: 0.504 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNASLOpt vs Afold Matthews Correlation Coefficient RNASLOpt: 0.479 Afold: 0.477 Sensitivity RNASLOpt: 0.507 Afold: 0.520 Positive Predictive Value RNASLOpt: 0.463 Afold: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 RNASLOpt vs ProbKnot Matthews Correlation Coefficient RNASLOpt: 0.449 ProbKnot: 0.441 Sensitivity RNASLOpt: 0.438 ProbKnot: 0.469 Positive Predictive Value RNASLOpt: 0.475 ProbKnot: 0.430 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.602 RNASLOpt: 0.493 Sensitivity Cylofold: 0.600 RNASLOpt: 0.445 Positive Predictive Value Cylofold: 0.623 RNASLOpt: 0.570 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.449 RNAsubopt: 0.402 Sensitivity RNASLOpt: 0.438 RNAsubopt: 0.423 Positive Predictive Value RNASLOpt: 0.475 RNAsubopt: 0.399 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASLOpt vs Fold Matthews Correlation Coefficient RNASLOpt: 0.449 Fold: 0.348 Sensitivity RNASLOpt: 0.438 Fold: 0.362 Positive Predictive Value RNASLOpt: 0.475 Fold: 0.353 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.459 RSpredict(20): 0.351 Sensitivity RNASLOpt: 0.456 RSpredict(20): 0.304 Positive Predictive Value RNASLOpt: 0.474 RSpredict(20): 0.421 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 Vsfold4 vs RNASLOpt Matthews Correlation Coefficient Vsfold4: 0.461 RNASLOpt: 0.449 Sensitivity Vsfold4: 0.446 RNASLOpt: 0.438 Positive Predictive Value Vsfold4: 0.492 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.495 RNASLOpt: 0.461 Sensitivity Murlet(seed): 0.340 RNASLOpt: 0.443 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.379 Alterna: 0.362 Sensitivity RNASLOpt: 0.310 Alterna: 0.345 Positive Predictive Value RNASLOpt: 0.500 Alterna: 0.417 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.459 Mastr(20): 0.386 Sensitivity RNASLOpt: 0.456 Mastr(20): 0.228 Positive Predictive Value RNASLOpt: 0.474 Mastr(20): 0.667 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 Vsfold5 vs RNASLOpt Matthews Correlation Coefficient Vsfold5: 0.450 RNASLOpt: 0.449 Sensitivity Vsfold5: 0.462 RNASLOpt: 0.438 Positive Predictive Value Vsfold5: 0.455 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.499 RDfolder: 0.299 Sensitivity RNASLOpt: 0.420 RDfolder: 0.261 Positive Predictive Value RNASLOpt: 0.617 RDfolder: 0.377 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.483 MCFold: 0.436 Sensitivity RNASLOpt: 0.485 MCFold: 0.475 Positive Predictive Value RNASLOpt: 0.495 MCFold: 0.414 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 RSpredict(seed): 0.203 Sensitivity RNASLOpt: 0.443 RSpredict(seed): 0.124 Positive Predictive Value RNASLOpt: 0.494 RSpredict(seed): 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 Carnac(seed): 0.202 Sensitivity RNASLOpt: 0.443 Carnac(seed): 0.041 Positive Predictive Value RNASLOpt: 0.494 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs RNASLOpt Matthews Correlation Coefficient NanoFolder: 0.427 RNASLOpt: 0.420 Sensitivity NanoFolder: 0.519 RNASLOpt: 0.423 Positive Predictive Value NanoFolder: 0.365 RNASLOpt: 0.431 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.565 RNASLOpt: 0.449 Sensitivity CentroidHomfold‑LAST: 0.492 RNASLOpt: 0.438 Positive Predictive Value CentroidHomfold‑LAST: 0.660 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	2 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.458 RNASLOpt: 0.375 Sensitivity Multilign(seed): 0.404 RNASLOpt: 0.319 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 RNASLOpt vs Multilign(20) Matthews Correlation Coefficient RNASLOpt: 0.459 Multilign(20): 0.446 Sensitivity RNASLOpt: 0.456 Multilign(20): 0.443 Positive Predictive Value RNASLOpt: 0.474 Multilign(20): 0.461 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNASLOpt: 0.461 Sensitivity PETfold_pre2.0(seed): 0.619 RNASLOpt: 0.443 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.554 RNASLOpt: 0.459 Sensitivity TurboFold(20): 0.506 RNASLOpt: 0.456 Positive Predictive Value TurboFold(20): 0.615 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.449 RNAwolf: 0.325 Sensitivity RNASLOpt: 0.438 RNAwolf: 0.331 Positive Predictive Value RNASLOpt: 0.475 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.531 RNASLOpt: 0.449 Sensitivity IPknot: 0.508 RNASLOpt: 0.438 Positive Predictive Value IPknot: 0.569 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	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	4 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 RNASLOpt: 0.459 Sensitivity PETfold_pre2.0(20): 0.570 RNASLOpt: 0.456 Positive Predictive Value PETfold_pre2.0(20): 0.682 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 PPfold(seed): 0.194 Sensitivity RNASLOpt: 0.443 PPfold(seed): 0.072 Positive Predictive Value RNASLOpt: 0.494 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.662 RNASLOpt: 0.449 Sensitivity ContextFold: 0.608 RNASLOpt: 0.438 Positive Predictive Value ContextFold: 0.731 RNASLOpt: 0.475 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs TurboFold(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 TurboFold(seed): 0.431 Sensitivity RNASLOpt: 0.443 TurboFold(seed): 0.412 Positive Predictive Value RNASLOpt: 0.494 TurboFold(seed): 0.465 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.473 RNASLOpt: 0.449 Sensitivity CRWrnafold: 0.485 RNASLOpt: 0.438 Positive Predictive Value CRWrnafold: 0.477 RNASLOpt: 0.475 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: 0.358 RNASampler(seed): 0.232 Sensitivity RNASLOpt: 0.395 RNASampler(seed): 0.211 Positive Predictive Value RNASLOpt: 0.333 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): 0.630 RNASLOpt: 0.459 Sensitivity PPfold(20): 0.557 RNASLOpt: 0.456 Positive Predictive Value PPfold(20): 0.721 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.443 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.494 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PPfold(20)	6 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.764 PPfold(20): 0.715 Sensitivity CentroidAlifold(20): 0.636 PPfold(20): 0.644 Positive Predictive Value CentroidAlifold(20): 0.923 PPfold(20): 0.802 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 PPfold(20): 0.715 Sensitivity CentroidAlifold(seed): 0.674 PPfold(20): 0.644 Positive Predictive Value CentroidAlifold(seed): 0.978 PPfold(20): 0.802 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.715 RNAalifold(20): 0.658 Sensitivity PPfold(20): 0.644 RNAalifold(20): 0.591 Positive Predictive Value PPfold(20): 0.802 RNAalifold(20): 0.743 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.715 MXScarna(seed): 0.663 Sensitivity PPfold(20): 0.644 MXScarna(seed): 0.606 Positive Predictive Value PPfold(20): 0.802 MXScarna(seed): 0.734 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.715 CentroidFold: 0.633 Sensitivity PPfold(20): 0.644 CentroidFold: 0.614 Positive Predictive Value PPfold(20): 0.802 CentroidFold: 0.664 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.715 RNASampler(20): 0.693 Sensitivity PPfold(20): 0.644 RNASampler(20): 0.606 Positive Predictive Value PPfold(20): 0.802 RNASampler(20): 0.800 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.715 MXScarna(20): 0.606 Sensitivity PPfold(20): 0.644 MXScarna(20): 0.561 Positive Predictive Value PPfold(20): 0.802 MXScarna(20): 0.667 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.715 Contrafold: 0.628 Sensitivity PPfold(20): 0.644 Contrafold: 0.621 Positive Predictive Value PPfold(20): 0.802 Contrafold: 0.646 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.715 Sfold: 0.636 Sensitivity PPfold(20): 0.644 Sfold: 0.598 Positive Predictive Value PPfold(20): 0.802 Sfold: 0.687 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.715 MaxExpect: 0.590 Sensitivity PPfold(20): 0.644 MaxExpect: 0.591 Positive Predictive Value PPfold(20): 0.802 MaxExpect: 0.600 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.715 HotKnots: 0.689 Sensitivity PPfold(20): 0.644 HotKnots: 0.712 Positive Predictive Value PPfold(20): 0.802 HotKnots: 0.676 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): 0.715 RNAalifold(seed): 0.701 Sensitivity PPfold(20): 0.644 RNAalifold(seed): 0.538 Positive Predictive Value PPfold(20): 0.802 RNAalifold(seed): 0.922 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.715 Murlet(20): 0.654 Sensitivity PPfold(20): 0.644 Murlet(20): 0.576 Positive Predictive Value PPfold(20): 0.802 Murlet(20): 0.752 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.715 UNAFold: 0.605 Sensitivity PPfold(20): 0.644 UNAFold: 0.606 Positive Predictive Value PPfold(20): 0.802 UNAFold: 0.615 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.715 Carnac(20): 0.600 Sensitivity PPfold(20): 0.644 Carnac(20): 0.417 Positive Predictive Value PPfold(20): 0.802 Carnac(20): 0.873 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.715 McQFold: 0.685 Sensitivity PPfold(20): 0.644 McQFold: 0.705 Positive Predictive Value PPfold(20): 0.802 McQFold: 0.674 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.715 RNAshapes: 0.608 Sensitivity PPfold(20): 0.644 RNAshapes: 0.606 Positive Predictive Value PPfold(20): 0.802 RNAshapes: 0.620 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.715 RNAfold: 0.603 Sensitivity PPfold(20): 0.644 RNAfold: 0.606 Positive Predictive Value PPfold(20): 0.802 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.715 PknotsRG: 0.675 Sensitivity PPfold(20): 0.644 PknotsRG: 0.705 Positive Predictive Value PPfold(20): 0.802 PknotsRG: 0.655 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.715 Pknots: 0.644 Sensitivity PPfold(20): 0.644 Pknots: 0.659 Positive Predictive Value PPfold(20): 0.802 Pknots: 0.640 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.598 Afold: 0.577 Sensitivity PPfold(20): 0.525 Afold: 0.610 Positive Predictive Value PPfold(20): 0.689 Afold: 0.554 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.715 ProbKnot: 0.577 Sensitivity PPfold(20): 0.644 ProbKnot: 0.614 Positive Predictive Value PPfold(20): 0.802 ProbKnot: 0.555 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.797 Cylofold: 0.756 Sensitivity PPfold(20): 0.714 Cylofold: 0.723 Positive Predictive Value PPfold(20): 0.899 Cylofold: 0.802 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.715 RNAsubopt: 0.596 Sensitivity PPfold(20): 0.644 RNAsubopt: 0.606 Positive Predictive Value PPfold(20): 0.802 RNAsubopt: 0.597 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.715 Fold: 0.537 Sensitivity PPfold(20): 0.644 Fold: 0.545 Positive Predictive Value PPfold(20): 0.802 Fold: 0.541 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.715 RSpredict(20): 0.573 Sensitivity PPfold(20): 0.644 RSpredict(20): 0.530 Positive Predictive Value PPfold(20): 0.802 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.715 Vsfold4: 0.544 Sensitivity PPfold(20): 0.644 Vsfold4: 0.523 Positive Predictive Value PPfold(20): 0.802 Vsfold4: 0.580 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.715 Murlet(seed): 0.621 Sensitivity PPfold(20): 0.644 Murlet(seed): 0.424 Positive Predictive Value PPfold(20): 0.802 Murlet(seed): 0.918 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	2 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.836 Alterna: 0.673 Sensitivity PPfold(20): 0.774 Alterna: 0.660 Positive Predictive Value PPfold(20): 0.911 Alterna: 0.700 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.715 Mastr(20): 0.570 Sensitivity PPfold(20): 0.644 Mastr(20): 0.424 Positive Predictive Value PPfold(20): 0.802 Mastr(20): 0.778 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.715 Vsfold5: 0.518 Sensitivity PPfold(20): 0.644 Vsfold5: 0.530 Positive Predictive Value PPfold(20): 0.802 Vsfold5: 0.519 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.797 RDfolder: 0.533 Sensitivity PPfold(20): 0.714 RDfolder: 0.446 Positive Predictive Value PPfold(20): 0.899 RDfolder: 0.658 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.668 MCFold: 0.498 Sensitivity PPfold(20): 0.592 MCFold: 0.534 Positive Predictive Value PPfold(20): 0.763 MCFold: 0.478 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.715 RSpredict(seed): 0.409 Sensitivity PPfold(20): 0.644 RSpredict(seed): 0.227 Positive Predictive Value PPfold(20): 0.802 RSpredict(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.715 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.644 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.802 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.632 NanoFolder: 0.285 Sensitivity PPfold(20): 0.578 NanoFolder: 0.359 Positive Predictive Value PPfold(20): 0.698 NanoFolder: 0.240 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 PPfold(20): 0.715 Sensitivity CentroidHomfold‑LAST: 0.644 PPfold(20): 0.644 Positive Predictive Value CentroidHomfold‑LAST: 0.825 PPfold(20): 0.802 Number of pairs reference - predicted secondary structure: 6 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): 0.849 Multilign(seed): 0.755 Sensitivity PPfold(20): 0.793 Multilign(seed): 0.707 Positive Predictive Value PPfold(20): 0.915 Multilign(seed): 0.817 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.715 Multilign(20): 0.581 Sensitivity PPfold(20): 0.644 Multilign(20): 0.576 Positive Predictive Value PPfold(20): 0.802 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.751 PPfold(20): 0.630 Sensitivity PETfold_pre2.0(seed): 0.684 PPfold(20): 0.557 Positive Predictive Value PETfold_pre2.0(seed): 0.831 PPfold(20): 0.721 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.715 TurboFold(20): 0.653 Sensitivity PPfold(20): 0.644 TurboFold(20): 0.606 Positive Predictive Value PPfold(20): 0.802 TurboFold(20): 0.714 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.715 RNAwolf: 0.442 Sensitivity PPfold(20): 0.644 RNAwolf: 0.439 Positive Predictive Value PPfold(20): 0.802 RNAwolf: 0.460 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.715 IPknot: 0.623 Sensitivity PPfold(20): 0.644 IPknot: 0.591 Positive Predictive Value PPfold(20): 0.802 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 6 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	4 PPfold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(20): 0.630 PETfold_pre2.0(20): 0.619 Sensitivity PPfold(20): 0.557 PETfold_pre2.0(20): 0.570 Positive Predictive Value PPfold(20): 0.721 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.715 PPfold(seed): 0.036 Sensitivity PPfold(20): 0.644 PPfold(seed): 0.008 Positive Predictive Value PPfold(20): 0.802 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.630 ContextFold: 0.567 Sensitivity PPfold(20): 0.557 ContextFold: 0.506 Positive Predictive Value PPfold(20): 0.721 ContextFold: 0.645 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.715 TurboFold(seed): 0.636 Sensitivity PPfold(20): 0.644 TurboFold(seed): 0.606 Positive Predictive Value PPfold(20): 0.802 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.681 CRWrnafold: 0.592 Sensitivity PPfold(20): 0.611 CRWrnafold: 0.611 Positive Predictive Value PPfold(20): 0.767 CRWrnafold: 0.584 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.681 RNASampler(seed): 0.679 Sensitivity PPfold(20): 0.630 RNASampler(seed): 0.603 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	4 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.630 RNASLOpt: 0.459 Sensitivity PPfold(20): 0.557 RNASLOpt: 0.456 Positive Predictive Value PPfold(20): 0.721 RNASLOpt: 0.474 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.715 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.644 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.802 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
Mastr(seed)	15 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.803 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.932 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	19 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.730 Mastr(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.598 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.894 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.48104284388e-08	15 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.753 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.656 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.869 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.57237423209e-08	19 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.711 Mastr(seed): 0.000 Sensitivity MXScarna(seed): 0.663 Mastr(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.768 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	19 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.675 Mastr(seed): 0.000 Sensitivity CentroidFold: 0.675 Mastr(seed): 0.000 Positive Predictive Value CentroidFold: 0.681 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	15 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.732 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.639 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	15 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.703 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.659 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.755 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.39551335374e-08	19 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.623 Mastr(seed): 0.000 Sensitivity Contrafold: 0.647 Mastr(seed): 0.000 Positive Predictive Value Contrafold: 0.606 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.57327336088e-08	19 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.632 Mastr(seed): 0.000 Sensitivity Sfold: 0.623 Mastr(seed): 0.000 Positive Predictive Value Sfold: 0.646 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08	17 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.591 Mastr(seed): 0.000 Sensitivity MaxExpect: 0.614 Mastr(seed): 0.000 Positive Predictive Value MaxExpect: 0.575 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	19 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.616 Mastr(seed): 0.000 Sensitivity HotKnots: 0.657 Mastr(seed): 0.000 Positive Predictive Value HotKnots: 0.582 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.27388928538e-08	16 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.634 Mastr(seed): 0.000 Sensitivity RNAalifold(seed): 0.479 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.842 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.84361416392e-08	15 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.666 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.548 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.814 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	19 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.613 Mastr(seed): 0.000 Sensitivity UNAFold: 0.638 Mastr(seed): 0.000 Positive Predictive Value UNAFold: 0.594 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.78993384543e-08	15 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.662 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.469 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.938 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.89169006118e-08	19 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.613 Mastr(seed): 0.000 Sensitivity McQFold: 0.640 Mastr(seed): 0.000 Positive Predictive Value McQFold: 0.593 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.84041289224e-08	19 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.594 Mastr(seed): 0.000 Sensitivity RNAshapes: 0.617 Mastr(seed): 0.000 Positive Predictive Value RNAshapes: 0.578 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	19 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.618 Mastr(seed): 0.000 Sensitivity RNAfold: 0.652 Mastr(seed): 0.000 Positive Predictive Value RNAfold: 0.591 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08	19 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.634 Mastr(seed): 0.000 Sensitivity PknotsRG: 0.675 Mastr(seed): 0.000 Positive Predictive Value PknotsRG: 0.602 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.97012568641e-08	17 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.710 Mastr(seed): 0.000 Sensitivity Pknots: 0.727 Mastr(seed): 0.000 Positive Predictive Value Pknots: 0.701 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	14 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.551 Mastr(seed): 0.000 Sensitivity Afold: 0.597 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.514 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	12 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.542 Mastr(seed): 0.000 Sensitivity ProbKnot: 0.593 Mastr(seed): 0.000 Positive Predictive Value ProbKnot: 0.501 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.00627773251e-08	8 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.723 Mastr(seed): 0.000 Sensitivity Cylofold: 0.703 Mastr(seed): 0.000 Positive Predictive Value Cylofold: 0.751 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	19 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.573 Mastr(seed): 0.000 Sensitivity RNAsubopt: 0.603 Mastr(seed): 0.000 Positive Predictive Value RNAsubopt: 0.550 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.42071836373e-08	12 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.532 Mastr(seed): 0.000 Sensitivity Fold: 0.570 Mastr(seed): 0.000 Positive Predictive Value Fold: 0.502 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.00475527001e-08	15 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.624 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.559 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.702 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.9966815982e-08	19 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.531 Mastr(seed): 0.000 Sensitivity Vsfold4: 0.530 Mastr(seed): 0.000 Positive Predictive Value Vsfold4: 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	14 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.571 Mastr(seed): 0.000 Sensitivity Murlet(seed): 0.386 Mastr(seed): 0.000 Positive Predictive Value Murlet(seed): 0.855 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.24019667966e-08	10 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.657 Mastr(seed): 0.000 Sensitivity Alterna: 0.651 Mastr(seed): 0.000 Positive Predictive Value Alterna: 0.677 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.07229227445e-09	15 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.506 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.337 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.769 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.86109605532e-08	19 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.498 Mastr(seed): 0.000 Sensitivity Vsfold5: 0.496 Mastr(seed): 0.000 Positive Predictive Value Vsfold5: 0.508 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.34821445183e-08	13 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.600 Mastr(seed): 0.000 Sensitivity RDfolder: 0.543 Mastr(seed): 0.000 Positive Predictive Value RDfolder: 0.679 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.66062906821e-08	15 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.551 Mastr(seed): 0.000 Sensitivity MCFold: 0.587 Mastr(seed): 0.000 Positive Predictive Value MCFold: 0.530 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	19 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.324 Mastr(seed): 0.000 Sensitivity RSpredict(seed): 0.177 Mastr(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.600 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.05041766982e-08	14 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.104 Mastr(seed): 0.000 Sensitivity Carnac(seed): 0.011 Mastr(seed): 0.000 Positive Predictive Value Carnac(seed): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 7.95923378787e-08	4 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.336 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.415 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.288 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.567 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.746 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): 0.629 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.580 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	6 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.581 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.576 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.598 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.619 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.653 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.606 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.714 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.451 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.447 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.472 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.601 Mastr(seed): 0.000 Sensitivity IPknot: 0.560 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.656 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(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	4 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.619 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.570 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.682 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.155 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.047 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.570 Mastr(seed): 0.000 Sensitivity ContextFold: 0.515 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.641 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.560 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.533 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.602 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.524 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.516 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.640 Mastr(seed): 0.000 Sensitivity RNASampler(seed): 0.554 Mastr(seed): 0.000 Positive Predictive Value RNASampler(seed): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.461 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.443 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.494 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.715 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.644 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.802 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 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 RNAsstandard base pair definition

Summary of pairwise comparisons

Detailed results of pairwise comparisons between methods

Pseudoknotted RNAs
standard base pair definition