CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Pseudoknotted short RNAs from RNAStrand dataset

	Only pseudoknotted RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. 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. 3, 2012
Base pair definition: extended
Type of RNA structures: pseudoknotted
RNA sequence length range: 20, 200
Number of RNA sequences: 53
Robustness test: no

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	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	Cylofold	no	35	0	0	18	53	45
2	McQFold	yes	35	1	0	17	53	53
3	Pknots	no	33	2	1	17	53	46
4	PknotsRG	no	32	3	1	17	53	53
4	CentroidAlifold(seed)	yes	32	3	1	17	19	17
6	PETfold_pre2.0(seed)	no	31	5	0	17	19	19
7	RNASampler(seed)	no	30	6	0	17	19	13
8	IPknot	yes	27	8	1	17	53	53
9	RNAalifold(seed)	no	27	9	0	17	19	17
10	CentroidFold	yes	26	10	0	17	53	53
11	Vsfold5	no	25	9	2	17	53	53
11	CentroidHomfold‑LAST	yes	25	9	2	17	53	53
13	Carnac(seed)	no	22	11	3	17	19	13
14	ProbKnot	yes	21	13	2	17	53	53
15	RNASLOpt	no	19	12	5	17	53	53
16	Contrafold	yes	18	12	6	17	53	53
17	HotKnots	no	17	14	5	17	53	53
18	RDfolder	no	17	15	4	17	53	46
19	Fold	no	16	15	5	17	53	53
20	ContextFold	yes	16	16	4	17	53	53
21	MaxExpect	yes	16	18	2	17	53	53
22	Murlet(seed)	yes	15	19	2	17	19	13
23	Sfold	no	13	21	2	17	53	53
24	UNAFold	no	11	25	0	17	53	53
25	Vsfold4	no	10	24	2	17	53	53
26	RNAshapes	no	10	26	0	17	53	53
27	RNAfold	no	9	26	1	17	53	53
28	MXScarna(seed)	no	8	25	3	17	19	17
29	RNAsubopt	no	7	27	2	17	53	53
30	RSpredict(seed)	no	6	28	2	17	19	17
31	CRWrnafold	yes	6	29	1	17	53	53
32	CMfinder(seed)	yes	4	23	6	20	19	11
33	RNAwolf	yes	4	32	0	17	53	53
34	Afold	no	3	31	1	18	53	33
35	Alterna	no	3	33	0	17	53	46
36	Mastr(seed)	yes	1	35	0	17	19	17
37	MCFold	yes	0	35	0	18	53	48
N/A	NanoFolder	yes	0	0	0	53	53	7
N/A	TurboFold(seed)	no	0	0	0	53	19	9
N/A	PPfold(seed)	yes	0	0	0	53	19	8
N/A	Multilign(seed)	no	0	0	0	53	19	8
N/A	Mastr(20)	yes	0	0	0	53	5	5
N/A	RNASampler(20)	no	0	0	0	53	5	5
N/A	Carnac(20)	no	0	0	0	53	5	5
N/A	Murlet(20)	yes	0	0	0	53	5	5
N/A	Multilign(20)	no	0	0	0	53	5	5
N/A	RSpredict(20)	no	0	0	0	53	5	5
N/A	TurboFold(20)	no	0	0	0	53	5	5
N/A	PPfold(20)	yes	0	0	0	53	5	5
N/A	CMfinder(20)	yes	0	0	0	53	5	5
N/A	CentroidAlifold(20)	yes	0	0	0	53	5	5
N/A	MXScarna(20)	no	0	0	0	53	5	5
N/A	RNAalifold(20)	no	0	0	0	53	5	5
N/A	PETfold_pre2.0(20)	no	0	0	0	53	5	5

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.


Cylofold		+ Cylofold vs McQFold Matthews Correlation Coefficient Cylofold: 0.764 McQFold: 0.699 Sensitivity Cylofold: 0.742 McQFold: 0.673 Positive Predictive Value Cylofold: 0.791 McQFold: 0.732 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.764 Pknots: 0.691 Sensitivity Cylofold: 0.742 Pknots: 0.662 Positive Predictive Value Cylofold: 0.791 Pknots: 0.728 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 CentroidAlifold(seed): 0.780 Sensitivity Cylofold: 0.772 CentroidAlifold(seed): 0.646 Positive Predictive Value Cylofold: 0.828 CentroidAlifold(seed): 0.946 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.10784607058e-08	+ Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.764 PknotsRG: 0.620 Sensitivity Cylofold: 0.742 PknotsRG: 0.594 Positive Predictive Value Cylofold: 0.791 PknotsRG: 0.655 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: 0.809 PETfold_pre2.0(seed): 0.737 Sensitivity Cylofold: 0.782 PETfold_pre2.0(seed): 0.666 Positive Predictive Value Cylofold: 0.841 PETfold_pre2.0(seed): 0.821 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.831 RNASampler(seed): 0.646 Sensitivity Cylofold: 0.834 RNASampler(seed): 0.562 Positive Predictive Value Cylofold: 0.830 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ Cylofold vs IPknot Matthews Correlation Coefficient Cylofold: 0.764 IPknot: 0.555 Sensitivity Cylofold: 0.742 IPknot: 0.499 Positive Predictive Value Cylofold: 0.791 IPknot: 0.628 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 RNAalifold(seed): 0.647 Sensitivity Cylofold: 0.772 RNAalifold(seed): 0.517 Positive Predictive Value Cylofold: 0.828 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ Cylofold vs CentroidFold Matthews Correlation Coefficient Cylofold: 0.764 CentroidFold: 0.541 Sensitivity Cylofold: 0.742 CentroidFold: 0.483 Positive Predictive Value Cylofold: 0.791 CentroidFold: 0.616 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Cylofold: 0.764 CentroidHomfold‑LAST: 0.538 Sensitivity Cylofold: 0.742 CentroidHomfold‑LAST: 0.469 Positive Predictive Value Cylofold: 0.791 CentroidHomfold‑LAST: 0.627 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.764 Vsfold5: 0.589 Sensitivity Cylofold: 0.742 Vsfold5: 0.541 Positive Predictive Value Cylofold: 0.791 Vsfold5: 0.649 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.831 Carnac(seed): 0.550 Sensitivity Cylofold: 0.834 Carnac(seed): 0.313 Positive Predictive Value Cylofold: 0.830 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.08220657796e-09	+ Cylofold vs ProbKnot Matthews Correlation Coefficient Cylofold: 0.764 ProbKnot: 0.525 Sensitivity Cylofold: 0.742 ProbKnot: 0.495 Positive Predictive Value Cylofold: 0.791 ProbKnot: 0.567 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.764 RNASLOpt: 0.546 Sensitivity Cylofold: 0.742 RNASLOpt: 0.488 Positive Predictive Value Cylofold: 0.791 RNASLOpt: 0.621 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Contrafold Matthews Correlation Coefficient Cylofold: 0.764 Contrafold: 0.512 Sensitivity Cylofold: 0.742 Contrafold: 0.475 Positive Predictive Value Cylofold: 0.791 Contrafold: 0.563 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: 0.764 HotKnots: 0.524 Sensitivity Cylofold: 0.742 HotKnots: 0.501 Positive Predictive Value Cylofold: 0.791 HotKnots: 0.560 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.764 RDfolder: 0.505 Sensitivity Cylofold: 0.742 RDfolder: 0.429 Positive Predictive Value Cylofold: 0.791 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Fold Matthews Correlation Coefficient Cylofold: 0.764 Fold: 0.515 Sensitivity Cylofold: 0.742 Fold: 0.475 Positive Predictive Value Cylofold: 0.791 Fold: 0.568 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs ContextFold Matthews Correlation Coefficient Cylofold: 0.764 ContextFold: 0.498 Sensitivity Cylofold: 0.742 ContextFold: 0.441 Positive Predictive Value Cylofold: 0.791 ContextFold: 0.574 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MaxExpect Matthews Correlation Coefficient Cylofold: 0.764 MaxExpect: 0.501 Sensitivity Cylofold: 0.742 MaxExpect: 0.461 Positive Predictive Value Cylofold: 0.791 MaxExpect: 0.556 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.831 Murlet(seed): 0.405 Sensitivity Cylofold: 0.834 Murlet(seed): 0.263 Positive Predictive Value Cylofold: 0.830 Murlet(seed): 0.633 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ Cylofold vs Sfold Matthews Correlation Coefficient Cylofold: 0.764 Sfold: 0.492 Sensitivity Cylofold: 0.742 Sfold: 0.443 Positive Predictive Value Cylofold: 0.791 Sfold: 0.558 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs UNAFold Matthews Correlation Coefficient Cylofold: 0.764 UNAFold: 0.478 Sensitivity Cylofold: 0.742 UNAFold: 0.439 Positive Predictive Value Cylofold: 0.791 UNAFold: 0.532 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.764 Vsfold4: 0.477 Sensitivity Cylofold: 0.742 Vsfold4: 0.420 Positive Predictive Value Cylofold: 0.791 Vsfold4: 0.554 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.764 RNAshapes: 0.473 Sensitivity Cylofold: 0.742 RNAshapes: 0.434 Positive Predictive Value Cylofold: 0.791 RNAshapes: 0.526 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.764 RNAfold: 0.486 Sensitivity Cylofold: 0.742 RNAfold: 0.447 Positive Predictive Value Cylofold: 0.791 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.798 MXScarna(seed): 0.542 Sensitivity Cylofold: 0.772 MXScarna(seed): 0.505 Positive Predictive Value Cylofold: 0.828 MXScarna(seed): 0.590 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.764 RNAsubopt: 0.480 Sensitivity Cylofold: 0.742 RNAsubopt: 0.443 Positive Predictive Value Cylofold: 0.791 RNAsubopt: 0.531 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.798 RSpredict(seed): 0.514 Sensitivity Cylofold: 0.772 RSpredict(seed): 0.434 Positive Predictive Value Cylofold: 0.828 RSpredict(seed): 0.618 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.13392142882e-08	+ Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.764 CRWrnafold: 0.468 Sensitivity Cylofold: 0.742 CRWrnafold: 0.422 Positive Predictive Value Cylofold: 0.791 CRWrnafold: 0.530 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: 0.797 CMfinder(seed): 0.439 Sensitivity Cylofold: 0.801 CMfinder(seed): 0.348 Positive Predictive Value Cylofold: 0.797 CMfinder(seed): 0.563 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.764 RNAwolf: 0.396 Sensitivity Cylofold: 0.742 RNAwolf: 0.378 Positive Predictive Value Cylofold: 0.791 RNAwolf: 0.429 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Afold Matthews Correlation Coefficient Cylofold: 0.735 Afold: 0.318 Sensitivity Cylofold: 0.722 Afold: 0.304 Positive Predictive Value Cylofold: 0.755 Afold: 0.348 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.764 Alterna: 0.401 Sensitivity Cylofold: 0.742 Alterna: 0.372 Positive Predictive Value Cylofold: 0.791 Alterna: 0.446 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.798 Mastr(seed): 0.406 Sensitivity Cylofold: 0.772 Mastr(seed): 0.212 Positive Predictive Value Cylofold: 0.828 Mastr(seed): 0.784 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08	? Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.756 Mastr(20): 0.561 Sensitivity Cylofold: 0.677 Mastr(20): 0.459 Positive Predictive Value Cylofold: 0.849 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.784 NanoFolder: 0.242 Sensitivity Cylofold: 0.720 NanoFolder: 0.273 Positive Predictive Value Cylofold: 0.857 NanoFolder: 0.228 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.821 Cylofold: 0.756 Sensitivity Carnac(20): 0.684 Cylofold: 0.677 Positive Predictive Value Carnac(20): 0.989 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.943 Multilign(seed): 0.572 Sensitivity Cylofold: 0.935 Multilign(seed): 0.532 Positive Predictive Value Cylofold: 0.951 Multilign(seed): 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.862 Cylofold: 0.756 Sensitivity Multilign(20): 0.752 Cylofold: 0.677 Positive Predictive Value Multilign(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.857 Cylofold: 0.756 Sensitivity TurboFold(20): 0.744 Cylofold: 0.677 Positive Predictive Value TurboFold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.844 Cylofold: 0.756 Sensitivity RNAalifold(20): 0.722 Cylofold: 0.677 Positive Predictive Value RNAalifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.840 Cylofold: 0.756 Sensitivity RNASampler(20): 0.714 Cylofold: 0.677 Positive Predictive Value RNASampler(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.779 Cylofold: 0.756 Sensitivity CMfinder(20): 0.617 Cylofold: 0.677 Positive Predictive Value CMfinder(20): 0.988 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Cylofold: 0.756 Sensitivity PETfold_pre2.0(20): 0.759 Cylofold: 0.677 Positive Predictive Value PETfold_pre2.0(20): 0.962 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.943 PPfold(seed): 0.656 Sensitivity Cylofold: 0.935 PPfold(seed): 0.532 Positive Predictive Value Cylofold: 0.951 PPfold(seed): 0.815 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.911 TurboFold(seed): 0.587 Sensitivity Cylofold: 0.914 TurboFold(seed): 0.513 Positive Predictive Value Cylofold: 0.908 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.837 Cylofold: 0.756 Sensitivity MXScarna(20): 0.752 Cylofold: 0.677 Positive Predictive Value MXScarna(20): 0.935 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.756 RSpredict(20): 0.672 Sensitivity Cylofold: 0.677 RSpredict(20): 0.549 Positive Predictive Value Cylofold: 0.849 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Cylofold: 0.756 Sensitivity CentroidAlifold(20): 0.752 Cylofold: 0.677 Positive Predictive Value CentroidAlifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: 0.756 Murlet(20): 0.741 Sensitivity Cylofold: 0.677 Murlet(20): 0.594 Positive Predictive Value Cylofold: 0.849 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.840 Cylofold: 0.756 Sensitivity PPfold(20): 0.737 Cylofold: 0.677 Positive Predictive Value PPfold(20): 0.961 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.771 MCFold: 0.294 Sensitivity Cylofold: 0.749 MCFold: 0.323 Positive Predictive Value Cylofold: 0.799 MCFold: 0.284 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08
McQFold	45 Cylofold vs McQFold Matthews Correlation Coefficient Cylofold: 0.764 McQFold: 0.699 Sensitivity Cylofold: 0.742 McQFold: 0.673 Positive Predictive Value Cylofold: 0.791 McQFold: 0.732 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.705 Pknots: 0.697 Sensitivity McQFold: 0.679 Pknots: 0.668 Positive Predictive Value McQFold: 0.738 Pknots: 0.733 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 1.59823887228e-06	+ McQFold vs CentroidAlifold(seed) Matthews Correlation Coefficient McQFold: 0.834 CentroidAlifold(seed): 0.767 Sensitivity McQFold: 0.799 CentroidAlifold(seed): 0.634 Positive Predictive Value McQFold: 0.872 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ McQFold vs PknotsRG Matthews Correlation Coefficient McQFold: 0.594 PknotsRG: 0.531 Sensitivity McQFold: 0.583 PknotsRG: 0.525 Positive Predictive Value McQFold: 0.611 PknotsRG: 0.544 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient McQFold: 0.839 PETfold_pre2.0(seed): 0.729 Sensitivity McQFold: 0.804 PETfold_pre2.0(seed): 0.649 Positive Predictive Value McQFold: 0.878 PETfold_pre2.0(seed): 0.824 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.36849473644e-08	+ McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.862 RNASampler(seed): 0.655 Sensitivity McQFold: 0.849 RNASampler(seed): 0.572 Positive Predictive Value McQFold: 0.877 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ McQFold vs IPknot Matthews Correlation Coefficient McQFold: 0.594 IPknot: 0.489 Sensitivity McQFold: 0.583 IPknot: 0.435 Positive Predictive Value McQFold: 0.611 IPknot: 0.556 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAalifold(seed) Matthews Correlation Coefficient McQFold: 0.834 RNAalifold(seed): 0.657 Sensitivity McQFold: 0.799 RNAalifold(seed): 0.522 Positive Predictive Value McQFold: 0.872 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ McQFold vs CentroidFold Matthews Correlation Coefficient McQFold: 0.594 CentroidFold: 0.482 Sensitivity McQFold: 0.583 CentroidFold: 0.430 Positive Predictive Value McQFold: 0.611 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient McQFold: 0.594 CentroidHomfold‑LAST: 0.488 Sensitivity McQFold: 0.583 CentroidHomfold‑LAST: 0.407 Positive Predictive Value McQFold: 0.611 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.594 Vsfold5: 0.534 Sensitivity McQFold: 0.583 Vsfold5: 0.505 Positive Predictive Value McQFold: 0.611 Vsfold5: 0.572 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.862 Carnac(seed): 0.582 Sensitivity McQFold: 0.849 Carnac(seed): 0.354 Positive Predictive Value McQFold: 0.877 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ McQFold vs ProbKnot Matthews Correlation Coefficient McQFold: 0.594 ProbKnot: 0.459 Sensitivity McQFold: 0.583 ProbKnot: 0.440 Positive Predictive Value McQFold: 0.611 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.594 RNASLOpt: 0.458 Sensitivity McQFold: 0.583 RNASLOpt: 0.419 Positive Predictive Value McQFold: 0.611 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Contrafold Matthews Correlation Coefficient McQFold: 0.594 Contrafold: 0.458 Sensitivity McQFold: 0.583 Contrafold: 0.435 Positive Predictive Value McQFold: 0.611 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs HotKnots Matthews Correlation Coefficient McQFold: 0.594 HotKnots: 0.453 Sensitivity McQFold: 0.583 HotKnots: 0.445 Positive Predictive Value McQFold: 0.611 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.705 RDfolder: 0.508 Sensitivity McQFold: 0.679 RDfolder: 0.432 Positive Predictive Value McQFold: 0.738 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Fold Matthews Correlation Coefficient McQFold: 0.594 Fold: 0.453 Sensitivity McQFold: 0.583 Fold: 0.431 Positive Predictive Value McQFold: 0.611 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs ContextFold Matthews Correlation Coefficient McQFold: 0.594 ContextFold: 0.447 Sensitivity McQFold: 0.583 ContextFold: 0.407 Positive Predictive Value McQFold: 0.611 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MaxExpect Matthews Correlation Coefficient McQFold: 0.594 MaxExpect: 0.440 Sensitivity McQFold: 0.583 MaxExpect: 0.414 Positive Predictive Value McQFold: 0.611 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.862 Murlet(seed): 0.482 Sensitivity McQFold: 0.849 Murlet(seed): 0.319 Positive Predictive Value McQFold: 0.877 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ McQFold vs Sfold Matthews Correlation Coefficient McQFold: 0.594 Sfold: 0.425 Sensitivity McQFold: 0.583 Sfold: 0.377 Positive Predictive Value McQFold: 0.611 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs UNAFold Matthews Correlation Coefficient McQFold: 0.594 UNAFold: 0.412 Sensitivity McQFold: 0.583 UNAFold: 0.390 Positive Predictive Value McQFold: 0.611 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.594 Vsfold4: 0.423 Sensitivity McQFold: 0.583 Vsfold4: 0.380 Positive Predictive Value McQFold: 0.611 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.594 RNAshapes: 0.416 Sensitivity McQFold: 0.583 RNAshapes: 0.395 Positive Predictive Value McQFold: 0.611 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAfold Matthews Correlation Coefficient McQFold: 0.594 RNAfold: 0.409 Sensitivity McQFold: 0.583 RNAfold: 0.390 Positive Predictive Value McQFold: 0.611 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MXScarna(seed) Matthews Correlation Coefficient McQFold: 0.834 MXScarna(seed): 0.539 Sensitivity McQFold: 0.799 MXScarna(seed): 0.501 Positive Predictive Value McQFold: 0.872 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ McQFold vs RNAsubopt Matthews Correlation Coefficient McQFold: 0.594 RNAsubopt: 0.394 Sensitivity McQFold: 0.583 RNAsubopt: 0.378 Positive Predictive Value McQFold: 0.611 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.834 RSpredict(seed): 0.514 Sensitivity McQFold: 0.799 RSpredict(seed): 0.427 Positive Predictive Value McQFold: 0.872 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.36849473644e-08	+ McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.594 CRWrnafold: 0.374 Sensitivity McQFold: 0.583 CRWrnafold: 0.351 Positive Predictive Value McQFold: 0.611 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.842 CMfinder(seed): 0.443 Sensitivity McQFold: 0.827 CMfinder(seed): 0.333 Positive Predictive Value McQFold: 0.858 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.594 RNAwolf: 0.362 Sensitivity McQFold: 0.583 RNAwolf: 0.353 Positive Predictive Value McQFold: 0.611 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Afold Matthews Correlation Coefficient McQFold: 0.619 Afold: 0.316 Sensitivity McQFold: 0.610 Afold: 0.305 Positive Predictive Value McQFold: 0.634 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.705 Alterna: 0.393 Sensitivity McQFold: 0.679 Alterna: 0.365 Positive Predictive Value McQFold: 0.738 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.834 Mastr(seed): 0.341 Sensitivity McQFold: 0.799 Mastr(seed): 0.176 Positive Predictive Value McQFold: 0.872 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	? McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.777 Mastr(20): 0.561 Sensitivity McQFold: 0.692 Mastr(20): 0.459 Positive Predictive Value McQFold: 0.876 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.813 NanoFolder: 0.304 Sensitivity McQFold: 0.759 NanoFolder: 0.343 Positive Predictive Value McQFold: 0.875 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.821 McQFold: 0.777 Sensitivity Carnac(20): 0.684 McQFold: 0.692 Positive Predictive Value Carnac(20): 0.989 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.932 Multilign(seed): 0.575 Sensitivity McQFold: 0.936 Multilign(seed): 0.536 Positive Predictive Value McQFold: 0.929 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.862 McQFold: 0.777 Sensitivity Multilign(20): 0.752 McQFold: 0.692 Positive Predictive Value Multilign(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.857 McQFold: 0.777 Sensitivity TurboFold(20): 0.744 McQFold: 0.692 Positive Predictive Value TurboFold(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.844 McQFold: 0.777 Sensitivity RNAalifold(20): 0.722 McQFold: 0.692 Positive Predictive Value RNAalifold(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.840 McQFold: 0.777 Sensitivity RNASampler(20): 0.714 McQFold: 0.692 Positive Predictive Value RNASampler(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.779 McQFold: 0.777 Sensitivity CMfinder(20): 0.617 McQFold: 0.692 Positive Predictive Value CMfinder(20): 0.988 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 McQFold: 0.777 Sensitivity PETfold_pre2.0(20): 0.759 McQFold: 0.692 Positive Predictive Value PETfold_pre2.0(20): 0.962 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.932 PPfold(seed): 0.666 Sensitivity McQFold: 0.936 PPfold(seed): 0.536 Positive Predictive Value McQFold: 0.929 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? McQFold vs TurboFold(seed) Matthews Correlation Coefficient McQFold: 0.898 TurboFold(seed): 0.600 Sensitivity McQFold: 0.899 TurboFold(seed): 0.518 Positive Predictive Value McQFold: 0.899 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.837 McQFold: 0.777 Sensitivity MXScarna(20): 0.752 McQFold: 0.692 Positive Predictive Value MXScarna(20): 0.935 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.777 RSpredict(20): 0.672 Sensitivity McQFold: 0.692 RSpredict(20): 0.549 Positive Predictive Value McQFold: 0.876 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 McQFold: 0.777 Sensitivity CentroidAlifold(20): 0.752 McQFold: 0.692 Positive Predictive Value CentroidAlifold(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? McQFold vs Murlet(20) Matthews Correlation Coefficient McQFold: 0.777 Murlet(20): 0.741 Sensitivity McQFold: 0.692 Murlet(20): 0.594 Positive Predictive Value McQFold: 0.876 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.840 McQFold: 0.777 Sensitivity PPfold(20): 0.737 McQFold: 0.692 Positive Predictive Value PPfold(20): 0.961 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.652 MCFold: 0.290 Sensitivity McQFold: 0.631 MCFold: 0.320 Positive Predictive Value McQFold: 0.681 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Pknots	45 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.764 Pknots: 0.691 Sensitivity Cylofold: 0.742 Pknots: 0.662 Positive Predictive Value Cylofold: 0.791 Pknots: 0.728 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.705 Pknots: 0.697 Sensitivity McQFold: 0.679 Pknots: 0.668 Positive Predictive Value McQFold: 0.738 Pknots: 0.733 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 1.59823887228e-06		= CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Pknots: 0.768 Sensitivity CentroidAlifold(seed): 0.642 Pknots: 0.748 Positive Predictive Value CentroidAlifold(seed): 0.936 Pknots: 0.792 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.119719389721	+ Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.697 PknotsRG: 0.627 Sensitivity Pknots: 0.668 PknotsRG: 0.601 Positive Predictive Value Pknots: 0.733 PknotsRG: 0.662 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: 0.781 PETfold_pre2.0(seed): 0.736 Sensitivity Pknots: 0.760 PETfold_pre2.0(seed): 0.661 Positive Predictive Value Pknots: 0.808 PETfold_pre2.0(seed): 0.823 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.803 RNASampler(seed): 0.641 Sensitivity Pknots: 0.820 RNASampler(seed): 0.562 Positive Predictive Value Pknots: 0.789 RNASampler(seed): 0.736 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.20383511129e-08	+ Pknots vs IPknot Matthews Correlation Coefficient Pknots: 0.697 IPknot: 0.558 Sensitivity Pknots: 0.668 IPknot: 0.501 Positive Predictive Value Pknots: 0.733 IPknot: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: 0.768 RNAalifold(seed): 0.651 Sensitivity Pknots: 0.748 RNAalifold(seed): 0.519 Positive Predictive Value Pknots: 0.792 RNAalifold(seed): 0.823 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.18141491686e-08	+ Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: 0.697 CentroidFold: 0.544 Sensitivity Pknots: 0.668 CentroidFold: 0.485 Positive Predictive Value Pknots: 0.733 CentroidFold: 0.621 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: 0.697 CentroidHomfold‑LAST: 0.541 Sensitivity Pknots: 0.668 CentroidHomfold‑LAST: 0.471 Positive Predictive Value Pknots: 0.733 CentroidHomfold‑LAST: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.697 Vsfold5: 0.597 Sensitivity Pknots: 0.668 Vsfold5: 0.550 Positive Predictive Value Pknots: 0.733 Vsfold5: 0.657 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.803 Carnac(seed): 0.531 Sensitivity Pknots: 0.820 Carnac(seed): 0.292 Positive Predictive Value Pknots: 0.789 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ Pknots vs ProbKnot Matthews Correlation Coefficient Pknots: 0.697 ProbKnot: 0.527 Sensitivity Pknots: 0.668 ProbKnot: 0.496 Positive Predictive Value Pknots: 0.733 ProbKnot: 0.570 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: 0.697 RNASLOpt: 0.549 Sensitivity Pknots: 0.668 RNASLOpt: 0.489 Positive Predictive Value Pknots: 0.733 RNASLOpt: 0.626 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Contrafold Matthews Correlation Coefficient Pknots: 0.697 Contrafold: 0.515 Sensitivity Pknots: 0.668 Contrafold: 0.477 Positive Predictive Value Pknots: 0.733 Contrafold: 0.567 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.697 HotKnots: 0.534 Sensitivity Pknots: 0.668 HotKnots: 0.510 Positive Predictive Value Pknots: 0.733 HotKnots: 0.569 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.697 RDfolder: 0.508 Sensitivity Pknots: 0.668 RDfolder: 0.432 Positive Predictive Value Pknots: 0.733 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Fold Matthews Correlation Coefficient Pknots: 0.697 Fold: 0.504 Sensitivity Pknots: 0.668 Fold: 0.466 Positive Predictive Value Pknots: 0.733 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs ContextFold Matthews Correlation Coefficient Pknots: 0.697 ContextFold: 0.500 Sensitivity Pknots: 0.668 ContextFold: 0.441 Positive Predictive Value Pknots: 0.733 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MaxExpect Matthews Correlation Coefficient Pknots: 0.697 MaxExpect: 0.503 Sensitivity Pknots: 0.668 MaxExpect: 0.463 Positive Predictive Value Pknots: 0.733 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.803 Murlet(seed): 0.432 Sensitivity Pknots: 0.820 Murlet(seed): 0.283 Positive Predictive Value Pknots: 0.789 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.697 Sfold: 0.482 Sensitivity Pknots: 0.668 Sfold: 0.435 Positive Predictive Value Pknots: 0.733 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.697 UNAFold: 0.468 Sensitivity Pknots: 0.668 UNAFold: 0.431 Positive Predictive Value Pknots: 0.733 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.697 Vsfold4: 0.480 Sensitivity Pknots: 0.668 Vsfold4: 0.423 Positive Predictive Value Pknots: 0.733 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.697 RNAshapes: 0.463 Sensitivity Pknots: 0.668 RNAshapes: 0.426 Positive Predictive Value Pknots: 0.733 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.697 RNAfold: 0.476 Sensitivity Pknots: 0.668 RNAfold: 0.439 Positive Predictive Value Pknots: 0.733 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: 0.768 MXScarna(seed): 0.514 Sensitivity Pknots: 0.748 MXScarna(seed): 0.481 Positive Predictive Value Pknots: 0.792 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: 0.697 RNAsubopt: 0.470 Sensitivity Pknots: 0.668 RNAsubopt: 0.435 Positive Predictive Value Pknots: 0.733 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.768 RSpredict(seed): 0.518 Sensitivity Pknots: 0.748 RSpredict(seed): 0.437 Positive Predictive Value Pknots: 0.792 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: 0.697 CRWrnafold: 0.458 Sensitivity Pknots: 0.668 CRWrnafold: 0.415 Positive Predictive Value Pknots: 0.733 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: 0.767 CMfinder(seed): 0.459 Sensitivity Pknots: 0.787 CMfinder(seed): 0.365 Positive Predictive Value Pknots: 0.752 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.697 RNAwolf: 0.401 Sensitivity Pknots: 0.668 RNAwolf: 0.381 Positive Predictive Value Pknots: 0.733 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.653 Afold: 0.309 Sensitivity Pknots: 0.630 Afold: 0.296 Positive Predictive Value Pknots: 0.684 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.697 Alterna: 0.393 Sensitivity Pknots: 0.668 Alterna: 0.365 Positive Predictive Value Pknots: 0.733 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.768 Mastr(seed): 0.365 Sensitivity Pknots: 0.748 Mastr(seed): 0.202 Positive Predictive Value Pknots: 0.792 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.02510705504e-08	? Pknots vs Mastr(20) Matthews Correlation Coefficient Pknots: 0.723 Mastr(20): 0.561 Sensitivity Pknots: 0.632 Mastr(20): 0.459 Positive Predictive Value Pknots: 0.832 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.808 NanoFolder: 0.304 Sensitivity Pknots: 0.759 NanoFolder: 0.343 Positive Predictive Value Pknots: 0.863 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.821 Pknots: 0.723 Sensitivity Carnac(20): 0.684 Pknots: 0.632 Positive Predictive Value Carnac(20): 0.989 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.886 Multilign(seed): 0.575 Sensitivity Pknots: 0.893 Multilign(seed): 0.536 Positive Predictive Value Pknots: 0.880 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.862 Pknots: 0.723 Sensitivity Multilign(20): 0.752 Pknots: 0.632 Positive Predictive Value Multilign(20): 0.990 Pknots: 0.832 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): 0.857 Pknots: 0.723 Sensitivity TurboFold(20): 0.744 Pknots: 0.632 Positive Predictive Value TurboFold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.844 Pknots: 0.723 Sensitivity RNAalifold(20): 0.722 Pknots: 0.632 Positive Predictive Value RNAalifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.840 Pknots: 0.723 Sensitivity RNASampler(20): 0.714 Pknots: 0.632 Positive Predictive Value RNASampler(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.779 Pknots: 0.723 Sensitivity CMfinder(20): 0.617 Pknots: 0.632 Positive Predictive Value CMfinder(20): 0.988 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Pknots: 0.723 Sensitivity PETfold_pre2.0(20): 0.759 Pknots: 0.632 Positive Predictive Value PETfold_pre2.0(20): 0.962 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.886 PPfold(seed): 0.666 Sensitivity Pknots: 0.893 PPfold(seed): 0.536 Positive Predictive Value Pknots: 0.880 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Pknots vs TurboFold(seed) Matthews Correlation Coefficient Pknots: 0.870 TurboFold(seed): 0.600 Sensitivity Pknots: 0.887 TurboFold(seed): 0.518 Positive Predictive Value Pknots: 0.856 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.837 Pknots: 0.723 Sensitivity MXScarna(20): 0.752 Pknots: 0.632 Positive Predictive Value MXScarna(20): 0.935 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RSpredict(20) Matthews Correlation Coefficient Pknots: 0.723 RSpredict(20): 0.672 Sensitivity Pknots: 0.632 RSpredict(20): 0.549 Positive Predictive Value Pknots: 0.832 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Pknots: 0.723 Sensitivity CentroidAlifold(20): 0.752 Pknots: 0.632 Positive Predictive Value CentroidAlifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.741 Pknots: 0.723 Sensitivity Murlet(20): 0.594 Pknots: 0.632 Positive Predictive Value Murlet(20): 0.929 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.840 Pknots: 0.723 Sensitivity PPfold(20): 0.737 Pknots: 0.632 Positive Predictive Value PPfold(20): 0.961 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.707 MCFold: 0.296 Sensitivity Pknots: 0.676 MCFold: 0.325 Positive Predictive Value Pknots: 0.747 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	15 Cylofold vs CentroidAlifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 CentroidAlifold(seed): 0.780 Sensitivity Cylofold: 0.772 CentroidAlifold(seed): 0.646 Positive Predictive Value Cylofold: 0.828 CentroidAlifold(seed): 0.946 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.10784607058e-08	17 McQFold vs CentroidAlifold(seed) Matthews Correlation Coefficient McQFold: 0.834 CentroidAlifold(seed): 0.767 Sensitivity McQFold: 0.799 CentroidAlifold(seed): 0.634 Positive Predictive Value McQFold: 0.872 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	16 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Pknots: 0.768 Sensitivity CentroidAlifold(seed): 0.642 Pknots: 0.748 Positive Predictive Value CentroidAlifold(seed): 0.936 Pknots: 0.792 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.119719389721		- PknotsRG vs CentroidAlifold(seed) Matthews Correlation Coefficient PknotsRG: 0.787 CentroidAlifold(seed): 0.767 Sensitivity PknotsRG: 0.761 CentroidAlifold(seed): 0.634 Positive Predictive Value PknotsRG: 0.817 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ CentroidAlifold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 PETfold_pre2.0(seed): 0.710 Sensitivity CentroidAlifold(seed): 0.634 PETfold_pre2.0(seed): 0.626 Positive Predictive Value CentroidAlifold(seed): 0.933 PETfold_pre2.0(seed): 0.809 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 RNASampler(seed): 0.655 Sensitivity CentroidAlifold(seed): 0.579 RNASampler(seed): 0.572 Positive Predictive Value CentroidAlifold(seed): 0.902 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 IPknot: 0.671 Sensitivity CentroidAlifold(seed): 0.634 IPknot: 0.590 Positive Predictive Value CentroidAlifold(seed): 0.933 IPknot: 0.768 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAalifold(seed): 0.657 Sensitivity CentroidAlifold(seed): 0.634 RNAalifold(seed): 0.522 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.28538098861e-09	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 CentroidFold: 0.695 Sensitivity CentroidAlifold(seed): 0.634 CentroidFold: 0.608 Positive Predictive Value CentroidAlifold(seed): 0.933 CentroidFold: 0.799 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 CentroidHomfold‑LAST: 0.654 Sensitivity CentroidAlifold(seed): 0.634 CentroidHomfold‑LAST: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.933 CentroidHomfold‑LAST: 0.769 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Vsfold5: 0.531 Sensitivity CentroidAlifold(seed): 0.634 Vsfold5: 0.501 Positive Predictive Value CentroidAlifold(seed): 0.933 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 Carnac(seed): 0.582 Sensitivity CentroidAlifold(seed): 0.579 Carnac(seed): 0.354 Positive Predictive Value CentroidAlifold(seed): 0.902 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.52214427071e-09	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 ProbKnot: 0.603 Sensitivity CentroidAlifold(seed): 0.634 ProbKnot: 0.565 Positive Predictive Value CentroidAlifold(seed): 0.933 ProbKnot: 0.649 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNASLOpt: 0.635 Sensitivity CentroidAlifold(seed): 0.634 RNASLOpt: 0.565 Positive Predictive Value CentroidAlifold(seed): 0.933 RNASLOpt: 0.718 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Contrafold: 0.653 Sensitivity CentroidAlifold(seed): 0.634 Contrafold: 0.598 Positive Predictive Value CentroidAlifold(seed): 0.933 Contrafold: 0.719 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 HotKnots: 0.603 Sensitivity CentroidAlifold(seed): 0.634 HotKnots: 0.588 Positive Predictive Value CentroidAlifold(seed): 0.933 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.45076534967e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RDfolder: 0.616 Sensitivity CentroidAlifold(seed): 0.642 RDfolder: 0.531 Positive Predictive Value CentroidAlifold(seed): 0.936 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Fold: 0.572 Sensitivity CentroidAlifold(seed): 0.634 Fold: 0.534 Positive Predictive Value CentroidAlifold(seed): 0.933 Fold: 0.619 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ CentroidAlifold(seed) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 ContextFold: 0.567 Sensitivity CentroidAlifold(seed): 0.634 ContextFold: 0.506 Positive Predictive Value CentroidAlifold(seed): 0.933 ContextFold: 0.642 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 MaxExpect: 0.603 Sensitivity CentroidAlifold(seed): 0.634 MaxExpect: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.933 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 Murlet(seed): 0.482 Sensitivity CentroidAlifold(seed): 0.579 Murlet(seed): 0.319 Positive Predictive Value CentroidAlifold(seed): 0.902 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Sfold: 0.571 Sensitivity CentroidAlifold(seed): 0.634 Sfold: 0.519 Positive Predictive Value CentroidAlifold(seed): 0.933 Sfold: 0.636 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 UNAFold: 0.552 Sensitivity CentroidAlifold(seed): 0.634 UNAFold: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.933 UNAFold: 0.597 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Vsfold4: 0.488 Sensitivity CentroidAlifold(seed): 0.634 Vsfold4: 0.445 Positive Predictive Value CentroidAlifold(seed): 0.933 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAshapes: 0.526 Sensitivity CentroidAlifold(seed): 0.634 RNAshapes: 0.496 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAfold: 0.566 Sensitivity CentroidAlifold(seed): 0.634 RNAfold: 0.532 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 MXScarna(seed): 0.539 Sensitivity CentroidAlifold(seed): 0.634 MXScarna(seed): 0.501 Positive Predictive Value CentroidAlifold(seed): 0.933 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAsubopt: 0.538 Sensitivity CentroidAlifold(seed): 0.634 RNAsubopt: 0.506 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RSpredict(seed): 0.514 Sensitivity CentroidAlifold(seed): 0.634 RSpredict(seed): 0.427 Positive Predictive Value CentroidAlifold(seed): 0.933 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 CRWrnafold: 0.527 Sensitivity CentroidAlifold(seed): 0.634 CRWrnafold: 0.491 Positive Predictive Value CentroidAlifold(seed): 0.933 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.718 CMfinder(seed): 0.443 Sensitivity CentroidAlifold(seed): 0.582 CMfinder(seed): 0.333 Positive Predictive Value CentroidAlifold(seed): 0.890 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.67568292565e-09	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAwolf: 0.487 Sensitivity CentroidAlifold(seed): 0.634 RNAwolf: 0.461 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.748 Afold: 0.517 Sensitivity CentroidAlifold(seed): 0.615 Afold: 0.480 Positive Predictive Value CentroidAlifold(seed): 0.912 Afold: 0.564 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Alterna: 0.486 Sensitivity CentroidAlifold(seed): 0.642 Alterna: 0.455 Positive Predictive Value CentroidAlifold(seed): 0.936 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Mastr(seed): 0.341 Sensitivity CentroidAlifold(seed): 0.634 Mastr(seed): 0.176 Positive Predictive Value CentroidAlifold(seed): 0.933 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.69265863073e-08	? CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Mastr(20): 0.705 Sensitivity CentroidAlifold(seed): 0.778 Mastr(20): 0.565 Positive Predictive Value CentroidAlifold(seed): 1.000 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.771 NanoFolder: 0.489 Sensitivity CentroidAlifold(seed): 0.633 NanoFolder: 0.544 Positive Predictive Value CentroidAlifold(seed): 0.943 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Carnac(20): 0.832 Sensitivity CentroidAlifold(seed): 0.778 Carnac(20): 0.694 Positive Predictive Value CentroidAlifold(seed): 1.000 Carnac(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Multilign(seed): 0.575 Sensitivity CentroidAlifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Multilign(20): 0.865 Sensitivity CentroidAlifold(seed): 0.778 Multilign(20): 0.750 Positive Predictive Value CentroidAlifold(seed): 1.000 Multilign(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 TurboFold(20): 0.860 Sensitivity CentroidAlifold(seed): 0.778 TurboFold(20): 0.741 Positive Predictive Value CentroidAlifold(seed): 1.000 TurboFold(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 RNAalifold(20): 0.838 Sensitivity CentroidAlifold(seed): 0.778 RNAalifold(20): 0.704 Positive Predictive Value CentroidAlifold(seed): 1.000 RNAalifold(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 RNASampler(20): 0.832 Sensitivity CentroidAlifold(seed): 0.778 RNASampler(20): 0.694 Positive Predictive Value CentroidAlifold(seed): 1.000 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 CMfinder(20): 0.756 Sensitivity CentroidAlifold(seed): 0.778 CMfinder(20): 0.574 Positive Predictive Value CentroidAlifold(seed): 1.000 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 PETfold_pre2.0(20): 0.849 Sensitivity CentroidAlifold(seed): 0.778 PETfold_pre2.0(20): 0.750 Positive Predictive Value CentroidAlifold(seed): 1.000 PETfold_pre2.0(20): 0.964 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): 0.690 PPfold(seed): 0.666 Sensitivity CentroidAlifold(seed): 0.536 PPfold(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.706 TurboFold(seed): 0.600 Sensitivity CentroidAlifold(seed): 0.560 TurboFold(seed): 0.518 Positive Predictive Value CentroidAlifold(seed): 0.895 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 MXScarna(20): 0.855 Sensitivity CentroidAlifold(seed): 0.778 MXScarna(20): 0.769 Positive Predictive Value CentroidAlifold(seed): 1.000 MXScarna(20): 0.954 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 RSpredict(20): 0.676 Sensitivity CentroidAlifold(seed): 0.778 RSpredict(20): 0.546 Positive Predictive Value CentroidAlifold(seed): 1.000 RSpredict(20): 0.843 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 CentroidAlifold(20): 0.860 Sensitivity CentroidAlifold(seed): 0.778 CentroidAlifold(20): 0.741 Positive Predictive Value CentroidAlifold(seed): 1.000 CentroidAlifold(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Murlet(20): 0.780 Sensitivity CentroidAlifold(seed): 0.778 Murlet(20): 0.611 Positive Predictive Value CentroidAlifold(seed): 1.000 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 PPfold(20): 0.833 Sensitivity CentroidAlifold(seed): 0.778 PPfold(20): 0.722 Positive Predictive Value CentroidAlifold(seed): 1.000 PPfold(20): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 MCFold: 0.358 Sensitivity CentroidAlifold(seed): 0.642 MCFold: 0.409 Positive Predictive Value CentroidAlifold(seed): 0.944 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.63136857368e-09
PknotsRG	45 Cylofold vs PknotsRG Matthews Correlation Coefficient Cylofold: 0.764 PknotsRG: 0.620 Sensitivity Cylofold: 0.742 PknotsRG: 0.594 Positive Predictive Value Cylofold: 0.791 PknotsRG: 0.655 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs PknotsRG Matthews Correlation Coefficient McQFold: 0.594 PknotsRG: 0.531 Sensitivity McQFold: 0.583 PknotsRG: 0.525 Positive Predictive Value McQFold: 0.611 PknotsRG: 0.544 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.697 PknotsRG: 0.627 Sensitivity Pknots: 0.668 PknotsRG: 0.601 Positive Predictive Value Pknots: 0.733 PknotsRG: 0.662 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PknotsRG vs CentroidAlifold(seed) Matthews Correlation Coefficient PknotsRG: 0.787 CentroidAlifold(seed): 0.767 Sensitivity PknotsRG: 0.761 CentroidAlifold(seed): 0.634 Positive Predictive Value PknotsRG: 0.817 CentroidAlifold(seed): 0.933 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52609899389e-08		+ PknotsRG vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PknotsRG: 0.739 PETfold_pre2.0(seed): 0.729 Sensitivity PknotsRG: 0.718 PETfold_pre2.0(seed): 0.649 Positive Predictive Value PknotsRG: 0.765 PETfold_pre2.0(seed): 0.824 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000640500069683	+ PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.819 RNASampler(seed): 0.655 Sensitivity PknotsRG: 0.818 RNASampler(seed): 0.572 Positive Predictive Value PknotsRG: 0.823 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ PknotsRG vs IPknot Matthews Correlation Coefficient PknotsRG: 0.531 IPknot: 0.489 Sensitivity PknotsRG: 0.525 IPknot: 0.435 Positive Predictive Value PknotsRG: 0.544 IPknot: 0.556 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.787 RNAalifold(seed): 0.657 Sensitivity PknotsRG: 0.761 RNAalifold(seed): 0.522 Positive Predictive Value PknotsRG: 0.817 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ PknotsRG vs CentroidFold Matthews Correlation Coefficient PknotsRG: 0.531 CentroidFold: 0.482 Sensitivity PknotsRG: 0.525 CentroidFold: 0.430 Positive Predictive Value PknotsRG: 0.544 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CentroidHomfold‑LAST Matthews Correlation Coefficient PknotsRG: 0.531 CentroidHomfold‑LAST: 0.488 Sensitivity PknotsRG: 0.525 CentroidHomfold‑LAST: 0.407 Positive Predictive Value PknotsRG: 0.544 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Vsfold5 vs PknotsRG Matthews Correlation Coefficient Vsfold5: 0.534 PknotsRG: 0.531 Sensitivity Vsfold5: 0.505 PknotsRG: 0.525 Positive Predictive Value Vsfold5: 0.572 PknotsRG: 0.544 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.501542402616	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.819 Carnac(seed): 0.582 Sensitivity PknotsRG: 0.818 Carnac(seed): 0.354 Positive Predictive Value PknotsRG: 0.823 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.531 ProbKnot: 0.459 Sensitivity PknotsRG: 0.525 ProbKnot: 0.440 Positive Predictive Value PknotsRG: 0.544 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.531 RNASLOpt: 0.458 Sensitivity PknotsRG: 0.525 RNASLOpt: 0.419 Positive Predictive Value PknotsRG: 0.544 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Contrafold Matthews Correlation Coefficient PknotsRG: 0.531 Contrafold: 0.458 Sensitivity PknotsRG: 0.525 Contrafold: 0.435 Positive Predictive Value PknotsRG: 0.544 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.531 HotKnots: 0.453 Sensitivity PknotsRG: 0.525 HotKnots: 0.445 Positive Predictive Value PknotsRG: 0.544 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.627 RDfolder: 0.508 Sensitivity PknotsRG: 0.601 RDfolder: 0.432 Positive Predictive Value PknotsRG: 0.662 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.531 Fold: 0.453 Sensitivity PknotsRG: 0.525 Fold: 0.431 Positive Predictive Value PknotsRG: 0.544 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs ContextFold Matthews Correlation Coefficient PknotsRG: 0.531 ContextFold: 0.447 Sensitivity PknotsRG: 0.525 ContextFold: 0.407 Positive Predictive Value PknotsRG: 0.544 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MaxExpect Matthews Correlation Coefficient PknotsRG: 0.531 MaxExpect: 0.440 Sensitivity PknotsRG: 0.525 MaxExpect: 0.414 Positive Predictive Value PknotsRG: 0.544 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.819 Murlet(seed): 0.482 Sensitivity PknotsRG: 0.818 Murlet(seed): 0.319 Positive Predictive Value PknotsRG: 0.823 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ PknotsRG vs Sfold Matthews Correlation Coefficient PknotsRG: 0.531 Sfold: 0.425 Sensitivity PknotsRG: 0.525 Sfold: 0.377 Positive Predictive Value PknotsRG: 0.544 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs UNAFold Matthews Correlation Coefficient PknotsRG: 0.531 UNAFold: 0.412 Sensitivity PknotsRG: 0.525 UNAFold: 0.390 Positive Predictive Value PknotsRG: 0.544 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.531 Vsfold4: 0.423 Sensitivity PknotsRG: 0.525 Vsfold4: 0.380 Positive Predictive Value PknotsRG: 0.544 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.531 RNAshapes: 0.416 Sensitivity PknotsRG: 0.525 RNAshapes: 0.395 Positive Predictive Value PknotsRG: 0.544 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.531 RNAfold: 0.409 Sensitivity PknotsRG: 0.525 RNAfold: 0.390 Positive Predictive Value PknotsRG: 0.544 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MXScarna(seed) Matthews Correlation Coefficient PknotsRG: 0.787 MXScarna(seed): 0.539 Sensitivity PknotsRG: 0.761 MXScarna(seed): 0.501 Positive Predictive Value PknotsRG: 0.817 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.531 RNAsubopt: 0.394 Sensitivity PknotsRG: 0.525 RNAsubopt: 0.378 Positive Predictive Value PknotsRG: 0.544 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.787 RSpredict(seed): 0.514 Sensitivity PknotsRG: 0.761 RSpredict(seed): 0.427 Positive Predictive Value PknotsRG: 0.817 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.531 CRWrnafold: 0.374 Sensitivity PknotsRG: 0.525 CRWrnafold: 0.351 Positive Predictive Value PknotsRG: 0.544 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.793 CMfinder(seed): 0.443 Sensitivity PknotsRG: 0.791 CMfinder(seed): 0.333 Positive Predictive Value PknotsRG: 0.798 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.531 RNAwolf: 0.362 Sensitivity PknotsRG: 0.525 RNAwolf: 0.353 Positive Predictive Value PknotsRG: 0.544 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.538 Afold: 0.316 Sensitivity PknotsRG: 0.533 Afold: 0.305 Positive Predictive Value PknotsRG: 0.551 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.627 Alterna: 0.393 Sensitivity PknotsRG: 0.601 Alterna: 0.365 Positive Predictive Value PknotsRG: 0.662 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.787 Mastr(seed): 0.341 Sensitivity PknotsRG: 0.761 Mastr(seed): 0.176 Positive Predictive Value PknotsRG: 0.817 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.50323628132e-08	? PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.592 Mastr(20): 0.561 Sensitivity PknotsRG: 0.526 Mastr(20): 0.459 Positive Predictive Value PknotsRG: 0.673 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.646 NanoFolder: 0.304 Sensitivity PknotsRG: 0.608 NanoFolder: 0.343 Positive Predictive Value PknotsRG: 0.692 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.821 PknotsRG: 0.592 Sensitivity Carnac(20): 0.684 PknotsRG: 0.526 Positive Predictive Value Carnac(20): 0.989 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.949 Multilign(seed): 0.575 Sensitivity PknotsRG: 0.943 Multilign(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.862 PknotsRG: 0.592 Sensitivity Multilign(20): 0.752 PknotsRG: 0.526 Positive Predictive Value Multilign(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.857 PknotsRG: 0.592 Sensitivity TurboFold(20): 0.744 PknotsRG: 0.526 Positive Predictive Value TurboFold(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.844 PknotsRG: 0.592 Sensitivity RNAalifold(20): 0.722 PknotsRG: 0.526 Positive Predictive Value RNAalifold(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.840 PknotsRG: 0.592 Sensitivity RNASampler(20): 0.714 PknotsRG: 0.526 Positive Predictive Value RNASampler(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs PknotsRG Matthews Correlation Coefficient CMfinder(20): 0.779 PknotsRG: 0.592 Sensitivity CMfinder(20): 0.617 PknotsRG: 0.526 Positive Predictive Value CMfinder(20): 0.988 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 PknotsRG: 0.592 Sensitivity PETfold_pre2.0(20): 0.759 PknotsRG: 0.526 Positive Predictive Value PETfold_pre2.0(20): 0.962 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.949 PPfold(seed): 0.666 Sensitivity PknotsRG: 0.943 PPfold(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.949 TurboFold(seed): 0.600 Sensitivity PknotsRG: 0.946 TurboFold(seed): 0.518 Positive Predictive Value PknotsRG: 0.952 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.837 PknotsRG: 0.592 Sensitivity MXScarna(20): 0.752 PknotsRG: 0.526 Positive Predictive Value MXScarna(20): 0.935 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.672 PknotsRG: 0.592 Sensitivity RSpredict(20): 0.549 PknotsRG: 0.526 Positive Predictive Value RSpredict(20): 0.830 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PknotsRG: 0.592 Sensitivity CentroidAlifold(20): 0.752 PknotsRG: 0.526 Positive Predictive Value CentroidAlifold(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.741 PknotsRG: 0.592 Sensitivity Murlet(20): 0.594 PknotsRG: 0.526 Positive Predictive Value Murlet(20): 0.929 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.840 PknotsRG: 0.592 Sensitivity PPfold(20): 0.737 PknotsRG: 0.526 Positive Predictive Value PPfold(20): 0.961 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.537 MCFold: 0.290 Sensitivity PknotsRG: 0.522 MCFold: 0.320 Positive Predictive Value PknotsRG: 0.560 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(seed)	17 Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: 0.809 PETfold_pre2.0(seed): 0.737 Sensitivity Cylofold: 0.782 PETfold_pre2.0(seed): 0.666 Positive Predictive Value Cylofold: 0.841 PETfold_pre2.0(seed): 0.821 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	19 McQFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient McQFold: 0.839 PETfold_pre2.0(seed): 0.729 Sensitivity McQFold: 0.804 PETfold_pre2.0(seed): 0.649 Positive Predictive Value McQFold: 0.878 PETfold_pre2.0(seed): 0.824 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.36849473644e-08	18 Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: 0.781 PETfold_pre2.0(seed): 0.736 Sensitivity Pknots: 0.760 PETfold_pre2.0(seed): 0.661 Positive Predictive Value Pknots: 0.808 PETfold_pre2.0(seed): 0.823 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	17 CentroidAlifold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 PETfold_pre2.0(seed): 0.710 Sensitivity CentroidAlifold(seed): 0.634 PETfold_pre2.0(seed): 0.626 Positive Predictive Value CentroidAlifold(seed): 0.933 PETfold_pre2.0(seed): 0.809 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.24019667966e-08	19 PknotsRG vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PknotsRG: 0.739 PETfold_pre2.0(seed): 0.729 Sensitivity PknotsRG: 0.718 PETfold_pre2.0(seed): 0.649 Positive Predictive Value PknotsRG: 0.765 PETfold_pre2.0(seed): 0.824 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000640500069683		+ PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 RNASampler(seed): 0.655 Sensitivity PETfold_pre2.0(seed): 0.572 RNASampler(seed): 0.572 Positive Predictive Value PETfold_pre2.0(seed): 0.769 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.04375264657e-07	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 IPknot: 0.680 Sensitivity PETfold_pre2.0(seed): 0.649 IPknot: 0.610 Positive Predictive Value PETfold_pre2.0(seed): 0.824 IPknot: 0.761 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RNAalifold(seed): 0.657 Sensitivity PETfold_pre2.0(seed): 0.626 RNAalifold(seed): 0.522 Positive Predictive Value PETfold_pre2.0(seed): 0.809 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.95070920198e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidFold: 0.683 Sensitivity PETfold_pre2.0(seed): 0.649 CentroidFold: 0.606 Positive Predictive Value PETfold_pre2.0(seed): 0.824 CentroidFold: 0.776 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidHomfold‑LAST: 0.683 Sensitivity PETfold_pre2.0(seed): 0.649 CentroidHomfold‑LAST: 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.824 CentroidHomfold‑LAST: 0.794 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold5: 0.569 Sensitivity PETfold_pre2.0(seed): 0.649 Vsfold5: 0.538 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Vsfold5: 0.608 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 Carnac(seed): 0.582 Sensitivity PETfold_pre2.0(seed): 0.572 Carnac(seed): 0.354 Positive Predictive Value PETfold_pre2.0(seed): 0.769 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 ProbKnot: 0.599 Sensitivity PETfold_pre2.0(seed): 0.649 ProbKnot: 0.567 Positive Predictive Value PETfold_pre2.0(seed): 0.824 ProbKnot: 0.638 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNASLOpt: 0.663 Sensitivity PETfold_pre2.0(seed): 0.649 RNASLOpt: 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNASLOpt: 0.744 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Contrafold: 0.653 Sensitivity PETfold_pre2.0(seed): 0.649 Contrafold: 0.606 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 HotKnots: 0.575 Sensitivity PETfold_pre2.0(seed): 0.649 HotKnots: 0.563 Positive Predictive Value PETfold_pre2.0(seed): 0.824 HotKnots: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 RDfolder: 0.586 Sensitivity PETfold_pre2.0(seed): 0.661 RDfolder: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.823 RDfolder: 0.682 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Fold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.649 Fold: 0.547 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Fold: 0.622 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 ContextFold: 0.601 Sensitivity PETfold_pre2.0(seed): 0.649 ContextFold: 0.540 Positive Predictive Value PETfold_pre2.0(seed): 0.824 ContextFold: 0.675 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 MaxExpect: 0.588 Sensitivity PETfold_pre2.0(seed): 0.649 MaxExpect: 0.549 Positive Predictive Value PETfold_pre2.0(seed): 0.824 MaxExpect: 0.636 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 Murlet(seed): 0.482 Sensitivity PETfold_pre2.0(seed): 0.572 Murlet(seed): 0.319 Positive Predictive Value PETfold_pre2.0(seed): 0.769 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.97952969696e-09	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Sfold: 0.543 Sensitivity PETfold_pre2.0(seed): 0.649 Sfold: 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Sfold: 0.596 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 UNAFold: 0.531 Sensitivity PETfold_pre2.0(seed): 0.649 UNAFold: 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.824 UNAFold: 0.570 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.42071836373e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold4: 0.532 Sensitivity PETfold_pre2.0(seed): 0.649 Vsfold4: 0.487 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Vsfold4: 0.588 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAshapes: 0.506 Sensitivity PETfold_pre2.0(seed): 0.649 RNAshapes: 0.481 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.86290426071e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAfold: 0.541 Sensitivity PETfold_pre2.0(seed): 0.649 RNAfold: 0.513 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAfold: 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 MXScarna(seed): 0.539 Sensitivity PETfold_pre2.0(seed): 0.626 MXScarna(seed): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.809 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAsubopt: 0.514 Sensitivity PETfold_pre2.0(seed): 0.649 RNAsubopt: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAsubopt: 0.547 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RSpredict(seed): 0.514 Sensitivity PETfold_pre2.0(seed): 0.626 RSpredict(seed): 0.427 Positive Predictive Value PETfold_pre2.0(seed): 0.809 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CRWrnafold: 0.564 Sensitivity PETfold_pre2.0(seed): 0.649 CRWrnafold: 0.526 Positive Predictive Value PETfold_pre2.0(seed): 0.824 CRWrnafold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.666 CMfinder(seed): 0.443 Sensitivity PETfold_pre2.0(seed): 0.574 CMfinder(seed): 0.333 Positive Predictive Value PETfold_pre2.0(seed): 0.777 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.16590079822e-09	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAwolf: 0.507 Sensitivity PETfold_pre2.0(seed): 0.649 RNAwolf: 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAwolf: 0.538 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.73174208038e-08	+ PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Afold: 0.481 Sensitivity PETfold_pre2.0(seed): 0.640 Afold: 0.451 Positive Predictive Value PETfold_pre2.0(seed): 0.812 Afold: 0.521 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Alterna: 0.503 Sensitivity PETfold_pre2.0(seed): 0.661 Alterna: 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.823 Alterna: 0.543 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 Mastr(seed): 0.341 Sensitivity PETfold_pre2.0(seed): 0.626 Mastr(seed): 0.176 Positive Predictive Value PETfold_pre2.0(seed): 0.809 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	? PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Mastr(20): 0.561 Sensitivity PETfold_pre2.0(seed): 0.774 Mastr(20): 0.459 Positive Predictive Value PETfold_pre2.0(seed): 0.904 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.783 NanoFolder: 0.346 Sensitivity PETfold_pre2.0(seed): 0.712 NanoFolder: 0.400 Positive Predictive Value PETfold_pre2.0(seed): 0.864 NanoFolder: 0.311 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): 0.835 Carnac(20): 0.821 Sensitivity PETfold_pre2.0(seed): 0.774 Carnac(20): 0.684 Positive Predictive Value PETfold_pre2.0(seed): 0.904 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.619 Multilign(seed): 0.575 Sensitivity PETfold_pre2.0(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PETfold_pre2.0(seed): 0.721 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Multilign(20): 0.862 PETfold_pre2.0(seed): 0.835 Sensitivity Multilign(20): 0.752 PETfold_pre2.0(seed): 0.774 Positive Predictive Value Multilign(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(20): 0.857 PETfold_pre2.0(seed): 0.835 Sensitivity TurboFold(20): 0.744 PETfold_pre2.0(seed): 0.774 Positive Predictive Value TurboFold(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RNAalifold(20): 0.844 PETfold_pre2.0(seed): 0.835 Sensitivity RNAalifold(20): 0.722 PETfold_pre2.0(seed): 0.774 Positive Predictive Value RNAalifold(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RNASampler(20): 0.840 PETfold_pre2.0(seed): 0.835 Sensitivity RNASampler(20): 0.714 PETfold_pre2.0(seed): 0.774 Positive Predictive Value RNASampler(20): 0.990 PETfold_pre2.0(seed): 0.904 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): 0.835 CMfinder(20): 0.779 Sensitivity PETfold_pre2.0(seed): 0.774 CMfinder(20): 0.617 Positive Predictive Value PETfold_pre2.0(seed): 0.904 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 PETfold_pre2.0(seed): 0.835 Sensitivity PETfold_pre2.0(20): 0.759 PETfold_pre2.0(seed): 0.774 Positive Predictive Value PETfold_pre2.0(20): 0.962 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 PETfold_pre2.0(seed): 0.619 Sensitivity PPfold(seed): 0.536 PETfold_pre2.0(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 PETfold_pre2.0(seed): 0.721 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.638 TurboFold(seed): 0.600 Sensitivity PETfold_pre2.0(seed): 0.560 TurboFold(seed): 0.518 Positive Predictive Value PETfold_pre2.0(seed): 0.734 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient MXScarna(20): 0.837 PETfold_pre2.0(seed): 0.835 Sensitivity MXScarna(20): 0.752 PETfold_pre2.0(seed): 0.774 Positive Predictive Value MXScarna(20): 0.935 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RSpredict(20): 0.672 Sensitivity PETfold_pre2.0(seed): 0.774 RSpredict(20): 0.549 Positive Predictive Value PETfold_pre2.0(seed): 0.904 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PETfold_pre2.0(seed): 0.835 Sensitivity CentroidAlifold(20): 0.752 PETfold_pre2.0(seed): 0.774 Positive Predictive Value CentroidAlifold(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Murlet(20): 0.741 Sensitivity PETfold_pre2.0(seed): 0.774 Murlet(20): 0.594 Positive Predictive Value PETfold_pre2.0(seed): 0.904 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PPfold(20): 0.840 PETfold_pre2.0(seed): 0.835 Sensitivity PPfold(20): 0.737 PETfold_pre2.0(seed): 0.774 Positive Predictive Value PPfold(20): 0.961 PETfold_pre2.0(seed): 0.904 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): 0.739 MCFold: 0.336 Sensitivity PETfold_pre2.0(seed): 0.663 MCFold: 0.387 Positive Predictive Value PETfold_pre2.0(seed): 0.829 MCFold: 0.303 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08
RNASampler(seed)	11 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.831 RNASampler(seed): 0.646 Sensitivity Cylofold: 0.834 RNASampler(seed): 0.562 Positive Predictive Value Cylofold: 0.830 RNASampler(seed): 0.748 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	13 McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.862 RNASampler(seed): 0.655 Sensitivity McQFold: 0.849 RNASampler(seed): 0.572 Positive Predictive Value McQFold: 0.877 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.59816551561e-08	12 Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.803 RNASampler(seed): 0.641 Sensitivity Pknots: 0.820 RNASampler(seed): 0.562 Positive Predictive Value Pknots: 0.789 RNASampler(seed): 0.736 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.20383511129e-08	13 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 RNASampler(seed): 0.655 Sensitivity CentroidAlifold(seed): 0.579 RNASampler(seed): 0.572 Positive Predictive Value CentroidAlifold(seed): 0.902 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	13 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.819 RNASampler(seed): 0.655 Sensitivity PknotsRG: 0.818 RNASampler(seed): 0.572 Positive Predictive Value PknotsRG: 0.823 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.22210847902e-08	13 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 RNASampler(seed): 0.655 Sensitivity PETfold_pre2.0(seed): 0.572 RNASampler(seed): 0.572 Positive Predictive Value PETfold_pre2.0(seed): 0.769 RNASampler(seed): 0.755 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.04375264657e-07		+ RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): 0.655 IPknot: 0.604 Sensitivity RNASampler(seed): 0.572 IPknot: 0.537 Positive Predictive Value RNASampler(seed): 0.755 IPknot: 0.686 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAalifold(seed): 0.619 Sensitivity RNASampler(seed): 0.572 RNAalifold(seed): 0.477 Positive Predictive Value RNASampler(seed): 0.755 RNAalifold(seed): 0.810 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.42992852122e-09	+ RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidFold: 0.631 Sensitivity RNASampler(seed): 0.572 CentroidFold: 0.554 Positive Predictive Value RNASampler(seed): 0.755 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.74569091494e-09	+ RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidHomfold‑LAST: 0.583 Sensitivity RNASampler(seed): 0.572 CentroidHomfold‑LAST: 0.502 Positive Predictive Value RNASampler(seed): 0.755 CentroidHomfold‑LAST: 0.684 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.26497248087e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold5: 0.452 Sensitivity RNASampler(seed): 0.572 Vsfold5: 0.435 Positive Predictive Value RNASampler(seed): 0.755 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Carnac(seed): 0.582 Sensitivity RNASampler(seed): 0.572 Carnac(seed): 0.354 Positive Predictive Value RNASampler(seed): 0.755 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.655 ProbKnot: 0.514 Sensitivity RNASampler(seed): 0.572 ProbKnot: 0.495 Positive Predictive Value RNASampler(seed): 0.755 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNASLOpt: 0.584 Sensitivity RNASampler(seed): 0.572 RNASLOpt: 0.526 Positive Predictive Value RNASampler(seed): 0.755 RNASLOpt: 0.655 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.655 Contrafold: 0.582 Sensitivity RNASampler(seed): 0.572 Contrafold: 0.540 Positive Predictive Value RNASampler(seed): 0.755 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.655 HotKnots: 0.522 Sensitivity RNASampler(seed): 0.572 HotKnots: 0.526 Positive Predictive Value RNASampler(seed): 0.755 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.641 RDfolder: 0.561 Sensitivity RNASampler(seed): 0.562 RDfolder: 0.481 Positive Predictive Value RNASampler(seed): 0.736 RDfolder: 0.663 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.655 Fold: 0.472 Sensitivity RNASampler(seed): 0.572 Fold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): 0.655 ContextFold: 0.504 Sensitivity RNASampler(seed): 0.572 ContextFold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 ContextFold: 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.655 MaxExpect: 0.513 Sensitivity RNASampler(seed): 0.572 MaxExpect: 0.488 Positive Predictive Value RNASampler(seed): 0.755 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Murlet(seed): 0.482 Sensitivity RNASampler(seed): 0.572 Murlet(seed): 0.319 Positive Predictive Value RNASampler(seed): 0.755 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.655 Sfold: 0.475 Sensitivity RNASampler(seed): 0.572 Sfold: 0.442 Positive Predictive Value RNASampler(seed): 0.755 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.655 UNAFold: 0.481 Sensitivity RNASampler(seed): 0.572 UNAFold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold4: 0.392 Sensitivity RNASampler(seed): 0.572 Vsfold4: 0.365 Positive Predictive Value RNASampler(seed): 0.755 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAshapes: 0.447 Sensitivity RNASampler(seed): 0.572 RNAshapes: 0.432 Positive Predictive Value RNASampler(seed): 0.755 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.36983135185e-08	+ RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAfold: 0.476 Sensitivity RNASampler(seed): 0.572 RNAfold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 MXScarna(seed): 0.440 Sensitivity RNASampler(seed): 0.572 MXScarna(seed): 0.421 Positive Predictive Value RNASampler(seed): 0.755 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.72523032126e-08	+ RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAsubopt: 0.463 Sensitivity RNASampler(seed): 0.572 RNAsubopt: 0.446 Positive Predictive Value RNASampler(seed): 0.755 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RSpredict(seed): 0.488 Sensitivity RNASampler(seed): 0.572 RSpredict(seed): 0.425 Positive Predictive Value RNASampler(seed): 0.755 RSpredict(seed): 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.655 CRWrnafold: 0.446 Sensitivity RNASampler(seed): 0.572 CRWrnafold: 0.425 Positive Predictive Value RNASampler(seed): 0.755 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 CMfinder(seed): 0.443 Sensitivity RNASampler(seed): 0.574 CMfinder(seed): 0.333 Positive Predictive Value RNASampler(seed): 0.753 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.89166989468e-09	+ RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAwolf: 0.438 Sensitivity RNASampler(seed): 0.572 RNAwolf: 0.407 Positive Predictive Value RNASampler(seed): 0.755 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.642 Afold: 0.454 Sensitivity RNASampler(seed): 0.561 Afold: 0.427 Positive Predictive Value RNASampler(seed): 0.740 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.641 Alterna: 0.384 Sensitivity RNASampler(seed): 0.562 Alterna: 0.365 Positive Predictive Value RNASampler(seed): 0.736 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.40919803867e-08	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Mastr(seed): 0.400 Sensitivity RNASampler(seed): 0.572 Mastr(seed): 0.242 Positive Predictive Value RNASampler(seed): 0.755 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	? Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): N/A RNASampler(seed): N/A Sensitivity Mastr(20): N/A RNASampler(seed): N/A Positive Predictive Value Mastr(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs RNASampler(seed) Matthews Correlation Coefficient NanoFolder: 0.585 RNASampler(seed): 0.559 Sensitivity NanoFolder: 0.654 RNASampler(seed): 0.481 Positive Predictive Value NanoFolder: 0.531 RNASampler(seed): 0.658 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(20): N/A Sensitivity RNASampler(seed): N/A Carnac(20): N/A Positive Predictive Value RNASampler(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 RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RNASampler(seed): 0.569 Sensitivity Multilign(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value Multilign(seed): 0.625 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(20): N/A Sensitivity RNASampler(seed): N/A Multilign(20): N/A Positive Predictive Value RNASampler(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): N/A TurboFold(20): N/A Sensitivity RNASampler(seed): N/A TurboFold(20): N/A Positive Predictive Value RNASampler(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(20): N/A Sensitivity RNASampler(seed): N/A RNAalifold(20): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): N/A RNASampler(seed): N/A Sensitivity RNASampler(20): N/A RNASampler(seed): N/A Positive Predictive Value RNASampler(20): N/A RNASampler(seed): 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	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNASampler(seed): 0.569 Sensitivity PPfold(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value PPfold(seed): 0.833 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.615 TurboFold(seed): 0.600 Sensitivity RNASampler(seed): 0.548 TurboFold(seed): 0.518 Positive Predictive Value RNASampler(seed): 0.697 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(20): N/A Sensitivity RNASampler(seed): N/A MXScarna(20): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): N/A RNASampler(seed): N/A Sensitivity RSpredict(20): N/A RNASampler(seed): N/A Positive Predictive Value RSpredict(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(20): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(20): N/A Sensitivity RNASampler(seed): N/A Murlet(20): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(20): N/A Sensitivity RNASampler(seed): N/A PPfold(20): N/A Positive Predictive Value RNASampler(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.621 MCFold: 0.354 Sensitivity RNASampler(seed): 0.546 MCFold: 0.415 Positive Predictive Value RNASampler(seed): 0.713 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08
IPknot	45 Cylofold vs IPknot Matthews Correlation Coefficient Cylofold: 0.764 IPknot: 0.555 Sensitivity Cylofold: 0.742 IPknot: 0.499 Positive Predictive Value Cylofold: 0.791 IPknot: 0.628 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs IPknot Matthews Correlation Coefficient McQFold: 0.594 IPknot: 0.489 Sensitivity McQFold: 0.583 IPknot: 0.435 Positive Predictive Value McQFold: 0.611 IPknot: 0.556 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs IPknot Matthews Correlation Coefficient Pknots: 0.697 IPknot: 0.558 Sensitivity Pknots: 0.668 IPknot: 0.501 Positive Predictive Value Pknots: 0.733 IPknot: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 IPknot: 0.671 Sensitivity CentroidAlifold(seed): 0.634 IPknot: 0.590 Positive Predictive Value CentroidAlifold(seed): 0.933 IPknot: 0.768 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.07760058607e-08	53 PknotsRG vs IPknot Matthews Correlation Coefficient PknotsRG: 0.531 IPknot: 0.489 Sensitivity PknotsRG: 0.525 IPknot: 0.435 Positive Predictive Value PknotsRG: 0.544 IPknot: 0.556 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 IPknot: 0.680 Sensitivity PETfold_pre2.0(seed): 0.649 IPknot: 0.610 Positive Predictive Value PETfold_pre2.0(seed): 0.824 IPknot: 0.761 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.51155234096e-08	13 RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): 0.655 IPknot: 0.604 Sensitivity RNASampler(seed): 0.572 IPknot: 0.537 Positive Predictive Value RNASampler(seed): 0.755 IPknot: 0.686 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.04409141234e-08		+ IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.671 RNAalifold(seed): 0.657 Sensitivity IPknot: 0.590 RNAalifold(seed): 0.522 Positive Predictive Value IPknot: 0.768 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.05036736369e-07	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.489 CentroidFold: 0.482 Sensitivity IPknot: 0.435 CentroidFold: 0.430 Positive Predictive Value IPknot: 0.556 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.03703286746e-07	= IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.489 CentroidHomfold‑LAST: 0.488 Sensitivity IPknot: 0.435 CentroidHomfold‑LAST: 0.407 Positive Predictive Value IPknot: 0.556 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.326486874811	- Vsfold5 vs IPknot Matthews Correlation Coefficient Vsfold5: 0.534 IPknot: 0.489 Sensitivity Vsfold5: 0.505 IPknot: 0.435 Positive Predictive Value Vsfold5: 0.572 IPknot: 0.556 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.604 Carnac(seed): 0.582 Sensitivity IPknot: 0.537 Carnac(seed): 0.354 Positive Predictive Value IPknot: 0.686 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.81284138222e-07	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.489 ProbKnot: 0.459 Sensitivity IPknot: 0.435 ProbKnot: 0.440 Positive Predictive Value IPknot: 0.556 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.489 RNASLOpt: 0.458 Sensitivity IPknot: 0.435 RNASLOpt: 0.419 Positive Predictive Value IPknot: 0.556 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.489 Contrafold: 0.458 Sensitivity IPknot: 0.435 Contrafold: 0.435 Positive Predictive Value IPknot: 0.556 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.489 HotKnots: 0.453 Sensitivity IPknot: 0.435 HotKnots: 0.445 Positive Predictive Value IPknot: 0.556 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.558 RDfolder: 0.508 Sensitivity IPknot: 0.501 RDfolder: 0.432 Positive Predictive Value IPknot: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.489 Fold: 0.453 Sensitivity IPknot: 0.435 Fold: 0.431 Positive Predictive Value IPknot: 0.556 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ContextFold Matthews Correlation Coefficient IPknot: 0.489 ContextFold: 0.447 Sensitivity IPknot: 0.435 ContextFold: 0.407 Positive Predictive Value IPknot: 0.556 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.489 MaxExpect: 0.440 Sensitivity IPknot: 0.435 MaxExpect: 0.414 Positive Predictive Value IPknot: 0.556 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.604 Murlet(seed): 0.482 Sensitivity IPknot: 0.537 Murlet(seed): 0.319 Positive Predictive Value IPknot: 0.686 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.29209047668e-09	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.489 Sfold: 0.425 Sensitivity IPknot: 0.435 Sfold: 0.377 Positive Predictive Value IPknot: 0.556 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.489 UNAFold: 0.412 Sensitivity IPknot: 0.435 UNAFold: 0.390 Positive Predictive Value IPknot: 0.556 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.489 Vsfold4: 0.423 Sensitivity IPknot: 0.435 Vsfold4: 0.380 Positive Predictive Value IPknot: 0.556 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.489 RNAshapes: 0.416 Sensitivity IPknot: 0.435 RNAshapes: 0.395 Positive Predictive Value IPknot: 0.556 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.489 RNAfold: 0.409 Sensitivity IPknot: 0.435 RNAfold: 0.390 Positive Predictive Value IPknot: 0.556 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.671 MXScarna(seed): 0.539 Sensitivity IPknot: 0.590 MXScarna(seed): 0.501 Positive Predictive Value IPknot: 0.768 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.489 RNAsubopt: 0.394 Sensitivity IPknot: 0.435 RNAsubopt: 0.378 Positive Predictive Value IPknot: 0.556 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.671 RSpredict(seed): 0.514 Sensitivity IPknot: 0.590 RSpredict(seed): 0.427 Positive Predictive Value IPknot: 0.768 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.489 CRWrnafold: 0.374 Sensitivity IPknot: 0.435 CRWrnafold: 0.351 Positive Predictive Value IPknot: 0.556 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.564 CMfinder(seed): 0.443 Sensitivity IPknot: 0.502 CMfinder(seed): 0.333 Positive Predictive Value IPknot: 0.641 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.489 RNAwolf: 0.362 Sensitivity IPknot: 0.435 RNAwolf: 0.353 Positive Predictive Value IPknot: 0.556 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.468 Afold: 0.316 Sensitivity IPknot: 0.430 Afold: 0.305 Positive Predictive Value IPknot: 0.518 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.558 Alterna: 0.393 Sensitivity IPknot: 0.501 Alterna: 0.365 Positive Predictive Value IPknot: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.671 Mastr(seed): 0.341 Sensitivity IPknot: 0.590 Mastr(seed): 0.176 Positive Predictive Value IPknot: 0.768 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.89649746203e-08	? IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.840 Mastr(20): 0.561 Sensitivity IPknot: 0.737 Mastr(20): 0.459 Positive Predictive Value IPknot: 0.961 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.674 NanoFolder: 0.304 Sensitivity IPknot: 0.614 NanoFolder: 0.343 Positive Predictive Value IPknot: 0.745 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.840 Carnac(20): 0.821 Sensitivity IPknot: 0.737 Carnac(20): 0.684 Positive Predictive Value IPknot: 0.961 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.684 Multilign(seed): 0.575 Sensitivity IPknot: 0.586 Multilign(seed): 0.536 Positive Predictive Value IPknot: 0.804 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.862 IPknot: 0.840 Sensitivity Multilign(20): 0.752 IPknot: 0.737 Positive Predictive Value Multilign(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.857 IPknot: 0.840 Sensitivity TurboFold(20): 0.744 IPknot: 0.737 Positive Predictive Value TurboFold(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.844 IPknot: 0.840 Sensitivity RNAalifold(20): 0.722 IPknot: 0.737 Positive Predictive Value RNAalifold(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.840 RNASampler(20): 0.840 Sensitivity IPknot: 0.737 RNASampler(20): 0.714 Positive Predictive Value IPknot: 0.961 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.840 CMfinder(20): 0.779 Sensitivity IPknot: 0.737 CMfinder(20): 0.617 Positive Predictive Value IPknot: 0.961 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 IPknot: 0.840 Sensitivity PETfold_pre2.0(20): 0.759 IPknot: 0.737 Positive Predictive Value PETfold_pre2.0(20): 0.962 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.684 PPfold(seed): 0.666 Sensitivity IPknot: 0.586 PPfold(seed): 0.536 Positive Predictive Value IPknot: 0.804 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.677 TurboFold(seed): 0.600 Sensitivity IPknot: 0.595 TurboFold(seed): 0.518 Positive Predictive Value IPknot: 0.775 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.840 MXScarna(20): 0.837 Sensitivity IPknot: 0.737 MXScarna(20): 0.752 Positive Predictive Value IPknot: 0.961 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.840 RSpredict(20): 0.672 Sensitivity IPknot: 0.737 RSpredict(20): 0.549 Positive Predictive Value IPknot: 0.961 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.862 IPknot: 0.840 Sensitivity CentroidAlifold(20): 0.752 IPknot: 0.737 Positive Predictive Value CentroidAlifold(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.840 Murlet(20): 0.741 Sensitivity IPknot: 0.737 Murlet(20): 0.594 Positive Predictive Value IPknot: 0.961 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.840 IPknot: 0.840 Sensitivity PPfold(20): 0.737 IPknot: 0.737 Positive Predictive Value PPfold(20): 0.961 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.503 MCFold: 0.290 Sensitivity IPknot: 0.457 MCFold: 0.320 Positive Predictive Value IPknot: 0.562 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(seed)	15 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.798 RNAalifold(seed): 0.647 Sensitivity Cylofold: 0.772 RNAalifold(seed): 0.517 Positive Predictive Value Cylofold: 0.828 RNAalifold(seed): 0.816 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.5677163434e-08	17 McQFold vs RNAalifold(seed) Matthews Correlation Coefficient McQFold: 0.834 RNAalifold(seed): 0.657 Sensitivity McQFold: 0.799 RNAalifold(seed): 0.522 Positive Predictive Value McQFold: 0.872 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	16 Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: 0.768 RNAalifold(seed): 0.651 Sensitivity Pknots: 0.748 RNAalifold(seed): 0.519 Positive Predictive Value Pknots: 0.792 RNAalifold(seed): 0.823 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.18141491686e-08	17 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAalifold(seed): 0.657 Sensitivity CentroidAlifold(seed): 0.634 RNAalifold(seed): 0.522 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.28538098861e-09	17 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.787 RNAalifold(seed): 0.657 Sensitivity PknotsRG: 0.761 RNAalifold(seed): 0.522 Positive Predictive Value PknotsRG: 0.817 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.89649746203e-08	17 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RNAalifold(seed): 0.657 Sensitivity PETfold_pre2.0(seed): 0.626 RNAalifold(seed): 0.522 Positive Predictive Value PETfold_pre2.0(seed): 0.809 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.95070920198e-08	13 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAalifold(seed): 0.619 Sensitivity RNASampler(seed): 0.572 RNAalifold(seed): 0.477 Positive Predictive Value RNASampler(seed): 0.755 RNAalifold(seed): 0.810 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.42992852122e-09	17 IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.671 RNAalifold(seed): 0.657 Sensitivity IPknot: 0.590 RNAalifold(seed): 0.522 Positive Predictive Value IPknot: 0.768 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.05036736369e-07		- CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.695 RNAalifold(seed): 0.657 Sensitivity CentroidFold: 0.608 RNAalifold(seed): 0.522 Positive Predictive Value CentroidFold: 0.799 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.657 CentroidHomfold‑LAST: 0.654 Sensitivity RNAalifold(seed): 0.522 CentroidHomfold‑LAST: 0.560 Positive Predictive Value RNAalifold(seed): 0.833 CentroidHomfold‑LAST: 0.769 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000126832858459	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.657 Vsfold5: 0.531 Sensitivity RNAalifold(seed): 0.522 Vsfold5: 0.501 Positive Predictive Value RNAalifold(seed): 0.833 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.619 Carnac(seed): 0.582 Sensitivity RNAalifold(seed): 0.477 Carnac(seed): 0.354 Positive Predictive Value RNAalifold(seed): 0.810 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.42992852122e-09	+ RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.657 ProbKnot: 0.603 Sensitivity RNAalifold(seed): 0.522 ProbKnot: 0.565 Positive Predictive Value RNAalifold(seed): 0.833 ProbKnot: 0.649 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNASLOpt: 0.635 Sensitivity RNAalifold(seed): 0.522 RNASLOpt: 0.565 Positive Predictive Value RNAalifold(seed): 0.833 RNASLOpt: 0.718 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 6.9050074835e-07	+ RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.657 Contrafold: 0.653 Sensitivity RNAalifold(seed): 0.522 Contrafold: 0.598 Positive Predictive Value RNAalifold(seed): 0.833 Contrafold: 0.719 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71428824004e-05	+ RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.657 HotKnots: 0.603 Sensitivity RNAalifold(seed): 0.522 HotKnots: 0.588 Positive Predictive Value RNAalifold(seed): 0.833 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.651 RDfolder: 0.616 Sensitivity RNAalifold(seed): 0.519 RDfolder: 0.531 Positive Predictive Value RNAalifold(seed): 0.823 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.06136423953e-07	+ RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.657 Fold: 0.572 Sensitivity RNAalifold(seed): 0.522 Fold: 0.534 Positive Predictive Value RNAalifold(seed): 0.833 Fold: 0.619 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 8.09700314043e-09	+ RNAalifold(seed) vs ContextFold Matthews Correlation Coefficient RNAalifold(seed): 0.657 ContextFold: 0.567 Sensitivity RNAalifold(seed): 0.522 ContextFold: 0.506 Positive Predictive Value RNAalifold(seed): 0.833 ContextFold: 0.642 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.657 MaxExpect: 0.603 Sensitivity RNAalifold(seed): 0.522 MaxExpect: 0.560 Positive Predictive Value RNAalifold(seed): 0.833 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.619 Murlet(seed): 0.482 Sensitivity RNAalifold(seed): 0.477 Murlet(seed): 0.319 Positive Predictive Value RNAalifold(seed): 0.810 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.657 Sfold: 0.571 Sensitivity RNAalifold(seed): 0.522 Sfold: 0.519 Positive Predictive Value RNAalifold(seed): 0.833 Sfold: 0.636 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.657 UNAFold: 0.552 Sensitivity RNAalifold(seed): 0.522 UNAFold: 0.517 Positive Predictive Value RNAalifold(seed): 0.833 UNAFold: 0.597 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.657 Vsfold4: 0.488 Sensitivity RNAalifold(seed): 0.522 Vsfold4: 0.445 Positive Predictive Value RNAalifold(seed): 0.833 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAshapes: 0.526 Sensitivity RNAalifold(seed): 0.522 RNAshapes: 0.496 Positive Predictive Value RNAalifold(seed): 0.833 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAfold: 0.566 Sensitivity RNAalifold(seed): 0.522 RNAfold: 0.532 Positive Predictive Value RNAalifold(seed): 0.833 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ RNAalifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 MXScarna(seed): 0.539 Sensitivity RNAalifold(seed): 0.522 MXScarna(seed): 0.501 Positive Predictive Value RNAalifold(seed): 0.833 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.64481516727e-08	+ RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAsubopt: 0.538 Sensitivity RNAalifold(seed): 0.522 RNAsubopt: 0.506 Positive Predictive Value RNAalifold(seed): 0.833 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 RSpredict(seed): 0.514 Sensitivity RNAalifold(seed): 0.522 RSpredict(seed): 0.427 Positive Predictive Value RNAalifold(seed): 0.833 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.657 CRWrnafold: 0.527 Sensitivity RNAalifold(seed): 0.522 CRWrnafold: 0.491 Positive Predictive Value RNAalifold(seed): 0.833 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.615 CMfinder(seed): 0.443 Sensitivity RNAalifold(seed): 0.466 CMfinder(seed): 0.333 Positive Predictive Value RNAalifold(seed): 0.817 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.93000771886e-09	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAwolf: 0.487 Sensitivity RNAalifold(seed): 0.522 RNAwolf: 0.461 Positive Predictive Value RNAalifold(seed): 0.833 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	+ RNAalifold(seed) vs Afold Matthews Correlation Coefficient RNAalifold(seed): 0.638 Afold: 0.517 Sensitivity RNAalifold(seed): 0.503 Afold: 0.480 Positive Predictive Value RNAalifold(seed): 0.814 Afold: 0.564 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.651 Alterna: 0.486 Sensitivity RNAalifold(seed): 0.519 Alterna: 0.455 Positive Predictive Value RNAalifold(seed): 0.823 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 Mastr(seed): 0.341 Sensitivity RNAalifold(seed): 0.522 Mastr(seed): 0.176 Positive Predictive Value RNAalifold(seed): 0.833 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.22210847902e-08	? RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.750 Mastr(20): 0.705 Sensitivity RNAalifold(seed): 0.639 Mastr(20): 0.565 Positive Predictive Value RNAalifold(seed): 0.885 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.687 NanoFolder: 0.489 Sensitivity RNAalifold(seed): 0.570 NanoFolder: 0.544 Positive Predictive Value RNAalifold(seed): 0.833 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNAalifold(seed) Matthews Correlation Coefficient Carnac(20): 0.832 RNAalifold(seed): 0.750 Sensitivity Carnac(20): 0.694 RNAalifold(seed): 0.639 Positive Predictive Value Carnac(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Multilign(seed): 0.575 Sensitivity RNAalifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value RNAalifold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.865 RNAalifold(seed): 0.750 Sensitivity Multilign(20): 0.750 RNAalifold(seed): 0.639 Positive Predictive Value Multilign(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 RNAalifold(seed): 0.750 Sensitivity TurboFold(20): 0.741 RNAalifold(seed): 0.639 Positive Predictive Value TurboFold(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 RNAalifold(seed): 0.750 Sensitivity RNAalifold(20): 0.704 RNAalifold(seed): 0.639 Positive Predictive Value RNAalifold(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 RNAalifold(seed): 0.750 Sensitivity RNASampler(20): 0.694 RNAalifold(seed): 0.639 Positive Predictive Value RNASampler(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.756 RNAalifold(seed): 0.750 Sensitivity CMfinder(20): 0.574 RNAalifold(seed): 0.639 Positive Predictive Value CMfinder(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 RNAalifold(seed): 0.750 Sensitivity PETfold_pre2.0(20): 0.750 RNAalifold(seed): 0.639 Positive Predictive Value PETfold_pre2.0(20): 0.964 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNAalifold(seed): 0.644 Sensitivity PPfold(seed): 0.536 RNAalifold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 RNAalifold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.621 TurboFold(seed): 0.600 Sensitivity RNAalifold(seed): 0.500 TurboFold(seed): 0.518 Positive Predictive Value RNAalifold(seed): 0.778 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 RNAalifold(seed): 0.750 Sensitivity MXScarna(20): 0.769 RNAalifold(seed): 0.639 Positive Predictive Value MXScarna(20): 0.954 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.750 RSpredict(20): 0.676 Sensitivity RNAalifold(seed): 0.639 RSpredict(20): 0.546 Positive Predictive Value RNAalifold(seed): 0.885 RSpredict(20): 0.843 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 RNAalifold(seed): 0.750 Sensitivity CentroidAlifold(20): 0.741 RNAalifold(seed): 0.639 Positive Predictive Value CentroidAlifold(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.780 RNAalifold(seed): 0.750 Sensitivity Murlet(20): 0.611 RNAalifold(seed): 0.639 Positive Predictive Value Murlet(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.833 RNAalifold(seed): 0.750 Sensitivity PPfold(20): 0.722 RNAalifold(seed): 0.639 Positive Predictive Value PPfold(20): 0.963 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.664 MCFold: 0.358 Sensitivity RNAalifold(seed): 0.537 MCFold: 0.409 Positive Predictive Value RNAalifold(seed): 0.828 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.80908287419e-08
CentroidFold	45 Cylofold vs CentroidFold Matthews Correlation Coefficient Cylofold: 0.764 CentroidFold: 0.541 Sensitivity Cylofold: 0.742 CentroidFold: 0.483 Positive Predictive Value Cylofold: 0.791 CentroidFold: 0.616 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs CentroidFold Matthews Correlation Coefficient McQFold: 0.594 CentroidFold: 0.482 Sensitivity McQFold: 0.583 CentroidFold: 0.430 Positive Predictive Value McQFold: 0.611 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: 0.697 CentroidFold: 0.544 Sensitivity Pknots: 0.668 CentroidFold: 0.485 Positive Predictive Value Pknots: 0.733 CentroidFold: 0.621 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 CentroidFold: 0.695 Sensitivity CentroidAlifold(seed): 0.634 CentroidFold: 0.608 Positive Predictive Value CentroidAlifold(seed): 0.933 CentroidFold: 0.799 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	53 PknotsRG vs CentroidFold Matthews Correlation Coefficient PknotsRG: 0.531 CentroidFold: 0.482 Sensitivity PknotsRG: 0.525 CentroidFold: 0.430 Positive Predictive Value PknotsRG: 0.544 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidFold: 0.683 Sensitivity PETfold_pre2.0(seed): 0.649 CentroidFold: 0.606 Positive Predictive Value PETfold_pre2.0(seed): 0.824 CentroidFold: 0.776 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.39162260866e-08	13 RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidFold: 0.631 Sensitivity RNASampler(seed): 0.572 CentroidFold: 0.554 Positive Predictive Value RNASampler(seed): 0.755 CentroidFold: 0.725 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.74569091494e-09	53 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.489 CentroidFold: 0.482 Sensitivity IPknot: 0.435 CentroidFold: 0.430 Positive Predictive Value IPknot: 0.556 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.03703286746e-07	17 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.695 RNAalifold(seed): 0.657 Sensitivity CentroidFold: 0.608 RNAalifold(seed): 0.522 Positive Predictive Value CentroidFold: 0.799 RNAalifold(seed): 0.833 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08		- CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 CentroidFold: 0.482 Sensitivity CentroidHomfold‑LAST: 0.407 CentroidFold: 0.430 Positive Predictive Value CentroidHomfold‑LAST: 0.592 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 1.5875416339e-07	- Vsfold5 vs CentroidFold Matthews Correlation Coefficient Vsfold5: 0.534 CentroidFold: 0.482 Sensitivity Vsfold5: 0.505 CentroidFold: 0.430 Positive Predictive Value Vsfold5: 0.572 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.631 Carnac(seed): 0.582 Sensitivity CentroidFold: 0.554 Carnac(seed): 0.354 Positive Predictive Value CentroidFold: 0.725 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.482 ProbKnot: 0.459 Sensitivity CentroidFold: 0.430 ProbKnot: 0.440 Positive Predictive Value CentroidFold: 0.548 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.482 RNASLOpt: 0.458 Sensitivity CentroidFold: 0.430 RNASLOpt: 0.419 Positive Predictive Value CentroidFold: 0.548 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.482 Contrafold: 0.458 Sensitivity CentroidFold: 0.430 Contrafold: 0.435 Positive Predictive Value CentroidFold: 0.548 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.482 HotKnots: 0.453 Sensitivity CentroidFold: 0.430 HotKnots: 0.445 Positive Predictive Value CentroidFold: 0.548 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.544 RDfolder: 0.508 Sensitivity CentroidFold: 0.485 RDfolder: 0.432 Positive Predictive Value CentroidFold: 0.621 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.482 Fold: 0.453 Sensitivity CentroidFold: 0.430 Fold: 0.431 Positive Predictive Value CentroidFold: 0.548 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ContextFold Matthews Correlation Coefficient CentroidFold: 0.482 ContextFold: 0.447 Sensitivity CentroidFold: 0.430 ContextFold: 0.407 Positive Predictive Value CentroidFold: 0.548 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.482 MaxExpect: 0.440 Sensitivity CentroidFold: 0.430 MaxExpect: 0.414 Positive Predictive Value CentroidFold: 0.548 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.631 Murlet(seed): 0.482 Sensitivity CentroidFold: 0.554 Murlet(seed): 0.319 Positive Predictive Value CentroidFold: 0.725 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.482 Sfold: 0.425 Sensitivity CentroidFold: 0.430 Sfold: 0.377 Positive Predictive Value CentroidFold: 0.548 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.482 UNAFold: 0.412 Sensitivity CentroidFold: 0.430 UNAFold: 0.390 Positive Predictive Value CentroidFold: 0.548 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.482 Vsfold4: 0.423 Sensitivity CentroidFold: 0.430 Vsfold4: 0.380 Positive Predictive Value CentroidFold: 0.548 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.482 RNAshapes: 0.416 Sensitivity CentroidFold: 0.430 RNAshapes: 0.395 Positive Predictive Value CentroidFold: 0.548 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.482 RNAfold: 0.409 Sensitivity CentroidFold: 0.430 RNAfold: 0.390 Positive Predictive Value CentroidFold: 0.548 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MXScarna(seed) Matthews Correlation Coefficient CentroidFold: 0.695 MXScarna(seed): 0.539 Sensitivity CentroidFold: 0.608 MXScarna(seed): 0.501 Positive Predictive Value CentroidFold: 0.799 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.482 RNAsubopt: 0.394 Sensitivity CentroidFold: 0.430 RNAsubopt: 0.378 Positive Predictive Value CentroidFold: 0.548 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.695 RSpredict(seed): 0.514 Sensitivity CentroidFold: 0.608 RSpredict(seed): 0.427 Positive Predictive Value CentroidFold: 0.799 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.482 CRWrnafold: 0.374 Sensitivity CentroidFold: 0.430 CRWrnafold: 0.351 Positive Predictive Value CentroidFold: 0.548 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.640 CMfinder(seed): 0.443 Sensitivity CentroidFold: 0.562 CMfinder(seed): 0.333 Positive Predictive Value CentroidFold: 0.733 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.482 RNAwolf: 0.362 Sensitivity CentroidFold: 0.430 RNAwolf: 0.353 Positive Predictive Value CentroidFold: 0.548 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.466 Afold: 0.316 Sensitivity CentroidFold: 0.423 Afold: 0.305 Positive Predictive Value CentroidFold: 0.521 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.544 Alterna: 0.393 Sensitivity CentroidFold: 0.485 Alterna: 0.365 Positive Predictive Value CentroidFold: 0.621 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.695 Mastr(seed): 0.341 Sensitivity CentroidFold: 0.608 Mastr(seed): 0.176 Positive Predictive Value CentroidFold: 0.799 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.39162260866e-08	? CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.849 Mastr(20): 0.561 Sensitivity CentroidFold: 0.729 Mastr(20): 0.459 Positive Predictive Value CentroidFold: 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.628 NanoFolder: 0.304 Sensitivity CentroidFold: 0.554 NanoFolder: 0.343 Positive Predictive Value CentroidFold: 0.719 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.849 Carnac(20): 0.821 Sensitivity CentroidFold: 0.729 Carnac(20): 0.684 Positive Predictive Value CentroidFold: 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.618 Multilign(seed): 0.575 Sensitivity CentroidFold: 0.514 Multilign(seed): 0.536 Positive Predictive Value CentroidFold: 0.750 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.862 CentroidFold: 0.849 Sensitivity Multilign(20): 0.752 CentroidFold: 0.729 Positive Predictive Value Multilign(20): 0.990 CentroidFold: 0.990 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): 0.857 CentroidFold: 0.849 Sensitivity TurboFold(20): 0.744 CentroidFold: 0.729 Positive Predictive Value TurboFold(20): 0.990 CentroidFold: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs RNAalifold(20) Matthews Correlation Coefficient CentroidFold: 0.849 RNAalifold(20): 0.844 Sensitivity CentroidFold: 0.729 RNAalifold(20): 0.722 Positive Predictive Value CentroidFold: 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs RNASampler(20) Matthews Correlation Coefficient CentroidFold: 0.849 RNASampler(20): 0.840 Sensitivity CentroidFold: 0.729 RNASampler(20): 0.714 Positive Predictive Value CentroidFold: 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.849 CMfinder(20): 0.779 Sensitivity CentroidFold: 0.729 CMfinder(20): 0.617 Positive Predictive Value CentroidFold: 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CentroidFold: 0.849 Sensitivity PETfold_pre2.0(20): 0.759 CentroidFold: 0.729 Positive Predictive Value PETfold_pre2.0(20): 0.962 CentroidFold: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidFold: 0.618 Sensitivity PPfold(seed): 0.536 CentroidFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.621 TurboFold(seed): 0.600 Sensitivity CentroidFold: 0.536 TurboFold(seed): 0.518 Positive Predictive Value CentroidFold: 0.726 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs MXScarna(20) Matthews Correlation Coefficient CentroidFold: 0.849 MXScarna(20): 0.837 Sensitivity CentroidFold: 0.729 MXScarna(20): 0.752 Positive Predictive Value CentroidFold: 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.849 RSpredict(20): 0.672 Sensitivity CentroidFold: 0.729 RSpredict(20): 0.549 Positive Predictive Value CentroidFold: 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CentroidFold: 0.849 Sensitivity CentroidAlifold(20): 0.752 CentroidFold: 0.729 Positive Predictive Value CentroidAlifold(20): 0.990 CentroidFold: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.849 Murlet(20): 0.741 Sensitivity CentroidFold: 0.729 Murlet(20): 0.594 Positive Predictive Value CentroidFold: 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs PPfold(20) Matthews Correlation Coefficient CentroidFold: 0.849 PPfold(20): 0.840 Sensitivity CentroidFold: 0.729 PPfold(20): 0.737 Positive Predictive Value CentroidFold: 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.486 MCFold: 0.290 Sensitivity CentroidFold: 0.436 MCFold: 0.320 Positive Predictive Value CentroidFold: 0.550 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidHomfold‑LAST	45 Cylofold vs CentroidHomfold‑LAST Matthews Correlation Coefficient Cylofold: 0.764 CentroidHomfold‑LAST: 0.538 Sensitivity Cylofold: 0.742 CentroidHomfold‑LAST: 0.469 Positive Predictive Value Cylofold: 0.791 CentroidHomfold‑LAST: 0.627 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient McQFold: 0.594 CentroidHomfold‑LAST: 0.488 Sensitivity McQFold: 0.583 CentroidHomfold‑LAST: 0.407 Positive Predictive Value McQFold: 0.611 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: 0.697 CentroidHomfold‑LAST: 0.541 Sensitivity Pknots: 0.668 CentroidHomfold‑LAST: 0.471 Positive Predictive Value Pknots: 0.733 CentroidHomfold‑LAST: 0.632 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 CentroidHomfold‑LAST: 0.654 Sensitivity CentroidAlifold(seed): 0.634 CentroidHomfold‑LAST: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.933 CentroidHomfold‑LAST: 0.769 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.59816551561e-08	53 PknotsRG vs CentroidHomfold‑LAST Matthews Correlation Coefficient PknotsRG: 0.531 CentroidHomfold‑LAST: 0.488 Sensitivity PknotsRG: 0.525 CentroidHomfold‑LAST: 0.407 Positive Predictive Value PknotsRG: 0.544 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CentroidHomfold‑LAST: 0.683 Sensitivity PETfold_pre2.0(seed): 0.649 CentroidHomfold‑LAST: 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.824 CentroidHomfold‑LAST: 0.794 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.89169006118e-08	13 RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): 0.655 CentroidHomfold‑LAST: 0.583 Sensitivity RNASampler(seed): 0.572 CentroidHomfold‑LAST: 0.502 Positive Predictive Value RNASampler(seed): 0.755 CentroidHomfold‑LAST: 0.684 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.26497248087e-08	53 IPknot vs CentroidHomfold‑LAST Matthews Correlation Coefficient IPknot: 0.489 CentroidHomfold‑LAST: 0.488 Sensitivity IPknot: 0.435 CentroidHomfold‑LAST: 0.407 Positive Predictive Value IPknot: 0.556 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.326486874811	17 RNAalifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNAalifold(seed): 0.657 CentroidHomfold‑LAST: 0.654 Sensitivity RNAalifold(seed): 0.522 CentroidHomfold‑LAST: 0.560 Positive Predictive Value RNAalifold(seed): 0.833 CentroidHomfold‑LAST: 0.769 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000126832858459	53 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 CentroidFold: 0.482 Sensitivity CentroidHomfold‑LAST: 0.407 CentroidFold: 0.430 Positive Predictive Value CentroidHomfold‑LAST: 0.592 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 1.5875416339e-07		- Vsfold5 vs CentroidHomfold‑LAST Matthews Correlation Coefficient Vsfold5: 0.534 CentroidHomfold‑LAST: 0.488 Sensitivity Vsfold5: 0.505 CentroidHomfold‑LAST: 0.407 Positive Predictive Value Vsfold5: 0.572 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08	= CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Carnac(seed): 0.582 Sensitivity CentroidHomfold‑LAST: 0.502 Carnac(seed): 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.684 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.220070679653	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 ProbKnot: 0.459 Sensitivity CentroidHomfold‑LAST: 0.407 ProbKnot: 0.440 Positive Predictive Value CentroidHomfold‑LAST: 0.592 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNASLOpt: 0.458 Sensitivity CentroidHomfold‑LAST: 0.407 RNASLOpt: 0.419 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Contrafold: 0.458 Sensitivity CentroidHomfold‑LAST: 0.407 Contrafold: 0.435 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 HotKnots: 0.453 Sensitivity CentroidHomfold‑LAST: 0.407 HotKnots: 0.445 Positive Predictive Value CentroidHomfold‑LAST: 0.592 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 RDfolder: 0.508 Sensitivity CentroidHomfold‑LAST: 0.471 RDfolder: 0.432 Positive Predictive Value CentroidHomfold‑LAST: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Fold: 0.453 Sensitivity CentroidHomfold‑LAST: 0.407 Fold: 0.431 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ContextFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 ContextFold: 0.447 Sensitivity CentroidHomfold‑LAST: 0.407 ContextFold: 0.407 Positive Predictive Value CentroidHomfold‑LAST: 0.592 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 MaxExpect: 0.440 Sensitivity CentroidHomfold‑LAST: 0.407 MaxExpect: 0.414 Positive Predictive Value CentroidHomfold‑LAST: 0.592 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Murlet(seed): 0.482 Sensitivity CentroidHomfold‑LAST: 0.502 Murlet(seed): 0.319 Positive Predictive Value CentroidHomfold‑LAST: 0.684 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Sfold: 0.425 Sensitivity CentroidHomfold‑LAST: 0.407 Sfold: 0.377 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 UNAFold: 0.412 Sensitivity CentroidHomfold‑LAST: 0.407 UNAFold: 0.390 Positive Predictive Value CentroidHomfold‑LAST: 0.592 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Vsfold4: 0.423 Sensitivity CentroidHomfold‑LAST: 0.407 Vsfold4: 0.380 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAshapes: 0.416 Sensitivity CentroidHomfold‑LAST: 0.407 RNAshapes: 0.395 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAfold: 0.409 Sensitivity CentroidHomfold‑LAST: 0.407 RNAfold: 0.390 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 MXScarna(seed): 0.539 Sensitivity CentroidHomfold‑LAST: 0.560 MXScarna(seed): 0.501 Positive Predictive Value CentroidHomfold‑LAST: 0.769 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAsubopt: 0.394 Sensitivity CentroidHomfold‑LAST: 0.407 RNAsubopt: 0.378 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RSpredict(seed): 0.514 Sensitivity CentroidHomfold‑LAST: 0.560 RSpredict(seed): 0.427 Positive Predictive Value CentroidHomfold‑LAST: 0.769 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 CRWrnafold: 0.374 Sensitivity CentroidHomfold‑LAST: 0.407 CRWrnafold: 0.351 Positive Predictive Value CentroidHomfold‑LAST: 0.592 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.577 CMfinder(seed): 0.443 Sensitivity CentroidHomfold‑LAST: 0.510 CMfinder(seed): 0.333 Positive Predictive Value CentroidHomfold‑LAST: 0.658 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAwolf: 0.362 Sensitivity CentroidHomfold‑LAST: 0.407 RNAwolf: 0.353 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.450 Afold: 0.316 Sensitivity CentroidHomfold‑LAST: 0.388 Afold: 0.305 Positive Predictive Value CentroidHomfold‑LAST: 0.531 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 Alterna: 0.393 Sensitivity CentroidHomfold‑LAST: 0.471 Alterna: 0.365 Positive Predictive Value CentroidHomfold‑LAST: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Mastr(seed): 0.341 Sensitivity CentroidHomfold‑LAST: 0.560 Mastr(seed): 0.176 Positive Predictive Value CentroidHomfold‑LAST: 0.769 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	? CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 Mastr(20): 0.561 Sensitivity CentroidHomfold‑LAST: 0.729 Mastr(20): 0.459 Positive Predictive Value CentroidHomfold‑LAST: 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.692 NanoFolder: 0.304 Sensitivity CentroidHomfold‑LAST: 0.602 NanoFolder: 0.343 Positive Predictive Value CentroidHomfold‑LAST: 0.800 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 Carnac(20): 0.821 Sensitivity CentroidHomfold‑LAST: 0.729 Carnac(20): 0.684 Positive Predictive Value CentroidHomfold‑LAST: 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Multilign(seed): 0.575 Sensitivity CentroidHomfold‑LAST: 0.486 Multilign(seed): 0.536 Positive Predictive Value CentroidHomfold‑LAST: 0.708 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Multilign(20): 0.862 CentroidHomfold‑LAST: 0.849 Sensitivity Multilign(20): 0.752 CentroidHomfold‑LAST: 0.729 Positive Predictive Value Multilign(20): 0.990 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.857 CentroidHomfold‑LAST: 0.849 Sensitivity TurboFold(20): 0.744 CentroidHomfold‑LAST: 0.729 Positive Predictive Value TurboFold(20): 0.990 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 RNAalifold(20): 0.844 Sensitivity CentroidHomfold‑LAST: 0.729 RNAalifold(20): 0.722 Positive Predictive Value CentroidHomfold‑LAST: 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 RNASampler(20): 0.840 Sensitivity CentroidHomfold‑LAST: 0.729 RNASampler(20): 0.714 Positive Predictive Value CentroidHomfold‑LAST: 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 CMfinder(20): 0.779 Sensitivity CentroidHomfold‑LAST: 0.729 CMfinder(20): 0.617 Positive Predictive Value CentroidHomfold‑LAST: 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CentroidHomfold‑LAST: 0.849 Sensitivity PETfold_pre2.0(20): 0.759 CentroidHomfold‑LAST: 0.729 Positive Predictive Value PETfold_pre2.0(20): 0.962 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidHomfold‑LAST: 0.584 Sensitivity PPfold(seed): 0.536 CentroidHomfold‑LAST: 0.486 Positive Predictive Value PPfold(seed): 0.833 CentroidHomfold‑LAST: 0.708 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.600 CentroidHomfold‑LAST: 0.593 Sensitivity TurboFold(seed): 0.518 CentroidHomfold‑LAST: 0.512 Positive Predictive Value TurboFold(seed): 0.702 CentroidHomfold‑LAST: 0.694 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 MXScarna(20): 0.837 Sensitivity CentroidHomfold‑LAST: 0.729 MXScarna(20): 0.752 Positive Predictive Value CentroidHomfold‑LAST: 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 RSpredict(20): 0.672 Sensitivity CentroidHomfold‑LAST: 0.729 RSpredict(20): 0.549 Positive Predictive Value CentroidHomfold‑LAST: 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CentroidHomfold‑LAST: 0.849 Sensitivity CentroidAlifold(20): 0.752 CentroidHomfold‑LAST: 0.729 Positive Predictive Value CentroidAlifold(20): 0.990 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 Murlet(20): 0.741 Sensitivity CentroidHomfold‑LAST: 0.729 Murlet(20): 0.594 Positive Predictive Value CentroidHomfold‑LAST: 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 PPfold(20): 0.840 Sensitivity CentroidHomfold‑LAST: 0.729 PPfold(20): 0.737 Positive Predictive Value CentroidHomfold‑LAST: 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.487 MCFold: 0.290 Sensitivity CentroidHomfold‑LAST: 0.422 MCFold: 0.320 Positive Predictive Value CentroidHomfold‑LAST: 0.570 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold5	45 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.764 Vsfold5: 0.589 Sensitivity Cylofold: 0.742 Vsfold5: 0.541 Positive Predictive Value Cylofold: 0.791 Vsfold5: 0.649 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.594 Vsfold5: 0.534 Sensitivity McQFold: 0.583 Vsfold5: 0.505 Positive Predictive Value McQFold: 0.611 Vsfold5: 0.572 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.697 Vsfold5: 0.597 Sensitivity Pknots: 0.668 Vsfold5: 0.550 Positive Predictive Value Pknots: 0.733 Vsfold5: 0.657 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Vsfold5: 0.531 Sensitivity CentroidAlifold(seed): 0.634 Vsfold5: 0.501 Positive Predictive Value CentroidAlifold(seed): 0.933 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.87872347734e-08	53 Vsfold5 vs PknotsRG Matthews Correlation Coefficient Vsfold5: 0.534 PknotsRG: 0.531 Sensitivity Vsfold5: 0.505 PknotsRG: 0.525 Positive Predictive Value Vsfold5: 0.572 PknotsRG: 0.544 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.501542402616	19 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold5: 0.569 Sensitivity PETfold_pre2.0(seed): 0.649 Vsfold5: 0.538 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Vsfold5: 0.608 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.54914456376e-08	13 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold5: 0.452 Sensitivity RNASampler(seed): 0.572 Vsfold5: 0.435 Positive Predictive Value RNASampler(seed): 0.755 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.87872347734e-08	53 Vsfold5 vs IPknot Matthews Correlation Coefficient Vsfold5: 0.534 IPknot: 0.489 Sensitivity Vsfold5: 0.505 IPknot: 0.435 Positive Predictive Value Vsfold5: 0.572 IPknot: 0.556 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08	17 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.657 Vsfold5: 0.531 Sensitivity RNAalifold(seed): 0.522 Vsfold5: 0.501 Positive Predictive Value RNAalifold(seed): 0.833 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.07760058607e-08	53 Vsfold5 vs CentroidFold Matthews Correlation Coefficient Vsfold5: 0.534 CentroidFold: 0.482 Sensitivity Vsfold5: 0.505 CentroidFold: 0.430 Positive Predictive Value Vsfold5: 0.572 CentroidFold: 0.548 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs CentroidHomfold‑LAST Matthews Correlation Coefficient Vsfold5: 0.534 CentroidHomfold‑LAST: 0.488 Sensitivity Vsfold5: 0.505 CentroidHomfold‑LAST: 0.407 Positive Predictive Value Vsfold5: 0.572 CentroidHomfold‑LAST: 0.592 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08		- Carnac(seed) vs Vsfold5 Matthews Correlation Coefficient Carnac(seed): 0.582 Vsfold5: 0.452 Sensitivity Carnac(seed): 0.354 Vsfold5: 0.435 Positive Predictive Value Carnac(seed): 0.962 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ Vsfold5 vs ProbKnot Matthews Correlation Coefficient Vsfold5: 0.534 ProbKnot: 0.459 Sensitivity Vsfold5: 0.505 ProbKnot: 0.440 Positive Predictive Value Vsfold5: 0.572 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RNASLOpt Matthews Correlation Coefficient Vsfold5: 0.534 RNASLOpt: 0.458 Sensitivity Vsfold5: 0.505 RNASLOpt: 0.419 Positive Predictive Value Vsfold5: 0.572 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Contrafold Matthews Correlation Coefficient Vsfold5: 0.534 Contrafold: 0.458 Sensitivity Vsfold5: 0.505 Contrafold: 0.435 Positive Predictive Value Vsfold5: 0.572 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs HotKnots Matthews Correlation Coefficient Vsfold5: 0.534 HotKnots: 0.453 Sensitivity Vsfold5: 0.505 HotKnots: 0.445 Positive Predictive Value Vsfold5: 0.572 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.597 RDfolder: 0.508 Sensitivity Vsfold5: 0.550 RDfolder: 0.432 Positive Predictive Value Vsfold5: 0.657 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Fold Matthews Correlation Coefficient Vsfold5: 0.534 Fold: 0.453 Sensitivity Vsfold5: 0.505 Fold: 0.431 Positive Predictive Value Vsfold5: 0.572 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs ContextFold Matthews Correlation Coefficient Vsfold5: 0.534 ContextFold: 0.447 Sensitivity Vsfold5: 0.505 ContextFold: 0.407 Positive Predictive Value Vsfold5: 0.572 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs MaxExpect Matthews Correlation Coefficient Vsfold5: 0.534 MaxExpect: 0.440 Sensitivity Vsfold5: 0.505 MaxExpect: 0.414 Positive Predictive Value Vsfold5: 0.572 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold5: 0.452 Sensitivity Murlet(seed): 0.319 Vsfold5: 0.435 Positive Predictive Value Murlet(seed): 0.734 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ Vsfold5 vs Sfold Matthews Correlation Coefficient Vsfold5: 0.534 Sfold: 0.425 Sensitivity Vsfold5: 0.505 Sfold: 0.377 Positive Predictive Value Vsfold5: 0.572 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs UNAFold Matthews Correlation Coefficient Vsfold5: 0.534 UNAFold: 0.412 Sensitivity Vsfold5: 0.505 UNAFold: 0.390 Positive Predictive Value Vsfold5: 0.572 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Vsfold4 Matthews Correlation Coefficient Vsfold5: 0.534 Vsfold4: 0.423 Sensitivity Vsfold5: 0.505 Vsfold4: 0.380 Positive Predictive Value Vsfold5: 0.572 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RNAshapes Matthews Correlation Coefficient Vsfold5: 0.534 RNAshapes: 0.416 Sensitivity Vsfold5: 0.505 RNAshapes: 0.395 Positive Predictive Value Vsfold5: 0.572 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RNAfold Matthews Correlation Coefficient Vsfold5: 0.534 RNAfold: 0.409 Sensitivity Vsfold5: 0.505 RNAfold: 0.390 Positive Predictive Value Vsfold5: 0.572 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.539 Vsfold5: 0.531 Sensitivity MXScarna(seed): 0.501 Vsfold5: 0.501 Positive Predictive Value MXScarna(seed): 0.586 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00909249161262	+ Vsfold5 vs RNAsubopt Matthews Correlation Coefficient Vsfold5: 0.534 RNAsubopt: 0.394 Sensitivity Vsfold5: 0.505 RNAsubopt: 0.378 Positive Predictive Value Vsfold5: 0.572 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.531 RSpredict(seed): 0.514 Sensitivity Vsfold5: 0.501 RSpredict(seed): 0.427 Positive Predictive Value Vsfold5: 0.569 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.9656853596e-05	+ Vsfold5 vs CRWrnafold Matthews Correlation Coefficient Vsfold5: 0.534 CRWrnafold: 0.374 Sensitivity Vsfold5: 0.505 CRWrnafold: 0.351 Positive Predictive Value Vsfold5: 0.572 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: 0.504 CMfinder(seed): 0.443 Sensitivity Vsfold5: 0.482 CMfinder(seed): 0.333 Positive Predictive Value Vsfold5: 0.533 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.34632741202e-08	+ Vsfold5 vs RNAwolf Matthews Correlation Coefficient Vsfold5: 0.534 RNAwolf: 0.362 Sensitivity Vsfold5: 0.505 RNAwolf: 0.353 Positive Predictive Value Vsfold5: 0.572 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Afold Matthews Correlation Coefficient Vsfold5: 0.531 Afold: 0.316 Sensitivity Vsfold5: 0.504 Afold: 0.305 Positive Predictive Value Vsfold5: 0.567 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.597 Alterna: 0.393 Sensitivity Vsfold5: 0.550 Alterna: 0.365 Positive Predictive Value Vsfold5: 0.657 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.531 Mastr(seed): 0.341 Sensitivity Vsfold5: 0.501 Mastr(seed): 0.176 Positive Predictive Value Vsfold5: 0.569 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	? Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.774 Mastr(20): 0.561 Sensitivity Vsfold5: 0.699 Mastr(20): 0.459 Positive Predictive Value Vsfold5: 0.861 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.686 NanoFolder: 0.304 Sensitivity Vsfold5: 0.620 NanoFolder: 0.343 Positive Predictive Value Vsfold5: 0.763 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.821 Vsfold5: 0.774 Sensitivity Carnac(20): 0.684 Vsfold5: 0.699 Positive Predictive Value Carnac(20): 0.989 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold5: 0.423 Sensitivity Multilign(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value Multilign(seed): 0.625 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.862 Vsfold5: 0.774 Sensitivity Multilign(20): 0.752 Vsfold5: 0.699 Positive Predictive Value Multilign(20): 0.990 Vsfold5: 0.861 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): 0.857 Vsfold5: 0.774 Sensitivity TurboFold(20): 0.744 Vsfold5: 0.699 Positive Predictive Value TurboFold(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.844 Vsfold5: 0.774 Sensitivity RNAalifold(20): 0.722 Vsfold5: 0.699 Positive Predictive Value RNAalifold(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.840 Vsfold5: 0.774 Sensitivity RNASampler(20): 0.714 Vsfold5: 0.699 Positive Predictive Value RNASampler(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.779 Vsfold5: 0.774 Sensitivity CMfinder(20): 0.617 Vsfold5: 0.699 Positive Predictive Value CMfinder(20): 0.988 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Vsfold5: 0.774 Sensitivity PETfold_pre2.0(20): 0.759 Vsfold5: 0.699 Positive Predictive Value PETfold_pre2.0(20): 0.962 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold5: 0.423 Sensitivity PPfold(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value PPfold(seed): 0.833 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.600 Vsfold5: 0.449 Sensitivity TurboFold(seed): 0.518 Vsfold5: 0.435 Positive Predictive Value TurboFold(seed): 0.702 Vsfold5: 0.474 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.837 Vsfold5: 0.774 Sensitivity MXScarna(20): 0.752 Vsfold5: 0.699 Positive Predictive Value MXScarna(20): 0.935 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs RSpredict(20) Matthews Correlation Coefficient Vsfold5: 0.774 RSpredict(20): 0.672 Sensitivity Vsfold5: 0.699 RSpredict(20): 0.549 Positive Predictive Value Vsfold5: 0.861 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Vsfold5: 0.774 Sensitivity CentroidAlifold(20): 0.752 Vsfold5: 0.699 Positive Predictive Value CentroidAlifold(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs Murlet(20) Matthews Correlation Coefficient Vsfold5: 0.774 Murlet(20): 0.741 Sensitivity Vsfold5: 0.699 Murlet(20): 0.594 Positive Predictive Value Vsfold5: 0.861 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.840 Vsfold5: 0.774 Sensitivity PPfold(20): 0.737 Vsfold5: 0.699 Positive Predictive Value PPfold(20): 0.961 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.555 MCFold: 0.290 Sensitivity Vsfold5: 0.517 MCFold: 0.320 Positive Predictive Value Vsfold5: 0.604 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(seed)	11 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.831 Carnac(seed): 0.550 Sensitivity Cylofold: 0.834 Carnac(seed): 0.313 Positive Predictive Value Cylofold: 0.830 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.08220657796e-09	13 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.862 Carnac(seed): 0.582 Sensitivity McQFold: 0.849 Carnac(seed): 0.354 Positive Predictive Value McQFold: 0.877 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	12 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.803 Carnac(seed): 0.531 Sensitivity Pknots: 0.820 Carnac(seed): 0.292 Positive Predictive Value Pknots: 0.789 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.53777893337e-08	13 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 Carnac(seed): 0.582 Sensitivity CentroidAlifold(seed): 0.579 Carnac(seed): 0.354 Positive Predictive Value CentroidAlifold(seed): 0.902 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.52214427071e-09	13 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.819 Carnac(seed): 0.582 Sensitivity PknotsRG: 0.818 Carnac(seed): 0.354 Positive Predictive Value PknotsRG: 0.823 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.34193807955e-08	13 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 Carnac(seed): 0.582 Sensitivity PETfold_pre2.0(seed): 0.572 Carnac(seed): 0.354 Positive Predictive Value PETfold_pre2.0(seed): 0.769 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.5677163434e-08	13 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Carnac(seed): 0.582 Sensitivity RNASampler(seed): 0.572 Carnac(seed): 0.354 Positive Predictive Value RNASampler(seed): 0.755 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	13 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.604 Carnac(seed): 0.582 Sensitivity IPknot: 0.537 Carnac(seed): 0.354 Positive Predictive Value IPknot: 0.686 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.81284138222e-07	13 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.619 Carnac(seed): 0.582 Sensitivity RNAalifold(seed): 0.477 Carnac(seed): 0.354 Positive Predictive Value RNAalifold(seed): 0.810 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.42992852122e-09	13 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.631 Carnac(seed): 0.582 Sensitivity CentroidFold: 0.554 Carnac(seed): 0.354 Positive Predictive Value CentroidFold: 0.725 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	13 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Carnac(seed): 0.582 Sensitivity CentroidHomfold‑LAST: 0.502 Carnac(seed): 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.684 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.220070679653	13 Carnac(seed) vs Vsfold5 Matthews Correlation Coefficient Carnac(seed): 0.582 Vsfold5: 0.452 Sensitivity Carnac(seed): 0.354 Vsfold5: 0.435 Positive Predictive Value Carnac(seed): 0.962 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.08252958266e-08		+ Carnac(seed) vs ProbKnot Matthews Correlation Coefficient Carnac(seed): 0.582 ProbKnot: 0.514 Sensitivity Carnac(seed): 0.354 ProbKnot: 0.495 Positive Predictive Value Carnac(seed): 0.962 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.26036189514e-09	= RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.584 Carnac(seed): 0.582 Sensitivity RNASLOpt: 0.526 Carnac(seed): 0.354 Positive Predictive Value RNASLOpt: 0.655 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.652002798179	= Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.582 Carnac(seed): 0.582 Sensitivity Contrafold: 0.540 Carnac(seed): 0.354 Positive Predictive Value Contrafold: 0.634 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00256031511034	+ Carnac(seed) vs HotKnots Matthews Correlation Coefficient Carnac(seed): 0.582 HotKnots: 0.522 Sensitivity Carnac(seed): 0.354 HotKnots: 0.526 Positive Predictive Value Carnac(seed): 0.962 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.32883086441e-08	- RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.561 Carnac(seed): 0.531 Sensitivity RDfolder: 0.481 Carnac(seed): 0.292 Positive Predictive Value RDfolder: 0.663 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.76300197125e-07	+ Carnac(seed) vs Fold Matthews Correlation Coefficient Carnac(seed): 0.582 Fold: 0.472 Sensitivity Carnac(seed): 0.354 Fold: 0.453 Positive Predictive Value Carnac(seed): 0.962 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ Carnac(seed) vs ContextFold Matthews Correlation Coefficient Carnac(seed): 0.582 ContextFold: 0.504 Sensitivity Carnac(seed): 0.354 ContextFold: 0.453 Positive Predictive Value Carnac(seed): 0.962 ContextFold: 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ Carnac(seed) vs MaxExpect Matthews Correlation Coefficient Carnac(seed): 0.582 MaxExpect: 0.513 Sensitivity Carnac(seed): 0.354 MaxExpect: 0.488 Positive Predictive Value Carnac(seed): 0.962 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.36849473644e-08	+ Carnac(seed) vs Murlet(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 Murlet(seed): 0.482 Sensitivity Carnac(seed): 0.354 Murlet(seed): 0.319 Positive Predictive Value Carnac(seed): 0.962 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ Carnac(seed) vs Sfold Matthews Correlation Coefficient Carnac(seed): 0.582 Sfold: 0.475 Sensitivity Carnac(seed): 0.354 Sfold: 0.442 Positive Predictive Value Carnac(seed): 0.962 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ Carnac(seed) vs UNAFold Matthews Correlation Coefficient Carnac(seed): 0.582 UNAFold: 0.481 Sensitivity Carnac(seed): 0.354 UNAFold: 0.460 Positive Predictive Value Carnac(seed): 0.962 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	+ Carnac(seed) vs Vsfold4 Matthews Correlation Coefficient Carnac(seed): 0.582 Vsfold4: 0.392 Sensitivity Carnac(seed): 0.354 Vsfold4: 0.365 Positive Predictive Value Carnac(seed): 0.962 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ Carnac(seed) vs RNAshapes Matthews Correlation Coefficient Carnac(seed): 0.582 RNAshapes: 0.447 Sensitivity Carnac(seed): 0.354 RNAshapes: 0.432 Positive Predictive Value Carnac(seed): 0.962 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ Carnac(seed) vs RNAfold Matthews Correlation Coefficient Carnac(seed): 0.582 RNAfold: 0.476 Sensitivity Carnac(seed): 0.354 RNAfold: 0.460 Positive Predictive Value Carnac(seed): 0.962 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	+ Carnac(seed) vs MXScarna(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 MXScarna(seed): 0.440 Sensitivity Carnac(seed): 0.354 MXScarna(seed): 0.421 Positive Predictive Value Carnac(seed): 0.962 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.46296269841e-09	+ Carnac(seed) vs RNAsubopt Matthews Correlation Coefficient Carnac(seed): 0.582 RNAsubopt: 0.463 Sensitivity Carnac(seed): 0.354 RNAsubopt: 0.446 Positive Predictive Value Carnac(seed): 0.962 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.69265863073e-08	+ Carnac(seed) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 RSpredict(seed): 0.488 Sensitivity Carnac(seed): 0.354 RSpredict(seed): 0.425 Positive Predictive Value Carnac(seed): 0.962 RSpredict(seed): 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ Carnac(seed) vs CRWrnafold Matthews Correlation Coefficient Carnac(seed): 0.582 CRWrnafold: 0.446 Sensitivity Carnac(seed): 0.354 CRWrnafold: 0.425 Positive Predictive Value Carnac(seed): 0.962 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ Carnac(seed) vs CMfinder(seed) Matthews Correlation Coefficient Carnac(seed): 0.555 CMfinder(seed): 0.443 Sensitivity Carnac(seed): 0.325 CMfinder(seed): 0.333 Positive Predictive Value Carnac(seed): 0.953 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.582 RNAwolf: 0.438 Sensitivity Carnac(seed): 0.354 RNAwolf: 0.407 Positive Predictive Value Carnac(seed): 0.962 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ Carnac(seed) vs Afold Matthews Correlation Coefficient Carnac(seed): 0.547 Afold: 0.454 Sensitivity Carnac(seed): 0.316 Afold: 0.427 Positive Predictive Value Carnac(seed): 0.952 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.10032755566e-08	+ Carnac(seed) vs Alterna Matthews Correlation Coefficient Carnac(seed): 0.531 Alterna: 0.384 Sensitivity Carnac(seed): 0.292 Alterna: 0.365 Positive Predictive Value Carnac(seed): 0.971 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 Mastr(seed): 0.400 Sensitivity Carnac(seed): 0.354 Mastr(seed): 0.242 Positive Predictive Value Carnac(seed): 0.962 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 6.42028829171e-09	? Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): N/A Carnac(seed): N/A Sensitivity Mastr(20): N/A Carnac(seed): N/A Positive Predictive Value Mastr(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.585 Carnac(seed): 0.554 Sensitivity NanoFolder: 0.654 Carnac(seed): 0.327 Positive Predictive Value NanoFolder: 0.531 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): N/A Carnac(seed): N/A Sensitivity Carnac(20): N/A Carnac(seed): N/A Positive Predictive Value Carnac(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(seed) vs Multilign(seed) Matthews Correlation Coefficient Carnac(seed): 0.625 Multilign(seed): 0.575 Sensitivity Carnac(seed): 0.407 Multilign(seed): 0.536 Positive Predictive Value Carnac(seed): 0.966 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs Multilign(20) Matthews Correlation Coefficient Carnac(seed): N/A Multilign(20): N/A Sensitivity Carnac(seed): N/A Multilign(20): N/A Positive Predictive Value Carnac(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): N/A Carnac(seed): N/A Sensitivity TurboFold(20): N/A Carnac(seed): N/A Positive Predictive Value TurboFold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Carnac(seed): N/A Sensitivity RNAalifold(20): N/A Carnac(seed): N/A Positive Predictive Value RNAalifold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): N/A Carnac(seed): N/A Sensitivity RNASampler(20): N/A Carnac(seed): N/A Positive Predictive Value RNASampler(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(seed) vs 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): N/A Carnac(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Carnac(seed): 0.625 Sensitivity PPfold(seed): 0.536 Carnac(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Carnac(seed): 0.571 Sensitivity TurboFold(seed): 0.518 Carnac(seed): 0.339 Positive Predictive Value TurboFold(seed): 0.702 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): N/A Carnac(seed): N/A Sensitivity MXScarna(20): N/A Carnac(seed): N/A Positive Predictive Value MXScarna(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): N/A Carnac(seed): N/A Sensitivity RSpredict(20): N/A Carnac(seed): N/A Positive Predictive Value RSpredict(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): N/A Carnac(seed): N/A Sensitivity CentroidAlifold(20): N/A Carnac(seed): N/A Positive Predictive Value CentroidAlifold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): N/A Carnac(seed): N/A Sensitivity Murlet(20): N/A Carnac(seed): N/A Positive Predictive Value Murlet(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): N/A Carnac(seed): N/A Sensitivity PPfold(20): N/A Carnac(seed): N/A Positive Predictive Value PPfold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Carnac(seed) vs MCFold Matthews Correlation Coefficient Carnac(seed): 0.566 MCFold: 0.354 Sensitivity Carnac(seed): 0.332 MCFold: 0.415 Positive Predictive Value Carnac(seed): 0.971 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.26545642304e-09
ProbKnot	45 Cylofold vs ProbKnot Matthews Correlation Coefficient Cylofold: 0.764 ProbKnot: 0.525 Sensitivity Cylofold: 0.742 ProbKnot: 0.495 Positive Predictive Value Cylofold: 0.791 ProbKnot: 0.567 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs ProbKnot Matthews Correlation Coefficient McQFold: 0.594 ProbKnot: 0.459 Sensitivity McQFold: 0.583 ProbKnot: 0.440 Positive Predictive Value McQFold: 0.611 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs ProbKnot Matthews Correlation Coefficient Pknots: 0.697 ProbKnot: 0.527 Sensitivity Pknots: 0.668 ProbKnot: 0.496 Positive Predictive Value Pknots: 0.733 ProbKnot: 0.570 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 ProbKnot: 0.603 Sensitivity CentroidAlifold(seed): 0.634 ProbKnot: 0.565 Positive Predictive Value CentroidAlifold(seed): 0.933 ProbKnot: 0.649 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	53 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.531 ProbKnot: 0.459 Sensitivity PknotsRG: 0.525 ProbKnot: 0.440 Positive Predictive Value PknotsRG: 0.544 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 ProbKnot: 0.599 Sensitivity PETfold_pre2.0(seed): 0.649 ProbKnot: 0.567 Positive Predictive Value PETfold_pre2.0(seed): 0.824 ProbKnot: 0.638 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.43573297697e-08	13 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.655 ProbKnot: 0.514 Sensitivity RNASampler(seed): 0.572 ProbKnot: 0.495 Positive Predictive Value RNASampler(seed): 0.755 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.1413769576e-08	53 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.489 ProbKnot: 0.459 Sensitivity IPknot: 0.435 ProbKnot: 0.440 Positive Predictive Value IPknot: 0.556 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs ProbKnot Matthews Correlation Coefficient RNAalifold(seed): 0.657 ProbKnot: 0.603 Sensitivity RNAalifold(seed): 0.522 ProbKnot: 0.565 Positive Predictive Value RNAalifold(seed): 0.833 ProbKnot: 0.649 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.02510705504e-08	53 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.482 ProbKnot: 0.459 Sensitivity CentroidFold: 0.430 ProbKnot: 0.440 Positive Predictive Value CentroidFold: 0.548 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 ProbKnot: 0.459 Sensitivity CentroidHomfold‑LAST: 0.407 ProbKnot: 0.440 Positive Predictive Value CentroidHomfold‑LAST: 0.592 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs ProbKnot Matthews Correlation Coefficient Vsfold5: 0.534 ProbKnot: 0.459 Sensitivity Vsfold5: 0.505 ProbKnot: 0.440 Positive Predictive Value Vsfold5: 0.572 ProbKnot: 0.487 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs ProbKnot Matthews Correlation Coefficient Carnac(seed): 0.582 ProbKnot: 0.514 Sensitivity Carnac(seed): 0.354 ProbKnot: 0.495 Positive Predictive Value Carnac(seed): 0.962 ProbKnot: 0.542 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.26036189514e-09		= ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.459 RNASLOpt: 0.458 Sensitivity ProbKnot: 0.440 RNASLOpt: 0.419 Positive Predictive Value ProbKnot: 0.487 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0139030957526	= ProbKnot vs Contrafold Matthews Correlation Coefficient ProbKnot: 0.459 Contrafold: 0.458 Sensitivity ProbKnot: 0.440 Contrafold: 0.435 Positive Predictive Value ProbKnot: 0.487 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.264581540075	+ ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.459 HotKnots: 0.453 Sensitivity ProbKnot: 0.440 HotKnots: 0.445 Positive Predictive Value ProbKnot: 0.487 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.000108348164592	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.527 RDfolder: 0.508 Sensitivity ProbKnot: 0.496 RDfolder: 0.432 Positive Predictive Value ProbKnot: 0.570 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 2.63254822069e-07	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.459 Fold: 0.453 Sensitivity ProbKnot: 0.440 Fold: 0.431 Positive Predictive Value ProbKnot: 0.487 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.000207424631753	+ ProbKnot vs ContextFold Matthews Correlation Coefficient ProbKnot: 0.459 ContextFold: 0.447 Sensitivity ProbKnot: 0.440 ContextFold: 0.407 Positive Predictive Value ProbKnot: 0.487 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.03351724933e-07	+ ProbKnot vs MaxExpect Matthews Correlation Coefficient ProbKnot: 0.459 MaxExpect: 0.440 Sensitivity ProbKnot: 0.440 MaxExpect: 0.414 Positive Predictive Value ProbKnot: 0.487 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.514 Murlet(seed): 0.482 Sensitivity ProbKnot: 0.495 Murlet(seed): 0.319 Positive Predictive Value ProbKnot: 0.542 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ ProbKnot vs Sfold Matthews Correlation Coefficient ProbKnot: 0.459 Sfold: 0.425 Sensitivity ProbKnot: 0.440 Sfold: 0.377 Positive Predictive Value ProbKnot: 0.487 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.459 UNAFold: 0.412 Sensitivity ProbKnot: 0.440 UNAFold: 0.390 Positive Predictive Value ProbKnot: 0.487 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.459 Vsfold4: 0.423 Sensitivity ProbKnot: 0.440 Vsfold4: 0.380 Positive Predictive Value ProbKnot: 0.487 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.459 RNAshapes: 0.416 Sensitivity ProbKnot: 0.440 RNAshapes: 0.395 Positive Predictive Value ProbKnot: 0.487 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.459 RNAfold: 0.409 Sensitivity ProbKnot: 0.440 RNAfold: 0.390 Positive Predictive Value ProbKnot: 0.487 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs MXScarna(seed) Matthews Correlation Coefficient ProbKnot: 0.603 MXScarna(seed): 0.539 Sensitivity ProbKnot: 0.565 MXScarna(seed): 0.501 Positive Predictive Value ProbKnot: 0.649 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.459 RNAsubopt: 0.394 Sensitivity ProbKnot: 0.440 RNAsubopt: 0.378 Positive Predictive Value ProbKnot: 0.487 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.603 RSpredict(seed): 0.514 Sensitivity ProbKnot: 0.565 RSpredict(seed): 0.427 Positive Predictive Value ProbKnot: 0.649 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.459 CRWrnafold: 0.374 Sensitivity ProbKnot: 0.440 CRWrnafold: 0.351 Positive Predictive Value ProbKnot: 0.487 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.513 CMfinder(seed): 0.443 Sensitivity ProbKnot: 0.494 CMfinder(seed): 0.333 Positive Predictive Value ProbKnot: 0.539 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.459 RNAwolf: 0.362 Sensitivity ProbKnot: 0.440 RNAwolf: 0.353 Positive Predictive Value ProbKnot: 0.487 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.407 Afold: 0.316 Sensitivity ProbKnot: 0.393 Afold: 0.305 Positive Predictive Value ProbKnot: 0.431 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.527 Alterna: 0.393 Sensitivity ProbKnot: 0.496 Alterna: 0.365 Positive Predictive Value ProbKnot: 0.570 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.603 Mastr(seed): 0.341 Sensitivity ProbKnot: 0.565 Mastr(seed): 0.176 Positive Predictive Value ProbKnot: 0.649 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-08	? ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.803 Mastr(20): 0.561 Sensitivity ProbKnot: 0.722 Mastr(20): 0.459 Positive Predictive Value ProbKnot: 0.897 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.594 NanoFolder: 0.304 Sensitivity ProbKnot: 0.560 NanoFolder: 0.343 Positive Predictive Value ProbKnot: 0.637 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.821 ProbKnot: 0.803 Sensitivity Carnac(20): 0.684 ProbKnot: 0.722 Positive Predictive Value Carnac(20): 0.989 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.575 ProbKnot: 0.539 Sensitivity Multilign(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value Multilign(seed): 0.625 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.862 ProbKnot: 0.803 Sensitivity Multilign(20): 0.752 ProbKnot: 0.722 Positive Predictive Value Multilign(20): 0.990 ProbKnot: 0.897 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): 0.857 ProbKnot: 0.803 Sensitivity TurboFold(20): 0.744 ProbKnot: 0.722 Positive Predictive Value TurboFold(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.844 ProbKnot: 0.803 Sensitivity RNAalifold(20): 0.722 ProbKnot: 0.722 Positive Predictive Value RNAalifold(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.840 ProbKnot: 0.803 Sensitivity RNASampler(20): 0.714 ProbKnot: 0.722 Positive Predictive Value RNASampler(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.803 CMfinder(20): 0.779 Sensitivity ProbKnot: 0.722 CMfinder(20): 0.617 Positive Predictive Value ProbKnot: 0.897 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 ProbKnot: 0.803 Sensitivity PETfold_pre2.0(20): 0.759 ProbKnot: 0.722 Positive Predictive Value PETfold_pre2.0(20): 0.962 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs ProbKnot Matthews Correlation Coefficient PPfold(seed): 0.666 ProbKnot: 0.539 Sensitivity PPfold(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value PPfold(seed): 0.833 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.600 ProbKnot: 0.522 Sensitivity TurboFold(seed): 0.518 ProbKnot: 0.512 Positive Predictive Value TurboFold(seed): 0.702 ProbKnot: 0.541 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.837 ProbKnot: 0.803 Sensitivity MXScarna(20): 0.752 ProbKnot: 0.722 Positive Predictive Value MXScarna(20): 0.935 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.803 RSpredict(20): 0.672 Sensitivity ProbKnot: 0.722 RSpredict(20): 0.549 Positive Predictive Value ProbKnot: 0.897 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.862 ProbKnot: 0.803 Sensitivity CentroidAlifold(20): 0.752 ProbKnot: 0.722 Positive Predictive Value CentroidAlifold(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.803 Murlet(20): 0.741 Sensitivity ProbKnot: 0.722 Murlet(20): 0.594 Positive Predictive Value ProbKnot: 0.897 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.840 ProbKnot: 0.803 Sensitivity PPfold(20): 0.737 ProbKnot: 0.722 Positive Predictive Value PPfold(20): 0.961 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.479 MCFold: 0.290 Sensitivity ProbKnot: 0.456 MCFold: 0.320 Positive Predictive Value ProbKnot: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASLOpt	45 Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.764 RNASLOpt: 0.546 Sensitivity Cylofold: 0.742 RNASLOpt: 0.488 Positive Predictive Value Cylofold: 0.791 RNASLOpt: 0.621 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.594 RNASLOpt: 0.458 Sensitivity McQFold: 0.583 RNASLOpt: 0.419 Positive Predictive Value McQFold: 0.611 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: 0.697 RNASLOpt: 0.549 Sensitivity Pknots: 0.668 RNASLOpt: 0.489 Positive Predictive Value Pknots: 0.733 RNASLOpt: 0.626 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNASLOpt: 0.635 Sensitivity CentroidAlifold(seed): 0.634 RNASLOpt: 0.565 Positive Predictive Value CentroidAlifold(seed): 0.933 RNASLOpt: 0.718 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	53 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.531 RNASLOpt: 0.458 Sensitivity PknotsRG: 0.525 RNASLOpt: 0.419 Positive Predictive Value PknotsRG: 0.544 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNASLOpt: 0.663 Sensitivity PETfold_pre2.0(seed): 0.649 RNASLOpt: 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNASLOpt: 0.744 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.04409141234e-08	13 RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNASLOpt: 0.584 Sensitivity RNASampler(seed): 0.572 RNASLOpt: 0.526 Positive Predictive Value RNASampler(seed): 0.755 RNASLOpt: 0.655 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.91441904741e-08	53 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.489 RNASLOpt: 0.458 Sensitivity IPknot: 0.435 RNASLOpt: 0.419 Positive Predictive Value IPknot: 0.556 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNASLOpt: 0.635 Sensitivity RNAalifold(seed): 0.522 RNASLOpt: 0.565 Positive Predictive Value RNAalifold(seed): 0.833 RNASLOpt: 0.718 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 6.9050074835e-07	53 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.482 RNASLOpt: 0.458 Sensitivity CentroidFold: 0.430 RNASLOpt: 0.419 Positive Predictive Value CentroidFold: 0.548 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNASLOpt: 0.458 Sensitivity CentroidHomfold‑LAST: 0.407 RNASLOpt: 0.419 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs RNASLOpt Matthews Correlation Coefficient Vsfold5: 0.534 RNASLOpt: 0.458 Sensitivity Vsfold5: 0.505 RNASLOpt: 0.419 Positive Predictive Value Vsfold5: 0.572 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.584 Carnac(seed): 0.582 Sensitivity RNASLOpt: 0.526 Carnac(seed): 0.354 Positive Predictive Value RNASLOpt: 0.655 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.652002798179	53 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.459 RNASLOpt: 0.458 Sensitivity ProbKnot: 0.440 RNASLOpt: 0.419 Positive Predictive Value ProbKnot: 0.487 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0139030957526		= Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.458 RNASLOpt: 0.458 Sensitivity Contrafold: 0.435 RNASLOpt: 0.419 Positive Predictive Value Contrafold: 0.491 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.187755798617	= RNASLOpt vs HotKnots Matthews Correlation Coefficient RNASLOpt: 0.458 HotKnots: 0.453 Sensitivity RNASLOpt: 0.419 HotKnots: 0.445 Positive Predictive Value RNASLOpt: 0.508 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0563054219211	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.549 RDfolder: 0.508 Sensitivity RNASLOpt: 0.489 RDfolder: 0.432 Positive Predictive Value RNASLOpt: 0.626 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASLOpt vs Fold Matthews Correlation Coefficient RNASLOpt: 0.458 Fold: 0.453 Sensitivity RNASLOpt: 0.419 Fold: 0.431 Positive Predictive Value RNASLOpt: 0.508 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.696686202358	+ RNASLOpt vs ContextFold Matthews Correlation Coefficient RNASLOpt: 0.458 ContextFold: 0.447 Sensitivity RNASLOpt: 0.419 ContextFold: 0.407 Positive Predictive Value RNASLOpt: 0.508 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 8.09943589199e-07	+ RNASLOpt vs MaxExpect Matthews Correlation Coefficient RNASLOpt: 0.458 MaxExpect: 0.440 Sensitivity RNASLOpt: 0.419 MaxExpect: 0.414 Positive Predictive Value RNASLOpt: 0.508 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.584 Murlet(seed): 0.482 Sensitivity RNASLOpt: 0.526 Murlet(seed): 0.319 Positive Predictive Value RNASLOpt: 0.655 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.03576421863e-08	+ RNASLOpt vs Sfold Matthews Correlation Coefficient RNASLOpt: 0.458 Sfold: 0.425 Sensitivity RNASLOpt: 0.419 Sfold: 0.377 Positive Predictive Value RNASLOpt: 0.508 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs UNAFold Matthews Correlation Coefficient RNASLOpt: 0.458 UNAFold: 0.412 Sensitivity RNASLOpt: 0.419 UNAFold: 0.390 Positive Predictive Value RNASLOpt: 0.508 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.458 Vsfold4: 0.423 Sensitivity RNASLOpt: 0.419 Vsfold4: 0.380 Positive Predictive Value RNASLOpt: 0.508 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.458 RNAshapes: 0.416 Sensitivity RNASLOpt: 0.419 RNAshapes: 0.395 Positive Predictive Value RNASLOpt: 0.508 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAfold Matthews Correlation Coefficient RNASLOpt: 0.458 RNAfold: 0.409 Sensitivity RNASLOpt: 0.419 RNAfold: 0.390 Positive Predictive Value RNASLOpt: 0.508 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs MXScarna(seed) Matthews Correlation Coefficient RNASLOpt: 0.635 MXScarna(seed): 0.539 Sensitivity RNASLOpt: 0.565 MXScarna(seed): 0.501 Positive Predictive Value RNASLOpt: 0.718 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.458 RNAsubopt: 0.394 Sensitivity RNASLOpt: 0.419 RNAsubopt: 0.378 Positive Predictive Value RNASLOpt: 0.508 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.635 RSpredict(seed): 0.514 Sensitivity RNASLOpt: 0.565 RSpredict(seed): 0.427 Positive Predictive Value RNASLOpt: 0.718 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ RNASLOpt vs CRWrnafold Matthews Correlation Coefficient RNASLOpt: 0.458 CRWrnafold: 0.374 Sensitivity RNASLOpt: 0.419 CRWrnafold: 0.351 Positive Predictive Value RNASLOpt: 0.508 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.580 CMfinder(seed): 0.443 Sensitivity RNASLOpt: 0.522 CMfinder(seed): 0.333 Positive Predictive Value RNASLOpt: 0.650 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.458 RNAwolf: 0.362 Sensitivity RNASLOpt: 0.419 RNAwolf: 0.353 Positive Predictive Value RNASLOpt: 0.508 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Afold Matthews Correlation Coefficient RNASLOpt: 0.445 Afold: 0.316 Sensitivity RNASLOpt: 0.415 Afold: 0.305 Positive Predictive Value RNASLOpt: 0.487 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.549 Alterna: 0.393 Sensitivity RNASLOpt: 0.489 Alterna: 0.365 Positive Predictive Value RNASLOpt: 0.626 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.635 Mastr(seed): 0.341 Sensitivity RNASLOpt: 0.565 Mastr(seed): 0.176 Positive Predictive Value RNASLOpt: 0.718 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.75835195567e-08	? RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.792 Mastr(20): 0.561 Sensitivity RNASLOpt: 0.692 Mastr(20): 0.459 Positive Predictive Value RNASLOpt: 0.911 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.692 NanoFolder: 0.304 Sensitivity RNASLOpt: 0.614 NanoFolder: 0.343 Positive Predictive Value RNASLOpt: 0.785 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.821 RNASLOpt: 0.792 Sensitivity Carnac(20): 0.684 RNASLOpt: 0.692 Positive Predictive Value Carnac(20): 0.989 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Multilign(seed) Matthews Correlation Coefficient RNASLOpt: 0.588 Multilign(seed): 0.575 Sensitivity RNASLOpt: 0.514 Multilign(seed): 0.536 Positive Predictive Value RNASLOpt: 0.679 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.862 RNASLOpt: 0.792 Sensitivity Multilign(20): 0.752 RNASLOpt: 0.692 Positive Predictive Value Multilign(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.857 RNASLOpt: 0.792 Sensitivity TurboFold(20): 0.744 RNASLOpt: 0.692 Positive Predictive Value TurboFold(20): 0.990 RNASLOpt: 0.911 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): 0.844 RNASLOpt: 0.792 Sensitivity RNAalifold(20): 0.722 RNASLOpt: 0.692 Positive Predictive Value RNAalifold(20): 0.990 RNASLOpt: 0.911 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): 0.840 RNASLOpt: 0.792 Sensitivity RNASampler(20): 0.714 RNASLOpt: 0.692 Positive Predictive Value RNASampler(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: 0.792 CMfinder(20): 0.779 Sensitivity RNASLOpt: 0.692 CMfinder(20): 0.617 Positive Predictive Value RNASLOpt: 0.911 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNASLOpt: 0.792 Sensitivity PETfold_pre2.0(20): 0.759 RNASLOpt: 0.692 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.666 RNASLOpt: 0.588 Sensitivity PPfold(seed): 0.536 RNASLOpt: 0.514 Positive Predictive Value PPfold(seed): 0.833 RNASLOpt: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.600 RNASLOpt: 0.599 Sensitivity TurboFold(seed): 0.518 RNASLOpt: 0.536 Positive Predictive Value TurboFold(seed): 0.702 RNASLOpt: 0.677 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.837 RNASLOpt: 0.792 Sensitivity MXScarna(20): 0.752 RNASLOpt: 0.692 Positive Predictive Value MXScarna(20): 0.935 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.792 RSpredict(20): 0.672 Sensitivity RNASLOpt: 0.692 RSpredict(20): 0.549 Positive Predictive Value RNASLOpt: 0.911 RSpredict(20): 0.830 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): 0.862 RNASLOpt: 0.792 Sensitivity CentroidAlifold(20): 0.752 RNASLOpt: 0.692 Positive Predictive Value CentroidAlifold(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Murlet(20) Matthews Correlation Coefficient RNASLOpt: 0.792 Murlet(20): 0.741 Sensitivity RNASLOpt: 0.692 Murlet(20): 0.594 Positive Predictive Value RNASLOpt: 0.911 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.840 RNASLOpt: 0.792 Sensitivity PPfold(20): 0.737 RNASLOpt: 0.692 Positive Predictive Value PPfold(20): 0.961 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.489 MCFold: 0.290 Sensitivity RNASLOpt: 0.442 MCFold: 0.320 Positive Predictive Value RNASLOpt: 0.549 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Contrafold	45 Cylofold vs Contrafold Matthews Correlation Coefficient Cylofold: 0.764 Contrafold: 0.512 Sensitivity Cylofold: 0.742 Contrafold: 0.475 Positive Predictive Value Cylofold: 0.791 Contrafold: 0.563 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs Contrafold Matthews Correlation Coefficient McQFold: 0.594 Contrafold: 0.458 Sensitivity McQFold: 0.583 Contrafold: 0.435 Positive Predictive Value McQFold: 0.611 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Contrafold Matthews Correlation Coefficient Pknots: 0.697 Contrafold: 0.515 Sensitivity Pknots: 0.668 Contrafold: 0.477 Positive Predictive Value Pknots: 0.733 Contrafold: 0.567 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Contrafold: 0.653 Sensitivity CentroidAlifold(seed): 0.634 Contrafold: 0.598 Positive Predictive Value CentroidAlifold(seed): 0.933 Contrafold: 0.719 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.77512146924e-08	53 PknotsRG vs Contrafold Matthews Correlation Coefficient PknotsRG: 0.531 Contrafold: 0.458 Sensitivity PknotsRG: 0.525 Contrafold: 0.435 Positive Predictive Value PknotsRG: 0.544 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Contrafold: 0.653 Sensitivity PETfold_pre2.0(seed): 0.649 Contrafold: 0.606 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.50323628132e-08	13 RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.655 Contrafold: 0.582 Sensitivity RNASampler(seed): 0.572 Contrafold: 0.540 Positive Predictive Value RNASampler(seed): 0.755 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	53 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.489 Contrafold: 0.458 Sensitivity IPknot: 0.435 Contrafold: 0.435 Positive Predictive Value IPknot: 0.556 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs Contrafold Matthews Correlation Coefficient RNAalifold(seed): 0.657 Contrafold: 0.653 Sensitivity RNAalifold(seed): 0.522 Contrafold: 0.598 Positive Predictive Value RNAalifold(seed): 0.833 Contrafold: 0.719 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71428824004e-05	53 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.482 Contrafold: 0.458 Sensitivity CentroidFold: 0.430 Contrafold: 0.435 Positive Predictive Value CentroidFold: 0.548 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Contrafold: 0.458 Sensitivity CentroidHomfold‑LAST: 0.407 Contrafold: 0.435 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs Contrafold Matthews Correlation Coefficient Vsfold5: 0.534 Contrafold: 0.458 Sensitivity Vsfold5: 0.505 Contrafold: 0.435 Positive Predictive Value Vsfold5: 0.572 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.582 Carnac(seed): 0.582 Sensitivity Contrafold: 0.540 Carnac(seed): 0.354 Positive Predictive Value Contrafold: 0.634 Carnac(seed): 0.962 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00256031511034	53 ProbKnot vs Contrafold Matthews Correlation Coefficient ProbKnot: 0.459 Contrafold: 0.458 Sensitivity ProbKnot: 0.440 Contrafold: 0.435 Positive Predictive Value ProbKnot: 0.487 Contrafold: 0.491 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.264581540075	53 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.458 RNASLOpt: 0.458 Sensitivity Contrafold: 0.435 RNASLOpt: 0.419 Positive Predictive Value Contrafold: 0.491 RNASLOpt: 0.508 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.187755798617		= Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.458 HotKnots: 0.453 Sensitivity Contrafold: 0.435 HotKnots: 0.445 Positive Predictive Value Contrafold: 0.491 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.00476252034473	= Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.515 RDfolder: 0.508 Sensitivity Contrafold: 0.477 RDfolder: 0.432 Positive Predictive Value Contrafold: 0.567 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00985919189012	= Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.458 Fold: 0.453 Sensitivity Contrafold: 0.435 Fold: 0.431 Positive Predictive Value Contrafold: 0.491 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.196924117351	+ Contrafold vs ContextFold Matthews Correlation Coefficient Contrafold: 0.458 ContextFold: 0.447 Sensitivity Contrafold: 0.435 ContextFold: 0.407 Positive Predictive Value Contrafold: 0.491 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.000990829372106	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.458 MaxExpect: 0.440 Sensitivity Contrafold: 0.435 MaxExpect: 0.414 Positive Predictive Value Contrafold: 0.491 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 8.1815824276e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.582 Murlet(seed): 0.482 Sensitivity Contrafold: 0.540 Murlet(seed): 0.319 Positive Predictive Value Contrafold: 0.634 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.49381627234e-08	+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.458 Sfold: 0.425 Sensitivity Contrafold: 0.435 Sfold: 0.377 Positive Predictive Value Contrafold: 0.491 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.458 UNAFold: 0.412 Sensitivity Contrafold: 0.435 UNAFold: 0.390 Positive Predictive Value Contrafold: 0.491 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.458 Vsfold4: 0.423 Sensitivity Contrafold: 0.435 Vsfold4: 0.380 Positive Predictive Value Contrafold: 0.491 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.458 RNAshapes: 0.416 Sensitivity Contrafold: 0.435 RNAshapes: 0.395 Positive Predictive Value Contrafold: 0.491 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.458 RNAfold: 0.409 Sensitivity Contrafold: 0.435 RNAfold: 0.390 Positive Predictive Value Contrafold: 0.491 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MXScarna(seed) Matthews Correlation Coefficient Contrafold: 0.653 MXScarna(seed): 0.539 Sensitivity Contrafold: 0.598 MXScarna(seed): 0.501 Positive Predictive Value Contrafold: 0.719 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.458 RNAsubopt: 0.394 Sensitivity Contrafold: 0.435 RNAsubopt: 0.378 Positive Predictive Value Contrafold: 0.491 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.653 RSpredict(seed): 0.514 Sensitivity Contrafold: 0.598 RSpredict(seed): 0.427 Positive Predictive Value Contrafold: 0.719 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.458 CRWrnafold: 0.374 Sensitivity Contrafold: 0.435 CRWrnafold: 0.351 Positive Predictive Value Contrafold: 0.491 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.584 CMfinder(seed): 0.443 Sensitivity Contrafold: 0.546 CMfinder(seed): 0.333 Positive Predictive Value Contrafold: 0.630 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.26710183075e-09	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.458 RNAwolf: 0.362 Sensitivity Contrafold: 0.435 RNAwolf: 0.353 Positive Predictive Value Contrafold: 0.491 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.447 Afold: 0.316 Sensitivity Contrafold: 0.430 Afold: 0.305 Positive Predictive Value Contrafold: 0.474 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.515 Alterna: 0.393 Sensitivity Contrafold: 0.477 Alterna: 0.365 Positive Predictive Value Contrafold: 0.567 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.653 Mastr(seed): 0.341 Sensitivity Contrafold: 0.598 Mastr(seed): 0.176 Positive Predictive Value Contrafold: 0.719 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	? Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.854 Mastr(20): 0.561 Sensitivity Contrafold: 0.759 Mastr(20): 0.459 Positive Predictive Value Contrafold: 0.962 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.645 NanoFolder: 0.304 Sensitivity Contrafold: 0.584 NanoFolder: 0.343 Positive Predictive Value Contrafold: 0.719 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.854 Carnac(20): 0.821 Sensitivity Contrafold: 0.759 Carnac(20): 0.684 Positive Predictive Value Contrafold: 0.962 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.596 Multilign(seed): 0.575 Sensitivity Contrafold: 0.521 Multilign(seed): 0.536 Positive Predictive Value Contrafold: 0.689 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.862 Contrafold: 0.854 Sensitivity Multilign(20): 0.752 Contrafold: 0.759 Positive Predictive Value Multilign(20): 0.990 Contrafold: 0.962 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): 0.857 Contrafold: 0.854 Sensitivity TurboFold(20): 0.744 Contrafold: 0.759 Positive Predictive Value TurboFold(20): 0.990 Contrafold: 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs RNAalifold(20) Matthews Correlation Coefficient Contrafold: 0.854 RNAalifold(20): 0.844 Sensitivity Contrafold: 0.759 RNAalifold(20): 0.722 Positive Predictive Value Contrafold: 0.962 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs RNASampler(20) Matthews Correlation Coefficient Contrafold: 0.854 RNASampler(20): 0.840 Sensitivity Contrafold: 0.759 RNASampler(20): 0.714 Positive Predictive Value Contrafold: 0.962 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.854 CMfinder(20): 0.779 Sensitivity Contrafold: 0.759 CMfinder(20): 0.617 Positive Predictive Value Contrafold: 0.962 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Contrafold: 0.854 Sensitivity PETfold_pre2.0(20): 0.759 Contrafold: 0.759 Positive Predictive Value PETfold_pre2.0(20): 0.962 Contrafold: 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): 0.666 Contrafold: 0.596 Sensitivity PPfold(seed): 0.536 Contrafold: 0.521 Positive Predictive Value PPfold(seed): 0.833 Contrafold: 0.689 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.600 Contrafold: 0.595 Sensitivity TurboFold(seed): 0.518 Contrafold: 0.542 Positive Predictive Value TurboFold(seed): 0.702 Contrafold: 0.659 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs MXScarna(20) Matthews Correlation Coefficient Contrafold: 0.854 MXScarna(20): 0.837 Sensitivity Contrafold: 0.759 MXScarna(20): 0.752 Positive Predictive Value Contrafold: 0.962 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.854 RSpredict(20): 0.672 Sensitivity Contrafold: 0.759 RSpredict(20): 0.549 Positive Predictive Value Contrafold: 0.962 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Contrafold: 0.854 Sensitivity CentroidAlifold(20): 0.752 Contrafold: 0.759 Positive Predictive Value CentroidAlifold(20): 0.990 Contrafold: 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs Murlet(20) Matthews Correlation Coefficient Contrafold: 0.854 Murlet(20): 0.741 Sensitivity Contrafold: 0.759 Murlet(20): 0.594 Positive Predictive Value Contrafold: 0.962 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs PPfold(20) Matthews Correlation Coefficient Contrafold: 0.854 PPfold(20): 0.840 Sensitivity Contrafold: 0.759 PPfold(20): 0.737 Positive Predictive Value Contrafold: 0.962 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.471 MCFold: 0.290 Sensitivity Contrafold: 0.440 MCFold: 0.320 Positive Predictive Value Contrafold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
HotKnots	45 Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: 0.764 HotKnots: 0.524 Sensitivity Cylofold: 0.742 HotKnots: 0.501 Positive Predictive Value Cylofold: 0.791 HotKnots: 0.560 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs HotKnots Matthews Correlation Coefficient McQFold: 0.594 HotKnots: 0.453 Sensitivity McQFold: 0.583 HotKnots: 0.445 Positive Predictive Value McQFold: 0.611 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.697 HotKnots: 0.534 Sensitivity Pknots: 0.668 HotKnots: 0.510 Positive Predictive Value Pknots: 0.733 HotKnots: 0.569 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 HotKnots: 0.603 Sensitivity CentroidAlifold(seed): 0.634 HotKnots: 0.588 Positive Predictive Value CentroidAlifold(seed): 0.933 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.45076534967e-08	53 PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.531 HotKnots: 0.453 Sensitivity PknotsRG: 0.525 HotKnots: 0.445 Positive Predictive Value PknotsRG: 0.544 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 HotKnots: 0.575 Sensitivity PETfold_pre2.0(seed): 0.649 HotKnots: 0.563 Positive Predictive Value PETfold_pre2.0(seed): 0.824 HotKnots: 0.594 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 1.80908287419e-08	13 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.655 HotKnots: 0.522 Sensitivity RNASampler(seed): 0.572 HotKnots: 0.526 Positive Predictive Value RNASampler(seed): 0.755 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	53 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.489 HotKnots: 0.453 Sensitivity IPknot: 0.435 HotKnots: 0.445 Positive Predictive Value IPknot: 0.556 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.657 HotKnots: 0.603 Sensitivity RNAalifold(seed): 0.522 HotKnots: 0.588 Positive Predictive Value RNAalifold(seed): 0.833 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.71568867205e-08	53 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.482 HotKnots: 0.453 Sensitivity CentroidFold: 0.430 HotKnots: 0.445 Positive Predictive Value CentroidFold: 0.548 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 HotKnots: 0.453 Sensitivity CentroidHomfold‑LAST: 0.407 HotKnots: 0.445 Positive Predictive Value CentroidHomfold‑LAST: 0.592 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs HotKnots Matthews Correlation Coefficient Vsfold5: 0.534 HotKnots: 0.453 Sensitivity Vsfold5: 0.505 HotKnots: 0.445 Positive Predictive Value Vsfold5: 0.572 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs HotKnots Matthews Correlation Coefficient Carnac(seed): 0.582 HotKnots: 0.522 Sensitivity Carnac(seed): 0.354 HotKnots: 0.526 Positive Predictive Value Carnac(seed): 0.962 HotKnots: 0.524 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.32883086441e-08	53 ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.459 HotKnots: 0.453 Sensitivity ProbKnot: 0.440 HotKnots: 0.445 Positive Predictive Value ProbKnot: 0.487 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.000108348164592	53 RNASLOpt vs HotKnots Matthews Correlation Coefficient RNASLOpt: 0.458 HotKnots: 0.453 Sensitivity RNASLOpt: 0.419 HotKnots: 0.445 Positive Predictive Value RNASLOpt: 0.508 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0563054219211	53 Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.458 HotKnots: 0.453 Sensitivity Contrafold: 0.435 HotKnots: 0.445 Positive Predictive Value Contrafold: 0.491 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.00476252034473		+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.534 RDfolder: 0.508 Sensitivity HotKnots: 0.510 RDfolder: 0.432 Positive Predictive Value HotKnots: 0.569 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 5.62644058675e-08	= Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.453 HotKnots: 0.453 Sensitivity Fold: 0.431 HotKnots: 0.445 Positive Predictive Value Fold: 0.485 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.590817397584	= HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: 0.453 ContextFold: 0.447 Sensitivity HotKnots: 0.445 ContextFold: 0.407 Positive Predictive Value HotKnots: 0.469 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0675470852546	+ HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.453 MaxExpect: 0.440 Sensitivity HotKnots: 0.445 MaxExpect: 0.414 Positive Predictive Value HotKnots: 0.469 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.522 Murlet(seed): 0.482 Sensitivity HotKnots: 0.526 Murlet(seed): 0.319 Positive Predictive Value HotKnots: 0.524 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	+ HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: 0.453 Sfold: 0.425 Sensitivity HotKnots: 0.445 Sfold: 0.377 Positive Predictive Value HotKnots: 0.469 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs UNAFold Matthews Correlation Coefficient HotKnots: 0.453 UNAFold: 0.412 Sensitivity HotKnots: 0.445 UNAFold: 0.390 Positive Predictive Value HotKnots: 0.469 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.453 Vsfold4: 0.423 Sensitivity HotKnots: 0.445 Vsfold4: 0.380 Positive Predictive Value HotKnots: 0.469 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.453 RNAshapes: 0.416 Sensitivity HotKnots: 0.445 RNAshapes: 0.395 Positive Predictive Value HotKnots: 0.469 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.453 RNAfold: 0.409 Sensitivity HotKnots: 0.445 RNAfold: 0.390 Positive Predictive Value HotKnots: 0.469 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: 0.603 MXScarna(seed): 0.539 Sensitivity HotKnots: 0.588 MXScarna(seed): 0.501 Positive Predictive Value HotKnots: 0.624 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.453 RNAsubopt: 0.394 Sensitivity HotKnots: 0.445 RNAsubopt: 0.378 Positive Predictive Value HotKnots: 0.469 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.603 RSpredict(seed): 0.514 Sensitivity HotKnots: 0.588 RSpredict(seed): 0.427 Positive Predictive Value HotKnots: 0.624 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.453 CRWrnafold: 0.374 Sensitivity HotKnots: 0.445 CRWrnafold: 0.351 Positive Predictive Value HotKnots: 0.469 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	= HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: 0.456 CMfinder(seed): 0.443 Sensitivity HotKnots: 0.458 CMfinder(seed): 0.333 Positive Predictive Value HotKnots: 0.462 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.483506955631	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.453 RNAwolf: 0.362 Sensitivity HotKnots: 0.445 RNAwolf: 0.353 Positive Predictive Value HotKnots: 0.469 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.390 Afold: 0.316 Sensitivity HotKnots: 0.385 Afold: 0.305 Positive Predictive Value HotKnots: 0.405 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.534 Alterna: 0.393 Sensitivity HotKnots: 0.510 Alterna: 0.365 Positive Predictive Value HotKnots: 0.569 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.603 Mastr(seed): 0.341 Sensitivity HotKnots: 0.588 Mastr(seed): 0.176 Positive Predictive Value HotKnots: 0.624 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	? HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.717 Mastr(20): 0.561 Sensitivity HotKnots: 0.639 Mastr(20): 0.459 Positive Predictive Value HotKnots: 0.810 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.431 NanoFolder: 0.304 Sensitivity HotKnots: 0.416 NanoFolder: 0.343 Positive Predictive Value HotKnots: 0.457 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.821 HotKnots: 0.717 Sensitivity Carnac(20): 0.684 HotKnots: 0.639 Positive Predictive Value Carnac(20): 0.989 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.575 HotKnots: 0.566 Sensitivity Multilign(seed): 0.536 HotKnots: 0.586 Positive Predictive Value Multilign(seed): 0.625 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.862 HotKnots: 0.717 Sensitivity Multilign(20): 0.752 HotKnots: 0.639 Positive Predictive Value Multilign(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.857 HotKnots: 0.717 Sensitivity TurboFold(20): 0.744 HotKnots: 0.639 Positive Predictive Value TurboFold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.844 HotKnots: 0.717 Sensitivity RNAalifold(20): 0.722 HotKnots: 0.639 Positive Predictive Value RNAalifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.840 HotKnots: 0.717 Sensitivity RNASampler(20): 0.714 HotKnots: 0.639 Positive Predictive Value RNASampler(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.779 HotKnots: 0.717 Sensitivity CMfinder(20): 0.617 HotKnots: 0.639 Positive Predictive Value CMfinder(20): 0.988 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 HotKnots: 0.717 Sensitivity PETfold_pre2.0(20): 0.759 HotKnots: 0.639 Positive Predictive Value PETfold_pre2.0(20): 0.962 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs HotKnots Matthews Correlation Coefficient PPfold(seed): 0.666 HotKnots: 0.566 Sensitivity PPfold(seed): 0.536 HotKnots: 0.586 Positive Predictive Value PPfold(seed): 0.833 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.600 HotKnots: 0.543 Sensitivity TurboFold(seed): 0.518 HotKnots: 0.560 Positive Predictive Value TurboFold(seed): 0.702 HotKnots: 0.534 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.837 HotKnots: 0.717 Sensitivity MXScarna(20): 0.752 HotKnots: 0.639 Positive Predictive Value MXScarna(20): 0.935 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.717 RSpredict(20): 0.672 Sensitivity HotKnots: 0.639 RSpredict(20): 0.549 Positive Predictive Value HotKnots: 0.810 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 HotKnots: 0.717 Sensitivity CentroidAlifold(20): 0.752 HotKnots: 0.639 Positive Predictive Value CentroidAlifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.741 HotKnots: 0.717 Sensitivity Murlet(20): 0.594 HotKnots: 0.639 Positive Predictive Value Murlet(20): 0.929 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.840 HotKnots: 0.717 Sensitivity PPfold(20): 0.737 HotKnots: 0.639 Positive Predictive Value PPfold(20): 0.961 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.480 MCFold: 0.290 Sensitivity HotKnots: 0.464 MCFold: 0.320 Positive Predictive Value HotKnots: 0.506 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RDfolder	45 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.764 RDfolder: 0.505 Sensitivity Cylofold: 0.742 RDfolder: 0.429 Positive Predictive Value Cylofold: 0.791 RDfolder: 0.605 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.705 RDfolder: 0.508 Sensitivity McQFold: 0.679 RDfolder: 0.432 Positive Predictive Value McQFold: 0.738 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.697 RDfolder: 0.508 Sensitivity Pknots: 0.668 RDfolder: 0.432 Positive Predictive Value Pknots: 0.733 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 RDfolder: 0.616 Sensitivity CentroidAlifold(seed): 0.642 RDfolder: 0.531 Positive Predictive Value CentroidAlifold(seed): 0.936 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.30549897711e-08	46 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.627 RDfolder: 0.508 Sensitivity PknotsRG: 0.601 RDfolder: 0.432 Positive Predictive Value PknotsRG: 0.662 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 RDfolder: 0.586 Sensitivity PETfold_pre2.0(seed): 0.661 RDfolder: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.823 RDfolder: 0.682 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.02344513449e-08	12 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.641 RDfolder: 0.561 Sensitivity RNASampler(seed): 0.562 RDfolder: 0.481 Positive Predictive Value RNASampler(seed): 0.736 RDfolder: 0.663 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.96907987703e-08	46 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.558 RDfolder: 0.508 Sensitivity IPknot: 0.501 RDfolder: 0.432 Positive Predictive Value IPknot: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.651 RDfolder: 0.616 Sensitivity RNAalifold(seed): 0.519 RDfolder: 0.531 Positive Predictive Value RNAalifold(seed): 0.823 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.06136423953e-07	46 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.544 RDfolder: 0.508 Sensitivity CentroidFold: 0.485 RDfolder: 0.432 Positive Predictive Value CentroidFold: 0.621 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 RDfolder: 0.508 Sensitivity CentroidHomfold‑LAST: 0.471 RDfolder: 0.432 Positive Predictive Value CentroidHomfold‑LAST: 0.632 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.597 RDfolder: 0.508 Sensitivity Vsfold5: 0.550 RDfolder: 0.432 Positive Predictive Value Vsfold5: 0.657 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.561 Carnac(seed): 0.531 Sensitivity RDfolder: 0.481 Carnac(seed): 0.292 Positive Predictive Value RDfolder: 0.663 Carnac(seed): 0.971 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.76300197125e-07	46 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.527 RDfolder: 0.508 Sensitivity ProbKnot: 0.496 RDfolder: 0.432 Positive Predictive Value ProbKnot: 0.570 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 2.63254822069e-07	46 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.549 RDfolder: 0.508 Sensitivity RNASLOpt: 0.489 RDfolder: 0.432 Positive Predictive Value RNASLOpt: 0.626 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.515 RDfolder: 0.508 Sensitivity Contrafold: 0.477 RDfolder: 0.432 Positive Predictive Value Contrafold: 0.567 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00985919189012	46 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.534 RDfolder: 0.508 Sensitivity HotKnots: 0.510 RDfolder: 0.432 Positive Predictive Value HotKnots: 0.569 RDfolder: 0.609 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 5.62644058675e-08		= RDfolder vs Fold Matthews Correlation Coefficient RDfolder: 0.508 Fold: 0.504 Sensitivity RDfolder: 0.432 Fold: 0.466 Positive Predictive Value RDfolder: 0.609 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.427756533344	= RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: 0.508 ContextFold: 0.500 Sensitivity RDfolder: 0.432 ContextFold: 0.441 Positive Predictive Value RDfolder: 0.609 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00119801349039	= RDfolder vs MaxExpect Matthews Correlation Coefficient RDfolder: 0.508 MaxExpect: 0.503 Sensitivity RDfolder: 0.432 MaxExpect: 0.463 Positive Predictive Value RDfolder: 0.609 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0829309738858	+ RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.561 Murlet(seed): 0.432 Sensitivity RDfolder: 0.481 Murlet(seed): 0.283 Positive Predictive Value RDfolder: 0.663 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: 0.508 Sfold: 0.482 Sensitivity RDfolder: 0.432 Sfold: 0.435 Positive Predictive Value RDfolder: 0.609 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ RDfolder vs UNAFold Matthews Correlation Coefficient RDfolder: 0.508 UNAFold: 0.468 Sensitivity RDfolder: 0.432 UNAFold: 0.431 Positive Predictive Value RDfolder: 0.609 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: 0.508 Vsfold4: 0.480 Sensitivity RDfolder: 0.432 Vsfold4: 0.423 Positive Predictive Value RDfolder: 0.609 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: 0.508 RNAshapes: 0.463 Sensitivity RDfolder: 0.432 RNAshapes: 0.426 Positive Predictive Value RDfolder: 0.609 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: 0.508 RNAfold: 0.476 Sensitivity RDfolder: 0.432 RNAfold: 0.439 Positive Predictive Value RDfolder: 0.609 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 6.06606238843e-08	+ RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: 0.616 MXScarna(seed): 0.514 Sensitivity RDfolder: 0.531 MXScarna(seed): 0.481 Positive Predictive Value RDfolder: 0.721 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: 0.508 RNAsubopt: 0.470 Sensitivity RDfolder: 0.432 RNAsubopt: 0.435 Positive Predictive Value RDfolder: 0.609 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.616 RSpredict(seed): 0.518 Sensitivity RDfolder: 0.531 RSpredict(seed): 0.437 Positive Predictive Value RDfolder: 0.721 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: 0.508 CRWrnafold: 0.458 Sensitivity RDfolder: 0.432 CRWrnafold: 0.415 Positive Predictive Value RDfolder: 0.609 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: 0.538 CMfinder(seed): 0.459 Sensitivity RDfolder: 0.472 CMfinder(seed): 0.365 Positive Predictive Value RDfolder: 0.620 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: 0.508 RNAwolf: 0.401 Sensitivity RDfolder: 0.432 RNAwolf: 0.381 Positive Predictive Value RDfolder: 0.609 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs Afold Matthews Correlation Coefficient RDfolder: 0.480 Afold: 0.309 Sensitivity RDfolder: 0.418 Afold: 0.296 Positive Predictive Value RDfolder: 0.561 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: 0.508 Alterna: 0.393 Sensitivity RDfolder: 0.432 Alterna: 0.365 Positive Predictive Value RDfolder: 0.609 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.616 Mastr(seed): 0.365 Sensitivity RDfolder: 0.531 Mastr(seed): 0.202 Positive Predictive Value RDfolder: 0.721 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	? RDfolder vs Mastr(20) Matthews Correlation Coefficient RDfolder: 0.664 Mastr(20): 0.561 Sensitivity RDfolder: 0.586 Mastr(20): 0.459 Positive Predictive Value RDfolder: 0.757 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.466 NanoFolder: 0.304 Sensitivity RDfolder: 0.398 NanoFolder: 0.343 Positive Predictive Value RDfolder: 0.555 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.821 RDfolder: 0.664 Sensitivity Carnac(20): 0.684 RDfolder: 0.586 Positive Predictive Value Carnac(20): 0.989 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: 0.593 Multilign(seed): 0.575 Sensitivity RDfolder: 0.486 Multilign(seed): 0.536 Positive Predictive Value RDfolder: 0.731 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.862 RDfolder: 0.664 Sensitivity Multilign(20): 0.752 RDfolder: 0.586 Positive Predictive Value Multilign(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.857 RDfolder: 0.664 Sensitivity TurboFold(20): 0.744 RDfolder: 0.586 Positive Predictive Value TurboFold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.844 RDfolder: 0.664 Sensitivity RNAalifold(20): 0.722 RDfolder: 0.586 Positive Predictive Value RNAalifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.840 RDfolder: 0.664 Sensitivity RNASampler(20): 0.714 RDfolder: 0.586 Positive Predictive Value RNASampler(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.779 RDfolder: 0.664 Sensitivity CMfinder(20): 0.617 RDfolder: 0.586 Positive Predictive Value CMfinder(20): 0.988 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RDfolder: 0.664 Sensitivity PETfold_pre2.0(20): 0.759 RDfolder: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.962 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RDfolder Matthews Correlation Coefficient PPfold(seed): 0.666 RDfolder: 0.593 Sensitivity PPfold(seed): 0.536 RDfolder: 0.486 Positive Predictive Value PPfold(seed): 0.833 RDfolder: 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs TurboFold(seed) Matthews Correlation Coefficient RDfolder: 0.603 TurboFold(seed): 0.600 Sensitivity RDfolder: 0.512 TurboFold(seed): 0.518 Positive Predictive Value RDfolder: 0.717 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.837 RDfolder: 0.664 Sensitivity MXScarna(20): 0.752 RDfolder: 0.586 Positive Predictive Value MXScarna(20): 0.935 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.672 RDfolder: 0.664 Sensitivity RSpredict(20): 0.549 RDfolder: 0.586 Positive Predictive Value RSpredict(20): 0.830 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RDfolder: 0.664 Sensitivity CentroidAlifold(20): 0.752 RDfolder: 0.586 Positive Predictive Value CentroidAlifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.741 RDfolder: 0.664 Sensitivity Murlet(20): 0.594 RDfolder: 0.586 Positive Predictive Value Murlet(20): 0.929 RDfolder: 0.757 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): 0.840 RDfolder: 0.664 Sensitivity PPfold(20): 0.737 RDfolder: 0.586 Positive Predictive Value PPfold(20): 0.961 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.505 MCFold: 0.296 Sensitivity RDfolder: 0.428 MCFold: 0.325 Positive Predictive Value RDfolder: 0.605 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	45 Cylofold vs Fold Matthews Correlation Coefficient Cylofold: 0.764 Fold: 0.515 Sensitivity Cylofold: 0.742 Fold: 0.475 Positive Predictive Value Cylofold: 0.791 Fold: 0.568 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs Fold Matthews Correlation Coefficient McQFold: 0.594 Fold: 0.453 Sensitivity McQFold: 0.583 Fold: 0.431 Positive Predictive Value McQFold: 0.611 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Fold Matthews Correlation Coefficient Pknots: 0.697 Fold: 0.504 Sensitivity Pknots: 0.668 Fold: 0.466 Positive Predictive Value Pknots: 0.733 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Fold: 0.572 Sensitivity CentroidAlifold(seed): 0.634 Fold: 0.534 Positive Predictive Value CentroidAlifold(seed): 0.933 Fold: 0.619 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	53 PknotsRG vs Fold Matthews Correlation Coefficient PknotsRG: 0.531 Fold: 0.453 Sensitivity PknotsRG: 0.525 Fold: 0.431 Positive Predictive Value PknotsRG: 0.544 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Fold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.649 Fold: 0.547 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Fold: 0.622 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.57237423209e-08	13 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.655 Fold: 0.472 Sensitivity RNASampler(seed): 0.572 Fold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	53 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.489 Fold: 0.453 Sensitivity IPknot: 0.435 Fold: 0.431 Positive Predictive Value IPknot: 0.556 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs Fold Matthews Correlation Coefficient RNAalifold(seed): 0.657 Fold: 0.572 Sensitivity RNAalifold(seed): 0.522 Fold: 0.534 Positive Predictive Value RNAalifold(seed): 0.833 Fold: 0.619 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 8.09700314043e-09	53 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.482 Fold: 0.453 Sensitivity CentroidFold: 0.430 Fold: 0.431 Positive Predictive Value CentroidFold: 0.548 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Fold: 0.453 Sensitivity CentroidHomfold‑LAST: 0.407 Fold: 0.431 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs Fold Matthews Correlation Coefficient Vsfold5: 0.534 Fold: 0.453 Sensitivity Vsfold5: 0.505 Fold: 0.431 Positive Predictive Value Vsfold5: 0.572 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs Fold Matthews Correlation Coefficient Carnac(seed): 0.582 Fold: 0.472 Sensitivity Carnac(seed): 0.354 Fold: 0.453 Positive Predictive Value Carnac(seed): 0.962 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	53 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.459 Fold: 0.453 Sensitivity ProbKnot: 0.440 Fold: 0.431 Positive Predictive Value ProbKnot: 0.487 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.000207424631753	53 RNASLOpt vs Fold Matthews Correlation Coefficient RNASLOpt: 0.458 Fold: 0.453 Sensitivity RNASLOpt: 0.419 Fold: 0.431 Positive Predictive Value RNASLOpt: 0.508 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.696686202358	53 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.458 Fold: 0.453 Sensitivity Contrafold: 0.435 Fold: 0.431 Positive Predictive Value Contrafold: 0.491 Fold: 0.485 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.196924117351	53 Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.453 HotKnots: 0.453 Sensitivity Fold: 0.431 HotKnots: 0.445 Positive Predictive Value Fold: 0.485 HotKnots: 0.469 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.590817397584	46 RDfolder vs Fold Matthews Correlation Coefficient RDfolder: 0.508 Fold: 0.504 Sensitivity RDfolder: 0.432 Fold: 0.466 Positive Predictive Value RDfolder: 0.609 Fold: 0.556 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.427756533344		= Fold vs ContextFold Matthews Correlation Coefficient Fold: 0.453 ContextFold: 0.447 Sensitivity Fold: 0.431 ContextFold: 0.407 Positive Predictive Value Fold: 0.485 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.00137891412487	+ Fold vs MaxExpect Matthews Correlation Coefficient Fold: 0.453 MaxExpect: 0.440 Sensitivity Fold: 0.431 MaxExpect: 0.414 Positive Predictive Value Fold: 0.485 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.48494289621e-08	- Murlet(seed) vs Fold Matthews Correlation Coefficient Murlet(seed): 0.482 Fold: 0.472 Sensitivity Murlet(seed): 0.319 Fold: 0.453 Positive Predictive Value Murlet(seed): 0.734 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00063186145056	+ Fold vs Sfold Matthews Correlation Coefficient Fold: 0.453 Sfold: 0.425 Sensitivity Fold: 0.431 Sfold: 0.377 Positive Predictive Value Fold: 0.485 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.453 UNAFold: 0.412 Sensitivity Fold: 0.431 UNAFold: 0.390 Positive Predictive Value Fold: 0.485 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.453 Vsfold4: 0.423 Sensitivity Fold: 0.431 Vsfold4: 0.380 Positive Predictive Value Fold: 0.485 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.453 RNAshapes: 0.416 Sensitivity Fold: 0.431 RNAshapes: 0.395 Positive Predictive Value Fold: 0.485 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.453 RNAfold: 0.409 Sensitivity Fold: 0.431 RNAfold: 0.390 Positive Predictive Value Fold: 0.485 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs MXScarna(seed) Matthews Correlation Coefficient Fold: 0.572 MXScarna(seed): 0.539 Sensitivity Fold: 0.534 MXScarna(seed): 0.501 Positive Predictive Value Fold: 0.619 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.453 RNAsubopt: 0.394 Sensitivity Fold: 0.431 RNAsubopt: 0.378 Positive Predictive Value Fold: 0.485 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.572 RSpredict(seed): 0.514 Sensitivity Fold: 0.534 RSpredict(seed): 0.427 Positive Predictive Value Fold: 0.619 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.453 CRWrnafold: 0.374 Sensitivity Fold: 0.431 CRWrnafold: 0.351 Positive Predictive Value Fold: 0.485 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.476 CMfinder(seed): 0.443 Sensitivity Fold: 0.454 CMfinder(seed): 0.333 Positive Predictive Value Fold: 0.507 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.04893053302e-05	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.453 RNAwolf: 0.362 Sensitivity Fold: 0.431 RNAwolf: 0.353 Positive Predictive Value Fold: 0.485 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.417 Afold: 0.316 Sensitivity Fold: 0.403 Afold: 0.305 Positive Predictive Value Fold: 0.441 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.504 Alterna: 0.393 Sensitivity Fold: 0.466 Alterna: 0.365 Positive Predictive Value Fold: 0.556 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.572 Mastr(seed): 0.341 Sensitivity Fold: 0.534 Mastr(seed): 0.176 Positive Predictive Value Fold: 0.619 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	? Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.862 Mastr(20): 0.561 Sensitivity Fold: 0.752 Mastr(20): 0.459 Positive Predictive Value Fold: 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.567 NanoFolder: 0.304 Sensitivity Fold: 0.524 NanoFolder: 0.343 Positive Predictive Value Fold: 0.621 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.862 Carnac(20): 0.821 Sensitivity Fold: 0.752 Carnac(20): 0.684 Positive Predictive Value Fold: 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.575 Fold: 0.457 Sensitivity Multilign(seed): 0.536 Fold: 0.443 Positive Predictive Value Multilign(seed): 0.625 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.862 Multilign(20): 0.862 Sensitivity Fold: 0.752 Multilign(20): 0.752 Positive Predictive Value Fold: 0.990 Multilign(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs TurboFold(20) Matthews Correlation Coefficient Fold: 0.862 TurboFold(20): 0.857 Sensitivity Fold: 0.752 TurboFold(20): 0.744 Positive Predictive Value Fold: 0.990 TurboFold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs RNAalifold(20) Matthews Correlation Coefficient Fold: 0.862 RNAalifold(20): 0.844 Sensitivity Fold: 0.752 RNAalifold(20): 0.722 Positive Predictive Value Fold: 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs RNASampler(20) Matthews Correlation Coefficient Fold: 0.862 RNASampler(20): 0.840 Sensitivity Fold: 0.752 RNASampler(20): 0.714 Positive Predictive Value Fold: 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.862 CMfinder(20): 0.779 Sensitivity Fold: 0.752 CMfinder(20): 0.617 Positive Predictive Value Fold: 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs PETfold_pre2.0(20) Matthews Correlation Coefficient Fold: 0.862 PETfold_pre2.0(20): 0.854 Sensitivity Fold: 0.752 PETfold_pre2.0(20): 0.759 Positive Predictive Value Fold: 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Fold Matthews Correlation Coefficient PPfold(seed): 0.666 Fold: 0.457 Sensitivity PPfold(seed): 0.536 Fold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.600 Fold: 0.451 Sensitivity TurboFold(seed): 0.518 Fold: 0.440 Positive Predictive Value TurboFold(seed): 0.702 Fold: 0.471 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Fold vs MXScarna(20) Matthews Correlation Coefficient Fold: 0.862 MXScarna(20): 0.837 Sensitivity Fold: 0.752 MXScarna(20): 0.752 Positive Predictive Value Fold: 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.862 RSpredict(20): 0.672 Sensitivity Fold: 0.752 RSpredict(20): 0.549 Positive Predictive Value Fold: 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs CentroidAlifold(20) Matthews Correlation Coefficient Fold: 0.862 CentroidAlifold(20): 0.862 Sensitivity Fold: 0.752 CentroidAlifold(20): 0.752 Positive Predictive Value Fold: 0.990 CentroidAlifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.862 Murlet(20): 0.741 Sensitivity Fold: 0.752 Murlet(20): 0.594 Positive Predictive Value Fold: 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Fold vs PPfold(20) Matthews Correlation Coefficient Fold: 0.862 PPfold(20): 0.840 Sensitivity Fold: 0.752 PPfold(20): 0.737 Positive Predictive Value Fold: 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.472 MCFold: 0.290 Sensitivity Fold: 0.443 MCFold: 0.320 Positive Predictive Value Fold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
ContextFold	45 Cylofold vs ContextFold Matthews Correlation Coefficient Cylofold: 0.764 ContextFold: 0.498 Sensitivity Cylofold: 0.742 ContextFold: 0.441 Positive Predictive Value Cylofold: 0.791 ContextFold: 0.574 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs ContextFold Matthews Correlation Coefficient McQFold: 0.594 ContextFold: 0.447 Sensitivity McQFold: 0.583 ContextFold: 0.407 Positive Predictive Value McQFold: 0.611 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs ContextFold Matthews Correlation Coefficient Pknots: 0.697 ContextFold: 0.500 Sensitivity Pknots: 0.668 ContextFold: 0.441 Positive Predictive Value Pknots: 0.733 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 ContextFold: 0.567 Sensitivity CentroidAlifold(seed): 0.634 ContextFold: 0.506 Positive Predictive Value CentroidAlifold(seed): 0.933 ContextFold: 0.642 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	53 PknotsRG vs ContextFold Matthews Correlation Coefficient PknotsRG: 0.531 ContextFold: 0.447 Sensitivity PknotsRG: 0.525 ContextFold: 0.407 Positive Predictive Value PknotsRG: 0.544 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 ContextFold: 0.601 Sensitivity PETfold_pre2.0(seed): 0.649 ContextFold: 0.540 Positive Predictive Value PETfold_pre2.0(seed): 0.824 ContextFold: 0.675 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	13 RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): 0.655 ContextFold: 0.504 Sensitivity RNASampler(seed): 0.572 ContextFold: 0.453 Positive Predictive Value RNASampler(seed): 0.755 ContextFold: 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.48055519165e-08	53 IPknot vs ContextFold Matthews Correlation Coefficient IPknot: 0.489 ContextFold: 0.447 Sensitivity IPknot: 0.435 ContextFold: 0.407 Positive Predictive Value IPknot: 0.556 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs ContextFold Matthews Correlation Coefficient RNAalifold(seed): 0.657 ContextFold: 0.567 Sensitivity RNAalifold(seed): 0.522 ContextFold: 0.506 Positive Predictive Value RNAalifold(seed): 0.833 ContextFold: 0.642 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	53 CentroidFold vs ContextFold Matthews Correlation Coefficient CentroidFold: 0.482 ContextFold: 0.447 Sensitivity CentroidFold: 0.430 ContextFold: 0.407 Positive Predictive Value CentroidFold: 0.548 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs ContextFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 ContextFold: 0.447 Sensitivity CentroidHomfold‑LAST: 0.407 ContextFold: 0.407 Positive Predictive Value CentroidHomfold‑LAST: 0.592 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs ContextFold Matthews Correlation Coefficient Vsfold5: 0.534 ContextFold: 0.447 Sensitivity Vsfold5: 0.505 ContextFold: 0.407 Positive Predictive Value Vsfold5: 0.572 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs ContextFold Matthews Correlation Coefficient Carnac(seed): 0.582 ContextFold: 0.504 Sensitivity Carnac(seed): 0.354 ContextFold: 0.453 Positive Predictive Value Carnac(seed): 0.962 ContextFold: 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	53 ProbKnot vs ContextFold Matthews Correlation Coefficient ProbKnot: 0.459 ContextFold: 0.447 Sensitivity ProbKnot: 0.440 ContextFold: 0.407 Positive Predictive Value ProbKnot: 0.487 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.03351724933e-07	53 RNASLOpt vs ContextFold Matthews Correlation Coefficient RNASLOpt: 0.458 ContextFold: 0.447 Sensitivity RNASLOpt: 0.419 ContextFold: 0.407 Positive Predictive Value RNASLOpt: 0.508 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 8.09943589199e-07	53 Contrafold vs ContextFold Matthews Correlation Coefficient Contrafold: 0.458 ContextFold: 0.447 Sensitivity Contrafold: 0.435 ContextFold: 0.407 Positive Predictive Value Contrafold: 0.491 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.000990829372106	53 HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: 0.453 ContextFold: 0.447 Sensitivity HotKnots: 0.445 ContextFold: 0.407 Positive Predictive Value HotKnots: 0.469 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.0675470852546	46 RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: 0.508 ContextFold: 0.500 Sensitivity RDfolder: 0.432 ContextFold: 0.441 Positive Predictive Value RDfolder: 0.609 ContextFold: 0.577 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.00119801349039	53 Fold vs ContextFold Matthews Correlation Coefficient Fold: 0.453 ContextFold: 0.447 Sensitivity Fold: 0.431 ContextFold: 0.407 Positive Predictive Value Fold: 0.485 ContextFold: 0.499 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.00137891412487		= ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.447 MaxExpect: 0.440 Sensitivity ContextFold: 0.407 MaxExpect: 0.414 Positive Predictive Value ContextFold: 0.499 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.00158471883626	+ ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.504 Murlet(seed): 0.482 Sensitivity ContextFold: 0.453 Murlet(seed): 0.319 Positive Predictive Value ContextFold: 0.568 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.07504388705e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.447 Sfold: 0.425 Sensitivity ContextFold: 0.407 Sfold: 0.377 Positive Predictive Value ContextFold: 0.499 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 8.81311508309e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.447 UNAFold: 0.412 Sensitivity ContextFold: 0.407 UNAFold: 0.390 Positive Predictive Value ContextFold: 0.499 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.447 Vsfold4: 0.423 Sensitivity ContextFold: 0.407 Vsfold4: 0.380 Positive Predictive Value ContextFold: 0.499 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.447 RNAshapes: 0.416 Sensitivity ContextFold: 0.407 RNAshapes: 0.395 Positive Predictive Value ContextFold: 0.499 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.447 RNAfold: 0.409 Sensitivity ContextFold: 0.407 RNAfold: 0.390 Positive Predictive Value ContextFold: 0.499 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.567 MXScarna(seed): 0.539 Sensitivity ContextFold: 0.506 MXScarna(seed): 0.501 Positive Predictive Value ContextFold: 0.642 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.447 RNAsubopt: 0.394 Sensitivity ContextFold: 0.407 RNAsubopt: 0.378 Positive Predictive Value ContextFold: 0.499 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.567 RSpredict(seed): 0.514 Sensitivity ContextFold: 0.506 RSpredict(seed): 0.427 Positive Predictive Value ContextFold: 0.642 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.447 CRWrnafold: 0.374 Sensitivity ContextFold: 0.407 CRWrnafold: 0.351 Positive Predictive Value ContextFold: 0.499 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.490 CMfinder(seed): 0.443 Sensitivity ContextFold: 0.438 CMfinder(seed): 0.333 Positive Predictive Value ContextFold: 0.556 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.38889354863e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.447 RNAwolf: 0.362 Sensitivity ContextFold: 0.407 RNAwolf: 0.353 Positive Predictive Value ContextFold: 0.499 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.391 Afold: 0.316 Sensitivity ContextFold: 0.358 Afold: 0.305 Positive Predictive Value ContextFold: 0.436 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.500 Alterna: 0.393 Sensitivity ContextFold: 0.441 Alterna: 0.365 Positive Predictive Value ContextFold: 0.577 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.567 Mastr(seed): 0.341 Sensitivity ContextFold: 0.506 Mastr(seed): 0.176 Positive Predictive Value ContextFold: 0.642 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	? ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.759 Mastr(20): 0.561 Sensitivity ContextFold: 0.669 Mastr(20): 0.459 Positive Predictive Value ContextFold: 0.864 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.682 NanoFolder: 0.304 Sensitivity ContextFold: 0.608 NanoFolder: 0.343 Positive Predictive Value ContextFold: 0.771 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs ContextFold Matthews Correlation Coefficient Carnac(20): 0.821 ContextFold: 0.759 Sensitivity Carnac(20): 0.684 ContextFold: 0.669 Positive Predictive Value Carnac(20): 0.989 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.575 ContextFold: 0.566 Sensitivity Multilign(seed): 0.536 ContextFold: 0.514 Positive Predictive Value Multilign(seed): 0.625 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs ContextFold Matthews Correlation Coefficient Multilign(20): 0.862 ContextFold: 0.759 Sensitivity Multilign(20): 0.752 ContextFold: 0.669 Positive Predictive Value Multilign(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs ContextFold Matthews Correlation Coefficient TurboFold(20): 0.857 ContextFold: 0.759 Sensitivity TurboFold(20): 0.744 ContextFold: 0.669 Positive Predictive Value TurboFold(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs ContextFold Matthews Correlation Coefficient RNAalifold(20): 0.844 ContextFold: 0.759 Sensitivity RNAalifold(20): 0.722 ContextFold: 0.669 Positive Predictive Value RNAalifold(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs ContextFold Matthews Correlation Coefficient RNASampler(20): 0.840 ContextFold: 0.759 Sensitivity RNASampler(20): 0.714 ContextFold: 0.669 Positive Predictive Value RNASampler(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs ContextFold Matthews Correlation Coefficient CMfinder(20): 0.779 ContextFold: 0.759 Sensitivity CMfinder(20): 0.617 ContextFold: 0.669 Positive Predictive Value CMfinder(20): 0.988 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 ContextFold: 0.759 Sensitivity PETfold_pre2.0(20): 0.759 ContextFold: 0.669 Positive Predictive Value PETfold_pre2.0(20): 0.962 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs ContextFold Matthews Correlation Coefficient PPfold(seed): 0.666 ContextFold: 0.566 Sensitivity PPfold(seed): 0.536 ContextFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.600 ContextFold: 0.559 Sensitivity TurboFold(seed): 0.518 ContextFold: 0.500 Positive Predictive Value TurboFold(seed): 0.702 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs ContextFold Matthews Correlation Coefficient MXScarna(20): 0.837 ContextFold: 0.759 Sensitivity MXScarna(20): 0.752 ContextFold: 0.669 Positive Predictive Value MXScarna(20): 0.935 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.759 RSpredict(20): 0.672 Sensitivity ContextFold: 0.669 RSpredict(20): 0.549 Positive Predictive Value ContextFold: 0.864 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 ContextFold: 0.759 Sensitivity CentroidAlifold(20): 0.752 ContextFold: 0.669 Positive Predictive Value CentroidAlifold(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.759 Murlet(20): 0.741 Sensitivity ContextFold: 0.669 Murlet(20): 0.594 Positive Predictive Value ContextFold: 0.864 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.840 ContextFold: 0.759 Sensitivity PPfold(20): 0.737 ContextFold: 0.669 Positive Predictive Value PPfold(20): 0.961 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.449 MCFold: 0.290 Sensitivity ContextFold: 0.402 MCFold: 0.320 Positive Predictive Value ContextFold: 0.511 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
MaxExpect	45 Cylofold vs MaxExpect Matthews Correlation Coefficient Cylofold: 0.764 MaxExpect: 0.501 Sensitivity Cylofold: 0.742 MaxExpect: 0.461 Positive Predictive Value Cylofold: 0.791 MaxExpect: 0.556 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs MaxExpect Matthews Correlation Coefficient McQFold: 0.594 MaxExpect: 0.440 Sensitivity McQFold: 0.583 MaxExpect: 0.414 Positive Predictive Value McQFold: 0.611 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs MaxExpect Matthews Correlation Coefficient Pknots: 0.697 MaxExpect: 0.503 Sensitivity Pknots: 0.668 MaxExpect: 0.463 Positive Predictive Value Pknots: 0.733 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 MaxExpect: 0.603 Sensitivity CentroidAlifold(seed): 0.634 MaxExpect: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.933 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	53 PknotsRG vs MaxExpect Matthews Correlation Coefficient PknotsRG: 0.531 MaxExpect: 0.440 Sensitivity PknotsRG: 0.525 MaxExpect: 0.414 Positive Predictive Value PknotsRG: 0.544 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 MaxExpect: 0.588 Sensitivity PETfold_pre2.0(seed): 0.649 MaxExpect: 0.549 Positive Predictive Value PETfold_pre2.0(seed): 0.824 MaxExpect: 0.636 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	13 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.655 MaxExpect: 0.513 Sensitivity RNASampler(seed): 0.572 MaxExpect: 0.488 Positive Predictive Value RNASampler(seed): 0.755 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.10198558684e-08	53 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.489 MaxExpect: 0.440 Sensitivity IPknot: 0.435 MaxExpect: 0.414 Positive Predictive Value IPknot: 0.556 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.657 MaxExpect: 0.603 Sensitivity RNAalifold(seed): 0.522 MaxExpect: 0.560 Positive Predictive Value RNAalifold(seed): 0.833 MaxExpect: 0.657 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	53 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.482 MaxExpect: 0.440 Sensitivity CentroidFold: 0.430 MaxExpect: 0.414 Positive Predictive Value CentroidFold: 0.548 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 MaxExpect: 0.440 Sensitivity CentroidHomfold‑LAST: 0.407 MaxExpect: 0.414 Positive Predictive Value CentroidHomfold‑LAST: 0.592 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs MaxExpect Matthews Correlation Coefficient Vsfold5: 0.534 MaxExpect: 0.440 Sensitivity Vsfold5: 0.505 MaxExpect: 0.414 Positive Predictive Value Vsfold5: 0.572 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs MaxExpect Matthews Correlation Coefficient Carnac(seed): 0.582 MaxExpect: 0.513 Sensitivity Carnac(seed): 0.354 MaxExpect: 0.488 Positive Predictive Value Carnac(seed): 0.962 MaxExpect: 0.547 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.36849473644e-08	53 ProbKnot vs MaxExpect Matthews Correlation Coefficient ProbKnot: 0.459 MaxExpect: 0.440 Sensitivity ProbKnot: 0.440 MaxExpect: 0.414 Positive Predictive Value ProbKnot: 0.487 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs MaxExpect Matthews Correlation Coefficient RNASLOpt: 0.458 MaxExpect: 0.440 Sensitivity RNASLOpt: 0.419 MaxExpect: 0.414 Positive Predictive Value RNASLOpt: 0.508 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08	53 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.458 MaxExpect: 0.440 Sensitivity Contrafold: 0.435 MaxExpect: 0.414 Positive Predictive Value Contrafold: 0.491 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 8.1815824276e-08	53 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.453 MaxExpect: 0.440 Sensitivity HotKnots: 0.445 MaxExpect: 0.414 Positive Predictive Value HotKnots: 0.469 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.1569883686e-08	46 RDfolder vs MaxExpect Matthews Correlation Coefficient RDfolder: 0.508 MaxExpect: 0.503 Sensitivity RDfolder: 0.432 MaxExpect: 0.463 Positive Predictive Value RDfolder: 0.609 MaxExpect: 0.559 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 0.0829309738858	53 Fold vs MaxExpect Matthews Correlation Coefficient Fold: 0.453 MaxExpect: 0.440 Sensitivity Fold: 0.431 MaxExpect: 0.414 Positive Predictive Value Fold: 0.485 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.48494289621e-08	53 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.447 MaxExpect: 0.440 Sensitivity ContextFold: 0.407 MaxExpect: 0.414 Positive Predictive Value ContextFold: 0.499 MaxExpect: 0.476 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.00158471883626		+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.513 Murlet(seed): 0.482 Sensitivity MaxExpect: 0.488 Murlet(seed): 0.319 Positive Predictive Value MaxExpect: 0.547 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.440 Sfold: 0.425 Sensitivity MaxExpect: 0.414 Sfold: 0.377 Positive Predictive Value MaxExpect: 0.476 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.440 UNAFold: 0.412 Sensitivity MaxExpect: 0.414 UNAFold: 0.390 Positive Predictive Value MaxExpect: 0.476 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.440 Vsfold4: 0.423 Sensitivity MaxExpect: 0.414 Vsfold4: 0.380 Positive Predictive Value MaxExpect: 0.476 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.440 RNAshapes: 0.416 Sensitivity MaxExpect: 0.414 RNAshapes: 0.395 Positive Predictive Value MaxExpect: 0.476 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.440 RNAfold: 0.409 Sensitivity MaxExpect: 0.414 RNAfold: 0.390 Positive Predictive Value MaxExpect: 0.476 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs MXScarna(seed) Matthews Correlation Coefficient MaxExpect: 0.603 MXScarna(seed): 0.539 Sensitivity MaxExpect: 0.560 MXScarna(seed): 0.501 Positive Predictive Value MaxExpect: 0.657 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.440 RNAsubopt: 0.394 Sensitivity MaxExpect: 0.414 RNAsubopt: 0.378 Positive Predictive Value MaxExpect: 0.476 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.603 RSpredict(seed): 0.514 Sensitivity MaxExpect: 0.560 RSpredict(seed): 0.427 Positive Predictive Value MaxExpect: 0.657 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.440 CRWrnafold: 0.374 Sensitivity MaxExpect: 0.414 CRWrnafold: 0.351 Positive Predictive Value MaxExpect: 0.476 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.509 CMfinder(seed): 0.443 Sensitivity MaxExpect: 0.486 CMfinder(seed): 0.333 Positive Predictive Value MaxExpect: 0.540 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.65471383806e-09	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.440 RNAwolf: 0.362 Sensitivity MaxExpect: 0.414 RNAwolf: 0.353 Positive Predictive Value MaxExpect: 0.476 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.401 Afold: 0.316 Sensitivity MaxExpect: 0.383 Afold: 0.305 Positive Predictive Value MaxExpect: 0.429 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.503 Alterna: 0.393 Sensitivity MaxExpect: 0.463 Alterna: 0.365 Positive Predictive Value MaxExpect: 0.559 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.603 Mastr(seed): 0.341 Sensitivity MaxExpect: 0.560 Mastr(seed): 0.176 Positive Predictive Value MaxExpect: 0.657 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	? MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.783 Mastr(20): 0.561 Sensitivity MaxExpect: 0.677 Mastr(20): 0.459 Positive Predictive Value MaxExpect: 0.909 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.571 NanoFolder: 0.304 Sensitivity MaxExpect: 0.524 NanoFolder: 0.343 Positive Predictive Value MaxExpect: 0.630 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.821 MaxExpect: 0.783 Sensitivity Carnac(20): 0.684 MaxExpect: 0.677 Positive Predictive Value Carnac(20): 0.989 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.575 MaxExpect: 0.553 Sensitivity Multilign(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value Multilign(seed): 0.625 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.862 MaxExpect: 0.783 Sensitivity Multilign(20): 0.752 MaxExpect: 0.677 Positive Predictive Value Multilign(20): 0.990 MaxExpect: 0.909 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): 0.857 MaxExpect: 0.783 Sensitivity TurboFold(20): 0.744 MaxExpect: 0.677 Positive Predictive Value TurboFold(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.844 MaxExpect: 0.783 Sensitivity RNAalifold(20): 0.722 MaxExpect: 0.677 Positive Predictive Value RNAalifold(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.840 MaxExpect: 0.783 Sensitivity RNASampler(20): 0.714 MaxExpect: 0.677 Positive Predictive Value RNASampler(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.783 CMfinder(20): 0.779 Sensitivity MaxExpect: 0.677 CMfinder(20): 0.617 Positive Predictive Value MaxExpect: 0.909 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 MaxExpect: 0.783 Sensitivity PETfold_pre2.0(20): 0.759 MaxExpect: 0.677 Positive Predictive Value PETfold_pre2.0(20): 0.962 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs MaxExpect Matthews Correlation Coefficient PPfold(seed): 0.666 MaxExpect: 0.553 Sensitivity PPfold(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value PPfold(seed): 0.833 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.600 MaxExpect: 0.526 Sensitivity TurboFold(seed): 0.518 MaxExpect: 0.506 Positive Predictive Value TurboFold(seed): 0.702 MaxExpect: 0.556 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.837 MaxExpect: 0.783 Sensitivity MXScarna(20): 0.752 MaxExpect: 0.677 Positive Predictive Value MXScarna(20): 0.935 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.783 RSpredict(20): 0.672 Sensitivity MaxExpect: 0.677 RSpredict(20): 0.549 Positive Predictive Value MaxExpect: 0.909 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MaxExpect: 0.783 Sensitivity CentroidAlifold(20): 0.752 MaxExpect: 0.677 Positive Predictive Value CentroidAlifold(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.783 Murlet(20): 0.741 Sensitivity MaxExpect: 0.677 Murlet(20): 0.594 Positive Predictive Value MaxExpect: 0.909 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.840 MaxExpect: 0.783 Sensitivity PPfold(20): 0.737 MaxExpect: 0.677 Positive Predictive Value PPfold(20): 0.961 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.457 MCFold: 0.290 Sensitivity MaxExpect: 0.424 MCFold: 0.320 Positive Predictive Value MaxExpect: 0.502 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(seed)	11 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.831 Murlet(seed): 0.405 Sensitivity Cylofold: 0.834 Murlet(seed): 0.263 Positive Predictive Value Cylofold: 0.830 Murlet(seed): 0.633 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.5677163434e-08	13 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.862 Murlet(seed): 0.482 Sensitivity McQFold: 0.849 Murlet(seed): 0.319 Positive Predictive Value McQFold: 0.877 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.64481516727e-08	12 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.803 Murlet(seed): 0.432 Sensitivity Pknots: 0.820 Murlet(seed): 0.283 Positive Predictive Value Pknots: 0.789 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.79203144115e-08	13 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 Murlet(seed): 0.482 Sensitivity CentroidAlifold(seed): 0.579 Murlet(seed): 0.319 Positive Predictive Value CentroidAlifold(seed): 0.902 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	13 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.819 Murlet(seed): 0.482 Sensitivity PknotsRG: 0.818 Murlet(seed): 0.319 Positive Predictive Value PknotsRG: 0.823 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.74172190343e-08	13 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.661 Murlet(seed): 0.482 Sensitivity PETfold_pre2.0(seed): 0.572 Murlet(seed): 0.319 Positive Predictive Value PETfold_pre2.0(seed): 0.769 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.97952969696e-09	13 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Murlet(seed): 0.482 Sensitivity RNASampler(seed): 0.572 Murlet(seed): 0.319 Positive Predictive Value RNASampler(seed): 0.755 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	13 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.604 Murlet(seed): 0.482 Sensitivity IPknot: 0.537 Murlet(seed): 0.319 Positive Predictive Value IPknot: 0.686 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 7.29209047668e-09	13 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.619 Murlet(seed): 0.482 Sensitivity RNAalifold(seed): 0.477 Murlet(seed): 0.319 Positive Predictive Value RNAalifold(seed): 0.810 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	13 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.631 Murlet(seed): 0.482 Sensitivity CentroidFold: 0.554 Murlet(seed): 0.319 Positive Predictive Value CentroidFold: 0.725 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.61939086268e-08	13 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.583 Murlet(seed): 0.482 Sensitivity CentroidHomfold‑LAST: 0.502 Murlet(seed): 0.319 Positive Predictive Value CentroidHomfold‑LAST: 0.684 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	13 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold5: 0.452 Sensitivity Murlet(seed): 0.319 Vsfold5: 0.435 Positive Predictive Value Murlet(seed): 0.734 Vsfold5: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.43692248862e-08	13 Carnac(seed) vs Murlet(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 Murlet(seed): 0.482 Sensitivity Carnac(seed): 0.354 Murlet(seed): 0.319 Positive Predictive Value Carnac(seed): 0.962 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	13 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.514 Murlet(seed): 0.482 Sensitivity ProbKnot: 0.495 Murlet(seed): 0.319 Positive Predictive Value ProbKnot: 0.542 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.45805449719e-08	13 RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.584 Murlet(seed): 0.482 Sensitivity RNASLOpt: 0.526 Murlet(seed): 0.319 Positive Predictive Value RNASLOpt: 0.655 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.03576421863e-08	13 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.582 Murlet(seed): 0.482 Sensitivity Contrafold: 0.540 Murlet(seed): 0.319 Positive Predictive Value Contrafold: 0.634 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.49381627234e-08	13 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.522 Murlet(seed): 0.482 Sensitivity HotKnots: 0.526 Murlet(seed): 0.319 Positive Predictive Value HotKnots: 0.524 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	12 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.561 Murlet(seed): 0.432 Sensitivity RDfolder: 0.481 Murlet(seed): 0.283 Positive Predictive Value RDfolder: 0.663 Murlet(seed): 0.667 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	13 Murlet(seed) vs Fold Matthews Correlation Coefficient Murlet(seed): 0.482 Fold: 0.472 Sensitivity Murlet(seed): 0.319 Fold: 0.453 Positive Predictive Value Murlet(seed): 0.734 Fold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00063186145056	13 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.504 Murlet(seed): 0.482 Sensitivity ContextFold: 0.453 Murlet(seed): 0.319 Positive Predictive Value ContextFold: 0.568 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.07504388705e-08	13 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.513 Murlet(seed): 0.482 Sensitivity MaxExpect: 0.488 Murlet(seed): 0.319 Positive Predictive Value MaxExpect: 0.547 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08		= Murlet(seed) vs Sfold Matthews Correlation Coefficient Murlet(seed): 0.482 Sfold: 0.475 Sensitivity Murlet(seed): 0.319 Sfold: 0.442 Positive Predictive Value Murlet(seed): 0.734 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0139632814123	+ Murlet(seed) vs UNAFold Matthews Correlation Coefficient Murlet(seed): 0.482 UNAFold: 0.481 Sensitivity Murlet(seed): 0.319 UNAFold: 0.460 Positive Predictive Value Murlet(seed): 0.734 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000964840926149	+ Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold4: 0.392 Sensitivity Murlet(seed): 0.319 Vsfold4: 0.365 Positive Predictive Value Murlet(seed): 0.734 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): 0.482 RNAshapes: 0.447 Sensitivity Murlet(seed): 0.319 RNAshapes: 0.432 Positive Predictive Value Murlet(seed): 0.734 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.10353437966e-08	+ Murlet(seed) vs RNAfold Matthews Correlation Coefficient Murlet(seed): 0.482 RNAfold: 0.476 Sensitivity Murlet(seed): 0.319 RNAfold: 0.460 Positive Predictive Value Murlet(seed): 0.734 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000179548697844	+ Murlet(seed) vs MXScarna(seed) Matthews Correlation Coefficient Murlet(seed): 0.482 MXScarna(seed): 0.440 Sensitivity Murlet(seed): 0.319 MXScarna(seed): 0.421 Positive Predictive Value Murlet(seed): 0.734 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.34041282081e-08	+ Murlet(seed) vs RNAsubopt Matthews Correlation Coefficient Murlet(seed): 0.482 RNAsubopt: 0.463 Sensitivity Murlet(seed): 0.319 RNAsubopt: 0.446 Positive Predictive Value Murlet(seed): 0.734 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.385728764e-07	= RSpredict(seed) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(seed): 0.488 Murlet(seed): 0.482 Sensitivity RSpredict(seed): 0.425 Murlet(seed): 0.319 Positive Predictive Value RSpredict(seed): 0.568 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0107087209457	+ Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.482 CRWrnafold: 0.446 Sensitivity Murlet(seed): 0.319 CRWrnafold: 0.425 Positive Predictive Value Murlet(seed): 0.734 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18018834988e-08	+ Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.488 CMfinder(seed): 0.443 Sensitivity Murlet(seed): 0.321 CMfinder(seed): 0.333 Positive Predictive Value Murlet(seed): 0.748 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.85230291748e-05	+ Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.482 RNAwolf: 0.438 Sensitivity Murlet(seed): 0.319 RNAwolf: 0.407 Positive Predictive Value Murlet(seed): 0.734 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.33801301209e-08	+ Murlet(seed) vs Afold Matthews Correlation Coefficient Murlet(seed): 0.481 Afold: 0.454 Sensitivity Murlet(seed): 0.320 Afold: 0.427 Positive Predictive Value Murlet(seed): 0.730 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31873167448e-06	+ Murlet(seed) vs Alterna Matthews Correlation Coefficient Murlet(seed): 0.432 Alterna: 0.384 Sensitivity Murlet(seed): 0.283 Alterna: 0.365 Positive Predictive Value Murlet(seed): 0.667 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.63424715202e-08	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.482 Mastr(seed): 0.400 Sensitivity Murlet(seed): 0.319 Mastr(seed): 0.242 Positive Predictive Value Murlet(seed): 0.734 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 6.05123325482e-09	? Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): N/A Murlet(seed): N/A Sensitivity Mastr(20): N/A Murlet(seed): N/A Positive Predictive Value Mastr(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs Murlet(seed) Matthews Correlation Coefficient NanoFolder: 0.585 Murlet(seed): 0.574 Sensitivity NanoFolder: 0.654 Murlet(seed): 0.423 Positive Predictive Value NanoFolder: 0.531 Murlet(seed): 0.786 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): N/A Murlet(seed): N/A Sensitivity Carnac(20): N/A Murlet(seed): N/A Positive Predictive Value Carnac(20): 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): 0.575 Murlet(seed): 0.518 Sensitivity Multilign(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value Multilign(seed): 0.625 Murlet(seed): 0.716 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): N/A Multilign(20): N/A Sensitivity Murlet(seed): N/A Multilign(20): N/A Positive Predictive Value Murlet(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): N/A Murlet(seed): N/A Sensitivity TurboFold(20): N/A Murlet(seed): N/A Positive Predictive Value TurboFold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Murlet(seed): N/A Sensitivity RNAalifold(20): N/A Murlet(seed): N/A Positive Predictive Value RNAalifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): N/A Murlet(seed): N/A Sensitivity RNASampler(20): N/A Murlet(seed): N/A Positive Predictive Value RNASampler(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs 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	? PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Murlet(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Murlet(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Murlet(seed): 0.518 Sensitivity PPfold(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value PPfold(seed): 0.833 Murlet(seed): 0.716 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Murlet(seed): 0.477 Sensitivity TurboFold(seed): 0.518 Murlet(seed): 0.333 Positive Predictive Value TurboFold(seed): 0.702 Murlet(seed): 0.691 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs MXScarna(20) Matthews Correlation Coefficient Murlet(seed): N/A MXScarna(20): N/A Sensitivity Murlet(seed): N/A MXScarna(20): N/A Positive Predictive Value Murlet(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): N/A Murlet(seed): N/A Sensitivity RSpredict(20): N/A Murlet(seed): N/A Positive Predictive Value RSpredict(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): N/A Murlet(seed): N/A Sensitivity CentroidAlifold(20): N/A Murlet(seed): N/A Positive Predictive Value CentroidAlifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): N/A Murlet(seed): N/A Sensitivity Murlet(20): N/A Murlet(seed): N/A Positive Predictive Value Murlet(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): N/A Murlet(seed): N/A Sensitivity PPfold(20): N/A Murlet(seed): N/A Positive Predictive Value PPfold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.456 MCFold: 0.354 Sensitivity Murlet(seed): 0.307 MCFold: 0.415 Positive Predictive Value Murlet(seed): 0.685 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08
Sfold	45 Cylofold vs Sfold Matthews Correlation Coefficient Cylofold: 0.764 Sfold: 0.492 Sensitivity Cylofold: 0.742 Sfold: 0.443 Positive Predictive Value Cylofold: 0.791 Sfold: 0.558 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs Sfold Matthews Correlation Coefficient McQFold: 0.594 Sfold: 0.425 Sensitivity McQFold: 0.583 Sfold: 0.377 Positive Predictive Value McQFold: 0.611 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.697 Sfold: 0.482 Sensitivity Pknots: 0.668 Sfold: 0.435 Positive Predictive Value Pknots: 0.733 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Sfold: 0.571 Sensitivity CentroidAlifold(seed): 0.634 Sfold: 0.519 Positive Predictive Value CentroidAlifold(seed): 0.933 Sfold: 0.636 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	53 PknotsRG vs Sfold Matthews Correlation Coefficient PknotsRG: 0.531 Sfold: 0.425 Sensitivity PknotsRG: 0.525 Sfold: 0.377 Positive Predictive Value PknotsRG: 0.544 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Sfold: 0.543 Sensitivity PETfold_pre2.0(seed): 0.649 Sfold: 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Sfold: 0.596 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.86595104665e-08	13 RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.655 Sfold: 0.475 Sensitivity RNASampler(seed): 0.572 Sfold: 0.442 Positive Predictive Value RNASampler(seed): 0.755 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.72523032126e-08	53 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.489 Sfold: 0.425 Sensitivity IPknot: 0.435 Sfold: 0.377 Positive Predictive Value IPknot: 0.556 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs Sfold Matthews Correlation Coefficient RNAalifold(seed): 0.657 Sfold: 0.571 Sensitivity RNAalifold(seed): 0.522 Sfold: 0.519 Positive Predictive Value RNAalifold(seed): 0.833 Sfold: 0.636 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.39162260866e-08	53 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.482 Sfold: 0.425 Sensitivity CentroidFold: 0.430 Sfold: 0.377 Positive Predictive Value CentroidFold: 0.548 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Sfold: 0.425 Sensitivity CentroidHomfold‑LAST: 0.407 Sfold: 0.377 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs Sfold Matthews Correlation Coefficient Vsfold5: 0.534 Sfold: 0.425 Sensitivity Vsfold5: 0.505 Sfold: 0.377 Positive Predictive Value Vsfold5: 0.572 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs Sfold Matthews Correlation Coefficient Carnac(seed): 0.582 Sfold: 0.475 Sensitivity Carnac(seed): 0.354 Sfold: 0.442 Positive Predictive Value Carnac(seed): 0.962 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	53 ProbKnot vs Sfold Matthews Correlation Coefficient ProbKnot: 0.459 Sfold: 0.425 Sensitivity ProbKnot: 0.440 Sfold: 0.377 Positive Predictive Value ProbKnot: 0.487 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs Sfold Matthews Correlation Coefficient RNASLOpt: 0.458 Sfold: 0.425 Sensitivity RNASLOpt: 0.419 Sfold: 0.377 Positive Predictive Value RNASLOpt: 0.508 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.458 Sfold: 0.425 Sensitivity Contrafold: 0.435 Sfold: 0.377 Positive Predictive Value Contrafold: 0.491 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: 0.453 Sfold: 0.425 Sensitivity HotKnots: 0.445 Sfold: 0.377 Positive Predictive Value HotKnots: 0.469 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: 0.508 Sfold: 0.482 Sensitivity RDfolder: 0.432 Sfold: 0.435 Positive Predictive Value RDfolder: 0.609 Sfold: 0.545 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.83792096436e-08	53 Fold vs Sfold Matthews Correlation Coefficient Fold: 0.453 Sfold: 0.425 Sensitivity Fold: 0.431 Sfold: 0.377 Positive Predictive Value Fold: 0.485 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.447 Sfold: 0.425 Sensitivity ContextFold: 0.407 Sfold: 0.377 Positive Predictive Value ContextFold: 0.499 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 8.81311508309e-08	53 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.440 Sfold: 0.425 Sensitivity MaxExpect: 0.414 Sfold: 0.377 Positive Predictive Value MaxExpect: 0.476 Sfold: 0.488 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs Sfold Matthews Correlation Coefficient Murlet(seed): 0.482 Sfold: 0.475 Sensitivity Murlet(seed): 0.319 Sfold: 0.442 Positive Predictive Value Murlet(seed): 0.734 Sfold: 0.519 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0139632814123		+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.425 UNAFold: 0.412 Sensitivity Sfold: 0.377 UNAFold: 0.390 Positive Predictive Value Sfold: 0.488 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08	= Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.425 Vsfold4: 0.423 Sensitivity Sfold: 0.377 Vsfold4: 0.380 Positive Predictive Value Sfold: 0.488 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.326486874811	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.425 RNAshapes: 0.416 Sensitivity Sfold: 0.377 RNAshapes: 0.395 Positive Predictive Value Sfold: 0.488 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 6.06606238843e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.425 RNAfold: 0.409 Sensitivity Sfold: 0.377 RNAfold: 0.390 Positive Predictive Value Sfold: 0.488 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MXScarna(seed) Matthews Correlation Coefficient Sfold: 0.571 MXScarna(seed): 0.539 Sensitivity Sfold: 0.519 MXScarna(seed): 0.501 Positive Predictive Value Sfold: 0.636 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.425 RNAsubopt: 0.394 Sensitivity Sfold: 0.377 RNAsubopt: 0.378 Positive Predictive Value Sfold: 0.488 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.571 RSpredict(seed): 0.514 Sensitivity Sfold: 0.519 RSpredict(seed): 0.427 Positive Predictive Value Sfold: 0.636 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.425 CRWrnafold: 0.374 Sensitivity Sfold: 0.377 CRWrnafold: 0.351 Positive Predictive Value Sfold: 0.488 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.460 CMfinder(seed): 0.443 Sensitivity Sfold: 0.434 CMfinder(seed): 0.333 Positive Predictive Value Sfold: 0.495 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000237629262871	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.425 RNAwolf: 0.362 Sensitivity Sfold: 0.377 RNAwolf: 0.353 Positive Predictive Value Sfold: 0.488 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.379 Afold: 0.316 Sensitivity Sfold: 0.347 Afold: 0.305 Positive Predictive Value Sfold: 0.424 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.482 Alterna: 0.393 Sensitivity Sfold: 0.435 Alterna: 0.365 Positive Predictive Value Sfold: 0.545 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.571 Mastr(seed): 0.341 Sensitivity Sfold: 0.519 Mastr(seed): 0.176 Positive Predictive Value Sfold: 0.636 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08	? Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.721 Mastr(20): 0.561 Sensitivity Sfold: 0.624 Mastr(20): 0.459 Positive Predictive Value Sfold: 0.838 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.468 NanoFolder: 0.304 Sensitivity Sfold: 0.440 NanoFolder: 0.343 Positive Predictive Value Sfold: 0.507 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.821 Sfold: 0.721 Sensitivity Carnac(20): 0.684 Sfold: 0.624 Positive Predictive Value Carnac(20): 0.989 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.575 Sfold: 0.494 Sensitivity Multilign(seed): 0.536 Sfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.862 Sfold: 0.721 Sensitivity Multilign(20): 0.752 Sfold: 0.624 Positive Predictive Value Multilign(20): 0.990 Sfold: 0.838 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): 0.857 Sfold: 0.721 Sensitivity TurboFold(20): 0.744 Sfold: 0.624 Positive Predictive Value TurboFold(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.844 Sfold: 0.721 Sensitivity RNAalifold(20): 0.722 Sfold: 0.624 Positive Predictive Value RNAalifold(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.840 Sfold: 0.721 Sensitivity RNASampler(20): 0.714 Sfold: 0.624 Positive Predictive Value RNASampler(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Sfold Matthews Correlation Coefficient CMfinder(20): 0.779 Sfold: 0.721 Sensitivity CMfinder(20): 0.617 Sfold: 0.624 Positive Predictive Value CMfinder(20): 0.988 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Sfold: 0.721 Sensitivity PETfold_pre2.0(20): 0.759 Sfold: 0.624 Positive Predictive Value PETfold_pre2.0(20): 0.962 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Sfold Matthews Correlation Coefficient PPfold(seed): 0.666 Sfold: 0.494 Sensitivity PPfold(seed): 0.536 Sfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.600 Sfold: 0.476 Sensitivity TurboFold(seed): 0.518 Sfold: 0.446 Positive Predictive Value TurboFold(seed): 0.702 Sfold: 0.517 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.837 Sfold: 0.721 Sensitivity MXScarna(20): 0.752 Sfold: 0.624 Positive Predictive Value MXScarna(20): 0.935 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.721 RSpredict(20): 0.672 Sensitivity Sfold: 0.624 RSpredict(20): 0.549 Positive Predictive Value Sfold: 0.838 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Sfold: 0.721 Sensitivity CentroidAlifold(20): 0.752 Sfold: 0.624 Positive Predictive Value CentroidAlifold(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.741 Sfold: 0.721 Sensitivity Murlet(20): 0.594 Sfold: 0.624 Positive Predictive Value Murlet(20): 0.929 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.840 Sfold: 0.721 Sensitivity PPfold(20): 0.737 Sfold: 0.624 Positive Predictive Value PPfold(20): 0.961 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.441 MCFold: 0.290 Sensitivity Sfold: 0.399 MCFold: 0.320 Positive Predictive Value Sfold: 0.497 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
UNAFold	45 Cylofold vs UNAFold Matthews Correlation Coefficient Cylofold: 0.764 UNAFold: 0.478 Sensitivity Cylofold: 0.742 UNAFold: 0.439 Positive Predictive Value Cylofold: 0.791 UNAFold: 0.532 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs UNAFold Matthews Correlation Coefficient McQFold: 0.594 UNAFold: 0.412 Sensitivity McQFold: 0.583 UNAFold: 0.390 Positive Predictive Value McQFold: 0.611 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.697 UNAFold: 0.468 Sensitivity Pknots: 0.668 UNAFold: 0.431 Positive Predictive Value Pknots: 0.733 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 UNAFold: 0.552 Sensitivity CentroidAlifold(seed): 0.634 UNAFold: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.933 UNAFold: 0.597 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	53 PknotsRG vs UNAFold Matthews Correlation Coefficient PknotsRG: 0.531 UNAFold: 0.412 Sensitivity PknotsRG: 0.525 UNAFold: 0.390 Positive Predictive Value PknotsRG: 0.544 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 UNAFold: 0.531 Sensitivity PETfold_pre2.0(seed): 0.649 UNAFold: 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.824 UNAFold: 0.570 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.42071836373e-08	13 RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.655 UNAFold: 0.481 Sensitivity RNASampler(seed): 0.572 UNAFold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.52609899389e-08	53 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.489 UNAFold: 0.412 Sensitivity IPknot: 0.435 UNAFold: 0.390 Positive Predictive Value IPknot: 0.556 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs UNAFold Matthews Correlation Coefficient RNAalifold(seed): 0.657 UNAFold: 0.552 Sensitivity RNAalifold(seed): 0.522 UNAFold: 0.517 Positive Predictive Value RNAalifold(seed): 0.833 UNAFold: 0.597 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	53 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.482 UNAFold: 0.412 Sensitivity CentroidFold: 0.430 UNAFold: 0.390 Positive Predictive Value CentroidFold: 0.548 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 UNAFold: 0.412 Sensitivity CentroidHomfold‑LAST: 0.407 UNAFold: 0.390 Positive Predictive Value CentroidHomfold‑LAST: 0.592 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs UNAFold Matthews Correlation Coefficient Vsfold5: 0.534 UNAFold: 0.412 Sensitivity Vsfold5: 0.505 UNAFold: 0.390 Positive Predictive Value Vsfold5: 0.572 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs UNAFold Matthews Correlation Coefficient Carnac(seed): 0.582 UNAFold: 0.481 Sensitivity Carnac(seed): 0.354 UNAFold: 0.460 Positive Predictive Value Carnac(seed): 0.962 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.61358433984e-08	53 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.459 UNAFold: 0.412 Sensitivity ProbKnot: 0.440 UNAFold: 0.390 Positive Predictive Value ProbKnot: 0.487 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs UNAFold Matthews Correlation Coefficient RNASLOpt: 0.458 UNAFold: 0.412 Sensitivity RNASLOpt: 0.419 UNAFold: 0.390 Positive Predictive Value RNASLOpt: 0.508 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.458 UNAFold: 0.412 Sensitivity Contrafold: 0.435 UNAFold: 0.390 Positive Predictive Value Contrafold: 0.491 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs UNAFold Matthews Correlation Coefficient HotKnots: 0.453 UNAFold: 0.412 Sensitivity HotKnots: 0.445 UNAFold: 0.390 Positive Predictive Value HotKnots: 0.469 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs UNAFold Matthews Correlation Coefficient RDfolder: 0.508 UNAFold: 0.468 Sensitivity RDfolder: 0.432 UNAFold: 0.431 Positive Predictive Value RDfolder: 0.609 UNAFold: 0.521 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.453 UNAFold: 0.412 Sensitivity Fold: 0.431 UNAFold: 0.390 Positive Predictive Value Fold: 0.485 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.447 UNAFold: 0.412 Sensitivity ContextFold: 0.407 UNAFold: 0.390 Positive Predictive Value ContextFold: 0.499 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.440 UNAFold: 0.412 Sensitivity MaxExpect: 0.414 UNAFold: 0.390 Positive Predictive Value MaxExpect: 0.476 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs UNAFold Matthews Correlation Coefficient Murlet(seed): 0.482 UNAFold: 0.481 Sensitivity Murlet(seed): 0.319 UNAFold: 0.460 Positive Predictive Value Murlet(seed): 0.734 UNAFold: 0.512 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000964840926149	53 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.425 UNAFold: 0.412 Sensitivity Sfold: 0.377 UNAFold: 0.390 Positive Predictive Value Sfold: 0.488 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.85233844192e-08		- Vsfold4 vs UNAFold Matthews Correlation Coefficient Vsfold4: 0.423 UNAFold: 0.412 Sensitivity Vsfold4: 0.380 UNAFold: 0.390 Positive Predictive Value Vsfold4: 0.479 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.7281986208e-07	- RNAshapes vs UNAFold Matthews Correlation Coefficient RNAshapes: 0.416 UNAFold: 0.412 Sensitivity RNAshapes: 0.395 UNAFold: 0.390 Positive Predictive Value RNAshapes: 0.448 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 1.10039559051e-07	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.412 RNAfold: 0.409 Sensitivity UNAFold: 0.390 RNAfold: 0.390 Positive Predictive Value UNAFold: 0.443 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.19883461079e-06	+ UNAFold vs MXScarna(seed) Matthews Correlation Coefficient UNAFold: 0.552 MXScarna(seed): 0.539 Sensitivity UNAFold: 0.517 MXScarna(seed): 0.501 Positive Predictive Value UNAFold: 0.597 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.412 RNAsubopt: 0.394 Sensitivity UNAFold: 0.390 RNAsubopt: 0.378 Positive Predictive Value UNAFold: 0.443 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.552 RSpredict(seed): 0.514 Sensitivity UNAFold: 0.517 RSpredict(seed): 0.427 Positive Predictive Value UNAFold: 0.597 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.412 CRWrnafold: 0.374 Sensitivity UNAFold: 0.390 CRWrnafold: 0.351 Positive Predictive Value UNAFold: 0.443 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.472 CMfinder(seed): 0.443 Sensitivity UNAFold: 0.454 CMfinder(seed): 0.333 Positive Predictive Value UNAFold: 0.498 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00021235435813	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.412 RNAwolf: 0.362 Sensitivity UNAFold: 0.390 RNAwolf: 0.353 Positive Predictive Value UNAFold: 0.443 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.391 Afold: 0.316 Sensitivity UNAFold: 0.375 Afold: 0.305 Positive Predictive Value UNAFold: 0.418 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.468 Alterna: 0.393 Sensitivity UNAFold: 0.431 Alterna: 0.365 Positive Predictive Value UNAFold: 0.521 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.552 Mastr(seed): 0.341 Sensitivity UNAFold: 0.517 Mastr(seed): 0.176 Positive Predictive Value UNAFold: 0.597 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.36983135185e-08	? UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.649 Mastr(20): 0.561 Sensitivity UNAFold: 0.579 Mastr(20): 0.459 Positive Predictive Value UNAFold: 0.733 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.485 NanoFolder: 0.304 Sensitivity UNAFold: 0.446 NanoFolder: 0.343 Positive Predictive Value UNAFold: 0.536 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.821 UNAFold: 0.649 Sensitivity Carnac(20): 0.684 UNAFold: 0.579 Positive Predictive Value Carnac(20): 0.989 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.575 UNAFold: 0.483 Sensitivity Multilign(seed): 0.536 UNAFold: 0.457 Positive Predictive Value Multilign(seed): 0.625 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.862 UNAFold: 0.649 Sensitivity Multilign(20): 0.752 UNAFold: 0.579 Positive Predictive Value Multilign(20): 0.990 UNAFold: 0.733 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): 0.857 UNAFold: 0.649 Sensitivity TurboFold(20): 0.744 UNAFold: 0.579 Positive Predictive Value TurboFold(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.844 UNAFold: 0.649 Sensitivity RNAalifold(20): 0.722 UNAFold: 0.579 Positive Predictive Value RNAalifold(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.840 UNAFold: 0.649 Sensitivity RNASampler(20): 0.714 UNAFold: 0.579 Positive Predictive Value RNASampler(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs UNAFold Matthews Correlation Coefficient CMfinder(20): 0.779 UNAFold: 0.649 Sensitivity CMfinder(20): 0.617 UNAFold: 0.579 Positive Predictive Value CMfinder(20): 0.988 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 UNAFold: 0.649 Sensitivity PETfold_pre2.0(20): 0.759 UNAFold: 0.579 Positive Predictive Value PETfold_pre2.0(20): 0.962 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs UNAFold Matthews Correlation Coefficient PPfold(seed): 0.666 UNAFold: 0.483 Sensitivity PPfold(seed): 0.536 UNAFold: 0.457 Positive Predictive Value PPfold(seed): 0.833 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.600 UNAFold: 0.475 Sensitivity TurboFold(seed): 0.518 UNAFold: 0.452 Positive Predictive Value TurboFold(seed): 0.702 UNAFold: 0.507 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.837 UNAFold: 0.649 Sensitivity MXScarna(20): 0.752 UNAFold: 0.579 Positive Predictive Value MXScarna(20): 0.935 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.672 UNAFold: 0.649 Sensitivity RSpredict(20): 0.549 UNAFold: 0.579 Positive Predictive Value RSpredict(20): 0.830 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 UNAFold: 0.649 Sensitivity CentroidAlifold(20): 0.752 UNAFold: 0.579 Positive Predictive Value CentroidAlifold(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.741 UNAFold: 0.649 Sensitivity Murlet(20): 0.594 UNAFold: 0.579 Positive Predictive Value Murlet(20): 0.929 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.840 UNAFold: 0.649 Sensitivity PPfold(20): 0.737 UNAFold: 0.579 Positive Predictive Value PPfold(20): 0.961 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.423 MCFold: 0.290 Sensitivity UNAFold: 0.394 MCFold: 0.320 Positive Predictive Value UNAFold: 0.463 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold4	45 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.764 Vsfold4: 0.477 Sensitivity Cylofold: 0.742 Vsfold4: 0.420 Positive Predictive Value Cylofold: 0.791 Vsfold4: 0.554 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.594 Vsfold4: 0.423 Sensitivity McQFold: 0.583 Vsfold4: 0.380 Positive Predictive Value McQFold: 0.611 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.697 Vsfold4: 0.480 Sensitivity Pknots: 0.668 Vsfold4: 0.423 Positive Predictive Value Pknots: 0.733 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Vsfold4: 0.488 Sensitivity CentroidAlifold(seed): 0.634 Vsfold4: 0.445 Positive Predictive Value CentroidAlifold(seed): 0.933 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	53 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.531 Vsfold4: 0.423 Sensitivity PknotsRG: 0.525 Vsfold4: 0.380 Positive Predictive Value PknotsRG: 0.544 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 Vsfold4: 0.532 Sensitivity PETfold_pre2.0(seed): 0.649 Vsfold4: 0.487 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Vsfold4: 0.588 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.13260312532e-08	13 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.655 Vsfold4: 0.392 Sensitivity RNASampler(seed): 0.572 Vsfold4: 0.365 Positive Predictive Value RNASampler(seed): 0.755 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.78993384543e-08	53 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.489 Vsfold4: 0.423 Sensitivity IPknot: 0.435 Vsfold4: 0.380 Positive Predictive Value IPknot: 0.556 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.657 Vsfold4: 0.488 Sensitivity RNAalifold(seed): 0.522 Vsfold4: 0.445 Positive Predictive Value RNAalifold(seed): 0.833 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	53 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.482 Vsfold4: 0.423 Sensitivity CentroidFold: 0.430 Vsfold4: 0.380 Positive Predictive Value CentroidFold: 0.548 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 Vsfold4: 0.423 Sensitivity CentroidHomfold‑LAST: 0.407 Vsfold4: 0.380 Positive Predictive Value CentroidHomfold‑LAST: 0.592 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs Vsfold4 Matthews Correlation Coefficient Vsfold5: 0.534 Vsfold4: 0.423 Sensitivity Vsfold5: 0.505 Vsfold4: 0.380 Positive Predictive Value Vsfold5: 0.572 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs Vsfold4 Matthews Correlation Coefficient Carnac(seed): 0.582 Vsfold4: 0.392 Sensitivity Carnac(seed): 0.354 Vsfold4: 0.365 Positive Predictive Value Carnac(seed): 0.962 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.45805449719e-08	53 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.459 Vsfold4: 0.423 Sensitivity ProbKnot: 0.440 Vsfold4: 0.380 Positive Predictive Value ProbKnot: 0.487 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.458 Vsfold4: 0.423 Sensitivity RNASLOpt: 0.419 Vsfold4: 0.380 Positive Predictive Value RNASLOpt: 0.508 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.458 Vsfold4: 0.423 Sensitivity Contrafold: 0.435 Vsfold4: 0.380 Positive Predictive Value Contrafold: 0.491 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.453 Vsfold4: 0.423 Sensitivity HotKnots: 0.445 Vsfold4: 0.380 Positive Predictive Value HotKnots: 0.469 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.83792096436e-08	46 RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: 0.508 Vsfold4: 0.480 Sensitivity RDfolder: 0.432 Vsfold4: 0.423 Positive Predictive Value RDfolder: 0.609 Vsfold4: 0.557 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.48494289621e-08	53 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.453 Vsfold4: 0.423 Sensitivity Fold: 0.431 Vsfold4: 0.380 Positive Predictive Value Fold: 0.485 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.447 Vsfold4: 0.423 Sensitivity ContextFold: 0.407 Vsfold4: 0.380 Positive Predictive Value ContextFold: 0.499 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.83792096436e-08	53 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.440 Vsfold4: 0.423 Sensitivity MaxExpect: 0.414 Vsfold4: 0.380 Positive Predictive Value MaxExpect: 0.476 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.21776328505e-08	13 Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.482 Vsfold4: 0.392 Sensitivity Murlet(seed): 0.319 Vsfold4: 0.365 Positive Predictive Value Murlet(seed): 0.734 Vsfold4: 0.430 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	53 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.425 Vsfold4: 0.423 Sensitivity Sfold: 0.377 Vsfold4: 0.380 Positive Predictive Value Sfold: 0.488 Vsfold4: 0.479 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 0.326486874811	53 Vsfold4 vs UNAFold Matthews Correlation Coefficient Vsfold4: 0.423 UNAFold: 0.412 Sensitivity Vsfold4: 0.380 UNAFold: 0.390 Positive Predictive Value Vsfold4: 0.479 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.7281986208e-07		+ Vsfold4 vs RNAshapes Matthews Correlation Coefficient Vsfold4: 0.423 RNAshapes: 0.416 Sensitivity Vsfold4: 0.380 RNAshapes: 0.395 Positive Predictive Value Vsfold4: 0.479 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 9.17559933998e-05	+ Vsfold4 vs RNAfold Matthews Correlation Coefficient Vsfold4: 0.423 RNAfold: 0.409 Sensitivity Vsfold4: 0.380 RNAfold: 0.390 Positive Predictive Value Vsfold4: 0.479 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 1.59823887228e-06	- MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.539 Vsfold4: 0.488 Sensitivity MXScarna(seed): 0.501 Vsfold4: 0.445 Positive Predictive Value MXScarna(seed): 0.586 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.49381627234e-08	+ Vsfold4 vs RNAsubopt Matthews Correlation Coefficient Vsfold4: 0.423 RNAsubopt: 0.394 Sensitivity Vsfold4: 0.380 RNAsubopt: 0.378 Positive Predictive Value Vsfold4: 0.479 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RSpredict(seed) vs Vsfold4 Matthews Correlation Coefficient RSpredict(seed): 0.514 Vsfold4: 0.488 Sensitivity RSpredict(seed): 0.427 Vsfold4: 0.445 Positive Predictive Value RSpredict(seed): 0.625 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.98606912064e-08	+ Vsfold4 vs CRWrnafold Matthews Correlation Coefficient Vsfold4: 0.423 CRWrnafold: 0.374 Sensitivity Vsfold4: 0.380 CRWrnafold: 0.351 Positive Predictive Value Vsfold4: 0.479 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: 0.448 CMfinder(seed): 0.443 Sensitivity Vsfold4: 0.418 CMfinder(seed): 0.333 Positive Predictive Value Vsfold4: 0.488 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.216974056439	+ Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.423 RNAwolf: 0.362 Sensitivity Vsfold4: 0.380 RNAwolf: 0.353 Positive Predictive Value Vsfold4: 0.479 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Afold Matthews Correlation Coefficient Vsfold4: 0.391 Afold: 0.316 Sensitivity Vsfold4: 0.360 Afold: 0.305 Positive Predictive Value Vsfold4: 0.435 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.480 Alterna: 0.393 Sensitivity Vsfold4: 0.423 Alterna: 0.365 Positive Predictive Value Vsfold4: 0.557 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.488 Mastr(seed): 0.341 Sensitivity Vsfold4: 0.445 Mastr(seed): 0.176 Positive Predictive Value Vsfold4: 0.543 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	? Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.784 Mastr(20): 0.561 Sensitivity Vsfold4: 0.684 Mastr(20): 0.459 Positive Predictive Value Vsfold4: 0.901 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.582 NanoFolder: 0.304 Sensitivity Vsfold4: 0.518 NanoFolder: 0.343 Positive Predictive Value Vsfold4: 0.662 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.821 Vsfold4: 0.784 Sensitivity Carnac(20): 0.684 Vsfold4: 0.684 Positive Predictive Value Carnac(20): 0.989 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold4: 0.260 Sensitivity Multilign(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value Multilign(seed): 0.625 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.862 Vsfold4: 0.784 Sensitivity Multilign(20): 0.752 Vsfold4: 0.684 Positive Predictive Value Multilign(20): 0.990 Vsfold4: 0.901 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): 0.857 Vsfold4: 0.784 Sensitivity TurboFold(20): 0.744 Vsfold4: 0.684 Positive Predictive Value TurboFold(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.844 Vsfold4: 0.784 Sensitivity RNAalifold(20): 0.722 Vsfold4: 0.684 Positive Predictive Value RNAalifold(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.840 Vsfold4: 0.784 Sensitivity RNASampler(20): 0.714 Vsfold4: 0.684 Positive Predictive Value RNASampler(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: 0.784 CMfinder(20): 0.779 Sensitivity Vsfold4: 0.684 CMfinder(20): 0.617 Positive Predictive Value Vsfold4: 0.901 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Vsfold4: 0.784 Sensitivity PETfold_pre2.0(20): 0.759 Vsfold4: 0.684 Positive Predictive Value PETfold_pre2.0(20): 0.962 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold4: 0.260 Sensitivity PPfold(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value PPfold(seed): 0.833 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.600 Vsfold4: 0.316 Sensitivity TurboFold(seed): 0.518 Vsfold4: 0.298 Positive Predictive Value TurboFold(seed): 0.702 Vsfold4: 0.347 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.837 Vsfold4: 0.784 Sensitivity MXScarna(20): 0.752 Vsfold4: 0.684 Positive Predictive Value MXScarna(20): 0.935 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs RSpredict(20) Matthews Correlation Coefficient Vsfold4: 0.784 RSpredict(20): 0.672 Sensitivity Vsfold4: 0.684 RSpredict(20): 0.549 Positive Predictive Value Vsfold4: 0.901 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Vsfold4: 0.784 Sensitivity CentroidAlifold(20): 0.752 Vsfold4: 0.684 Positive Predictive Value CentroidAlifold(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs Murlet(20) Matthews Correlation Coefficient Vsfold4: 0.784 Murlet(20): 0.741 Sensitivity Vsfold4: 0.684 Murlet(20): 0.594 Positive Predictive Value Vsfold4: 0.901 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.840 Vsfold4: 0.784 Sensitivity PPfold(20): 0.737 Vsfold4: 0.684 Positive Predictive Value PPfold(20): 0.961 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.435 MCFold: 0.290 Sensitivity Vsfold4: 0.387 MCFold: 0.320 Positive Predictive Value Vsfold4: 0.498 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAshapes	45 Cylofold vs RNAshapes Matthews Correlation Coefficient Cylofold: 0.764 RNAshapes: 0.473 Sensitivity Cylofold: 0.742 RNAshapes: 0.434 Positive Predictive Value Cylofold: 0.791 RNAshapes: 0.526 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.594 RNAshapes: 0.416 Sensitivity McQFold: 0.583 RNAshapes: 0.395 Positive Predictive Value McQFold: 0.611 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.697 RNAshapes: 0.463 Sensitivity Pknots: 0.668 RNAshapes: 0.426 Positive Predictive Value Pknots: 0.733 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAshapes: 0.526 Sensitivity CentroidAlifold(seed): 0.634 RNAshapes: 0.496 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	53 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.531 RNAshapes: 0.416 Sensitivity PknotsRG: 0.525 RNAshapes: 0.395 Positive Predictive Value PknotsRG: 0.544 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAshapes: 0.506 Sensitivity PETfold_pre2.0(seed): 0.649 RNAshapes: 0.481 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAshapes: 0.540 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.86290426071e-08	13 RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAshapes: 0.447 Sensitivity RNASampler(seed): 0.572 RNAshapes: 0.432 Positive Predictive Value RNASampler(seed): 0.755 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.36983135185e-08	53 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.489 RNAshapes: 0.416 Sensitivity IPknot: 0.435 RNAshapes: 0.395 Positive Predictive Value IPknot: 0.556 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAshapes: 0.526 Sensitivity RNAalifold(seed): 0.522 RNAshapes: 0.496 Positive Predictive Value RNAalifold(seed): 0.833 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	53 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.482 RNAshapes: 0.416 Sensitivity CentroidFold: 0.430 RNAshapes: 0.395 Positive Predictive Value CentroidFold: 0.548 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAshapes: 0.416 Sensitivity CentroidHomfold‑LAST: 0.407 RNAshapes: 0.395 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs RNAshapes Matthews Correlation Coefficient Vsfold5: 0.534 RNAshapes: 0.416 Sensitivity Vsfold5: 0.505 RNAshapes: 0.395 Positive Predictive Value Vsfold5: 0.572 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs RNAshapes Matthews Correlation Coefficient Carnac(seed): 0.582 RNAshapes: 0.447 Sensitivity Carnac(seed): 0.354 RNAshapes: 0.432 Positive Predictive Value Carnac(seed): 0.962 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	53 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.459 RNAshapes: 0.416 Sensitivity ProbKnot: 0.440 RNAshapes: 0.395 Positive Predictive Value ProbKnot: 0.487 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.458 RNAshapes: 0.416 Sensitivity RNASLOpt: 0.419 RNAshapes: 0.395 Positive Predictive Value RNASLOpt: 0.508 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.458 RNAshapes: 0.416 Sensitivity Contrafold: 0.435 RNAshapes: 0.395 Positive Predictive Value Contrafold: 0.491 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.453 RNAshapes: 0.416 Sensitivity HotKnots: 0.445 RNAshapes: 0.395 Positive Predictive Value HotKnots: 0.469 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: 0.508 RNAshapes: 0.463 Sensitivity RDfolder: 0.432 RNAshapes: 0.426 Positive Predictive Value RDfolder: 0.609 RNAshapes: 0.515 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.1569883686e-08	53 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.453 RNAshapes: 0.416 Sensitivity Fold: 0.431 RNAshapes: 0.395 Positive Predictive Value Fold: 0.485 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.447 RNAshapes: 0.416 Sensitivity ContextFold: 0.407 RNAshapes: 0.395 Positive Predictive Value ContextFold: 0.499 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 4.1569883686e-08	53 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.440 RNAshapes: 0.416 Sensitivity MaxExpect: 0.414 RNAshapes: 0.395 Positive Predictive Value MaxExpect: 0.476 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): 0.482 RNAshapes: 0.447 Sensitivity Murlet(seed): 0.319 RNAshapes: 0.432 Positive Predictive Value Murlet(seed): 0.734 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.10353437966e-08	53 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.425 RNAshapes: 0.416 Sensitivity Sfold: 0.377 RNAshapes: 0.395 Positive Predictive Value Sfold: 0.488 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 6.06606238843e-08	53 RNAshapes vs UNAFold Matthews Correlation Coefficient RNAshapes: 0.416 UNAFold: 0.412 Sensitivity RNAshapes: 0.395 UNAFold: 0.390 Positive Predictive Value RNAshapes: 0.448 UNAFold: 0.443 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 1.10039559051e-07	53 Vsfold4 vs RNAshapes Matthews Correlation Coefficient Vsfold4: 0.423 RNAshapes: 0.416 Sensitivity Vsfold4: 0.380 RNAshapes: 0.395 Positive Predictive Value Vsfold4: 0.479 RNAshapes: 0.448 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 9.17559933998e-05		+ RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.416 RNAfold: 0.409 Sensitivity RNAshapes: 0.395 RNAfold: 0.390 Positive Predictive Value RNAshapes: 0.448 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.54175532786e-06	- MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.539 RNAshapes: 0.526 Sensitivity MXScarna(seed): 0.501 RNAshapes: 0.496 Positive Predictive Value MXScarna(seed): 0.586 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.43986829011e-07	+ RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.416 RNAsubopt: 0.394 Sensitivity RNAshapes: 0.395 RNAsubopt: 0.378 Positive Predictive Value RNAshapes: 0.448 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.526 RSpredict(seed): 0.514 Sensitivity RNAshapes: 0.496 RSpredict(seed): 0.427 Positive Predictive Value RNAshapes: 0.565 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000562659844894	+ RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.416 CRWrnafold: 0.374 Sensitivity RNAshapes: 0.395 CRWrnafold: 0.351 Positive Predictive Value RNAshapes: 0.448 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): 0.443 RNAshapes: 0.433 Sensitivity CMfinder(seed): 0.333 RNAshapes: 0.422 Positive Predictive Value CMfinder(seed): 0.597 RNAshapes: 0.453 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000492532411318	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.416 RNAwolf: 0.362 Sensitivity RNAshapes: 0.395 RNAwolf: 0.353 Positive Predictive Value RNAshapes: 0.448 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.398 Afold: 0.316 Sensitivity RNAshapes: 0.381 Afold: 0.305 Positive Predictive Value RNAshapes: 0.424 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.463 Alterna: 0.393 Sensitivity RNAshapes: 0.426 Alterna: 0.365 Positive Predictive Value RNAshapes: 0.515 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.526 Mastr(seed): 0.341 Sensitivity RNAshapes: 0.496 Mastr(seed): 0.176 Positive Predictive Value RNAshapes: 0.565 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	? RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.640 Mastr(20): 0.561 Sensitivity RNAshapes: 0.571 Mastr(20): 0.459 Positive Predictive Value RNAshapes: 0.724 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.455 NanoFolder: 0.304 Sensitivity RNAshapes: 0.416 NanoFolder: 0.343 Positive Predictive Value RNAshapes: 0.507 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.821 RNAshapes: 0.640 Sensitivity Carnac(20): 0.684 RNAshapes: 0.571 Positive Predictive Value Carnac(20): 0.989 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.575 RNAshapes: 0.481 Sensitivity Multilign(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.862 RNAshapes: 0.640 Sensitivity Multilign(20): 0.752 RNAshapes: 0.571 Positive Predictive Value Multilign(20): 0.990 RNAshapes: 0.724 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): 0.857 RNAshapes: 0.640 Sensitivity TurboFold(20): 0.744 RNAshapes: 0.571 Positive Predictive Value TurboFold(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAshapes: 0.640 Sensitivity RNAalifold(20): 0.722 RNAshapes: 0.571 Positive Predictive Value RNAalifold(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.840 RNAshapes: 0.640 Sensitivity RNASampler(20): 0.714 RNAshapes: 0.571 Positive Predictive Value RNASampler(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.779 RNAshapes: 0.640 Sensitivity CMfinder(20): 0.617 RNAshapes: 0.571 Positive Predictive Value CMfinder(20): 0.988 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAshapes: 0.640 Sensitivity PETfold_pre2.0(20): 0.759 RNAshapes: 0.571 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): 0.666 RNAshapes: 0.481 Sensitivity PPfold(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAshapes: 0.471 Sensitivity TurboFold(seed): 0.518 RNAshapes: 0.452 Positive Predictive Value TurboFold(seed): 0.702 RNAshapes: 0.500 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.837 RNAshapes: 0.640 Sensitivity MXScarna(20): 0.752 RNAshapes: 0.571 Positive Predictive Value MXScarna(20): 0.935 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.672 RNAshapes: 0.640 Sensitivity RSpredict(20): 0.549 RNAshapes: 0.571 Positive Predictive Value RSpredict(20): 0.830 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAshapes: 0.640 Sensitivity CentroidAlifold(20): 0.752 RNAshapes: 0.571 Positive Predictive Value CentroidAlifold(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.741 RNAshapes: 0.640 Sensitivity Murlet(20): 0.594 RNAshapes: 0.571 Positive Predictive Value Murlet(20): 0.929 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.840 RNAshapes: 0.640 Sensitivity PPfold(20): 0.737 RNAshapes: 0.571 Positive Predictive Value PPfold(20): 0.961 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.438 MCFold: 0.290 Sensitivity RNAshapes: 0.408 MCFold: 0.320 Positive Predictive Value RNAshapes: 0.481 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	45 Cylofold vs RNAfold Matthews Correlation Coefficient Cylofold: 0.764 RNAfold: 0.486 Sensitivity Cylofold: 0.742 RNAfold: 0.447 Positive Predictive Value Cylofold: 0.791 RNAfold: 0.539 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs RNAfold Matthews Correlation Coefficient McQFold: 0.594 RNAfold: 0.409 Sensitivity McQFold: 0.583 RNAfold: 0.390 Positive Predictive Value McQFold: 0.611 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.697 RNAfold: 0.476 Sensitivity Pknots: 0.668 RNAfold: 0.439 Positive Predictive Value Pknots: 0.733 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAfold: 0.566 Sensitivity CentroidAlifold(seed): 0.634 RNAfold: 0.532 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	53 PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.531 RNAfold: 0.409 Sensitivity PknotsRG: 0.525 RNAfold: 0.390 Positive Predictive Value PknotsRG: 0.544 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAfold: 0.541 Sensitivity PETfold_pre2.0(seed): 0.649 RNAfold: 0.513 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAfold: 0.578 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.16042554876e-08	13 RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAfold: 0.476 Sensitivity RNASampler(seed): 0.572 RNAfold: 0.460 Positive Predictive Value RNASampler(seed): 0.755 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	53 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.489 RNAfold: 0.409 Sensitivity IPknot: 0.435 RNAfold: 0.390 Positive Predictive Value IPknot: 0.556 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs RNAfold Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAfold: 0.566 Sensitivity RNAalifold(seed): 0.522 RNAfold: 0.532 Positive Predictive Value RNAalifold(seed): 0.833 RNAfold: 0.609 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.77512146924e-08	53 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.482 RNAfold: 0.409 Sensitivity CentroidFold: 0.430 RNAfold: 0.390 Positive Predictive Value CentroidFold: 0.548 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAfold: 0.409 Sensitivity CentroidHomfold‑LAST: 0.407 RNAfold: 0.390 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs RNAfold Matthews Correlation Coefficient Vsfold5: 0.534 RNAfold: 0.409 Sensitivity Vsfold5: 0.505 RNAfold: 0.390 Positive Predictive Value Vsfold5: 0.572 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs RNAfold Matthews Correlation Coefficient Carnac(seed): 0.582 RNAfold: 0.476 Sensitivity Carnac(seed): 0.354 RNAfold: 0.460 Positive Predictive Value Carnac(seed): 0.962 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	53 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.459 RNAfold: 0.409 Sensitivity ProbKnot: 0.440 RNAfold: 0.390 Positive Predictive Value ProbKnot: 0.487 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs RNAfold Matthews Correlation Coefficient RNASLOpt: 0.458 RNAfold: 0.409 Sensitivity RNASLOpt: 0.419 RNAfold: 0.390 Positive Predictive Value RNASLOpt: 0.508 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.458 RNAfold: 0.409 Sensitivity Contrafold: 0.435 RNAfold: 0.390 Positive Predictive Value Contrafold: 0.491 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.453 RNAfold: 0.409 Sensitivity HotKnots: 0.445 RNAfold: 0.390 Positive Predictive Value HotKnots: 0.469 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: 0.508 RNAfold: 0.476 Sensitivity RDfolder: 0.432 RNAfold: 0.439 Positive Predictive Value RDfolder: 0.609 RNAfold: 0.528 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 6.06606238843e-08	53 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.453 RNAfold: 0.409 Sensitivity Fold: 0.431 RNAfold: 0.390 Positive Predictive Value Fold: 0.485 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.447 RNAfold: 0.409 Sensitivity ContextFold: 0.407 RNAfold: 0.390 Positive Predictive Value ContextFold: 0.499 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.440 RNAfold: 0.409 Sensitivity MaxExpect: 0.414 RNAfold: 0.390 Positive Predictive Value MaxExpect: 0.476 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs RNAfold Matthews Correlation Coefficient Murlet(seed): 0.482 RNAfold: 0.476 Sensitivity Murlet(seed): 0.319 RNAfold: 0.460 Positive Predictive Value Murlet(seed): 0.734 RNAfold: 0.500 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.000179548697844	53 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.425 RNAfold: 0.409 Sensitivity Sfold: 0.377 RNAfold: 0.390 Positive Predictive Value Sfold: 0.488 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.412 RNAfold: 0.409 Sensitivity UNAFold: 0.390 RNAfold: 0.390 Positive Predictive Value UNAFold: 0.443 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.19883461079e-06	53 Vsfold4 vs RNAfold Matthews Correlation Coefficient Vsfold4: 0.423 RNAfold: 0.409 Sensitivity Vsfold4: 0.380 RNAfold: 0.390 Positive Predictive Value Vsfold4: 0.479 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 1.59823887228e-06	53 RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.416 RNAfold: 0.409 Sensitivity RNAshapes: 0.395 RNAfold: 0.390 Positive Predictive Value RNAshapes: 0.448 RNAfold: 0.438 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 5.54175532786e-06		+ RNAfold vs MXScarna(seed) Matthews Correlation Coefficient RNAfold: 0.566 MXScarna(seed): 0.539 Sensitivity RNAfold: 0.532 MXScarna(seed): 0.501 Positive Predictive Value RNAfold: 0.609 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.16131455263e-08	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.409 RNAsubopt: 0.394 Sensitivity RNAfold: 0.390 RNAsubopt: 0.378 Positive Predictive Value RNAfold: 0.438 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.566 RSpredict(seed): 0.514 Sensitivity RNAfold: 0.532 RSpredict(seed): 0.427 Positive Predictive Value RNAfold: 0.609 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.409 CRWrnafold: 0.374 Sensitivity RNAfold: 0.390 CRWrnafold: 0.351 Positive Predictive Value RNAfold: 0.438 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.465 CMfinder(seed): 0.443 Sensitivity RNAfold: 0.454 CMfinder(seed): 0.333 Positive Predictive Value RNAfold: 0.485 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0217436526037	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.409 RNAwolf: 0.362 Sensitivity RNAfold: 0.390 RNAwolf: 0.353 Positive Predictive Value RNAfold: 0.438 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.378 Afold: 0.316 Sensitivity RNAfold: 0.364 Afold: 0.305 Positive Predictive Value RNAfold: 0.403 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.476 Alterna: 0.393 Sensitivity RNAfold: 0.439 Alterna: 0.365 Positive Predictive Value RNAfold: 0.528 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.566 Mastr(seed): 0.341 Sensitivity RNAfold: 0.532 Mastr(seed): 0.176 Positive Predictive Value RNAfold: 0.609 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	? RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.702 Mastr(20): 0.561 Sensitivity RNAfold: 0.617 Mastr(20): 0.459 Positive Predictive Value RNAfold: 0.804 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.468 NanoFolder: 0.304 Sensitivity RNAfold: 0.440 NanoFolder: 0.343 Positive Predictive Value RNAfold: 0.507 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.821 RNAfold: 0.702 Sensitivity Carnac(20): 0.684 RNAfold: 0.617 Positive Predictive Value Carnac(20): 0.989 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.575 RNAfold: 0.472 Sensitivity Multilign(seed): 0.536 RNAfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAfold: 0.496 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.862 RNAfold: 0.702 Sensitivity Multilign(20): 0.752 RNAfold: 0.617 Positive Predictive Value Multilign(20): 0.990 RNAfold: 0.804 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): 0.857 RNAfold: 0.702 Sensitivity TurboFold(20): 0.744 RNAfold: 0.617 Positive Predictive Value TurboFold(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAfold: 0.702 Sensitivity RNAalifold(20): 0.722 RNAfold: 0.617 Positive Predictive Value RNAalifold(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.840 RNAfold: 0.702 Sensitivity RNASampler(20): 0.714 RNAfold: 0.617 Positive Predictive Value RNASampler(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RNAfold Matthews Correlation Coefficient CMfinder(20): 0.779 RNAfold: 0.702 Sensitivity CMfinder(20): 0.617 RNAfold: 0.617 Positive Predictive Value CMfinder(20): 0.988 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAfold: 0.702 Sensitivity PETfold_pre2.0(20): 0.759 RNAfold: 0.617 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAfold Matthews Correlation Coefficient PPfold(seed): 0.666 RNAfold: 0.472 Sensitivity PPfold(seed): 0.536 RNAfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAfold: 0.496 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAfold: 0.464 Sensitivity TurboFold(seed): 0.518 RNAfold: 0.452 Positive Predictive Value TurboFold(seed): 0.702 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.837 RNAfold: 0.702 Sensitivity MXScarna(20): 0.752 RNAfold: 0.617 Positive Predictive Value MXScarna(20): 0.935 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.702 RSpredict(20): 0.672 Sensitivity RNAfold: 0.617 RSpredict(20): 0.549 Positive Predictive Value RNAfold: 0.804 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAfold: 0.702 Sensitivity CentroidAlifold(20): 0.752 RNAfold: 0.617 Positive Predictive Value CentroidAlifold(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.741 RNAfold: 0.702 Sensitivity Murlet(20): 0.594 RNAfold: 0.617 Positive Predictive Value Murlet(20): 0.929 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.840 RNAfold: 0.702 Sensitivity PPfold(20): 0.737 RNAfold: 0.617 Positive Predictive Value PPfold(20): 0.961 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.417 MCFold: 0.290 Sensitivity RNAfold: 0.391 MCFold: 0.320 Positive Predictive Value RNAfold: 0.455 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(seed)	15 Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: 0.798 MXScarna(seed): 0.542 Sensitivity Cylofold: 0.772 MXScarna(seed): 0.505 Positive Predictive Value Cylofold: 0.828 MXScarna(seed): 0.590 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.00627773251e-08	17 McQFold vs MXScarna(seed) Matthews Correlation Coefficient McQFold: 0.834 MXScarna(seed): 0.539 Sensitivity McQFold: 0.799 MXScarna(seed): 0.501 Positive Predictive Value McQFold: 0.872 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	16 Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: 0.768 MXScarna(seed): 0.514 Sensitivity Pknots: 0.748 MXScarna(seed): 0.481 Positive Predictive Value Pknots: 0.792 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.53777893337e-08	17 CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 MXScarna(seed): 0.539 Sensitivity CentroidAlifold(seed): 0.634 MXScarna(seed): 0.501 Positive Predictive Value CentroidAlifold(seed): 0.933 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	17 PknotsRG vs MXScarna(seed) Matthews Correlation Coefficient PknotsRG: 0.787 MXScarna(seed): 0.539 Sensitivity PknotsRG: 0.761 MXScarna(seed): 0.501 Positive Predictive Value PknotsRG: 0.817 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	17 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 MXScarna(seed): 0.539 Sensitivity PETfold_pre2.0(seed): 0.626 MXScarna(seed): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.809 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.32883086441e-08	13 RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 MXScarna(seed): 0.440 Sensitivity RNASampler(seed): 0.572 MXScarna(seed): 0.421 Positive Predictive Value RNASampler(seed): 0.755 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.72523032126e-08	17 IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.671 MXScarna(seed): 0.539 Sensitivity IPknot: 0.590 MXScarna(seed): 0.501 Positive Predictive Value IPknot: 0.768 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	17 RNAalifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 MXScarna(seed): 0.539 Sensitivity RNAalifold(seed): 0.522 MXScarna(seed): 0.501 Positive Predictive Value RNAalifold(seed): 0.833 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.64481516727e-08	17 CentroidFold vs MXScarna(seed) Matthews Correlation Coefficient CentroidFold: 0.695 MXScarna(seed): 0.539 Sensitivity CentroidFold: 0.608 MXScarna(seed): 0.501 Positive Predictive Value CentroidFold: 0.799 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	17 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 MXScarna(seed): 0.539 Sensitivity CentroidHomfold‑LAST: 0.560 MXScarna(seed): 0.501 Positive Predictive Value CentroidHomfold‑LAST: 0.769 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	17 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.539 Vsfold5: 0.531 Sensitivity MXScarna(seed): 0.501 Vsfold5: 0.501 Positive Predictive Value MXScarna(seed): 0.586 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.00909249161262	13 Carnac(seed) vs MXScarna(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 MXScarna(seed): 0.440 Sensitivity Carnac(seed): 0.354 MXScarna(seed): 0.421 Positive Predictive Value Carnac(seed): 0.962 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.46296269841e-09	17 ProbKnot vs MXScarna(seed) Matthews Correlation Coefficient ProbKnot: 0.603 MXScarna(seed): 0.539 Sensitivity ProbKnot: 0.565 MXScarna(seed): 0.501 Positive Predictive Value ProbKnot: 0.649 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.70887622364e-08	17 RNASLOpt vs MXScarna(seed) Matthews Correlation Coefficient RNASLOpt: 0.635 MXScarna(seed): 0.539 Sensitivity RNASLOpt: 0.565 MXScarna(seed): 0.501 Positive Predictive Value RNASLOpt: 0.718 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	17 Contrafold vs MXScarna(seed) Matthews Correlation Coefficient Contrafold: 0.653 MXScarna(seed): 0.539 Sensitivity Contrafold: 0.598 MXScarna(seed): 0.501 Positive Predictive Value Contrafold: 0.719 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	17 HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: 0.603 MXScarna(seed): 0.539 Sensitivity HotKnots: 0.588 MXScarna(seed): 0.501 Positive Predictive Value HotKnots: 0.624 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	16 RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: 0.616 MXScarna(seed): 0.514 Sensitivity RDfolder: 0.531 MXScarna(seed): 0.481 Positive Predictive Value RDfolder: 0.721 MXScarna(seed): 0.558 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.98760236454e-08	17 Fold vs MXScarna(seed) Matthews Correlation Coefficient Fold: 0.572 MXScarna(seed): 0.539 Sensitivity Fold: 0.534 MXScarna(seed): 0.501 Positive Predictive Value Fold: 0.619 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	17 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.567 MXScarna(seed): 0.539 Sensitivity ContextFold: 0.506 MXScarna(seed): 0.501 Positive Predictive Value ContextFold: 0.642 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	17 MaxExpect vs MXScarna(seed) Matthews Correlation Coefficient MaxExpect: 0.603 MXScarna(seed): 0.539 Sensitivity MaxExpect: 0.560 MXScarna(seed): 0.501 Positive Predictive Value MaxExpect: 0.657 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.16042554876e-08	13 Murlet(seed) vs MXScarna(seed) Matthews Correlation Coefficient Murlet(seed): 0.482 MXScarna(seed): 0.440 Sensitivity Murlet(seed): 0.319 MXScarna(seed): 0.421 Positive Predictive Value Murlet(seed): 0.734 MXScarna(seed): 0.469 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.34041282081e-08	17 Sfold vs MXScarna(seed) Matthews Correlation Coefficient Sfold: 0.571 MXScarna(seed): 0.539 Sensitivity Sfold: 0.519 MXScarna(seed): 0.501 Positive Predictive Value Sfold: 0.636 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	17 UNAFold vs MXScarna(seed) Matthews Correlation Coefficient UNAFold: 0.552 MXScarna(seed): 0.539 Sensitivity UNAFold: 0.517 MXScarna(seed): 0.501 Positive Predictive Value UNAFold: 0.597 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	17 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.539 Vsfold4: 0.488 Sensitivity MXScarna(seed): 0.501 Vsfold4: 0.445 Positive Predictive Value MXScarna(seed): 0.586 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.49381627234e-08	17 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.539 RNAshapes: 0.526 Sensitivity MXScarna(seed): 0.501 RNAshapes: 0.496 Positive Predictive Value MXScarna(seed): 0.586 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.43986829011e-07	17 RNAfold vs MXScarna(seed) Matthews Correlation Coefficient RNAfold: 0.566 MXScarna(seed): 0.539 Sensitivity RNAfold: 0.532 MXScarna(seed): 0.501 Positive Predictive Value RNAfold: 0.609 MXScarna(seed): 0.586 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.16131455263e-08		= MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.539 RNAsubopt: 0.538 Sensitivity MXScarna(seed): 0.501 RNAsubopt: 0.506 Positive Predictive Value MXScarna(seed): 0.586 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0367606191363	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.539 RSpredict(seed): 0.514 Sensitivity MXScarna(seed): 0.501 RSpredict(seed): 0.427 Positive Predictive Value MXScarna(seed): 0.586 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.81985890439e-08	+ MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.539 CRWrnafold: 0.527 Sensitivity MXScarna(seed): 0.501 CRWrnafold: 0.491 Positive Predictive Value MXScarna(seed): 0.586 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.95320262584e-05	= CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): 0.443 MXScarna(seed): 0.419 Sensitivity CMfinder(seed): 0.333 MXScarna(seed): 0.402 Positive Predictive Value CMfinder(seed): 0.597 MXScarna(seed): 0.446 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00123904660847	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.539 RNAwolf: 0.487 Sensitivity MXScarna(seed): 0.501 RNAwolf: 0.461 Positive Predictive Value MXScarna(seed): 0.586 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.23753225208e-08	- Afold vs MXScarna(seed) Matthews Correlation Coefficient Afold: 0.517 MXScarna(seed): 0.488 Sensitivity Afold: 0.480 MXScarna(seed): 0.464 Positive Predictive Value Afold: 0.564 MXScarna(seed): 0.522 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.514 Alterna: 0.486 Sensitivity MXScarna(seed): 0.481 Alterna: 0.455 Positive Predictive Value MXScarna(seed): 0.558 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 7.52580889924e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.539 Mastr(seed): 0.341 Sensitivity MXScarna(seed): 0.501 Mastr(seed): 0.176 Positive Predictive Value MXScarna(seed): 0.586 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.43692248862e-08	? MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 Mastr(20): 0.705 Sensitivity MXScarna(seed): 0.713 Mastr(20): 0.565 Positive Predictive Value MXScarna(seed): 0.963 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.510 NanoFolder: 0.489 Sensitivity MXScarna(seed): 0.481 NanoFolder: 0.544 Positive Predictive Value MXScarna(seed): 0.551 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs MXScarna(seed) Matthews Correlation Coefficient Carnac(20): 0.832 MXScarna(seed): 0.827 Sensitivity Carnac(20): 0.694 MXScarna(seed): 0.713 Positive Predictive Value Carnac(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 MXScarna(seed): 0.468 Sensitivity Multilign(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value Multilign(seed): 0.625 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(20): 0.865 MXScarna(seed): 0.827 Sensitivity Multilign(20): 0.750 MXScarna(seed): 0.713 Positive Predictive Value Multilign(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 MXScarna(seed): 0.827 Sensitivity TurboFold(20): 0.741 MXScarna(seed): 0.713 Positive Predictive Value TurboFold(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 MXScarna(seed): 0.827 Sensitivity RNAalifold(20): 0.704 MXScarna(seed): 0.713 Positive Predictive Value RNAalifold(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 MXScarna(seed): 0.827 Sensitivity RNASampler(20): 0.694 MXScarna(seed): 0.713 Positive Predictive Value RNASampler(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 CMfinder(20): 0.756 Sensitivity MXScarna(seed): 0.713 CMfinder(20): 0.574 Positive Predictive Value MXScarna(seed): 0.963 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 MXScarna(seed): 0.827 Sensitivity PETfold_pre2.0(20): 0.750 MXScarna(seed): 0.713 Positive Predictive Value PETfold_pre2.0(20): 0.964 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 MXScarna(seed): 0.468 Sensitivity PPfold(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value PPfold(seed): 0.833 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 MXScarna(seed): 0.449 Sensitivity TurboFold(seed): 0.518 MXScarna(seed): 0.446 Positive Predictive Value TurboFold(seed): 0.702 MXScarna(seed): 0.460 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs MXScarna(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 MXScarna(seed): 0.827 Sensitivity MXScarna(20): 0.769 MXScarna(seed): 0.713 Positive Predictive Value MXScarna(20): 0.954 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 RSpredict(20): 0.676 Sensitivity MXScarna(seed): 0.713 RSpredict(20): 0.546 Positive Predictive Value MXScarna(seed): 0.963 RSpredict(20): 0.843 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 MXScarna(seed): 0.827 Sensitivity CentroidAlifold(20): 0.741 MXScarna(seed): 0.713 Positive Predictive Value CentroidAlifold(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 Murlet(20): 0.780 Sensitivity MXScarna(seed): 0.713 Murlet(20): 0.611 Positive Predictive Value MXScarna(seed): 0.963 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.833 MXScarna(seed): 0.827 Sensitivity PPfold(20): 0.722 MXScarna(seed): 0.713 Positive Predictive Value PPfold(20): 0.963 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.538 MCFold: 0.358 Sensitivity MXScarna(seed): 0.502 MCFold: 0.409 Positive Predictive Value MXScarna(seed): 0.586 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 9.9460272886e-09
RNAsubopt	45 Cylofold vs RNAsubopt Matthews Correlation Coefficient Cylofold: 0.764 RNAsubopt: 0.480 Sensitivity Cylofold: 0.742 RNAsubopt: 0.443 Positive Predictive Value Cylofold: 0.791 RNAsubopt: 0.531 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs RNAsubopt Matthews Correlation Coefficient McQFold: 0.594 RNAsubopt: 0.394 Sensitivity McQFold: 0.583 RNAsubopt: 0.378 Positive Predictive Value McQFold: 0.611 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: 0.697 RNAsubopt: 0.470 Sensitivity Pknots: 0.668 RNAsubopt: 0.435 Positive Predictive Value Pknots: 0.733 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAsubopt: 0.538 Sensitivity CentroidAlifold(seed): 0.634 RNAsubopt: 0.506 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	53 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.531 RNAsubopt: 0.394 Sensitivity PknotsRG: 0.525 RNAsubopt: 0.378 Positive Predictive Value PknotsRG: 0.544 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAsubopt: 0.514 Sensitivity PETfold_pre2.0(seed): 0.649 RNAsubopt: 0.490 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAsubopt: 0.547 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.33194562506e-08	13 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAsubopt: 0.463 Sensitivity RNASampler(seed): 0.572 RNAsubopt: 0.446 Positive Predictive Value RNASampler(seed): 0.755 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08	53 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.489 RNAsubopt: 0.394 Sensitivity IPknot: 0.435 RNAsubopt: 0.378 Positive Predictive Value IPknot: 0.556 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAsubopt: 0.538 Sensitivity RNAalifold(seed): 0.522 RNAsubopt: 0.506 Positive Predictive Value RNAalifold(seed): 0.833 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	53 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.482 RNAsubopt: 0.394 Sensitivity CentroidFold: 0.430 RNAsubopt: 0.378 Positive Predictive Value CentroidFold: 0.548 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAsubopt: 0.394 Sensitivity CentroidHomfold‑LAST: 0.407 RNAsubopt: 0.378 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs RNAsubopt Matthews Correlation Coefficient Vsfold5: 0.534 RNAsubopt: 0.394 Sensitivity Vsfold5: 0.505 RNAsubopt: 0.378 Positive Predictive Value Vsfold5: 0.572 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs RNAsubopt Matthews Correlation Coefficient Carnac(seed): 0.582 RNAsubopt: 0.463 Sensitivity Carnac(seed): 0.354 RNAsubopt: 0.446 Positive Predictive Value Carnac(seed): 0.962 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.69265863073e-08	53 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.459 RNAsubopt: 0.394 Sensitivity ProbKnot: 0.440 RNAsubopt: 0.378 Positive Predictive Value ProbKnot: 0.487 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.458 RNAsubopt: 0.394 Sensitivity RNASLOpt: 0.419 RNAsubopt: 0.378 Positive Predictive Value RNASLOpt: 0.508 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.458 RNAsubopt: 0.394 Sensitivity Contrafold: 0.435 RNAsubopt: 0.378 Positive Predictive Value Contrafold: 0.491 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.453 RNAsubopt: 0.394 Sensitivity HotKnots: 0.445 RNAsubopt: 0.378 Positive Predictive Value HotKnots: 0.469 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: 0.508 RNAsubopt: 0.470 Sensitivity RDfolder: 0.432 RNAsubopt: 0.435 Positive Predictive Value RDfolder: 0.609 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 4.1569883686e-08	53 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.453 RNAsubopt: 0.394 Sensitivity Fold: 0.431 RNAsubopt: 0.378 Positive Predictive Value Fold: 0.485 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.447 RNAsubopt: 0.394 Sensitivity ContextFold: 0.407 RNAsubopt: 0.378 Positive Predictive Value ContextFold: 0.499 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.440 RNAsubopt: 0.394 Sensitivity MaxExpect: 0.414 RNAsubopt: 0.378 Positive Predictive Value MaxExpect: 0.476 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs RNAsubopt Matthews Correlation Coefficient Murlet(seed): 0.482 RNAsubopt: 0.463 Sensitivity Murlet(seed): 0.319 RNAsubopt: 0.446 Positive Predictive Value Murlet(seed): 0.734 RNAsubopt: 0.488 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.385728764e-07	53 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.425 RNAsubopt: 0.394 Sensitivity Sfold: 0.377 RNAsubopt: 0.378 Positive Predictive Value Sfold: 0.488 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.412 RNAsubopt: 0.394 Sensitivity UNAFold: 0.390 RNAsubopt: 0.378 Positive Predictive Value UNAFold: 0.443 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold4 vs RNAsubopt Matthews Correlation Coefficient Vsfold4: 0.423 RNAsubopt: 0.394 Sensitivity Vsfold4: 0.380 RNAsubopt: 0.378 Positive Predictive Value Vsfold4: 0.479 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.416 RNAsubopt: 0.394 Sensitivity RNAshapes: 0.395 RNAsubopt: 0.378 Positive Predictive Value RNAshapes: 0.448 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.409 RNAsubopt: 0.394 Sensitivity RNAfold: 0.390 RNAsubopt: 0.378 Positive Predictive Value RNAfold: 0.438 RNAsubopt: 0.419 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.539 RNAsubopt: 0.538 Sensitivity MXScarna(seed): 0.501 RNAsubopt: 0.506 Positive Predictive Value MXScarna(seed): 0.586 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.0367606191363		+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.538 RSpredict(seed): 0.514 Sensitivity RNAsubopt: 0.506 RSpredict(seed): 0.427 Positive Predictive Value RNAsubopt: 0.578 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.394 CRWrnafold: 0.374 Sensitivity RNAsubopt: 0.378 CRWrnafold: 0.351 Positive Predictive Value RNAsubopt: 0.419 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.451 CMfinder(seed): 0.443 Sensitivity RNAsubopt: 0.438 CMfinder(seed): 0.333 Positive Predictive Value RNAsubopt: 0.472 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0230361572455	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.394 RNAwolf: 0.362 Sensitivity RNAsubopt: 0.378 RNAwolf: 0.353 Positive Predictive Value RNAsubopt: 0.419 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.376 Afold: 0.316 Sensitivity RNAsubopt: 0.364 Afold: 0.305 Positive Predictive Value RNAsubopt: 0.399 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.470 Alterna: 0.393 Sensitivity RNAsubopt: 0.435 Alterna: 0.365 Positive Predictive Value RNAsubopt: 0.520 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.538 Mastr(seed): 0.341 Sensitivity RNAsubopt: 0.506 Mastr(seed): 0.176 Positive Predictive Value RNAsubopt: 0.578 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	? RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.646 Mastr(20): 0.561 Sensitivity RNAsubopt: 0.579 Mastr(20): 0.459 Positive Predictive Value RNAsubopt: 0.726 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.471 NanoFolder: 0.304 Sensitivity RNAsubopt: 0.440 NanoFolder: 0.343 Positive Predictive Value RNAsubopt: 0.514 NanoFolder: 0.281 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): 0.821 RNAsubopt: 0.646 Sensitivity Carnac(20): 0.684 RNAsubopt: 0.579 Positive Predictive Value Carnac(20): 0.989 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.575 RNAsubopt: 0.478 Sensitivity Multilign(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.862 RNAsubopt: 0.646 Sensitivity Multilign(20): 0.752 RNAsubopt: 0.579 Positive Predictive Value Multilign(20): 0.990 RNAsubopt: 0.726 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): 0.857 RNAsubopt: 0.646 Sensitivity TurboFold(20): 0.744 RNAsubopt: 0.579 Positive Predictive Value TurboFold(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAsubopt: 0.646 Sensitivity RNAalifold(20): 0.722 RNAsubopt: 0.579 Positive Predictive Value RNAalifold(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.840 RNAsubopt: 0.646 Sensitivity RNASampler(20): 0.714 RNAsubopt: 0.579 Positive Predictive Value RNASampler(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RNAsubopt Matthews Correlation Coefficient CMfinder(20): 0.779 RNAsubopt: 0.646 Sensitivity CMfinder(20): 0.617 RNAsubopt: 0.579 Positive Predictive Value CMfinder(20): 0.988 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAsubopt: 0.646 Sensitivity PETfold_pre2.0(20): 0.759 RNAsubopt: 0.579 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): 0.666 RNAsubopt: 0.478 Sensitivity PPfold(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAsubopt: 0.468 Sensitivity TurboFold(seed): 0.518 RNAsubopt: 0.452 Positive Predictive Value TurboFold(seed): 0.702 RNAsubopt: 0.494 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.837 RNAsubopt: 0.646 Sensitivity MXScarna(20): 0.752 RNAsubopt: 0.579 Positive Predictive Value MXScarna(20): 0.935 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.672 RNAsubopt: 0.646 Sensitivity RSpredict(20): 0.549 RNAsubopt: 0.579 Positive Predictive Value RSpredict(20): 0.830 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAsubopt: 0.646 Sensitivity CentroidAlifold(20): 0.752 RNAsubopt: 0.579 Positive Predictive Value CentroidAlifold(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.741 RNAsubopt: 0.646 Sensitivity Murlet(20): 0.594 RNAsubopt: 0.579 Positive Predictive Value Murlet(20): 0.929 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.840 RNAsubopt: 0.646 Sensitivity PPfold(20): 0.737 RNAsubopt: 0.579 Positive Predictive Value PPfold(20): 0.961 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.416 MCFold: 0.290 Sensitivity RNAsubopt: 0.393 MCFold: 0.320 Positive Predictive Value RNAsubopt: 0.451 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(seed)	15 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.798 RSpredict(seed): 0.514 Sensitivity Cylofold: 0.772 RSpredict(seed): 0.434 Positive Predictive Value Cylofold: 0.828 RSpredict(seed): 0.618 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.13392142882e-08	17 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.834 RSpredict(seed): 0.514 Sensitivity McQFold: 0.799 RSpredict(seed): 0.427 Positive Predictive Value McQFold: 0.872 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.36849473644e-08	16 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.768 RSpredict(seed): 0.518 Sensitivity Pknots: 0.748 RSpredict(seed): 0.437 Positive Predictive Value Pknots: 0.792 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	17 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RSpredict(seed): 0.514 Sensitivity CentroidAlifold(seed): 0.634 RSpredict(seed): 0.427 Positive Predictive Value CentroidAlifold(seed): 0.933 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.5677163434e-08	17 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.787 RSpredict(seed): 0.514 Sensitivity PknotsRG: 0.761 RSpredict(seed): 0.427 Positive Predictive Value PknotsRG: 0.817 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	17 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 RSpredict(seed): 0.514 Sensitivity PETfold_pre2.0(seed): 0.626 RSpredict(seed): 0.427 Positive Predictive Value PETfold_pre2.0(seed): 0.809 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.32677072069e-08	13 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 RSpredict(seed): 0.488 Sensitivity RNASampler(seed): 0.572 RSpredict(seed): 0.425 Positive Predictive Value RNASampler(seed): 0.755 RSpredict(seed): 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.53777893337e-08	17 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.671 RSpredict(seed): 0.514 Sensitivity IPknot: 0.590 RSpredict(seed): 0.427 Positive Predictive Value IPknot: 0.768 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.69132796717e-08	17 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 RSpredict(seed): 0.514 Sensitivity RNAalifold(seed): 0.522 RSpredict(seed): 0.427 Positive Predictive Value RNAalifold(seed): 0.833 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.59816551561e-08	17 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.695 RSpredict(seed): 0.514 Sensitivity CentroidFold: 0.608 RSpredict(seed): 0.427 Positive Predictive Value CentroidFold: 0.799 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.36130997681e-08	17 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RSpredict(seed): 0.514 Sensitivity CentroidHomfold‑LAST: 0.560 RSpredict(seed): 0.427 Positive Predictive Value CentroidHomfold‑LAST: 0.769 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	17 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.531 RSpredict(seed): 0.514 Sensitivity Vsfold5: 0.501 RSpredict(seed): 0.427 Positive Predictive Value Vsfold5: 0.569 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.9656853596e-05	13 Carnac(seed) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 RSpredict(seed): 0.488 Sensitivity Carnac(seed): 0.354 RSpredict(seed): 0.425 Positive Predictive Value Carnac(seed): 0.962 RSpredict(seed): 0.568 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.1413769576e-08	17 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.603 RSpredict(seed): 0.514 Sensitivity ProbKnot: 0.565 RSpredict(seed): 0.427 Positive Predictive Value ProbKnot: 0.649 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	17 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.635 RSpredict(seed): 0.514 Sensitivity RNASLOpt: 0.565 RSpredict(seed): 0.427 Positive Predictive Value RNASLOpt: 0.718 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	17 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.653 RSpredict(seed): 0.514 Sensitivity Contrafold: 0.598 RSpredict(seed): 0.427 Positive Predictive Value Contrafold: 0.719 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	17 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.603 RSpredict(seed): 0.514 Sensitivity HotKnots: 0.588 RSpredict(seed): 0.427 Positive Predictive Value HotKnots: 0.624 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	16 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.616 RSpredict(seed): 0.518 Sensitivity RDfolder: 0.531 RSpredict(seed): 0.437 Positive Predictive Value RDfolder: 0.721 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	17 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.572 RSpredict(seed): 0.514 Sensitivity Fold: 0.534 RSpredict(seed): 0.427 Positive Predictive Value Fold: 0.619 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	17 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.567 RSpredict(seed): 0.514 Sensitivity ContextFold: 0.506 RSpredict(seed): 0.427 Positive Predictive Value ContextFold: 0.642 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.84041289224e-08	17 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.603 RSpredict(seed): 0.514 Sensitivity MaxExpect: 0.560 RSpredict(seed): 0.427 Positive Predictive Value MaxExpect: 0.657 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	13 RSpredict(seed) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(seed): 0.488 Murlet(seed): 0.482 Sensitivity RSpredict(seed): 0.425 Murlet(seed): 0.319 Positive Predictive Value RSpredict(seed): 0.568 Murlet(seed): 0.734 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0107087209457	17 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.571 RSpredict(seed): 0.514 Sensitivity Sfold: 0.519 RSpredict(seed): 0.427 Positive Predictive Value Sfold: 0.636 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	17 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.552 RSpredict(seed): 0.514 Sensitivity UNAFold: 0.517 RSpredict(seed): 0.427 Positive Predictive Value UNAFold: 0.597 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	17 RSpredict(seed) vs Vsfold4 Matthews Correlation Coefficient RSpredict(seed): 0.514 Vsfold4: 0.488 Sensitivity RSpredict(seed): 0.427 Vsfold4: 0.445 Positive Predictive Value RSpredict(seed): 0.625 Vsfold4: 0.543 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.98606912064e-08	17 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.526 RSpredict(seed): 0.514 Sensitivity RNAshapes: 0.496 RSpredict(seed): 0.427 Positive Predictive Value RNAshapes: 0.565 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 0.000562659844894	17 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.566 RSpredict(seed): 0.514 Sensitivity RNAfold: 0.532 RSpredict(seed): 0.427 Positive Predictive Value RNAfold: 0.609 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.75835195567e-08	17 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.539 RSpredict(seed): 0.514 Sensitivity MXScarna(seed): 0.501 RSpredict(seed): 0.427 Positive Predictive Value MXScarna(seed): 0.586 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.81985890439e-08	17 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.538 RSpredict(seed): 0.514 Sensitivity RNAsubopt: 0.506 RSpredict(seed): 0.427 Positive Predictive Value RNAsubopt: 0.578 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08		- CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.527 RSpredict(seed): 0.514 Sensitivity CRWrnafold: 0.491 RSpredict(seed): 0.427 Positive Predictive Value CRWrnafold: 0.573 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.77733876858e-05	+ RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): 0.530 CMfinder(seed): 0.443 Sensitivity RSpredict(seed): 0.462 CMfinder(seed): 0.333 Positive Predictive Value RSpredict(seed): 0.615 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.21732636221e-09	+ RSpredict(seed) vs RNAwolf Matthews Correlation Coefficient RSpredict(seed): 0.514 RNAwolf: 0.487 Sensitivity RSpredict(seed): 0.427 RNAwolf: 0.461 Positive Predictive Value RSpredict(seed): 0.625 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	= Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.517 RSpredict(seed): 0.502 Sensitivity Afold: 0.480 RSpredict(seed): 0.428 Positive Predictive Value Afold: 0.564 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00599080906887	+ RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): 0.518 Alterna: 0.486 Sensitivity RSpredict(seed): 0.437 Alterna: 0.455 Positive Predictive Value RSpredict(seed): 0.623 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.57565412286e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.514 Mastr(seed): 0.341 Sensitivity RSpredict(seed): 0.427 Mastr(seed): 0.176 Positive Predictive Value RSpredict(seed): 0.625 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.36983135185e-08	? Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.705 RSpredict(seed): 0.602 Sensitivity Mastr(20): 0.565 RSpredict(seed): 0.435 Positive Predictive Value Mastr(20): 0.884 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs NanoFolder Matthews Correlation Coefficient RSpredict(seed): 0.535 NanoFolder: 0.489 Sensitivity RSpredict(seed): 0.481 NanoFolder: 0.544 Positive Predictive Value RSpredict(seed): 0.603 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.832 RSpredict(seed): 0.602 Sensitivity Carnac(20): 0.694 RSpredict(seed): 0.435 Positive Predictive Value Carnac(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RSpredict(seed): 0.437 Sensitivity Multilign(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value Multilign(seed): 0.625 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.865 RSpredict(seed): 0.602 Sensitivity Multilign(20): 0.750 RSpredict(seed): 0.435 Positive Predictive Value Multilign(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 RSpredict(seed): 0.602 Sensitivity TurboFold(20): 0.741 RSpredict(seed): 0.435 Positive Predictive Value TurboFold(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 RSpredict(seed): 0.602 Sensitivity RNAalifold(20): 0.704 RSpredict(seed): 0.435 Positive Predictive Value RNAalifold(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 RSpredict(seed): 0.602 Sensitivity RNASampler(20): 0.694 RSpredict(seed): 0.435 Positive Predictive Value RNASampler(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.756 RSpredict(seed): 0.602 Sensitivity CMfinder(20): 0.574 RSpredict(seed): 0.435 Positive Predictive Value CMfinder(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 RSpredict(seed): 0.602 Sensitivity PETfold_pre2.0(20): 0.750 RSpredict(seed): 0.435 Positive Predictive Value PETfold_pre2.0(20): 0.964 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RSpredict(seed): 0.437 Sensitivity PPfold(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 RSpredict(seed): 0.465 Sensitivity TurboFold(seed): 0.518 RSpredict(seed): 0.429 Positive Predictive Value TurboFold(seed): 0.702 RSpredict(seed): 0.514 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 RSpredict(seed): 0.602 Sensitivity MXScarna(20): 0.769 RSpredict(seed): 0.435 Positive Predictive Value MXScarna(20): 0.954 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.676 RSpredict(seed): 0.602 Sensitivity RSpredict(20): 0.546 RSpredict(seed): 0.435 Positive Predictive Value RSpredict(20): 0.843 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 RSpredict(seed): 0.602 Sensitivity CentroidAlifold(20): 0.741 RSpredict(seed): 0.435 Positive Predictive Value CentroidAlifold(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.780 RSpredict(seed): 0.602 Sensitivity Murlet(20): 0.611 RSpredict(seed): 0.435 Positive Predictive Value Murlet(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.833 RSpredict(seed): 0.602 Sensitivity PPfold(20): 0.722 RSpredict(seed): 0.435 Positive Predictive Value PPfold(20): 0.963 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): 0.522 MCFold: 0.358 Sensitivity RSpredict(seed): 0.441 MCFold: 0.409 Positive Predictive Value RSpredict(seed): 0.627 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.12262428713e-08
CRWrnafold	45 Cylofold vs CRWrnafold Matthews Correlation Coefficient Cylofold: 0.764 CRWrnafold: 0.468 Sensitivity Cylofold: 0.742 CRWrnafold: 0.422 Positive Predictive Value Cylofold: 0.791 CRWrnafold: 0.530 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.594 CRWrnafold: 0.374 Sensitivity McQFold: 0.583 CRWrnafold: 0.351 Positive Predictive Value McQFold: 0.611 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: 0.697 CRWrnafold: 0.458 Sensitivity Pknots: 0.668 CRWrnafold: 0.415 Positive Predictive Value Pknots: 0.733 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 CRWrnafold: 0.527 Sensitivity CentroidAlifold(seed): 0.634 CRWrnafold: 0.491 Positive Predictive Value CentroidAlifold(seed): 0.933 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.39162260866e-08	53 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.531 CRWrnafold: 0.374 Sensitivity PknotsRG: 0.525 CRWrnafold: 0.351 Positive Predictive Value PknotsRG: 0.544 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 CRWrnafold: 0.564 Sensitivity PETfold_pre2.0(seed): 0.649 CRWrnafold: 0.526 Positive Predictive Value PETfold_pre2.0(seed): 0.824 CRWrnafold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.8150742666e-08	13 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.655 CRWrnafold: 0.446 Sensitivity RNASampler(seed): 0.572 CRWrnafold: 0.425 Positive Predictive Value RNASampler(seed): 0.755 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.20167918023e-08	53 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.489 CRWrnafold: 0.374 Sensitivity IPknot: 0.435 CRWrnafold: 0.351 Positive Predictive Value IPknot: 0.556 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.657 CRWrnafold: 0.527 Sensitivity RNAalifold(seed): 0.522 CRWrnafold: 0.491 Positive Predictive Value RNAalifold(seed): 0.833 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.89649746203e-08	53 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.482 CRWrnafold: 0.374 Sensitivity CentroidFold: 0.430 CRWrnafold: 0.351 Positive Predictive Value CentroidFold: 0.548 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 CRWrnafold: 0.374 Sensitivity CentroidHomfold‑LAST: 0.407 CRWrnafold: 0.351 Positive Predictive Value CentroidHomfold‑LAST: 0.592 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs CRWrnafold Matthews Correlation Coefficient Vsfold5: 0.534 CRWrnafold: 0.374 Sensitivity Vsfold5: 0.505 CRWrnafold: 0.351 Positive Predictive Value Vsfold5: 0.572 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs CRWrnafold Matthews Correlation Coefficient Carnac(seed): 0.582 CRWrnafold: 0.446 Sensitivity Carnac(seed): 0.354 CRWrnafold: 0.425 Positive Predictive Value Carnac(seed): 0.962 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	53 ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.459 CRWrnafold: 0.374 Sensitivity ProbKnot: 0.440 CRWrnafold: 0.351 Positive Predictive Value ProbKnot: 0.487 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs CRWrnafold Matthews Correlation Coefficient RNASLOpt: 0.458 CRWrnafold: 0.374 Sensitivity RNASLOpt: 0.419 CRWrnafold: 0.351 Positive Predictive Value RNASLOpt: 0.508 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.458 CRWrnafold: 0.374 Sensitivity Contrafold: 0.435 CRWrnafold: 0.351 Positive Predictive Value Contrafold: 0.491 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.453 CRWrnafold: 0.374 Sensitivity HotKnots: 0.445 CRWrnafold: 0.351 Positive Predictive Value HotKnots: 0.469 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: 0.508 CRWrnafold: 0.458 Sensitivity RDfolder: 0.432 CRWrnafold: 0.415 Positive Predictive Value RDfolder: 0.609 CRWrnafold: 0.518 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.453 CRWrnafold: 0.374 Sensitivity Fold: 0.431 CRWrnafold: 0.351 Positive Predictive Value Fold: 0.485 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.447 CRWrnafold: 0.374 Sensitivity ContextFold: 0.407 CRWrnafold: 0.351 Positive Predictive Value ContextFold: 0.499 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.440 CRWrnafold: 0.374 Sensitivity MaxExpect: 0.414 CRWrnafold: 0.351 Positive Predictive Value MaxExpect: 0.476 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.482 CRWrnafold: 0.446 Sensitivity Murlet(seed): 0.319 CRWrnafold: 0.425 Positive Predictive Value Murlet(seed): 0.734 CRWrnafold: 0.476 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.18018834988e-08	53 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.425 CRWrnafold: 0.374 Sensitivity Sfold: 0.377 CRWrnafold: 0.351 Positive Predictive Value Sfold: 0.488 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.412 CRWrnafold: 0.374 Sensitivity UNAFold: 0.390 CRWrnafold: 0.351 Positive Predictive Value UNAFold: 0.443 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold4 vs CRWrnafold Matthews Correlation Coefficient Vsfold4: 0.423 CRWrnafold: 0.374 Sensitivity Vsfold4: 0.380 CRWrnafold: 0.351 Positive Predictive Value Vsfold4: 0.479 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.416 CRWrnafold: 0.374 Sensitivity RNAshapes: 0.395 CRWrnafold: 0.351 Positive Predictive Value RNAshapes: 0.448 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.409 CRWrnafold: 0.374 Sensitivity RNAfold: 0.390 CRWrnafold: 0.351 Positive Predictive Value RNAfold: 0.438 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.539 CRWrnafold: 0.527 Sensitivity MXScarna(seed): 0.501 CRWrnafold: 0.491 Positive Predictive Value MXScarna(seed): 0.586 CRWrnafold: 0.573 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.95320262584e-05	53 RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.394 CRWrnafold: 0.374 Sensitivity RNAsubopt: 0.378 CRWrnafold: 0.351 Positive Predictive Value RNAsubopt: 0.419 CRWrnafold: 0.407 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.527 RSpredict(seed): 0.514 Sensitivity CRWrnafold: 0.491 RSpredict(seed): 0.427 Positive Predictive Value CRWrnafold: 0.573 RSpredict(seed): 0.625 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.77733876858e-05		= CMfinder(seed) vs CRWrnafold Matthews Correlation Coefficient CMfinder(seed): 0.443 CRWrnafold: 0.434 Sensitivity CMfinder(seed): 0.333 CRWrnafold: 0.414 Positive Predictive Value CMfinder(seed): 0.597 CRWrnafold: 0.464 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00278379982001	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.374 RNAwolf: 0.362 Sensitivity CRWrnafold: 0.351 RNAwolf: 0.353 Positive Predictive Value CRWrnafold: 0.407 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 2.58638884049e-05	+ CRWrnafold vs Afold Matthews Correlation Coefficient CRWrnafold: 0.350 Afold: 0.316 Sensitivity CRWrnafold: 0.329 Afold: 0.305 Positive Predictive Value CRWrnafold: 0.383 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.458 Alterna: 0.393 Sensitivity CRWrnafold: 0.415 Alterna: 0.365 Positive Predictive Value CRWrnafold: 0.518 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.527 Mastr(seed): 0.341 Sensitivity CRWrnafold: 0.491 Mastr(seed): 0.176 Positive Predictive Value CRWrnafold: 0.573 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.18141491686e-08	? CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.776 Mastr(20): 0.561 Sensitivity CRWrnafold: 0.684 Mastr(20): 0.459 Positive Predictive Value CRWrnafold: 0.883 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.550 NanoFolder: 0.304 Sensitivity CRWrnafold: 0.512 NanoFolder: 0.343 Positive Predictive Value CRWrnafold: 0.599 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs CRWrnafold Matthews Correlation Coefficient Carnac(20): 0.821 CRWrnafold: 0.776 Sensitivity Carnac(20): 0.684 CRWrnafold: 0.684 Positive Predictive Value Carnac(20): 0.989 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.575 CRWrnafold: 0.400 Sensitivity Multilign(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value Multilign(seed): 0.625 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.862 CRWrnafold: 0.776 Sensitivity Multilign(20): 0.752 CRWrnafold: 0.684 Positive Predictive Value Multilign(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.857 CRWrnafold: 0.776 Sensitivity TurboFold(20): 0.744 CRWrnafold: 0.684 Positive Predictive Value TurboFold(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.844 CRWrnafold: 0.776 Sensitivity RNAalifold(20): 0.722 CRWrnafold: 0.684 Positive Predictive Value RNAalifold(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.840 CRWrnafold: 0.776 Sensitivity RNASampler(20): 0.714 CRWrnafold: 0.684 Positive Predictive Value RNASampler(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.779 CRWrnafold: 0.776 Sensitivity CMfinder(20): 0.617 CRWrnafold: 0.684 Positive Predictive Value CMfinder(20): 0.988 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CRWrnafold: 0.776 Sensitivity PETfold_pre2.0(20): 0.759 CRWrnafold: 0.684 Positive Predictive Value PETfold_pre2.0(20): 0.962 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.666 CRWrnafold: 0.400 Sensitivity PPfold(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value PPfold(seed): 0.833 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.600 CRWrnafold: 0.418 Sensitivity TurboFold(seed): 0.518 CRWrnafold: 0.405 Positive Predictive Value TurboFold(seed): 0.702 CRWrnafold: 0.442 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.837 CRWrnafold: 0.776 Sensitivity MXScarna(20): 0.752 CRWrnafold: 0.684 Positive Predictive Value MXScarna(20): 0.935 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.776 RSpredict(20): 0.672 Sensitivity CRWrnafold: 0.684 RSpredict(20): 0.549 Positive Predictive Value CRWrnafold: 0.883 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CRWrnafold: 0.776 Sensitivity CentroidAlifold(20): 0.752 CRWrnafold: 0.684 Positive Predictive Value CentroidAlifold(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Murlet(20) Matthews Correlation Coefficient CRWrnafold: 0.776 Murlet(20): 0.741 Sensitivity CRWrnafold: 0.684 Murlet(20): 0.594 Positive Predictive Value CRWrnafold: 0.883 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.840 CRWrnafold: 0.776 Sensitivity PPfold(20): 0.737 CRWrnafold: 0.684 Positive Predictive Value PPfold(20): 0.961 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.411 MCFold: 0.290 Sensitivity CRWrnafold: 0.380 MCFold: 0.320 Positive Predictive Value CRWrnafold: 0.456 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(seed)	9 Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: 0.797 CMfinder(seed): 0.439 Sensitivity Cylofold: 0.801 CMfinder(seed): 0.348 Positive Predictive Value Cylofold: 0.797 CMfinder(seed): 0.563 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.842 CMfinder(seed): 0.443 Sensitivity McQFold: 0.827 CMfinder(seed): 0.333 Positive Predictive Value McQFold: 0.858 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.06761512825e-08	10 Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: 0.767 CMfinder(seed): 0.459 Sensitivity Pknots: 0.787 CMfinder(seed): 0.365 Positive Predictive Value Pknots: 0.752 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.32883086441e-08	11 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.718 CMfinder(seed): 0.443 Sensitivity CentroidAlifold(seed): 0.582 CMfinder(seed): 0.333 Positive Predictive Value CentroidAlifold(seed): 0.890 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.67568292565e-09	11 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.793 CMfinder(seed): 0.443 Sensitivity PknotsRG: 0.791 CMfinder(seed): 0.333 Positive Predictive Value PknotsRG: 0.798 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	11 PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.666 CMfinder(seed): 0.443 Sensitivity PETfold_pre2.0(seed): 0.574 CMfinder(seed): 0.333 Positive Predictive Value PETfold_pre2.0(seed): 0.777 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.16590079822e-09	11 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 CMfinder(seed): 0.443 Sensitivity RNASampler(seed): 0.574 CMfinder(seed): 0.333 Positive Predictive Value RNASampler(seed): 0.753 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 5.89166989468e-09	11 IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.564 CMfinder(seed): 0.443 Sensitivity IPknot: 0.502 CMfinder(seed): 0.333 Positive Predictive Value IPknot: 0.641 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.89649746203e-08	11 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.615 CMfinder(seed): 0.443 Sensitivity RNAalifold(seed): 0.466 CMfinder(seed): 0.333 Positive Predictive Value RNAalifold(seed): 0.817 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.93000771886e-09	11 CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.640 CMfinder(seed): 0.443 Sensitivity CentroidFold: 0.562 CMfinder(seed): 0.333 Positive Predictive Value CentroidFold: 0.733 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.74172190343e-08	11 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.577 CMfinder(seed): 0.443 Sensitivity CentroidHomfold‑LAST: 0.510 CMfinder(seed): 0.333 Positive Predictive Value CentroidHomfold‑LAST: 0.658 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.12262428713e-08	11 Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: 0.504 CMfinder(seed): 0.443 Sensitivity Vsfold5: 0.482 CMfinder(seed): 0.333 Positive Predictive Value Vsfold5: 0.533 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.34632741202e-08	11 Carnac(seed) vs CMfinder(seed) Matthews Correlation Coefficient Carnac(seed): 0.555 CMfinder(seed): 0.443 Sensitivity Carnac(seed): 0.325 CMfinder(seed): 0.333 Positive Predictive Value Carnac(seed): 0.953 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	11 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.513 CMfinder(seed): 0.443 Sensitivity ProbKnot: 0.494 CMfinder(seed): 0.333 Positive Predictive Value ProbKnot: 0.539 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.12160100812e-08	11 RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.580 CMfinder(seed): 0.443 Sensitivity RNASLOpt: 0.522 CMfinder(seed): 0.333 Positive Predictive Value RNASLOpt: 0.650 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	11 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.584 CMfinder(seed): 0.443 Sensitivity Contrafold: 0.546 CMfinder(seed): 0.333 Positive Predictive Value Contrafold: 0.630 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 8.26710183075e-09	11 HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: 0.456 CMfinder(seed): 0.443 Sensitivity HotKnots: 0.458 CMfinder(seed): 0.333 Positive Predictive Value HotKnots: 0.462 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.483506955631	10 RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: 0.538 CMfinder(seed): 0.459 Sensitivity RDfolder: 0.472 CMfinder(seed): 0.365 Positive Predictive Value RDfolder: 0.620 CMfinder(seed): 0.585 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.53777893337e-08	11 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.476 CMfinder(seed): 0.443 Sensitivity Fold: 0.454 CMfinder(seed): 0.333 Positive Predictive Value Fold: 0.507 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 3.04893053302e-05	11 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.490 CMfinder(seed): 0.443 Sensitivity ContextFold: 0.438 CMfinder(seed): 0.333 Positive Predictive Value ContextFold: 0.556 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.38889354863e-08	11 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.509 CMfinder(seed): 0.443 Sensitivity MaxExpect: 0.486 CMfinder(seed): 0.333 Positive Predictive Value MaxExpect: 0.540 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.65471383806e-09	11 Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.488 CMfinder(seed): 0.443 Sensitivity Murlet(seed): 0.321 CMfinder(seed): 0.333 Positive Predictive Value Murlet(seed): 0.748 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.85230291748e-05	11 Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.460 CMfinder(seed): 0.443 Sensitivity Sfold: 0.434 CMfinder(seed): 0.333 Positive Predictive Value Sfold: 0.495 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000237629262871	11 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.472 CMfinder(seed): 0.443 Sensitivity UNAFold: 0.454 CMfinder(seed): 0.333 Positive Predictive Value UNAFold: 0.498 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00021235435813	11 Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: 0.448 CMfinder(seed): 0.443 Sensitivity Vsfold4: 0.418 CMfinder(seed): 0.333 Positive Predictive Value Vsfold4: 0.488 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.216974056439	11 CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): 0.443 RNAshapes: 0.433 Sensitivity CMfinder(seed): 0.333 RNAshapes: 0.422 Positive Predictive Value CMfinder(seed): 0.597 RNAshapes: 0.453 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000492532411318	11 RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.465 CMfinder(seed): 0.443 Sensitivity RNAfold: 0.454 CMfinder(seed): 0.333 Positive Predictive Value RNAfold: 0.485 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0217436526037	11 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): 0.443 MXScarna(seed): 0.419 Sensitivity CMfinder(seed): 0.333 MXScarna(seed): 0.402 Positive Predictive Value CMfinder(seed): 0.597 MXScarna(seed): 0.446 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00123904660847	11 RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.451 CMfinder(seed): 0.443 Sensitivity RNAsubopt: 0.438 CMfinder(seed): 0.333 Positive Predictive Value RNAsubopt: 0.472 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.0230361572455	11 RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): 0.530 CMfinder(seed): 0.443 Sensitivity RSpredict(seed): 0.462 CMfinder(seed): 0.333 Positive Predictive Value RSpredict(seed): 0.615 CMfinder(seed): 0.597 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.21732636221e-09	11 CMfinder(seed) vs CRWrnafold Matthews Correlation Coefficient CMfinder(seed): 0.443 CRWrnafold: 0.434 Sensitivity CMfinder(seed): 0.333 CRWrnafold: 0.414 Positive Predictive Value CMfinder(seed): 0.597 CRWrnafold: 0.464 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.00278379982001		+ CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.443 RNAwolf: 0.430 Sensitivity CMfinder(seed): 0.333 RNAwolf: 0.402 Positive Predictive Value CMfinder(seed): 0.597 RNAwolf: 0.469 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000138300613835	? Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.438 CMfinder(seed): 0.421 Sensitivity Afold: 0.415 CMfinder(seed): 0.318 Positive Predictive Value Afold: 0.471 CMfinder(seed): 0.566 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.459 Alterna: 0.360 Sensitivity CMfinder(seed): 0.365 Alterna: 0.345 Positive Predictive Value CMfinder(seed): 0.585 Alterna: 0.386 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.95556389719e-09	+ CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.443 Mastr(seed): 0.345 Sensitivity CMfinder(seed): 0.333 Mastr(seed): 0.201 Positive Predictive Value CMfinder(seed): 0.597 Mastr(seed): 0.602 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61358433984e-08	? Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: 0.585 CMfinder(seed): 0.507 Sensitivity NanoFolder: 0.654 CMfinder(seed): 0.346 Positive Predictive Value NanoFolder: 0.531 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 3 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 CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.562 CMfinder(seed): 0.553 Sensitivity Multilign(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value Multilign(seed): 0.604 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 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	? 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	? 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	? 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	? 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): 0.662 CMfinder(seed): 0.553 Sensitivity PPfold(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value PPfold(seed): 0.833 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(seed): 0.589 TurboFold(seed): 0.569 Sensitivity CMfinder(seed): 0.455 TurboFold(seed): 0.508 Positive Predictive Value CMfinder(seed): 0.769 TurboFold(seed): 0.644 Number of pairs reference - predicted secondary structure: 7 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	? 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	? 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	? 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	? 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	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.499 MCFold: 0.352 Sensitivity CMfinder(seed): 0.385 MCFold: 0.408 Positive Predictive Value CMfinder(seed): 0.657 MCFold: 0.315 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
RNAwolf	45 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.764 RNAwolf: 0.396 Sensitivity Cylofold: 0.742 RNAwolf: 0.378 Positive Predictive Value Cylofold: 0.791 RNAwolf: 0.429 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.594 RNAwolf: 0.362 Sensitivity McQFold: 0.583 RNAwolf: 0.353 Positive Predictive Value McQFold: 0.611 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.697 RNAwolf: 0.401 Sensitivity Pknots: 0.668 RNAwolf: 0.381 Positive Predictive Value Pknots: 0.733 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 RNAwolf: 0.487 Sensitivity CentroidAlifold(seed): 0.634 RNAwolf: 0.461 Positive Predictive Value CentroidAlifold(seed): 0.933 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	53 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.531 RNAwolf: 0.362 Sensitivity PknotsRG: 0.525 RNAwolf: 0.353 Positive Predictive Value PknotsRG: 0.544 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.729 RNAwolf: 0.507 Sensitivity PETfold_pre2.0(seed): 0.649 RNAwolf: 0.485 Positive Predictive Value PETfold_pre2.0(seed): 0.824 RNAwolf: 0.538 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.73174208038e-08	13 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.655 RNAwolf: 0.438 Sensitivity RNASampler(seed): 0.572 RNAwolf: 0.407 Positive Predictive Value RNASampler(seed): 0.755 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	53 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.489 RNAwolf: 0.362 Sensitivity IPknot: 0.435 RNAwolf: 0.353 Positive Predictive Value IPknot: 0.556 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNAwolf: 0.487 Sensitivity RNAalifold(seed): 0.522 RNAwolf: 0.461 Positive Predictive Value RNAalifold(seed): 0.833 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	53 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.482 RNAwolf: 0.362 Sensitivity CentroidFold: 0.430 RNAwolf: 0.353 Positive Predictive Value CentroidFold: 0.548 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.488 RNAwolf: 0.362 Sensitivity CentroidHomfold‑LAST: 0.407 RNAwolf: 0.353 Positive Predictive Value CentroidHomfold‑LAST: 0.592 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold5 vs RNAwolf Matthews Correlation Coefficient Vsfold5: 0.534 RNAwolf: 0.362 Sensitivity Vsfold5: 0.505 RNAwolf: 0.353 Positive Predictive Value Vsfold5: 0.572 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs RNAwolf Matthews Correlation Coefficient Carnac(seed): 0.582 RNAwolf: 0.438 Sensitivity Carnac(seed): 0.354 RNAwolf: 0.407 Positive Predictive Value Carnac(seed): 0.962 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	53 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.459 RNAwolf: 0.362 Sensitivity ProbKnot: 0.440 RNAwolf: 0.353 Positive Predictive Value ProbKnot: 0.487 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.458 RNAwolf: 0.362 Sensitivity RNASLOpt: 0.419 RNAwolf: 0.353 Positive Predictive Value RNASLOpt: 0.508 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.458 RNAwolf: 0.362 Sensitivity Contrafold: 0.435 RNAwolf: 0.353 Positive Predictive Value Contrafold: 0.491 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.453 RNAwolf: 0.362 Sensitivity HotKnots: 0.445 RNAwolf: 0.353 Positive Predictive Value HotKnots: 0.469 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: 0.508 RNAwolf: 0.401 Sensitivity RDfolder: 0.432 RNAwolf: 0.381 Positive Predictive Value RDfolder: 0.609 RNAwolf: 0.434 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.453 RNAwolf: 0.362 Sensitivity Fold: 0.431 RNAwolf: 0.353 Positive Predictive Value Fold: 0.485 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.447 RNAwolf: 0.362 Sensitivity ContextFold: 0.407 RNAwolf: 0.353 Positive Predictive Value ContextFold: 0.499 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.440 RNAwolf: 0.362 Sensitivity MaxExpect: 0.414 RNAwolf: 0.353 Positive Predictive Value MaxExpect: 0.476 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.482 RNAwolf: 0.438 Sensitivity Murlet(seed): 0.319 RNAwolf: 0.407 Positive Predictive Value Murlet(seed): 0.734 RNAwolf: 0.479 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.33801301209e-08	53 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.425 RNAwolf: 0.362 Sensitivity Sfold: 0.377 RNAwolf: 0.353 Positive Predictive Value Sfold: 0.488 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.412 RNAwolf: 0.362 Sensitivity UNAFold: 0.390 RNAwolf: 0.353 Positive Predictive Value UNAFold: 0.443 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.423 RNAwolf: 0.362 Sensitivity Vsfold4: 0.380 RNAwolf: 0.353 Positive Predictive Value Vsfold4: 0.479 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.416 RNAwolf: 0.362 Sensitivity RNAshapes: 0.395 RNAwolf: 0.353 Positive Predictive Value RNAshapes: 0.448 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	53 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.409 RNAwolf: 0.362 Sensitivity RNAfold: 0.390 RNAwolf: 0.353 Positive Predictive Value RNAfold: 0.438 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.539 RNAwolf: 0.487 Sensitivity MXScarna(seed): 0.501 RNAwolf: 0.461 Positive Predictive Value MXScarna(seed): 0.586 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 5.23753225208e-08	53 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.394 RNAwolf: 0.362 Sensitivity RNAsubopt: 0.378 RNAwolf: 0.353 Positive Predictive Value RNAsubopt: 0.419 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RSpredict(seed) vs RNAwolf Matthews Correlation Coefficient RSpredict(seed): 0.514 RNAwolf: 0.487 Sensitivity RSpredict(seed): 0.427 RNAwolf: 0.461 Positive Predictive Value RSpredict(seed): 0.625 RNAwolf: 0.523 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	53 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.374 RNAwolf: 0.362 Sensitivity CRWrnafold: 0.351 RNAwolf: 0.353 Positive Predictive Value CRWrnafold: 0.407 RNAwolf: 0.380 Number of pairs reference - predicted secondary structure: 53 Wilcoxon single-rank test P-value: 2.58638884049e-05	11 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.443 RNAwolf: 0.430 Sensitivity CMfinder(seed): 0.333 RNAwolf: 0.402 Positive Predictive Value CMfinder(seed): 0.597 RNAwolf: 0.469 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.000138300613835		+ RNAwolf vs Afold Matthews Correlation Coefficient RNAwolf: 0.344 Afold: 0.316 Sensitivity RNAwolf: 0.333 Afold: 0.305 Positive Predictive Value RNAwolf: 0.367 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23907313115e-07	+ RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.401 Alterna: 0.393 Sensitivity RNAwolf: 0.381 Alterna: 0.365 Positive Predictive Value RNAwolf: 0.434 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 1.95308298399e-06	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.487 Mastr(seed): 0.341 Sensitivity RNAwolf: 0.461 Mastr(seed): 0.176 Positive Predictive Value RNAwolf: 0.523 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	? RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.661 Mastr(20): 0.561 Sensitivity RNAwolf: 0.647 Mastr(20): 0.459 Positive Predictive Value RNAwolf: 0.683 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.571 NanoFolder: 0.304 Sensitivity RNAwolf: 0.560 NanoFolder: 0.343 Positive Predictive Value RNAwolf: 0.589 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.821 RNAwolf: 0.661 Sensitivity Carnac(20): 0.684 RNAwolf: 0.647 Positive Predictive Value Carnac(20): 0.989 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.575 RNAwolf: 0.455 Sensitivity Multilign(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value Multilign(seed): 0.625 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.862 RNAwolf: 0.661 Sensitivity Multilign(20): 0.752 RNAwolf: 0.647 Positive Predictive Value Multilign(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.857 RNAwolf: 0.661 Sensitivity TurboFold(20): 0.744 RNAwolf: 0.647 Positive Predictive Value TurboFold(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAwolf: 0.661 Sensitivity RNAalifold(20): 0.722 RNAwolf: 0.647 Positive Predictive Value RNAalifold(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.840 RNAwolf: 0.661 Sensitivity RNASampler(20): 0.714 RNAwolf: 0.647 Positive Predictive Value RNASampler(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.779 RNAwolf: 0.661 Sensitivity CMfinder(20): 0.617 RNAwolf: 0.647 Positive Predictive Value CMfinder(20): 0.988 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAwolf: 0.661 Sensitivity PETfold_pre2.0(20): 0.759 RNAwolf: 0.647 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.666 RNAwolf: 0.455 Sensitivity PPfold(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value PPfold(seed): 0.833 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAwolf: 0.444 Sensitivity TurboFold(seed): 0.518 RNAwolf: 0.423 Positive Predictive Value TurboFold(seed): 0.702 RNAwolf: 0.477 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.837 RNAwolf: 0.661 Sensitivity MXScarna(20): 0.752 RNAwolf: 0.647 Positive Predictive Value MXScarna(20): 0.935 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.672 RNAwolf: 0.661 Sensitivity RSpredict(20): 0.549 RNAwolf: 0.647 Positive Predictive Value RSpredict(20): 0.830 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAwolf: 0.661 Sensitivity CentroidAlifold(20): 0.752 RNAwolf: 0.647 Positive Predictive Value CentroidAlifold(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.741 RNAwolf: 0.661 Sensitivity Murlet(20): 0.594 RNAwolf: 0.647 Positive Predictive Value Murlet(20): 0.929 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.840 RNAwolf: 0.661 Sensitivity PPfold(20): 0.737 RNAwolf: 0.647 Positive Predictive Value PPfold(20): 0.961 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.376 MCFold: 0.290 Sensitivity RNAwolf: 0.364 MCFold: 0.320 Positive Predictive Value RNAwolf: 0.400 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08
Afold	28 Cylofold vs Afold Matthews Correlation Coefficient Cylofold: 0.735 Afold: 0.318 Sensitivity Cylofold: 0.722 Afold: 0.304 Positive Predictive Value Cylofold: 0.755 Afold: 0.348 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	33 McQFold vs Afold Matthews Correlation Coefficient McQFold: 0.619 Afold: 0.316 Sensitivity McQFold: 0.610 Afold: 0.305 Positive Predictive Value McQFold: 0.634 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Pknots vs Afold Matthews Correlation Coefficient Pknots: 0.653 Afold: 0.309 Sensitivity Pknots: 0.630 Afold: 0.296 Positive Predictive Value Pknots: 0.684 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	13 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.748 Afold: 0.517 Sensitivity CentroidAlifold(seed): 0.615 Afold: 0.480 Positive Predictive Value CentroidAlifold(seed): 0.912 Afold: 0.564 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.1413769576e-08	33 PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.538 Afold: 0.316 Sensitivity PknotsRG: 0.533 Afold: 0.305 Positive Predictive Value PknotsRG: 0.551 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.719 Afold: 0.481 Sensitivity PETfold_pre2.0(seed): 0.640 Afold: 0.451 Positive Predictive Value PETfold_pre2.0(seed): 0.812 Afold: 0.521 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.86595104665e-08	11 RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.642 Afold: 0.454 Sensitivity RNASampler(seed): 0.561 Afold: 0.427 Positive Predictive Value RNASampler(seed): 0.740 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.06761512825e-08	33 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.468 Afold: 0.316 Sensitivity IPknot: 0.430 Afold: 0.305 Positive Predictive Value IPknot: 0.518 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNAalifold(seed) vs Afold Matthews Correlation Coefficient RNAalifold(seed): 0.638 Afold: 0.517 Sensitivity RNAalifold(seed): 0.503 Afold: 0.480 Positive Predictive Value RNAalifold(seed): 0.814 Afold: 0.564 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.10198558684e-08	33 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.466 Afold: 0.316 Sensitivity CentroidFold: 0.423 Afold: 0.305 Positive Predictive Value CentroidFold: 0.521 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.450 Afold: 0.316 Sensitivity CentroidHomfold‑LAST: 0.388 Afold: 0.305 Positive Predictive Value CentroidHomfold‑LAST: 0.531 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Vsfold5 vs Afold Matthews Correlation Coefficient Vsfold5: 0.531 Afold: 0.316 Sensitivity Vsfold5: 0.504 Afold: 0.305 Positive Predictive Value Vsfold5: 0.567 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 Carnac(seed) vs Afold Matthews Correlation Coefficient Carnac(seed): 0.547 Afold: 0.454 Sensitivity Carnac(seed): 0.316 Afold: 0.427 Positive Predictive Value Carnac(seed): 0.952 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.10032755566e-08	33 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.407 Afold: 0.316 Sensitivity ProbKnot: 0.393 Afold: 0.305 Positive Predictive Value ProbKnot: 0.431 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNASLOpt vs Afold Matthews Correlation Coefficient RNASLOpt: 0.445 Afold: 0.316 Sensitivity RNASLOpt: 0.415 Afold: 0.305 Positive Predictive Value RNASLOpt: 0.487 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.447 Afold: 0.316 Sensitivity Contrafold: 0.430 Afold: 0.305 Positive Predictive Value Contrafold: 0.474 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.390 Afold: 0.316 Sensitivity HotKnots: 0.385 Afold: 0.305 Positive Predictive Value HotKnots: 0.405 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RDfolder vs Afold Matthews Correlation Coefficient RDfolder: 0.480 Afold: 0.309 Sensitivity RDfolder: 0.418 Afold: 0.296 Positive Predictive Value RDfolder: 0.561 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	33 Fold vs Afold Matthews Correlation Coefficient Fold: 0.417 Afold: 0.316 Sensitivity Fold: 0.403 Afold: 0.305 Positive Predictive Value Fold: 0.441 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.391 Afold: 0.316 Sensitivity ContextFold: 0.358 Afold: 0.305 Positive Predictive Value ContextFold: 0.436 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.401 Afold: 0.316 Sensitivity MaxExpect: 0.383 Afold: 0.305 Positive Predictive Value MaxExpect: 0.429 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 Murlet(seed) vs Afold Matthews Correlation Coefficient Murlet(seed): 0.481 Afold: 0.454 Sensitivity Murlet(seed): 0.320 Afold: 0.427 Positive Predictive Value Murlet(seed): 0.730 Afold: 0.491 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.31873167448e-06	33 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.379 Afold: 0.316 Sensitivity Sfold: 0.347 Afold: 0.305 Positive Predictive Value Sfold: 0.424 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.391 Afold: 0.316 Sensitivity UNAFold: 0.375 Afold: 0.305 Positive Predictive Value UNAFold: 0.418 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Vsfold4 vs Afold Matthews Correlation Coefficient Vsfold4: 0.391 Afold: 0.316 Sensitivity Vsfold4: 0.360 Afold: 0.305 Positive Predictive Value Vsfold4: 0.435 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.398 Afold: 0.316 Sensitivity RNAshapes: 0.381 Afold: 0.305 Positive Predictive Value RNAshapes: 0.424 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	33 RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.378 Afold: 0.316 Sensitivity RNAfold: 0.364 Afold: 0.305 Positive Predictive Value RNAfold: 0.403 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Afold vs MXScarna(seed) Matthews Correlation Coefficient Afold: 0.517 MXScarna(seed): 0.488 Sensitivity Afold: 0.480 MXScarna(seed): 0.464 Positive Predictive Value Afold: 0.564 MXScarna(seed): 0.522 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.70887622364e-08	33 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.376 Afold: 0.316 Sensitivity RNAsubopt: 0.364 Afold: 0.305 Positive Predictive Value RNAsubopt: 0.399 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.517 RSpredict(seed): 0.502 Sensitivity Afold: 0.480 RSpredict(seed): 0.428 Positive Predictive Value Afold: 0.564 RSpredict(seed): 0.596 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.00599080906887	33 CRWrnafold vs Afold Matthews Correlation Coefficient CRWrnafold: 0.350 Afold: 0.316 Sensitivity CRWrnafold: 0.329 Afold: 0.305 Positive Predictive Value CRWrnafold: 0.383 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.438 CMfinder(seed): 0.421 Sensitivity Afold: 0.415 CMfinder(seed): 0.318 Positive Predictive Value Afold: 0.471 CMfinder(seed): 0.566 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	33 RNAwolf vs Afold Matthews Correlation Coefficient RNAwolf: 0.344 Afold: 0.316 Sensitivity RNAwolf: 0.333 Afold: 0.305 Positive Predictive Value RNAwolf: 0.367 Afold: 0.339 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23907313115e-07		- Alterna vs Afold Matthews Correlation Coefficient Alterna: 0.340 Afold: 0.309 Sensitivity Alterna: 0.326 Afold: 0.296 Positive Predictive Value Alterna: 0.369 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.517 Mastr(seed): 0.331 Sensitivity Afold: 0.480 Mastr(seed): 0.174 Positive Predictive Value Afold: 0.564 Mastr(seed): 0.639 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.84361416392e-08	? Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.574 Afold: 0.569 Sensitivity Mastr(20): 0.500 Afold: 0.500 Positive Predictive Value Mastr(20): 0.667 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.463 NanoFolder: 0.346 Sensitivity Afold: 0.424 NanoFolder: 0.400 Positive Predictive Value Afold: 0.515 NanoFolder: 0.311 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.842 Afold: 0.569 Sensitivity Carnac(20): 0.724 Afold: 0.500 Positive Predictive Value Carnac(20): 0.982 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.571 Afold: 0.480 Sensitivity Multilign(seed): 0.533 Afold: 0.443 Positive Predictive Value Multilign(seed): 0.619 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.865 Afold: 0.569 Sensitivity Multilign(20): 0.763 Afold: 0.500 Positive Predictive Value Multilign(20): 0.983 Afold: 0.655 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): 0.857 Afold: 0.569 Sensitivity TurboFold(20): 0.750 Afold: 0.500 Positive Predictive Value TurboFold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.857 Afold: 0.569 Sensitivity RNAalifold(20): 0.750 Afold: 0.500 Positive Predictive Value RNAalifold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.865 Afold: 0.569 Sensitivity RNASampler(20): 0.763 Afold: 0.500 Positive Predictive Value RNASampler(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Afold Matthews Correlation Coefficient CMfinder(20): 0.850 Afold: 0.569 Sensitivity CMfinder(20): 0.737 Afold: 0.500 Positive Predictive Value CMfinder(20): 0.982 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.873 Afold: 0.569 Sensitivity PETfold_pre2.0(20): 0.776 Afold: 0.500 Positive Predictive Value PETfold_pre2.0(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.664 Afold: 0.480 Sensitivity PPfold(seed): 0.533 Afold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.588 Afold: 0.469 Sensitivity TurboFold(seed): 0.513 Afold: 0.440 Positive Predictive Value TurboFold(seed): 0.681 Afold: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.835 Afold: 0.569 Sensitivity MXScarna(20): 0.737 Afold: 0.500 Positive Predictive Value MXScarna(20): 0.949 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.730 Afold: 0.569 Sensitivity RSpredict(20): 0.645 Afold: 0.500 Positive Predictive Value RSpredict(20): 0.831 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.873 Afold: 0.569 Sensitivity CentroidAlifold(20): 0.776 Afold: 0.500 Positive Predictive Value CentroidAlifold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.747 Afold: 0.569 Sensitivity Murlet(20): 0.632 Afold: 0.500 Positive Predictive Value Murlet(20): 0.889 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.857 Afold: 0.569 Sensitivity PPfold(20): 0.750 Afold: 0.500 Positive Predictive Value PPfold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.280 MCFold: 0.263 Sensitivity Afold: 0.274 MCFold: 0.294 Positive Predictive Value Afold: 0.299 MCFold: 0.247 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.13872543599e-05
Alterna	45 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.764 Alterna: 0.401 Sensitivity Cylofold: 0.742 Alterna: 0.372 Positive Predictive Value Cylofold: 0.791 Alterna: 0.446 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.705 Alterna: 0.393 Sensitivity McQFold: 0.679 Alterna: 0.365 Positive Predictive Value McQFold: 0.738 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.697 Alterna: 0.393 Sensitivity Pknots: 0.668 Alterna: 0.365 Positive Predictive Value Pknots: 0.733 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.774 Alterna: 0.486 Sensitivity CentroidAlifold(seed): 0.642 Alterna: 0.455 Positive Predictive Value CentroidAlifold(seed): 0.936 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	46 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.627 Alterna: 0.393 Sensitivity PknotsRG: 0.601 Alterna: 0.365 Positive Predictive Value PknotsRG: 0.662 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.736 Alterna: 0.503 Sensitivity PETfold_pre2.0(seed): 0.661 Alterna: 0.473 Positive Predictive Value PETfold_pre2.0(seed): 0.823 Alterna: 0.543 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.39162260866e-08	12 RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.641 Alterna: 0.384 Sensitivity RNASampler(seed): 0.562 Alterna: 0.365 Positive Predictive Value RNASampler(seed): 0.736 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.40919803867e-08	46 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.558 Alterna: 0.393 Sensitivity IPknot: 0.501 Alterna: 0.365 Positive Predictive Value IPknot: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.651 Alterna: 0.486 Sensitivity RNAalifold(seed): 0.519 Alterna: 0.455 Positive Predictive Value RNAalifold(seed): 0.823 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.59578924681e-08	46 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.544 Alterna: 0.393 Sensitivity CentroidFold: 0.485 Alterna: 0.365 Positive Predictive Value CentroidFold: 0.621 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.541 Alterna: 0.393 Sensitivity CentroidHomfold‑LAST: 0.471 Alterna: 0.365 Positive Predictive Value CentroidHomfold‑LAST: 0.632 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.597 Alterna: 0.393 Sensitivity Vsfold5: 0.550 Alterna: 0.365 Positive Predictive Value Vsfold5: 0.657 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 Carnac(seed) vs Alterna Matthews Correlation Coefficient Carnac(seed): 0.531 Alterna: 0.384 Sensitivity Carnac(seed): 0.292 Alterna: 0.365 Positive Predictive Value Carnac(seed): 0.971 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.77512146924e-08	46 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.527 Alterna: 0.393 Sensitivity ProbKnot: 0.496 Alterna: 0.365 Positive Predictive Value ProbKnot: 0.570 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.549 Alterna: 0.393 Sensitivity RNASLOpt: 0.489 Alterna: 0.365 Positive Predictive Value RNASLOpt: 0.626 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.515 Alterna: 0.393 Sensitivity Contrafold: 0.477 Alterna: 0.365 Positive Predictive Value Contrafold: 0.567 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.534 Alterna: 0.393 Sensitivity HotKnots: 0.510 Alterna: 0.365 Positive Predictive Value HotKnots: 0.569 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: 0.508 Alterna: 0.393 Sensitivity RDfolder: 0.432 Alterna: 0.365 Positive Predictive Value RDfolder: 0.609 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.504 Alterna: 0.393 Sensitivity Fold: 0.466 Alterna: 0.365 Positive Predictive Value Fold: 0.556 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.500 Alterna: 0.393 Sensitivity ContextFold: 0.441 Alterna: 0.365 Positive Predictive Value ContextFold: 0.577 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.503 Alterna: 0.393 Sensitivity MaxExpect: 0.463 Alterna: 0.365 Positive Predictive Value MaxExpect: 0.559 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 Murlet(seed) vs Alterna Matthews Correlation Coefficient Murlet(seed): 0.432 Alterna: 0.384 Sensitivity Murlet(seed): 0.283 Alterna: 0.365 Positive Predictive Value Murlet(seed): 0.667 Alterna: 0.415 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.63424715202e-08	46 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.482 Alterna: 0.393 Sensitivity Sfold: 0.435 Alterna: 0.365 Positive Predictive Value Sfold: 0.545 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.468 Alterna: 0.393 Sensitivity UNAFold: 0.431 Alterna: 0.365 Positive Predictive Value UNAFold: 0.521 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.480 Alterna: 0.393 Sensitivity Vsfold4: 0.423 Alterna: 0.365 Positive Predictive Value Vsfold4: 0.557 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.463 Alterna: 0.393 Sensitivity RNAshapes: 0.426 Alterna: 0.365 Positive Predictive Value RNAshapes: 0.515 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	46 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.476 Alterna: 0.393 Sensitivity RNAfold: 0.439 Alterna: 0.365 Positive Predictive Value RNAfold: 0.528 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.514 Alterna: 0.486 Sensitivity MXScarna(seed): 0.481 Alterna: 0.455 Positive Predictive Value MXScarna(seed): 0.558 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 7.52580889924e-08	46 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.470 Alterna: 0.393 Sensitivity RNAsubopt: 0.435 Alterna: 0.365 Positive Predictive Value RNAsubopt: 0.520 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): 0.518 Alterna: 0.486 Sensitivity RSpredict(seed): 0.437 Alterna: 0.455 Positive Predictive Value RSpredict(seed): 0.623 Alterna: 0.529 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 5.57565412286e-08	46 CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.458 Alterna: 0.393 Sensitivity CRWrnafold: 0.415 Alterna: 0.365 Positive Predictive Value CRWrnafold: 0.518 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.459 Alterna: 0.360 Sensitivity CMfinder(seed): 0.365 Alterna: 0.345 Positive Predictive Value CMfinder(seed): 0.585 Alterna: 0.386 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.95556389719e-09	46 RNAwolf vs Alterna Matthews Correlation Coefficient RNAwolf: 0.401 Alterna: 0.393 Sensitivity RNAwolf: 0.381 Alterna: 0.365 Positive Predictive Value RNAwolf: 0.434 Alterna: 0.435 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 1.95308298399e-06	29 Alterna vs Afold Matthews Correlation Coefficient Alterna: 0.340 Afold: 0.309 Sensitivity Alterna: 0.326 Afold: 0.296 Positive Predictive Value Alterna: 0.369 Afold: 0.338 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08		+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.486 Mastr(seed): 0.365 Sensitivity Alterna: 0.455 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.529 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.87872347734e-08	? Alterna vs Mastr(20) Matthews Correlation Coefficient Alterna: 0.656 Mastr(20): 0.561 Sensitivity Alterna: 0.602 Mastr(20): 0.459 Positive Predictive Value Alterna: 0.721 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.435 NanoFolder: 0.304 Sensitivity Alterna: 0.404 NanoFolder: 0.343 Positive Predictive Value Alterna: 0.479 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.821 Alterna: 0.656 Sensitivity Carnac(20): 0.684 Alterna: 0.602 Positive Predictive Value Carnac(20): 0.989 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.575 Alterna: 0.414 Sensitivity Multilign(seed): 0.536 Alterna: 0.386 Positive Predictive Value Multilign(seed): 0.625 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.862 Alterna: 0.656 Sensitivity Multilign(20): 0.752 Alterna: 0.602 Positive Predictive Value Multilign(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.857 Alterna: 0.656 Sensitivity TurboFold(20): 0.744 Alterna: 0.602 Positive Predictive Value TurboFold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.844 Alterna: 0.656 Sensitivity RNAalifold(20): 0.722 Alterna: 0.602 Positive Predictive Value RNAalifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.840 Alterna: 0.656 Sensitivity RNASampler(20): 0.714 Alterna: 0.602 Positive Predictive Value RNASampler(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.779 Alterna: 0.656 Sensitivity CMfinder(20): 0.617 Alterna: 0.602 Positive Predictive Value CMfinder(20): 0.988 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Alterna: 0.656 Sensitivity PETfold_pre2.0(20): 0.759 Alterna: 0.602 Positive Predictive Value PETfold_pre2.0(20): 0.962 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Alterna Matthews Correlation Coefficient PPfold(seed): 0.666 Alterna: 0.414 Sensitivity PPfold(seed): 0.536 Alterna: 0.386 Positive Predictive Value PPfold(seed): 0.833 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.600 Alterna: 0.428 Sensitivity TurboFold(seed): 0.518 Alterna: 0.399 Positive Predictive Value TurboFold(seed): 0.702 Alterna: 0.469 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.837 Alterna: 0.656 Sensitivity MXScarna(20): 0.752 Alterna: 0.602 Positive Predictive Value MXScarna(20): 0.935 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.672 Alterna: 0.656 Sensitivity RSpredict(20): 0.549 Alterna: 0.602 Positive Predictive Value RSpredict(20): 0.830 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Alterna: 0.656 Sensitivity CentroidAlifold(20): 0.752 Alterna: 0.602 Positive Predictive Value CentroidAlifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.741 Alterna: 0.656 Sensitivity Murlet(20): 0.594 Alterna: 0.602 Positive Predictive Value Murlet(20): 0.929 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.840 Alterna: 0.656 Sensitivity PPfold(20): 0.737 Alterna: 0.602 Positive Predictive Value PPfold(20): 0.961 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.399 MCFold: 0.296 Sensitivity Alterna: 0.369 MCFold: 0.325 Positive Predictive Value Alterna: 0.444 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08
Mastr(seed)	15 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.798 Mastr(seed): 0.406 Sensitivity Cylofold: 0.772 Mastr(seed): 0.212 Positive Predictive Value Cylofold: 0.828 Mastr(seed): 0.784 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08	17 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.834 Mastr(seed): 0.341 Sensitivity McQFold: 0.799 Mastr(seed): 0.176 Positive Predictive Value McQFold: 0.872 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	16 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.768 Mastr(seed): 0.365 Sensitivity Pknots: 0.748 Mastr(seed): 0.202 Positive Predictive Value Pknots: 0.792 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.02510705504e-08	17 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.767 Mastr(seed): 0.341 Sensitivity CentroidAlifold(seed): 0.634 Mastr(seed): 0.176 Positive Predictive Value CentroidAlifold(seed): 0.933 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.69265863073e-08	17 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.787 Mastr(seed): 0.341 Sensitivity PknotsRG: 0.761 Mastr(seed): 0.176 Positive Predictive Value PknotsRG: 0.817 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.50323628132e-08	17 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.710 Mastr(seed): 0.341 Sensitivity PETfold_pre2.0(seed): 0.626 Mastr(seed): 0.176 Positive Predictive Value PETfold_pre2.0(seed): 0.809 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	13 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.655 Mastr(seed): 0.400 Sensitivity RNASampler(seed): 0.572 Mastr(seed): 0.242 Positive Predictive Value RNASampler(seed): 0.755 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	17 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.671 Mastr(seed): 0.341 Sensitivity IPknot: 0.590 Mastr(seed): 0.176 Positive Predictive Value IPknot: 0.768 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.89649746203e-08	17 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 Mastr(seed): 0.341 Sensitivity RNAalifold(seed): 0.522 Mastr(seed): 0.176 Positive Predictive Value RNAalifold(seed): 0.833 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.22210847902e-08	17 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.695 Mastr(seed): 0.341 Sensitivity CentroidFold: 0.608 Mastr(seed): 0.176 Positive Predictive Value CentroidFold: 0.799 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.39162260866e-08	17 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 Mastr(seed): 0.341 Sensitivity CentroidHomfold‑LAST: 0.560 Mastr(seed): 0.176 Positive Predictive Value CentroidHomfold‑LAST: 0.769 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	17 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.531 Mastr(seed): 0.341 Sensitivity Vsfold5: 0.501 Mastr(seed): 0.176 Positive Predictive Value Vsfold5: 0.569 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	13 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.582 Mastr(seed): 0.400 Sensitivity Carnac(seed): 0.354 Mastr(seed): 0.242 Positive Predictive Value Carnac(seed): 0.962 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 6.42028829171e-09	17 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.603 Mastr(seed): 0.341 Sensitivity ProbKnot: 0.565 Mastr(seed): 0.176 Positive Predictive Value ProbKnot: 0.649 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-08	17 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.635 Mastr(seed): 0.341 Sensitivity RNASLOpt: 0.565 Mastr(seed): 0.176 Positive Predictive Value RNASLOpt: 0.718 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.75835195567e-08	17 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.653 Mastr(seed): 0.341 Sensitivity Contrafold: 0.598 Mastr(seed): 0.176 Positive Predictive Value Contrafold: 0.719 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	17 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.603 Mastr(seed): 0.341 Sensitivity HotKnots: 0.588 Mastr(seed): 0.176 Positive Predictive Value HotKnots: 0.624 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.61939086268e-08	16 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.616 Mastr(seed): 0.365 Sensitivity RDfolder: 0.531 Mastr(seed): 0.202 Positive Predictive Value RDfolder: 0.721 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.64318034126e-08	17 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.572 Mastr(seed): 0.341 Sensitivity Fold: 0.534 Mastr(seed): 0.176 Positive Predictive Value Fold: 0.619 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	17 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.567 Mastr(seed): 0.341 Sensitivity ContextFold: 0.506 Mastr(seed): 0.176 Positive Predictive Value ContextFold: 0.642 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	17 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.603 Mastr(seed): 0.341 Sensitivity MaxExpect: 0.560 Mastr(seed): 0.176 Positive Predictive Value MaxExpect: 0.657 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	13 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.482 Mastr(seed): 0.400 Sensitivity Murlet(seed): 0.319 Mastr(seed): 0.242 Positive Predictive Value Murlet(seed): 0.734 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 6.05123325482e-09	17 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.571 Mastr(seed): 0.341 Sensitivity Sfold: 0.519 Mastr(seed): 0.176 Positive Predictive Value Sfold: 0.636 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08	17 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.552 Mastr(seed): 0.341 Sensitivity UNAFold: 0.517 Mastr(seed): 0.176 Positive Predictive Value UNAFold: 0.597 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.36983135185e-08	17 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.488 Mastr(seed): 0.341 Sensitivity Vsfold4: 0.445 Mastr(seed): 0.176 Positive Predictive Value Vsfold4: 0.543 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.91763127434e-08	17 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.526 Mastr(seed): 0.341 Sensitivity RNAshapes: 0.496 Mastr(seed): 0.176 Positive Predictive Value RNAshapes: 0.565 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	17 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.566 Mastr(seed): 0.341 Sensitivity RNAfold: 0.532 Mastr(seed): 0.176 Positive Predictive Value RNAfold: 0.609 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	17 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.539 Mastr(seed): 0.341 Sensitivity MXScarna(seed): 0.501 Mastr(seed): 0.176 Positive Predictive Value MXScarna(seed): 0.586 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.43692248862e-08	17 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.538 Mastr(seed): 0.341 Sensitivity RNAsubopt: 0.506 Mastr(seed): 0.176 Positive Predictive Value RNAsubopt: 0.578 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	17 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.514 Mastr(seed): 0.341 Sensitivity RSpredict(seed): 0.427 Mastr(seed): 0.176 Positive Predictive Value RSpredict(seed): 0.625 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.36983135185e-08	17 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.527 Mastr(seed): 0.341 Sensitivity CRWrnafold: 0.491 Mastr(seed): 0.176 Positive Predictive Value CRWrnafold: 0.573 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.18141491686e-08	11 CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.443 Mastr(seed): 0.345 Sensitivity CMfinder(seed): 0.333 Mastr(seed): 0.201 Positive Predictive Value CMfinder(seed): 0.597 Mastr(seed): 0.602 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.61358433984e-08	17 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.487 Mastr(seed): 0.341 Sensitivity RNAwolf: 0.461 Mastr(seed): 0.176 Positive Predictive Value RNAwolf: 0.523 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	13 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.517 Mastr(seed): 0.331 Sensitivity Afold: 0.480 Mastr(seed): 0.174 Positive Predictive Value Afold: 0.564 Mastr(seed): 0.639 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.84361416392e-08	16 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.486 Mastr(seed): 0.365 Sensitivity Alterna: 0.455 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.529 Mastr(seed): 0.670 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.87872347734e-08		? Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.705 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.565 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.884 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.489 Mastr(seed): 0.343 Sensitivity NanoFolder: 0.544 Mastr(seed): 0.241 Positive Predictive Value NanoFolder: 0.448 Mastr(seed): 0.500 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.832 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 Mastr(seed): 0.540 Sensitivity Multilign(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value Multilign(seed): 0.625 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.865 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.750 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.741 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.704 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.756 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.574 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 1.000 Mastr(seed): 0.000 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): 0.849 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.750 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.964 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Mastr(seed): 0.540 Sensitivity PPfold(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value PPfold(seed): 0.833 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Mastr(seed): 0.493 Sensitivity TurboFold(seed): 0.518 Mastr(seed): 0.375 Positive Predictive Value TurboFold(seed): 0.702 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.769 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.954 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.676 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.546 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.741 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.780 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.611 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 1.000 Mastr(seed): 0.000 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): 0.833 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.722 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.963 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): 0.381 MCFold: 0.358 Sensitivity Mastr(seed): 0.220 MCFold: 0.409 Positive Predictive Value Mastr(seed): 0.670 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.81807643229e-05
Mastr(20)	5 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.756 Mastr(20): 0.561 Sensitivity Cylofold: 0.677 Mastr(20): 0.459 Positive Predictive Value Cylofold: 0.849 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.777 Mastr(20): 0.561 Sensitivity McQFold: 0.692 Mastr(20): 0.459 Positive Predictive Value McQFold: 0.876 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Pknots vs Mastr(20) Matthews Correlation Coefficient Pknots: 0.723 Mastr(20): 0.561 Sensitivity Pknots: 0.632 Mastr(20): 0.459 Positive Predictive Value Pknots: 0.832 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Mastr(20): 0.705 Sensitivity CentroidAlifold(seed): 0.778 Mastr(20): 0.565 Positive Predictive Value CentroidAlifold(seed): 1.000 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.592 Mastr(20): 0.561 Sensitivity PknotsRG: 0.526 Mastr(20): 0.459 Positive Predictive Value PknotsRG: 0.673 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Mastr(20): 0.561 Sensitivity PETfold_pre2.0(seed): 0.774 Mastr(20): 0.459 Positive Predictive Value PETfold_pre2.0(seed): 0.904 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): N/A RNASampler(seed): N/A Sensitivity Mastr(20): N/A RNASampler(seed): N/A Positive Predictive Value Mastr(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.840 Mastr(20): 0.561 Sensitivity IPknot: 0.737 Mastr(20): 0.459 Positive Predictive Value IPknot: 0.961 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.750 Mastr(20): 0.705 Sensitivity RNAalifold(seed): 0.639 Mastr(20): 0.565 Positive Predictive Value RNAalifold(seed): 0.885 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.849 Mastr(20): 0.561 Sensitivity CentroidFold: 0.729 Mastr(20): 0.459 Positive Predictive Value CentroidFold: 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 Mastr(20): 0.561 Sensitivity CentroidHomfold‑LAST: 0.729 Mastr(20): 0.459 Positive Predictive Value CentroidHomfold‑LAST: 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.774 Mastr(20): 0.561 Sensitivity Vsfold5: 0.699 Mastr(20): 0.459 Positive Predictive Value Vsfold5: 0.861 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): N/A Carnac(seed): N/A Sensitivity Mastr(20): N/A Carnac(seed): N/A Positive Predictive Value Mastr(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.803 Mastr(20): 0.561 Sensitivity ProbKnot: 0.722 Mastr(20): 0.459 Positive Predictive Value ProbKnot: 0.897 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.792 Mastr(20): 0.561 Sensitivity RNASLOpt: 0.692 Mastr(20): 0.459 Positive Predictive Value RNASLOpt: 0.911 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.854 Mastr(20): 0.561 Sensitivity Contrafold: 0.759 Mastr(20): 0.459 Positive Predictive Value Contrafold: 0.962 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.717 Mastr(20): 0.561 Sensitivity HotKnots: 0.639 Mastr(20): 0.459 Positive Predictive Value HotKnots: 0.810 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RDfolder vs Mastr(20) Matthews Correlation Coefficient RDfolder: 0.664 Mastr(20): 0.561 Sensitivity RDfolder: 0.586 Mastr(20): 0.459 Positive Predictive Value RDfolder: 0.757 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.862 Mastr(20): 0.561 Sensitivity Fold: 0.752 Mastr(20): 0.459 Positive Predictive Value Fold: 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.759 Mastr(20): 0.561 Sensitivity ContextFold: 0.669 Mastr(20): 0.459 Positive Predictive Value ContextFold: 0.864 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.783 Mastr(20): 0.561 Sensitivity MaxExpect: 0.677 Mastr(20): 0.459 Positive Predictive Value MaxExpect: 0.909 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): N/A Murlet(seed): N/A Sensitivity Mastr(20): N/A Murlet(seed): N/A Positive Predictive Value Mastr(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.721 Mastr(20): 0.561 Sensitivity Sfold: 0.624 Mastr(20): 0.459 Positive Predictive Value Sfold: 0.838 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.649 Mastr(20): 0.561 Sensitivity UNAFold: 0.579 Mastr(20): 0.459 Positive Predictive Value UNAFold: 0.733 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.784 Mastr(20): 0.561 Sensitivity Vsfold4: 0.684 Mastr(20): 0.459 Positive Predictive Value Vsfold4: 0.901 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.640 Mastr(20): 0.561 Sensitivity RNAshapes: 0.571 Mastr(20): 0.459 Positive Predictive Value RNAshapes: 0.724 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.702 Mastr(20): 0.561 Sensitivity RNAfold: 0.617 Mastr(20): 0.459 Positive Predictive Value RNAfold: 0.804 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 Mastr(20): 0.705 Sensitivity MXScarna(seed): 0.713 Mastr(20): 0.565 Positive Predictive Value MXScarna(seed): 0.963 Mastr(20): 0.884 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.646 Mastr(20): 0.561 Sensitivity RNAsubopt: 0.579 Mastr(20): 0.459 Positive Predictive Value RNAsubopt: 0.726 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.705 RSpredict(seed): 0.602 Sensitivity Mastr(20): 0.565 RSpredict(seed): 0.435 Positive Predictive Value Mastr(20): 0.884 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.776 Mastr(20): 0.561 Sensitivity CRWrnafold: 0.684 Mastr(20): 0.459 Positive Predictive Value CRWrnafold: 0.883 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.661 Mastr(20): 0.561 Sensitivity RNAwolf: 0.647 Mastr(20): 0.459 Positive Predictive Value RNAwolf: 0.683 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.574 Afold: 0.569 Sensitivity Mastr(20): 0.500 Afold: 0.500 Positive Predictive Value Mastr(20): 0.667 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Alterna vs Mastr(20) Matthews Correlation Coefficient Alterna: 0.656 Mastr(20): 0.561 Sensitivity Alterna: 0.602 Mastr(20): 0.459 Positive Predictive Value Alterna: 0.721 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.705 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.565 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.884 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.456 NanoFolder: 0.144 Sensitivity Mastr(20): 0.404 NanoFolder: 0.173 Positive Predictive Value Mastr(20): 0.525 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.821 Mastr(20): 0.561 Sensitivity Carnac(20): 0.684 Mastr(20): 0.459 Positive Predictive Value Carnac(20): 0.989 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): N/A Multilign(seed): N/A Sensitivity Mastr(20): N/A Multilign(seed): N/A Positive Predictive Value Mastr(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.862 Mastr(20): 0.561 Sensitivity Multilign(20): 0.752 Mastr(20): 0.459 Positive Predictive Value Multilign(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.857 Mastr(20): 0.561 Sensitivity TurboFold(20): 0.744 Mastr(20): 0.459 Positive Predictive Value TurboFold(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 Mastr(20): 0.561 Sensitivity RNAalifold(20): 0.722 Mastr(20): 0.459 Positive Predictive Value RNAalifold(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.840 Mastr(20): 0.561 Sensitivity RNASampler(20): 0.714 Mastr(20): 0.459 Positive Predictive Value RNASampler(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.779 Mastr(20): 0.561 Sensitivity CMfinder(20): 0.617 Mastr(20): 0.459 Positive Predictive Value CMfinder(20): 0.988 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Mastr(20): 0.561 Sensitivity PETfold_pre2.0(20): 0.759 Mastr(20): 0.459 Positive Predictive Value PETfold_pre2.0(20): 0.962 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): N/A PPfold(seed): N/A Sensitivity Mastr(20): N/A PPfold(seed): N/A Positive Predictive Value Mastr(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): N/A Mastr(20): N/A Sensitivity TurboFold(seed): N/A Mastr(20): N/A Positive Predictive Value TurboFold(seed): N/A Mastr(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.837 Mastr(20): 0.561 Sensitivity MXScarna(20): 0.752 Mastr(20): 0.459 Positive Predictive Value MXScarna(20): 0.935 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.672 Mastr(20): 0.561 Sensitivity RSpredict(20): 0.549 Mastr(20): 0.459 Positive Predictive Value RSpredict(20): 0.830 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Mastr(20): 0.561 Sensitivity CentroidAlifold(20): 0.752 Mastr(20): 0.459 Positive Predictive Value CentroidAlifold(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.741 Mastr(20): 0.561 Sensitivity Murlet(20): 0.594 Mastr(20): 0.459 Positive Predictive Value Murlet(20): 0.929 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.840 Mastr(20): 0.561 Sensitivity PPfold(20): 0.737 Mastr(20): 0.459 Positive Predictive Value PPfold(20): 0.961 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.561 MCFold: 0.291 Sensitivity Mastr(20): 0.459 MCFold: 0.323 Positive Predictive Value Mastr(20): 0.693 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
NanoFolder	6 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.784 NanoFolder: 0.242 Sensitivity Cylofold: 0.720 NanoFolder: 0.273 Positive Predictive Value Cylofold: 0.857 NanoFolder: 0.228 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.813 NanoFolder: 0.304 Sensitivity McQFold: 0.759 NanoFolder: 0.343 Positive Predictive Value McQFold: 0.875 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.808 NanoFolder: 0.304 Sensitivity Pknots: 0.759 NanoFolder: 0.343 Positive Predictive Value Pknots: 0.863 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.771 NanoFolder: 0.489 Sensitivity CentroidAlifold(seed): 0.633 NanoFolder: 0.544 Positive Predictive Value CentroidAlifold(seed): 0.943 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.646 NanoFolder: 0.304 Sensitivity PknotsRG: 0.608 NanoFolder: 0.343 Positive Predictive Value PknotsRG: 0.692 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.783 NanoFolder: 0.346 Sensitivity PETfold_pre2.0(seed): 0.712 NanoFolder: 0.400 Positive Predictive Value PETfold_pre2.0(seed): 0.864 NanoFolder: 0.311 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	3 NanoFolder vs RNASampler(seed) Matthews Correlation Coefficient NanoFolder: 0.585 RNASampler(seed): 0.559 Sensitivity NanoFolder: 0.654 RNASampler(seed): 0.481 Positive Predictive Value NanoFolder: 0.531 RNASampler(seed): 0.658 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	7 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.674 NanoFolder: 0.304 Sensitivity IPknot: 0.614 NanoFolder: 0.343 Positive Predictive Value IPknot: 0.745 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.687 NanoFolder: 0.489 Sensitivity RNAalifold(seed): 0.570 NanoFolder: 0.544 Positive Predictive Value RNAalifold(seed): 0.833 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.628 NanoFolder: 0.304 Sensitivity CentroidFold: 0.554 NanoFolder: 0.343 Positive Predictive Value CentroidFold: 0.719 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.692 NanoFolder: 0.304 Sensitivity CentroidHomfold‑LAST: 0.602 NanoFolder: 0.343 Positive Predictive Value CentroidHomfold‑LAST: 0.800 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.686 NanoFolder: 0.304 Sensitivity Vsfold5: 0.620 NanoFolder: 0.343 Positive Predictive Value Vsfold5: 0.763 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	3 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.585 Carnac(seed): 0.554 Sensitivity NanoFolder: 0.654 Carnac(seed): 0.327 Positive Predictive Value NanoFolder: 0.531 Carnac(seed): 0.944 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	7 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.594 NanoFolder: 0.304 Sensitivity ProbKnot: 0.560 NanoFolder: 0.343 Positive Predictive Value ProbKnot: 0.637 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.692 NanoFolder: 0.304 Sensitivity RNASLOpt: 0.614 NanoFolder: 0.343 Positive Predictive Value RNASLOpt: 0.785 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.645 NanoFolder: 0.304 Sensitivity Contrafold: 0.584 NanoFolder: 0.343 Positive Predictive Value Contrafold: 0.719 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.431 NanoFolder: 0.304 Sensitivity HotKnots: 0.416 NanoFolder: 0.343 Positive Predictive Value HotKnots: 0.457 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.466 NanoFolder: 0.304 Sensitivity RDfolder: 0.398 NanoFolder: 0.343 Positive Predictive Value RDfolder: 0.555 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.567 NanoFolder: 0.304 Sensitivity Fold: 0.524 NanoFolder: 0.343 Positive Predictive Value Fold: 0.621 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.682 NanoFolder: 0.304 Sensitivity ContextFold: 0.608 NanoFolder: 0.343 Positive Predictive Value ContextFold: 0.771 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.571 NanoFolder: 0.304 Sensitivity MaxExpect: 0.524 NanoFolder: 0.343 Positive Predictive Value MaxExpect: 0.630 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	3 NanoFolder vs Murlet(seed) Matthews Correlation Coefficient NanoFolder: 0.585 Murlet(seed): 0.574 Sensitivity NanoFolder: 0.654 Murlet(seed): 0.423 Positive Predictive Value NanoFolder: 0.531 Murlet(seed): 0.786 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	7 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.468 NanoFolder: 0.304 Sensitivity Sfold: 0.440 NanoFolder: 0.343 Positive Predictive Value Sfold: 0.507 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.485 NanoFolder: 0.304 Sensitivity UNAFold: 0.446 NanoFolder: 0.343 Positive Predictive Value UNAFold: 0.536 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.582 NanoFolder: 0.304 Sensitivity Vsfold4: 0.518 NanoFolder: 0.343 Positive Predictive Value Vsfold4: 0.662 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.455 NanoFolder: 0.304 Sensitivity RNAshapes: 0.416 NanoFolder: 0.343 Positive Predictive Value RNAshapes: 0.507 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.468 NanoFolder: 0.304 Sensitivity RNAfold: 0.440 NanoFolder: 0.343 Positive Predictive Value RNAfold: 0.507 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.510 NanoFolder: 0.489 Sensitivity MXScarna(seed): 0.481 NanoFolder: 0.544 Positive Predictive Value MXScarna(seed): 0.551 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.471 NanoFolder: 0.304 Sensitivity RNAsubopt: 0.440 NanoFolder: 0.343 Positive Predictive Value RNAsubopt: 0.514 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 RSpredict(seed) vs NanoFolder Matthews Correlation Coefficient RSpredict(seed): 0.535 NanoFolder: 0.489 Sensitivity RSpredict(seed): 0.481 NanoFolder: 0.544 Positive Predictive Value RSpredict(seed): 0.603 NanoFolder: 0.448 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.550 NanoFolder: 0.304 Sensitivity CRWrnafold: 0.512 NanoFolder: 0.343 Positive Predictive Value CRWrnafold: 0.599 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	3 NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: 0.585 CMfinder(seed): 0.507 Sensitivity NanoFolder: 0.654 CMfinder(seed): 0.346 Positive Predictive Value NanoFolder: 0.531 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	7 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.571 NanoFolder: 0.304 Sensitivity RNAwolf: 0.560 NanoFolder: 0.343 Positive Predictive Value RNAwolf: 0.589 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	6 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.463 NanoFolder: 0.346 Sensitivity Afold: 0.424 NanoFolder: 0.400 Positive Predictive Value Afold: 0.515 NanoFolder: 0.311 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	7 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.435 NanoFolder: 0.304 Sensitivity Alterna: 0.404 NanoFolder: 0.343 Positive Predictive Value Alterna: 0.479 NanoFolder: 0.281 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.489 Mastr(seed): 0.343 Sensitivity NanoFolder: 0.544 Mastr(seed): 0.241 Positive Predictive Value NanoFolder: 0.448 Mastr(seed): 0.500 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.456 NanoFolder: 0.144 Sensitivity Mastr(20): 0.404 NanoFolder: 0.173 Positive Predictive Value Mastr(20): 0.525 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0		? Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.831 NanoFolder: 0.144 Sensitivity Carnac(20): 0.712 NanoFolder: 0.173 Positive Predictive Value Carnac(20): 0.974 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.618 NanoFolder: 0.585 Sensitivity Multilign(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value Multilign(seed): 0.690 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.865 NanoFolder: 0.144 Sensitivity Multilign(20): 0.769 NanoFolder: 0.173 Positive Predictive Value Multilign(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.854 NanoFolder: 0.144 Sensitivity TurboFold(20): 0.750 NanoFolder: 0.173 Positive Predictive Value TurboFold(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.854 NanoFolder: 0.144 Sensitivity RNAalifold(20): 0.750 NanoFolder: 0.173 Positive Predictive Value RNAalifold(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.865 NanoFolder: 0.144 Sensitivity RNASampler(20): 0.769 NanoFolder: 0.173 Positive Predictive Value RNASampler(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.854 NanoFolder: 0.144 Sensitivity CMfinder(20): 0.750 NanoFolder: 0.173 Positive Predictive Value CMfinder(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.876 NanoFolder: 0.144 Sensitivity PETfold_pre2.0(20): 0.788 NanoFolder: 0.173 Positive Predictive Value PETfold_pre2.0(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.698 NanoFolder: 0.585 Sensitivity PPfold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value PPfold(seed): 0.879 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.709 NanoFolder: 0.585 Sensitivity TurboFold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value TurboFold(seed): 0.906 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.810 NanoFolder: 0.144 Sensitivity MXScarna(20): 0.712 NanoFolder: 0.173 Positive Predictive Value MXScarna(20): 0.925 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.744 NanoFolder: 0.144 Sensitivity RSpredict(20): 0.654 NanoFolder: 0.173 Positive Predictive Value RSpredict(20): 0.850 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.876 NanoFolder: 0.144 Sensitivity CentroidAlifold(20): 0.788 NanoFolder: 0.173 Positive Predictive Value CentroidAlifold(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.718 NanoFolder: 0.144 Sensitivity Murlet(20): 0.615 NanoFolder: 0.173 Positive Predictive Value Murlet(20): 0.842 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.854 NanoFolder: 0.144 Sensitivity PPfold(20): 0.750 NanoFolder: 0.173 Positive Predictive Value PPfold(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: 0.304 MCFold: 0.248 Sensitivity NanoFolder: 0.343 MCFold: 0.283 Positive Predictive Value NanoFolder: 0.281 MCFold: 0.229 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
Carnac(20)	5 Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.821 Cylofold: 0.756 Sensitivity Carnac(20): 0.684 Cylofold: 0.677 Positive Predictive Value Carnac(20): 0.989 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.821 McQFold: 0.777 Sensitivity Carnac(20): 0.684 McQFold: 0.692 Positive Predictive Value Carnac(20): 0.989 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.821 Pknots: 0.723 Sensitivity Carnac(20): 0.684 Pknots: 0.632 Positive Predictive Value Carnac(20): 0.989 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Carnac(20): 0.832 Sensitivity CentroidAlifold(seed): 0.778 Carnac(20): 0.694 Positive Predictive Value CentroidAlifold(seed): 1.000 Carnac(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs PknotsRG Matthews Correlation Coefficient Carnac(20): 0.821 PknotsRG: 0.592 Sensitivity Carnac(20): 0.684 PknotsRG: 0.526 Positive Predictive Value Carnac(20): 0.989 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Carnac(20): 0.821 Sensitivity PETfold_pre2.0(seed): 0.774 Carnac(20): 0.684 Positive Predictive Value PETfold_pre2.0(seed): 0.904 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(20): N/A Sensitivity RNASampler(seed): N/A Carnac(20): N/A Positive Predictive Value RNASampler(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.840 Carnac(20): 0.821 Sensitivity IPknot: 0.737 Carnac(20): 0.684 Positive Predictive Value IPknot: 0.961 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs RNAalifold(seed) Matthews Correlation Coefficient Carnac(20): 0.832 RNAalifold(seed): 0.750 Sensitivity Carnac(20): 0.694 RNAalifold(seed): 0.639 Positive Predictive Value Carnac(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.849 Carnac(20): 0.821 Sensitivity CentroidFold: 0.729 Carnac(20): 0.684 Positive Predictive Value CentroidFold: 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 Carnac(20): 0.821 Sensitivity CentroidHomfold‑LAST: 0.729 Carnac(20): 0.684 Positive Predictive Value CentroidHomfold‑LAST: 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.821 Vsfold5: 0.774 Sensitivity Carnac(20): 0.684 Vsfold5: 0.699 Positive Predictive Value Carnac(20): 0.989 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): N/A Carnac(seed): N/A Sensitivity Carnac(20): N/A Carnac(seed): N/A Positive Predictive Value Carnac(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Carnac(20) vs ProbKnot Matthews Correlation Coefficient Carnac(20): 0.821 ProbKnot: 0.803 Sensitivity Carnac(20): 0.684 ProbKnot: 0.722 Positive Predictive Value Carnac(20): 0.989 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.821 RNASLOpt: 0.792 Sensitivity Carnac(20): 0.684 RNASLOpt: 0.692 Positive Predictive Value Carnac(20): 0.989 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.854 Carnac(20): 0.821 Sensitivity Contrafold: 0.759 Carnac(20): 0.684 Positive Predictive Value Contrafold: 0.962 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs HotKnots Matthews Correlation Coefficient Carnac(20): 0.821 HotKnots: 0.717 Sensitivity Carnac(20): 0.684 HotKnots: 0.639 Positive Predictive Value Carnac(20): 0.989 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.821 RDfolder: 0.664 Sensitivity Carnac(20): 0.684 RDfolder: 0.586 Positive Predictive Value Carnac(20): 0.989 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.862 Carnac(20): 0.821 Sensitivity Fold: 0.752 Carnac(20): 0.684 Positive Predictive Value Fold: 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs ContextFold Matthews Correlation Coefficient Carnac(20): 0.821 ContextFold: 0.759 Sensitivity Carnac(20): 0.684 ContextFold: 0.669 Positive Predictive Value Carnac(20): 0.989 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs MaxExpect Matthews Correlation Coefficient Carnac(20): 0.821 MaxExpect: 0.783 Sensitivity Carnac(20): 0.684 MaxExpect: 0.677 Positive Predictive Value Carnac(20): 0.989 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): N/A Murlet(seed): N/A Sensitivity Carnac(20): N/A Murlet(seed): N/A Positive Predictive Value Carnac(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Carnac(20) vs Sfold Matthews Correlation Coefficient Carnac(20): 0.821 Sfold: 0.721 Sensitivity Carnac(20): 0.684 Sfold: 0.624 Positive Predictive Value Carnac(20): 0.989 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs UNAFold Matthews Correlation Coefficient Carnac(20): 0.821 UNAFold: 0.649 Sensitivity Carnac(20): 0.684 UNAFold: 0.579 Positive Predictive Value Carnac(20): 0.989 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.821 Vsfold4: 0.784 Sensitivity Carnac(20): 0.684 Vsfold4: 0.684 Positive Predictive Value Carnac(20): 0.989 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RNAshapes Matthews Correlation Coefficient Carnac(20): 0.821 RNAshapes: 0.640 Sensitivity Carnac(20): 0.684 RNAshapes: 0.571 Positive Predictive Value Carnac(20): 0.989 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.821 RNAfold: 0.702 Sensitivity Carnac(20): 0.684 RNAfold: 0.617 Positive Predictive Value Carnac(20): 0.989 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs MXScarna(seed) Matthews Correlation Coefficient Carnac(20): 0.832 MXScarna(seed): 0.827 Sensitivity Carnac(20): 0.694 MXScarna(seed): 0.713 Positive Predictive Value Carnac(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.821 RNAsubopt: 0.646 Sensitivity Carnac(20): 0.684 RNAsubopt: 0.579 Positive Predictive Value Carnac(20): 0.989 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.832 RSpredict(seed): 0.602 Sensitivity Carnac(20): 0.694 RSpredict(seed): 0.435 Positive Predictive Value Carnac(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs CRWrnafold Matthews Correlation Coefficient Carnac(20): 0.821 CRWrnafold: 0.776 Sensitivity Carnac(20): 0.684 CRWrnafold: 0.684 Positive Predictive Value Carnac(20): 0.989 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.821 RNAwolf: 0.661 Sensitivity Carnac(20): 0.684 RNAwolf: 0.647 Positive Predictive Value Carnac(20): 0.989 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.842 Afold: 0.569 Sensitivity Carnac(20): 0.724 Afold: 0.500 Positive Predictive Value Carnac(20): 0.982 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.821 Alterna: 0.656 Sensitivity Carnac(20): 0.684 Alterna: 0.602 Positive Predictive Value Carnac(20): 0.989 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.832 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.821 Mastr(20): 0.561 Sensitivity Carnac(20): 0.684 Mastr(20): 0.459 Positive Predictive Value Carnac(20): 0.989 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.831 NanoFolder: 0.144 Sensitivity Carnac(20): 0.712 NanoFolder: 0.173 Positive Predictive Value Carnac(20): 0.974 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0		? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(20): N/A Sensitivity Multilign(seed): N/A Carnac(20): N/A Positive Predictive Value Multilign(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.862 Carnac(20): 0.821 Sensitivity Multilign(20): 0.752 Carnac(20): 0.684 Positive Predictive Value Multilign(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.857 Carnac(20): 0.821 Sensitivity TurboFold(20): 0.744 Carnac(20): 0.684 Positive Predictive Value TurboFold(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 Carnac(20): 0.821 Sensitivity RNAalifold(20): 0.722 Carnac(20): 0.684 Positive Predictive Value RNAalifold(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.840 Carnac(20): 0.821 Sensitivity RNASampler(20): 0.714 Carnac(20): 0.684 Positive Predictive Value RNASampler(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.821 CMfinder(20): 0.779 Sensitivity Carnac(20): 0.684 CMfinder(20): 0.617 Positive Predictive Value Carnac(20): 0.989 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Carnac(20): 0.821 Sensitivity PETfold_pre2.0(20): 0.759 Carnac(20): 0.684 Positive Predictive Value PETfold_pre2.0(20): 0.962 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Carnac(20) Matthews Correlation Coefficient PPfold(seed): N/A Carnac(20): N/A Sensitivity PPfold(seed): N/A Carnac(20): N/A Positive Predictive Value PPfold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): N/A Carnac(20): N/A Sensitivity TurboFold(seed): N/A Carnac(20): N/A Positive Predictive Value TurboFold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.837 Carnac(20): 0.821 Sensitivity MXScarna(20): 0.752 Carnac(20): 0.684 Positive Predictive Value MXScarna(20): 0.935 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.821 RSpredict(20): 0.672 Sensitivity Carnac(20): 0.684 RSpredict(20): 0.549 Positive Predictive Value Carnac(20): 0.989 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Carnac(20): 0.821 Sensitivity CentroidAlifold(20): 0.752 Carnac(20): 0.684 Positive Predictive Value CentroidAlifold(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs Murlet(20) Matthews Correlation Coefficient Carnac(20): 0.821 Murlet(20): 0.741 Sensitivity Carnac(20): 0.684 Murlet(20): 0.594 Positive Predictive Value Carnac(20): 0.989 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.840 Carnac(20): 0.821 Sensitivity PPfold(20): 0.737 Carnac(20): 0.684 Positive Predictive Value PPfold(20): 0.961 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.821 MCFold: 0.291 Sensitivity Carnac(20): 0.684 MCFold: 0.323 Positive Predictive Value Carnac(20): 0.989 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Multilign(seed)	7 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.943 Multilign(seed): 0.572 Sensitivity Cylofold: 0.935 Multilign(seed): 0.532 Positive Predictive Value Cylofold: 0.951 Multilign(seed): 0.623 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.932 Multilign(seed): 0.575 Sensitivity McQFold: 0.936 Multilign(seed): 0.536 Positive Predictive Value McQFold: 0.929 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.886 Multilign(seed): 0.575 Sensitivity Pknots: 0.893 Multilign(seed): 0.536 Positive Predictive Value Pknots: 0.880 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Multilign(seed): 0.575 Sensitivity CentroidAlifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.949 Multilign(seed): 0.575 Sensitivity PknotsRG: 0.943 Multilign(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.619 Multilign(seed): 0.575 Sensitivity PETfold_pre2.0(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PETfold_pre2.0(seed): 0.721 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RNASampler(seed): 0.569 Sensitivity Multilign(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value Multilign(seed): 0.625 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.684 Multilign(seed): 0.575 Sensitivity IPknot: 0.586 Multilign(seed): 0.536 Positive Predictive Value IPknot: 0.804 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Multilign(seed): 0.575 Sensitivity RNAalifold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value RNAalifold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.618 Multilign(seed): 0.575 Sensitivity CentroidFold: 0.514 Multilign(seed): 0.536 Positive Predictive Value CentroidFold: 0.750 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.584 Multilign(seed): 0.575 Sensitivity CentroidHomfold‑LAST: 0.486 Multilign(seed): 0.536 Positive Predictive Value CentroidHomfold‑LAST: 0.708 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold5: 0.423 Sensitivity Multilign(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value Multilign(seed): 0.625 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Carnac(seed) vs Multilign(seed) Matthews Correlation Coefficient Carnac(seed): 0.625 Multilign(seed): 0.575 Sensitivity Carnac(seed): 0.407 Multilign(seed): 0.536 Positive Predictive Value Carnac(seed): 0.966 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.575 ProbKnot: 0.539 Sensitivity Multilign(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value Multilign(seed): 0.625 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASLOpt vs Multilign(seed) Matthews Correlation Coefficient RNASLOpt: 0.588 Multilign(seed): 0.575 Sensitivity RNASLOpt: 0.514 Multilign(seed): 0.536 Positive Predictive Value RNASLOpt: 0.679 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.596 Multilign(seed): 0.575 Sensitivity Contrafold: 0.521 Multilign(seed): 0.536 Positive Predictive Value Contrafold: 0.689 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs HotKnots Matthews Correlation Coefficient Multilign(seed): 0.575 HotKnots: 0.566 Sensitivity Multilign(seed): 0.536 HotKnots: 0.586 Positive Predictive Value Multilign(seed): 0.625 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: 0.593 Multilign(seed): 0.575 Sensitivity RDfolder: 0.486 Multilign(seed): 0.536 Positive Predictive Value RDfolder: 0.731 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.575 Fold: 0.457 Sensitivity Multilign(seed): 0.536 Fold: 0.443 Positive Predictive Value Multilign(seed): 0.625 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.575 ContextFold: 0.566 Sensitivity Multilign(seed): 0.536 ContextFold: 0.514 Positive Predictive Value Multilign(seed): 0.625 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.575 MaxExpect: 0.553 Sensitivity Multilign(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value Multilign(seed): 0.625 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 Murlet(seed): 0.518 Sensitivity Multilign(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value Multilign(seed): 0.625 Murlet(seed): 0.716 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.575 Sfold: 0.494 Sensitivity Multilign(seed): 0.536 Sfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.575 UNAFold: 0.483 Sensitivity Multilign(seed): 0.536 UNAFold: 0.457 Positive Predictive Value Multilign(seed): 0.625 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.575 Vsfold4: 0.260 Sensitivity Multilign(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value Multilign(seed): 0.625 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.575 RNAshapes: 0.481 Sensitivity Multilign(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.575 RNAfold: 0.472 Sensitivity Multilign(seed): 0.536 RNAfold: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAfold: 0.496 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 MXScarna(seed): 0.468 Sensitivity Multilign(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value Multilign(seed): 0.625 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.575 RNAsubopt: 0.478 Sensitivity Multilign(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value Multilign(seed): 0.625 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 RSpredict(seed): 0.437 Sensitivity Multilign(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value Multilign(seed): 0.625 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.575 CRWrnafold: 0.400 Sensitivity Multilign(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value Multilign(seed): 0.625 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.562 CMfinder(seed): 0.553 Sensitivity Multilign(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value Multilign(seed): 0.604 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.575 RNAwolf: 0.455 Sensitivity Multilign(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value Multilign(seed): 0.625 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.571 Afold: 0.480 Sensitivity Multilign(seed): 0.533 Afold: 0.443 Positive Predictive Value Multilign(seed): 0.619 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.575 Alterna: 0.414 Sensitivity Multilign(seed): 0.536 Alterna: 0.386 Positive Predictive Value Multilign(seed): 0.625 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.575 Mastr(seed): 0.540 Sensitivity Multilign(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value Multilign(seed): 0.625 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): N/A Multilign(seed): N/A Sensitivity Mastr(20): N/A Multilign(seed): N/A Positive Predictive Value Mastr(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	3 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.618 NanoFolder: 0.585 Sensitivity Multilign(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value Multilign(seed): 0.690 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(20): N/A Sensitivity Multilign(seed): N/A Carnac(20): N/A Positive Predictive Value Multilign(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 Multilign(20) Matthews Correlation Coefficient Multilign(seed): N/A Multilign(20): N/A Sensitivity Multilign(seed): N/A Multilign(20): N/A Positive Predictive Value Multilign(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): N/A Multilign(seed): N/A Sensitivity TurboFold(20): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(20): N/A Multilign(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): N/A Multilign(seed): N/A Sensitivity RNAalifold(20): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(20): N/A Multilign(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): N/A Multilign(seed): N/A Sensitivity RNASampler(20): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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): N/A Multilign(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Multilign(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Multilign(seed): 0.575 Sensitivity PPfold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.644 Multilign(seed): 0.575 Sensitivity TurboFold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value TurboFold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(20): N/A Sensitivity Multilign(seed): N/A MXScarna(20): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): N/A Multilign(seed): N/A Sensitivity RSpredict(20): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient Multilign(seed): N/A CentroidAlifold(20): N/A Sensitivity Multilign(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value Multilign(seed): N/A CentroidAlifold(20): 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): N/A Multilign(seed): N/A Sensitivity Murlet(20): N/A Multilign(seed): N/A Positive Predictive Value Murlet(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): N/A Multilign(seed): N/A Sensitivity PPfold(20): N/A Multilign(seed): N/A Positive Predictive Value PPfold(20): N/A Multilign(seed): 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): 0.575 MCFold: 0.340 Sensitivity Multilign(seed): 0.536 MCFold: 0.407 Positive Predictive Value Multilign(seed): 0.625 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Multilign(20)	5 Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.862 Cylofold: 0.756 Sensitivity Multilign(20): 0.752 Cylofold: 0.677 Positive Predictive Value Multilign(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.862 McQFold: 0.777 Sensitivity Multilign(20): 0.752 McQFold: 0.692 Positive Predictive Value Multilign(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.862 Pknots: 0.723 Sensitivity Multilign(20): 0.752 Pknots: 0.632 Positive Predictive Value Multilign(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Multilign(20): 0.865 Sensitivity CentroidAlifold(seed): 0.778 Multilign(20): 0.750 Positive Predictive Value CentroidAlifold(seed): 1.000 Multilign(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.862 PknotsRG: 0.592 Sensitivity Multilign(20): 0.752 PknotsRG: 0.526 Positive Predictive Value Multilign(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Multilign(20): 0.862 PETfold_pre2.0(seed): 0.835 Sensitivity Multilign(20): 0.752 PETfold_pre2.0(seed): 0.774 Positive Predictive Value Multilign(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(20): N/A Sensitivity RNASampler(seed): N/A Multilign(20): N/A Positive Predictive Value RNASampler(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.862 IPknot: 0.840 Sensitivity Multilign(20): 0.752 IPknot: 0.737 Positive Predictive Value Multilign(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.865 RNAalifold(seed): 0.750 Sensitivity Multilign(20): 0.750 RNAalifold(seed): 0.639 Positive Predictive Value Multilign(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.862 CentroidFold: 0.849 Sensitivity Multilign(20): 0.752 CentroidFold: 0.729 Positive Predictive Value Multilign(20): 0.990 CentroidFold: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Multilign(20): 0.862 CentroidHomfold‑LAST: 0.849 Sensitivity Multilign(20): 0.752 CentroidHomfold‑LAST: 0.729 Positive Predictive Value Multilign(20): 0.990 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.862 Vsfold5: 0.774 Sensitivity Multilign(20): 0.752 Vsfold5: 0.699 Positive Predictive Value Multilign(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Carnac(seed) vs Multilign(20) Matthews Correlation Coefficient Carnac(seed): N/A Multilign(20): N/A Sensitivity Carnac(seed): N/A Multilign(20): N/A Positive Predictive Value Carnac(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.862 ProbKnot: 0.803 Sensitivity Multilign(20): 0.752 ProbKnot: 0.722 Positive Predictive Value Multilign(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.862 RNASLOpt: 0.792 Sensitivity Multilign(20): 0.752 RNASLOpt: 0.692 Positive Predictive Value Multilign(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.862 Contrafold: 0.854 Sensitivity Multilign(20): 0.752 Contrafold: 0.759 Positive Predictive Value Multilign(20): 0.990 Contrafold: 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.862 HotKnots: 0.717 Sensitivity Multilign(20): 0.752 HotKnots: 0.639 Positive Predictive Value Multilign(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.862 RDfolder: 0.664 Sensitivity Multilign(20): 0.752 RDfolder: 0.586 Positive Predictive Value Multilign(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.862 Multilign(20): 0.862 Sensitivity Fold: 0.752 Multilign(20): 0.752 Positive Predictive Value Fold: 0.990 Multilign(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs ContextFold Matthews Correlation Coefficient Multilign(20): 0.862 ContextFold: 0.759 Sensitivity Multilign(20): 0.752 ContextFold: 0.669 Positive Predictive Value Multilign(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.862 MaxExpect: 0.783 Sensitivity Multilign(20): 0.752 MaxExpect: 0.677 Positive Predictive Value Multilign(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): N/A Multilign(20): N/A Sensitivity Murlet(seed): N/A Multilign(20): N/A Positive Predictive Value Murlet(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.862 Sfold: 0.721 Sensitivity Multilign(20): 0.752 Sfold: 0.624 Positive Predictive Value Multilign(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.862 UNAFold: 0.649 Sensitivity Multilign(20): 0.752 UNAFold: 0.579 Positive Predictive Value Multilign(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.862 Vsfold4: 0.784 Sensitivity Multilign(20): 0.752 Vsfold4: 0.684 Positive Predictive Value Multilign(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.862 RNAshapes: 0.640 Sensitivity Multilign(20): 0.752 RNAshapes: 0.571 Positive Predictive Value Multilign(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.862 RNAfold: 0.702 Sensitivity Multilign(20): 0.752 RNAfold: 0.617 Positive Predictive Value Multilign(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(20) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(20): 0.865 MXScarna(seed): 0.827 Sensitivity Multilign(20): 0.750 MXScarna(seed): 0.713 Positive Predictive Value Multilign(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.862 RNAsubopt: 0.646 Sensitivity Multilign(20): 0.752 RNAsubopt: 0.579 Positive Predictive Value Multilign(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.865 RSpredict(seed): 0.602 Sensitivity Multilign(20): 0.750 RSpredict(seed): 0.435 Positive Predictive Value Multilign(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.862 CRWrnafold: 0.776 Sensitivity Multilign(20): 0.752 CRWrnafold: 0.684 Positive Predictive Value Multilign(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 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	5 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.862 RNAwolf: 0.661 Sensitivity Multilign(20): 0.752 RNAwolf: 0.647 Positive Predictive Value Multilign(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.865 Afold: 0.569 Sensitivity Multilign(20): 0.763 Afold: 0.500 Positive Predictive Value Multilign(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.862 Alterna: 0.656 Sensitivity Multilign(20): 0.752 Alterna: 0.602 Positive Predictive Value Multilign(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.865 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.750 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.862 Mastr(20): 0.561 Sensitivity Multilign(20): 0.752 Mastr(20): 0.459 Positive Predictive Value Multilign(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.865 NanoFolder: 0.144 Sensitivity Multilign(20): 0.769 NanoFolder: 0.173 Positive Predictive Value Multilign(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.862 Carnac(20): 0.821 Sensitivity Multilign(20): 0.752 Carnac(20): 0.684 Positive Predictive Value Multilign(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): N/A Multilign(20): N/A Sensitivity Multilign(seed): N/A Multilign(20): N/A Positive Predictive Value Multilign(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Multilign(20) vs TurboFold(20) Matthews Correlation Coefficient Multilign(20): 0.862 TurboFold(20): 0.857 Sensitivity Multilign(20): 0.752 TurboFold(20): 0.744 Positive Predictive Value Multilign(20): 0.990 TurboFold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(20): 0.862 RNAalifold(20): 0.844 Sensitivity Multilign(20): 0.752 RNAalifold(20): 0.722 Positive Predictive Value Multilign(20): 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.862 RNASampler(20): 0.840 Sensitivity Multilign(20): 0.752 RNASampler(20): 0.714 Positive Predictive Value Multilign(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.862 CMfinder(20): 0.779 Sensitivity Multilign(20): 0.752 CMfinder(20): 0.617 Positive Predictive Value Multilign(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Multilign(20): 0.862 PETfold_pre2.0(20): 0.854 Sensitivity Multilign(20): 0.752 PETfold_pre2.0(20): 0.759 Positive Predictive Value Multilign(20): 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Multilign(20) Matthews Correlation Coefficient PPfold(seed): N/A Multilign(20): N/A Sensitivity PPfold(seed): N/A Multilign(20): N/A Positive Predictive Value PPfold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): N/A Multilign(20): N/A Sensitivity TurboFold(seed): N/A Multilign(20): N/A Positive Predictive Value TurboFold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.862 MXScarna(20): 0.837 Sensitivity Multilign(20): 0.752 MXScarna(20): 0.752 Positive Predictive Value Multilign(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.862 RSpredict(20): 0.672 Sensitivity Multilign(20): 0.752 RSpredict(20): 0.549 Positive Predictive Value Multilign(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Multilign(20): 0.862 Sensitivity CentroidAlifold(20): 0.752 Multilign(20): 0.752 Positive Predictive Value CentroidAlifold(20): 0.990 Multilign(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.862 Murlet(20): 0.741 Sensitivity Multilign(20): 0.752 Murlet(20): 0.594 Positive Predictive Value Multilign(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs PPfold(20) Matthews Correlation Coefficient Multilign(20): 0.862 PPfold(20): 0.840 Sensitivity Multilign(20): 0.752 PPfold(20): 0.737 Positive Predictive Value Multilign(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.862 MCFold: 0.291 Sensitivity Multilign(20): 0.752 MCFold: 0.323 Positive Predictive Value Multilign(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
TurboFold(20)	5 TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.857 Cylofold: 0.756 Sensitivity TurboFold(20): 0.744 Cylofold: 0.677 Positive Predictive Value TurboFold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.857 McQFold: 0.777 Sensitivity TurboFold(20): 0.744 McQFold: 0.692 Positive Predictive Value TurboFold(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.857 Pknots: 0.723 Sensitivity TurboFold(20): 0.744 Pknots: 0.632 Positive Predictive Value TurboFold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 TurboFold(20): 0.860 Sensitivity CentroidAlifold(seed): 0.778 TurboFold(20): 0.741 Positive Predictive Value CentroidAlifold(seed): 1.000 TurboFold(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.857 PknotsRG: 0.592 Sensitivity TurboFold(20): 0.744 PknotsRG: 0.526 Positive Predictive Value TurboFold(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(20): 0.857 PETfold_pre2.0(seed): 0.835 Sensitivity TurboFold(20): 0.744 PETfold_pre2.0(seed): 0.774 Positive Predictive Value TurboFold(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): N/A TurboFold(20): N/A Sensitivity RNASampler(seed): N/A TurboFold(20): N/A Positive Predictive Value RNASampler(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.857 IPknot: 0.840 Sensitivity TurboFold(20): 0.744 IPknot: 0.737 Positive Predictive Value TurboFold(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 RNAalifold(seed): 0.750 Sensitivity TurboFold(20): 0.741 RNAalifold(seed): 0.639 Positive Predictive Value TurboFold(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.857 CentroidFold: 0.849 Sensitivity TurboFold(20): 0.744 CentroidFold: 0.729 Positive Predictive Value TurboFold(20): 0.990 CentroidFold: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.857 CentroidHomfold‑LAST: 0.849 Sensitivity TurboFold(20): 0.744 CentroidHomfold‑LAST: 0.729 Positive Predictive Value TurboFold(20): 0.990 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.857 Vsfold5: 0.774 Sensitivity TurboFold(20): 0.744 Vsfold5: 0.699 Positive Predictive Value TurboFold(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): N/A Carnac(seed): N/A Sensitivity TurboFold(20): N/A Carnac(seed): N/A Positive Predictive Value TurboFold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.857 ProbKnot: 0.803 Sensitivity TurboFold(20): 0.744 ProbKnot: 0.722 Positive Predictive Value TurboFold(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.857 RNASLOpt: 0.792 Sensitivity TurboFold(20): 0.744 RNASLOpt: 0.692 Positive Predictive Value TurboFold(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.857 Contrafold: 0.854 Sensitivity TurboFold(20): 0.744 Contrafold: 0.759 Positive Predictive Value TurboFold(20): 0.990 Contrafold: 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.857 HotKnots: 0.717 Sensitivity TurboFold(20): 0.744 HotKnots: 0.639 Positive Predictive Value TurboFold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.857 RDfolder: 0.664 Sensitivity TurboFold(20): 0.744 RDfolder: 0.586 Positive Predictive Value TurboFold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs TurboFold(20) Matthews Correlation Coefficient Fold: 0.862 TurboFold(20): 0.857 Sensitivity Fold: 0.752 TurboFold(20): 0.744 Positive Predictive Value Fold: 0.990 TurboFold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs ContextFold Matthews Correlation Coefficient TurboFold(20): 0.857 ContextFold: 0.759 Sensitivity TurboFold(20): 0.744 ContextFold: 0.669 Positive Predictive Value TurboFold(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.857 MaxExpect: 0.783 Sensitivity TurboFold(20): 0.744 MaxExpect: 0.677 Positive Predictive Value TurboFold(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): N/A Murlet(seed): N/A Sensitivity TurboFold(20): N/A Murlet(seed): N/A Positive Predictive Value TurboFold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.857 Sfold: 0.721 Sensitivity TurboFold(20): 0.744 Sfold: 0.624 Positive Predictive Value TurboFold(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.857 UNAFold: 0.649 Sensitivity TurboFold(20): 0.744 UNAFold: 0.579 Positive Predictive Value TurboFold(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.857 Vsfold4: 0.784 Sensitivity TurboFold(20): 0.744 Vsfold4: 0.684 Positive Predictive Value TurboFold(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.857 RNAshapes: 0.640 Sensitivity TurboFold(20): 0.744 RNAshapes: 0.571 Positive Predictive Value TurboFold(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.857 RNAfold: 0.702 Sensitivity TurboFold(20): 0.744 RNAfold: 0.617 Positive Predictive Value TurboFold(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 MXScarna(seed): 0.827 Sensitivity TurboFold(20): 0.741 MXScarna(seed): 0.713 Positive Predictive Value TurboFold(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.857 RNAsubopt: 0.646 Sensitivity TurboFold(20): 0.744 RNAsubopt: 0.579 Positive Predictive Value TurboFold(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 RSpredict(seed): 0.602 Sensitivity TurboFold(20): 0.741 RSpredict(seed): 0.435 Positive Predictive Value TurboFold(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.857 CRWrnafold: 0.776 Sensitivity TurboFold(20): 0.744 CRWrnafold: 0.684 Positive Predictive Value TurboFold(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 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	5 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.857 RNAwolf: 0.661 Sensitivity TurboFold(20): 0.744 RNAwolf: 0.647 Positive Predictive Value TurboFold(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.857 Afold: 0.569 Sensitivity TurboFold(20): 0.750 Afold: 0.500 Positive Predictive Value TurboFold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.857 Alterna: 0.656 Sensitivity TurboFold(20): 0.744 Alterna: 0.602 Positive Predictive Value TurboFold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.860 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.741 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.857 Mastr(20): 0.561 Sensitivity TurboFold(20): 0.744 Mastr(20): 0.459 Positive Predictive Value TurboFold(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.854 NanoFolder: 0.144 Sensitivity TurboFold(20): 0.750 NanoFolder: 0.173 Positive Predictive Value TurboFold(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.857 Carnac(20): 0.821 Sensitivity TurboFold(20): 0.744 Carnac(20): 0.684 Positive Predictive Value TurboFold(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): N/A Multilign(seed): N/A Sensitivity TurboFold(20): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs TurboFold(20) Matthews Correlation Coefficient Multilign(20): 0.862 TurboFold(20): 0.857 Sensitivity Multilign(20): 0.752 TurboFold(20): 0.744 Positive Predictive Value Multilign(20): 0.990 TurboFold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.857 RNAalifold(20): 0.844 Sensitivity TurboFold(20): 0.744 RNAalifold(20): 0.722 Positive Predictive Value TurboFold(20): 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.857 RNASampler(20): 0.840 Sensitivity TurboFold(20): 0.744 RNASampler(20): 0.714 Positive Predictive Value TurboFold(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.857 CMfinder(20): 0.779 Sensitivity TurboFold(20): 0.744 CMfinder(20): 0.617 Positive Predictive Value TurboFold(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.857 PETfold_pre2.0(20): 0.854 Sensitivity TurboFold(20): 0.744 PETfold_pre2.0(20): 0.759 Positive Predictive Value TurboFold(20): 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): N/A PPfold(seed): N/A Sensitivity TurboFold(20): N/A PPfold(seed): N/A Positive Predictive Value TurboFold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs TurboFold(20) Matthews Correlation Coefficient TurboFold(seed): N/A TurboFold(20): N/A Sensitivity TurboFold(seed): N/A TurboFold(20): N/A Positive Predictive Value TurboFold(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.857 MXScarna(20): 0.837 Sensitivity TurboFold(20): 0.744 MXScarna(20): 0.752 Positive Predictive Value TurboFold(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.857 RSpredict(20): 0.672 Sensitivity TurboFold(20): 0.744 RSpredict(20): 0.549 Positive Predictive Value TurboFold(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 TurboFold(20): 0.857 Sensitivity CentroidAlifold(20): 0.752 TurboFold(20): 0.744 Positive Predictive Value CentroidAlifold(20): 0.990 TurboFold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.857 Murlet(20): 0.741 Sensitivity TurboFold(20): 0.744 Murlet(20): 0.594 Positive Predictive Value TurboFold(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.857 PPfold(20): 0.840 Sensitivity TurboFold(20): 0.744 PPfold(20): 0.737 Positive Predictive Value TurboFold(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.857 MCFold: 0.291 Sensitivity TurboFold(20): 0.744 MCFold: 0.323 Positive Predictive Value TurboFold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
RNAalifold(20)	5 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.844 Cylofold: 0.756 Sensitivity RNAalifold(20): 0.722 Cylofold: 0.677 Positive Predictive Value RNAalifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.844 McQFold: 0.777 Sensitivity RNAalifold(20): 0.722 McQFold: 0.692 Positive Predictive Value RNAalifold(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.844 Pknots: 0.723 Sensitivity RNAalifold(20): 0.722 Pknots: 0.632 Positive Predictive Value RNAalifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 RNAalifold(20): 0.838 Sensitivity CentroidAlifold(seed): 0.778 RNAalifold(20): 0.704 Positive Predictive Value CentroidAlifold(seed): 1.000 RNAalifold(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.844 PknotsRG: 0.592 Sensitivity RNAalifold(20): 0.722 PknotsRG: 0.526 Positive Predictive Value RNAalifold(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RNAalifold(20): 0.844 PETfold_pre2.0(seed): 0.835 Sensitivity RNAalifold(20): 0.722 PETfold_pre2.0(seed): 0.774 Positive Predictive Value RNAalifold(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(20): N/A Sensitivity RNASampler(seed): N/A RNAalifold(20): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.844 IPknot: 0.840 Sensitivity RNAalifold(20): 0.722 IPknot: 0.737 Positive Predictive Value RNAalifold(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 RNAalifold(seed): 0.750 Sensitivity RNAalifold(20): 0.704 RNAalifold(seed): 0.639 Positive Predictive Value RNAalifold(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs RNAalifold(20) Matthews Correlation Coefficient CentroidFold: 0.849 RNAalifold(20): 0.844 Sensitivity CentroidFold: 0.729 RNAalifold(20): 0.722 Positive Predictive Value CentroidFold: 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 RNAalifold(20): 0.844 Sensitivity CentroidHomfold‑LAST: 0.729 RNAalifold(20): 0.722 Positive Predictive Value CentroidHomfold‑LAST: 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.844 Vsfold5: 0.774 Sensitivity RNAalifold(20): 0.722 Vsfold5: 0.699 Positive Predictive Value RNAalifold(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Carnac(seed): N/A Sensitivity RNAalifold(20): N/A Carnac(seed): N/A Positive Predictive Value RNAalifold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.844 ProbKnot: 0.803 Sensitivity RNAalifold(20): 0.722 ProbKnot: 0.722 Positive Predictive Value RNAalifold(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.844 RNASLOpt: 0.792 Sensitivity RNAalifold(20): 0.722 RNASLOpt: 0.692 Positive Predictive Value RNAalifold(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs RNAalifold(20) Matthews Correlation Coefficient Contrafold: 0.854 RNAalifold(20): 0.844 Sensitivity Contrafold: 0.759 RNAalifold(20): 0.722 Positive Predictive Value Contrafold: 0.962 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.844 HotKnots: 0.717 Sensitivity RNAalifold(20): 0.722 HotKnots: 0.639 Positive Predictive Value RNAalifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.844 RDfolder: 0.664 Sensitivity RNAalifold(20): 0.722 RDfolder: 0.586 Positive Predictive Value RNAalifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs RNAalifold(20) Matthews Correlation Coefficient Fold: 0.862 RNAalifold(20): 0.844 Sensitivity Fold: 0.752 RNAalifold(20): 0.722 Positive Predictive Value Fold: 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs ContextFold Matthews Correlation Coefficient RNAalifold(20): 0.844 ContextFold: 0.759 Sensitivity RNAalifold(20): 0.722 ContextFold: 0.669 Positive Predictive Value RNAalifold(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.844 MaxExpect: 0.783 Sensitivity RNAalifold(20): 0.722 MaxExpect: 0.677 Positive Predictive Value RNAalifold(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Murlet(seed): N/A Sensitivity RNAalifold(20): N/A Murlet(seed): N/A Positive Predictive Value RNAalifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.844 Sfold: 0.721 Sensitivity RNAalifold(20): 0.722 Sfold: 0.624 Positive Predictive Value RNAalifold(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.844 UNAFold: 0.649 Sensitivity RNAalifold(20): 0.722 UNAFold: 0.579 Positive Predictive Value RNAalifold(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.844 Vsfold4: 0.784 Sensitivity RNAalifold(20): 0.722 Vsfold4: 0.684 Positive Predictive Value RNAalifold(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAshapes: 0.640 Sensitivity RNAalifold(20): 0.722 RNAshapes: 0.571 Positive Predictive Value RNAalifold(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAfold: 0.702 Sensitivity RNAalifold(20): 0.722 RNAfold: 0.617 Positive Predictive Value RNAalifold(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 MXScarna(seed): 0.827 Sensitivity RNAalifold(20): 0.704 MXScarna(seed): 0.713 Positive Predictive Value RNAalifold(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAsubopt: 0.646 Sensitivity RNAalifold(20): 0.722 RNAsubopt: 0.579 Positive Predictive Value RNAalifold(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 RSpredict(seed): 0.602 Sensitivity RNAalifold(20): 0.704 RSpredict(seed): 0.435 Positive Predictive Value RNAalifold(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.844 CRWrnafold: 0.776 Sensitivity RNAalifold(20): 0.722 CRWrnafold: 0.684 Positive Predictive Value RNAalifold(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.844 RNAwolf: 0.661 Sensitivity RNAalifold(20): 0.722 RNAwolf: 0.647 Positive Predictive Value RNAalifold(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.857 Afold: 0.569 Sensitivity RNAalifold(20): 0.750 Afold: 0.500 Positive Predictive Value RNAalifold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.844 Alterna: 0.656 Sensitivity RNAalifold(20): 0.722 Alterna: 0.602 Positive Predictive Value RNAalifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.838 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.704 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 Mastr(20): 0.561 Sensitivity RNAalifold(20): 0.722 Mastr(20): 0.459 Positive Predictive Value RNAalifold(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.854 NanoFolder: 0.144 Sensitivity RNAalifold(20): 0.750 NanoFolder: 0.173 Positive Predictive Value RNAalifold(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 Carnac(20): 0.821 Sensitivity RNAalifold(20): 0.722 Carnac(20): 0.684 Positive Predictive Value RNAalifold(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Multilign(seed): N/A Sensitivity RNAalifold(20): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(20): 0.862 RNAalifold(20): 0.844 Sensitivity Multilign(20): 0.752 RNAalifold(20): 0.722 Positive Predictive Value Multilign(20): 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.857 RNAalifold(20): 0.844 Sensitivity TurboFold(20): 0.744 RNAalifold(20): 0.722 Positive Predictive Value TurboFold(20): 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 RNASampler(20): 0.840 Sensitivity RNAalifold(20): 0.722 RNASampler(20): 0.714 Positive Predictive Value RNAalifold(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 CMfinder(20): 0.779 Sensitivity RNAalifold(20): 0.722 CMfinder(20): 0.617 Positive Predictive Value RNAalifold(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAalifold(20): 0.844 Sensitivity PETfold_pre2.0(20): 0.759 RNAalifold(20): 0.722 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): N/A PPfold(seed): N/A Sensitivity RNAalifold(20): N/A PPfold(seed): N/A Positive Predictive Value RNAalifold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A RNAalifold(20): N/A Sensitivity TurboFold(seed): N/A RNAalifold(20): N/A Positive Predictive Value TurboFold(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 MXScarna(20): 0.837 Sensitivity RNAalifold(20): 0.722 MXScarna(20): 0.752 Positive Predictive Value RNAalifold(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 RSpredict(20): 0.672 Sensitivity RNAalifold(20): 0.722 RSpredict(20): 0.549 Positive Predictive Value RNAalifold(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAalifold(20): 0.844 Sensitivity CentroidAlifold(20): 0.752 RNAalifold(20): 0.722 Positive Predictive Value CentroidAlifold(20): 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 Murlet(20): 0.741 Sensitivity RNAalifold(20): 0.722 Murlet(20): 0.594 Positive Predictive Value RNAalifold(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 PPfold(20): 0.840 Sensitivity RNAalifold(20): 0.722 PPfold(20): 0.737 Positive Predictive Value RNAalifold(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.844 MCFold: 0.291 Sensitivity RNAalifold(20): 0.722 MCFold: 0.323 Positive Predictive Value RNAalifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
RNASampler(20)	5 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.840 Cylofold: 0.756 Sensitivity RNASampler(20): 0.714 Cylofold: 0.677 Positive Predictive Value RNASampler(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.840 McQFold: 0.777 Sensitivity RNASampler(20): 0.714 McQFold: 0.692 Positive Predictive Value RNASampler(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.840 Pknots: 0.723 Sensitivity RNASampler(20): 0.714 Pknots: 0.632 Positive Predictive Value RNASampler(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 RNASampler(20): 0.832 Sensitivity CentroidAlifold(seed): 0.778 RNASampler(20): 0.694 Positive Predictive Value CentroidAlifold(seed): 1.000 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.840 PknotsRG: 0.592 Sensitivity RNASampler(20): 0.714 PknotsRG: 0.526 Positive Predictive Value RNASampler(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RNASampler(20): 0.840 PETfold_pre2.0(seed): 0.835 Sensitivity RNASampler(20): 0.714 PETfold_pre2.0(seed): 0.774 Positive Predictive Value RNASampler(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): N/A RNASampler(seed): N/A Sensitivity RNASampler(20): N/A RNASampler(seed): N/A Positive Predictive Value RNASampler(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.840 RNASampler(20): 0.840 Sensitivity IPknot: 0.737 RNASampler(20): 0.714 Positive Predictive Value IPknot: 0.961 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 RNAalifold(seed): 0.750 Sensitivity RNASampler(20): 0.694 RNAalifold(seed): 0.639 Positive Predictive Value RNASampler(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs RNASampler(20) Matthews Correlation Coefficient CentroidFold: 0.849 RNASampler(20): 0.840 Sensitivity CentroidFold: 0.729 RNASampler(20): 0.714 Positive Predictive Value CentroidFold: 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 RNASampler(20): 0.840 Sensitivity CentroidHomfold‑LAST: 0.729 RNASampler(20): 0.714 Positive Predictive Value CentroidHomfold‑LAST: 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.840 Vsfold5: 0.774 Sensitivity RNASampler(20): 0.714 Vsfold5: 0.699 Positive Predictive Value RNASampler(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): N/A Carnac(seed): N/A Sensitivity RNASampler(20): N/A Carnac(seed): N/A Positive Predictive Value RNASampler(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.840 ProbKnot: 0.803 Sensitivity RNASampler(20): 0.714 ProbKnot: 0.722 Positive Predictive Value RNASampler(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.840 RNASLOpt: 0.792 Sensitivity RNASampler(20): 0.714 RNASLOpt: 0.692 Positive Predictive Value RNASampler(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs RNASampler(20) Matthews Correlation Coefficient Contrafold: 0.854 RNASampler(20): 0.840 Sensitivity Contrafold: 0.759 RNASampler(20): 0.714 Positive Predictive Value Contrafold: 0.962 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.840 HotKnots: 0.717 Sensitivity RNASampler(20): 0.714 HotKnots: 0.639 Positive Predictive Value RNASampler(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.840 RDfolder: 0.664 Sensitivity RNASampler(20): 0.714 RDfolder: 0.586 Positive Predictive Value RNASampler(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs RNASampler(20) Matthews Correlation Coefficient Fold: 0.862 RNASampler(20): 0.840 Sensitivity Fold: 0.752 RNASampler(20): 0.714 Positive Predictive Value Fold: 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs ContextFold Matthews Correlation Coefficient RNASampler(20): 0.840 ContextFold: 0.759 Sensitivity RNASampler(20): 0.714 ContextFold: 0.669 Positive Predictive Value RNASampler(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.840 MaxExpect: 0.783 Sensitivity RNASampler(20): 0.714 MaxExpect: 0.677 Positive Predictive Value RNASampler(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): N/A Murlet(seed): N/A Sensitivity RNASampler(20): N/A Murlet(seed): N/A Positive Predictive Value RNASampler(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.840 Sfold: 0.721 Sensitivity RNASampler(20): 0.714 Sfold: 0.624 Positive Predictive Value RNASampler(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.840 UNAFold: 0.649 Sensitivity RNASampler(20): 0.714 UNAFold: 0.579 Positive Predictive Value RNASampler(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.840 Vsfold4: 0.784 Sensitivity RNASampler(20): 0.714 Vsfold4: 0.684 Positive Predictive Value RNASampler(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.840 RNAshapes: 0.640 Sensitivity RNASampler(20): 0.714 RNAshapes: 0.571 Positive Predictive Value RNASampler(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.840 RNAfold: 0.702 Sensitivity RNASampler(20): 0.714 RNAfold: 0.617 Positive Predictive Value RNASampler(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 MXScarna(seed): 0.827 Sensitivity RNASampler(20): 0.694 MXScarna(seed): 0.713 Positive Predictive Value RNASampler(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.840 RNAsubopt: 0.646 Sensitivity RNASampler(20): 0.714 RNAsubopt: 0.579 Positive Predictive Value RNASampler(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 RSpredict(seed): 0.602 Sensitivity RNASampler(20): 0.694 RSpredict(seed): 0.435 Positive Predictive Value RNASampler(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.840 CRWrnafold: 0.776 Sensitivity RNASampler(20): 0.714 CRWrnafold: 0.684 Positive Predictive Value RNASampler(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.840 RNAwolf: 0.661 Sensitivity RNASampler(20): 0.714 RNAwolf: 0.647 Positive Predictive Value RNASampler(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.865 Afold: 0.569 Sensitivity RNASampler(20): 0.763 Afold: 0.500 Positive Predictive Value RNASampler(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.840 Alterna: 0.656 Sensitivity RNASampler(20): 0.714 Alterna: 0.602 Positive Predictive Value RNASampler(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.832 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.840 Mastr(20): 0.561 Sensitivity RNASampler(20): 0.714 Mastr(20): 0.459 Positive Predictive Value RNASampler(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.865 NanoFolder: 0.144 Sensitivity RNASampler(20): 0.769 NanoFolder: 0.173 Positive Predictive Value RNASampler(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.840 Carnac(20): 0.821 Sensitivity RNASampler(20): 0.714 Carnac(20): 0.684 Positive Predictive Value RNASampler(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): N/A Multilign(seed): N/A Sensitivity RNASampler(20): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.862 RNASampler(20): 0.840 Sensitivity Multilign(20): 0.752 RNASampler(20): 0.714 Positive Predictive Value Multilign(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.857 RNASampler(20): 0.840 Sensitivity TurboFold(20): 0.744 RNASampler(20): 0.714 Positive Predictive Value TurboFold(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 RNASampler(20): 0.840 Sensitivity RNAalifold(20): 0.722 RNASampler(20): 0.714 Positive Predictive Value RNAalifold(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.840 CMfinder(20): 0.779 Sensitivity RNASampler(20): 0.714 CMfinder(20): 0.617 Positive Predictive Value RNASampler(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNASampler(20): 0.840 Sensitivity PETfold_pre2.0(20): 0.759 RNASampler(20): 0.714 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): N/A PPfold(seed): N/A Sensitivity RNASampler(20): N/A PPfold(seed): N/A Positive Predictive Value RNASampler(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): N/A TurboFold(seed): N/A Sensitivity RNASampler(20): N/A TurboFold(seed): N/A Positive Predictive Value RNASampler(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.840 MXScarna(20): 0.837 Sensitivity RNASampler(20): 0.714 MXScarna(20): 0.752 Positive Predictive Value RNASampler(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.840 RSpredict(20): 0.672 Sensitivity RNASampler(20): 0.714 RSpredict(20): 0.549 Positive Predictive Value RNASampler(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNASampler(20): 0.840 Sensitivity CentroidAlifold(20): 0.752 RNASampler(20): 0.714 Positive Predictive Value CentroidAlifold(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.840 Murlet(20): 0.741 Sensitivity RNASampler(20): 0.714 Murlet(20): 0.594 Positive Predictive Value RNASampler(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.840 RNASampler(20): 0.840 Sensitivity PPfold(20): 0.737 RNASampler(20): 0.714 Positive Predictive Value PPfold(20): 0.961 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.840 MCFold: 0.291 Sensitivity RNASampler(20): 0.714 MCFold: 0.323 Positive Predictive Value RNASampler(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
CMfinder(20)	5 CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.779 Cylofold: 0.756 Sensitivity CMfinder(20): 0.617 Cylofold: 0.677 Positive Predictive Value CMfinder(20): 0.988 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.779 McQFold: 0.777 Sensitivity CMfinder(20): 0.617 McQFold: 0.692 Positive Predictive Value CMfinder(20): 0.988 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.779 Pknots: 0.723 Sensitivity CMfinder(20): 0.617 Pknots: 0.632 Positive Predictive Value CMfinder(20): 0.988 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 CMfinder(20): 0.756 Sensitivity CentroidAlifold(seed): 0.778 CMfinder(20): 0.574 Positive Predictive Value CentroidAlifold(seed): 1.000 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs PknotsRG Matthews Correlation Coefficient CMfinder(20): 0.779 PknotsRG: 0.592 Sensitivity CMfinder(20): 0.617 PknotsRG: 0.526 Positive Predictive Value CMfinder(20): 0.988 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 CMfinder(20): 0.779 Sensitivity PETfold_pre2.0(seed): 0.774 CMfinder(20): 0.617 Positive Predictive Value PETfold_pre2.0(seed): 0.904 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 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	5 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.840 CMfinder(20): 0.779 Sensitivity IPknot: 0.737 CMfinder(20): 0.617 Positive Predictive Value IPknot: 0.961 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.756 RNAalifold(seed): 0.750 Sensitivity CMfinder(20): 0.574 RNAalifold(seed): 0.639 Positive Predictive Value CMfinder(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.849 CMfinder(20): 0.779 Sensitivity CentroidFold: 0.729 CMfinder(20): 0.617 Positive Predictive Value CentroidFold: 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 CMfinder(20): 0.779 Sensitivity CentroidHomfold‑LAST: 0.729 CMfinder(20): 0.617 Positive Predictive Value CentroidHomfold‑LAST: 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.779 Vsfold5: 0.774 Sensitivity CMfinder(20): 0.617 Vsfold5: 0.699 Positive Predictive Value CMfinder(20): 0.988 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.803 CMfinder(20): 0.779 Sensitivity ProbKnot: 0.722 CMfinder(20): 0.617 Positive Predictive Value ProbKnot: 0.897 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: 0.792 CMfinder(20): 0.779 Sensitivity RNASLOpt: 0.692 CMfinder(20): 0.617 Positive Predictive Value RNASLOpt: 0.911 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.854 CMfinder(20): 0.779 Sensitivity Contrafold: 0.759 CMfinder(20): 0.617 Positive Predictive Value Contrafold: 0.962 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.779 HotKnots: 0.717 Sensitivity CMfinder(20): 0.617 HotKnots: 0.639 Positive Predictive Value CMfinder(20): 0.988 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.779 RDfolder: 0.664 Sensitivity CMfinder(20): 0.617 RDfolder: 0.586 Positive Predictive Value CMfinder(20): 0.988 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.862 CMfinder(20): 0.779 Sensitivity Fold: 0.752 CMfinder(20): 0.617 Positive Predictive Value Fold: 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs ContextFold Matthews Correlation Coefficient CMfinder(20): 0.779 ContextFold: 0.759 Sensitivity CMfinder(20): 0.617 ContextFold: 0.669 Positive Predictive Value CMfinder(20): 0.988 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.783 CMfinder(20): 0.779 Sensitivity MaxExpect: 0.677 CMfinder(20): 0.617 Positive Predictive Value MaxExpect: 0.909 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 CMfinder(20) vs Sfold Matthews Correlation Coefficient CMfinder(20): 0.779 Sfold: 0.721 Sensitivity CMfinder(20): 0.617 Sfold: 0.624 Positive Predictive Value CMfinder(20): 0.988 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs UNAFold Matthews Correlation Coefficient CMfinder(20): 0.779 UNAFold: 0.649 Sensitivity CMfinder(20): 0.617 UNAFold: 0.579 Positive Predictive Value CMfinder(20): 0.988 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: 0.784 CMfinder(20): 0.779 Sensitivity Vsfold4: 0.684 CMfinder(20): 0.617 Positive Predictive Value Vsfold4: 0.901 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.779 RNAshapes: 0.640 Sensitivity CMfinder(20): 0.617 RNAshapes: 0.571 Positive Predictive Value CMfinder(20): 0.988 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs RNAfold Matthews Correlation Coefficient CMfinder(20): 0.779 RNAfold: 0.702 Sensitivity CMfinder(20): 0.617 RNAfold: 0.617 Positive Predictive Value CMfinder(20): 0.988 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 CMfinder(20): 0.756 Sensitivity MXScarna(seed): 0.713 CMfinder(20): 0.574 Positive Predictive Value MXScarna(seed): 0.963 CMfinder(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs RNAsubopt Matthews Correlation Coefficient CMfinder(20): 0.779 RNAsubopt: 0.646 Sensitivity CMfinder(20): 0.617 RNAsubopt: 0.579 Positive Predictive Value CMfinder(20): 0.988 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.756 RSpredict(seed): 0.602 Sensitivity CMfinder(20): 0.574 RSpredict(seed): 0.435 Positive Predictive Value CMfinder(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.779 CRWrnafold: 0.776 Sensitivity CMfinder(20): 0.617 CRWrnafold: 0.684 Positive Predictive Value CMfinder(20): 0.988 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.779 RNAwolf: 0.661 Sensitivity CMfinder(20): 0.617 RNAwolf: 0.647 Positive Predictive Value CMfinder(20): 0.988 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 CMfinder(20) vs Afold Matthews Correlation Coefficient CMfinder(20): 0.850 Afold: 0.569 Sensitivity CMfinder(20): 0.737 Afold: 0.500 Positive Predictive Value CMfinder(20): 0.982 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.779 Alterna: 0.656 Sensitivity CMfinder(20): 0.617 Alterna: 0.602 Positive Predictive Value CMfinder(20): 0.988 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.756 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.574 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.779 Mastr(20): 0.561 Sensitivity CMfinder(20): 0.617 Mastr(20): 0.459 Positive Predictive Value CMfinder(20): 0.988 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.854 NanoFolder: 0.144 Sensitivity CMfinder(20): 0.750 NanoFolder: 0.173 Positive Predictive Value CMfinder(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): 0.821 CMfinder(20): 0.779 Sensitivity Carnac(20): 0.684 CMfinder(20): 0.617 Positive Predictive Value Carnac(20): 0.989 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.862 CMfinder(20): 0.779 Sensitivity Multilign(20): 0.752 CMfinder(20): 0.617 Positive Predictive Value Multilign(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.857 CMfinder(20): 0.779 Sensitivity TurboFold(20): 0.744 CMfinder(20): 0.617 Positive Predictive Value TurboFold(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 CMfinder(20): 0.779 Sensitivity RNAalifold(20): 0.722 CMfinder(20): 0.617 Positive Predictive Value RNAalifold(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.840 CMfinder(20): 0.779 Sensitivity RNASampler(20): 0.714 CMfinder(20): 0.617 Positive Predictive Value RNASampler(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CMfinder(20): 0.779 Sensitivity PETfold_pre2.0(20): 0.759 CMfinder(20): 0.617 Positive Predictive Value PETfold_pre2.0(20): 0.962 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.837 CMfinder(20): 0.779 Sensitivity MXScarna(20): 0.752 CMfinder(20): 0.617 Positive Predictive Value MXScarna(20): 0.935 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.779 RSpredict(20): 0.672 Sensitivity CMfinder(20): 0.617 RSpredict(20): 0.549 Positive Predictive Value CMfinder(20): 0.988 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CMfinder(20): 0.779 Sensitivity CentroidAlifold(20): 0.752 CMfinder(20): 0.617 Positive Predictive Value CentroidAlifold(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs Murlet(20) Matthews Correlation Coefficient CMfinder(20): 0.779 Murlet(20): 0.741 Sensitivity CMfinder(20): 0.617 Murlet(20): 0.594 Positive Predictive Value CMfinder(20): 0.988 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.840 CMfinder(20): 0.779 Sensitivity PPfold(20): 0.737 CMfinder(20): 0.617 Positive Predictive Value PPfold(20): 0.961 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.779 MCFold: 0.291 Sensitivity CMfinder(20): 0.617 MCFold: 0.323 Positive Predictive Value CMfinder(20): 0.988 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PETfold_pre2.0(20)	5 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Cylofold: 0.756 Sensitivity PETfold_pre2.0(20): 0.759 Cylofold: 0.677 Positive Predictive Value PETfold_pre2.0(20): 0.962 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 McQFold: 0.777 Sensitivity PETfold_pre2.0(20): 0.759 McQFold: 0.692 Positive Predictive Value PETfold_pre2.0(20): 0.962 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Pknots: 0.723 Sensitivity PETfold_pre2.0(20): 0.759 Pknots: 0.632 Positive Predictive Value PETfold_pre2.0(20): 0.962 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 PETfold_pre2.0(20): 0.849 Sensitivity CentroidAlifold(seed): 0.778 PETfold_pre2.0(20): 0.750 Positive Predictive Value CentroidAlifold(seed): 1.000 PETfold_pre2.0(20): 0.964 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 PknotsRG: 0.592 Sensitivity PETfold_pre2.0(20): 0.759 PknotsRG: 0.526 Positive Predictive Value PETfold_pre2.0(20): 0.962 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 PETfold_pre2.0(seed): 0.835 Sensitivity PETfold_pre2.0(20): 0.759 PETfold_pre2.0(seed): 0.774 Positive Predictive Value PETfold_pre2.0(20): 0.962 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 IPknot: 0.840 Sensitivity PETfold_pre2.0(20): 0.759 IPknot: 0.737 Positive Predictive Value PETfold_pre2.0(20): 0.962 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 RNAalifold(seed): 0.750 Sensitivity PETfold_pre2.0(20): 0.750 RNAalifold(seed): 0.639 Positive Predictive Value PETfold_pre2.0(20): 0.964 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CentroidFold: 0.849 Sensitivity PETfold_pre2.0(20): 0.759 CentroidFold: 0.729 Positive Predictive Value PETfold_pre2.0(20): 0.962 CentroidFold: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CentroidHomfold‑LAST: 0.849 Sensitivity PETfold_pre2.0(20): 0.759 CentroidHomfold‑LAST: 0.729 Positive Predictive Value PETfold_pre2.0(20): 0.962 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Vsfold5: 0.774 Sensitivity PETfold_pre2.0(20): 0.759 Vsfold5: 0.699 Positive Predictive Value PETfold_pre2.0(20): 0.962 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Carnac(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Carnac(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 ProbKnot: 0.803 Sensitivity PETfold_pre2.0(20): 0.759 ProbKnot: 0.722 Positive Predictive Value PETfold_pre2.0(20): 0.962 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNASLOpt: 0.792 Sensitivity PETfold_pre2.0(20): 0.759 RNASLOpt: 0.692 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Contrafold: 0.854 Sensitivity PETfold_pre2.0(20): 0.759 Contrafold: 0.759 Positive Predictive Value PETfold_pre2.0(20): 0.962 Contrafold: 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 HotKnots: 0.717 Sensitivity PETfold_pre2.0(20): 0.759 HotKnots: 0.639 Positive Predictive Value PETfold_pre2.0(20): 0.962 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RDfolder: 0.664 Sensitivity PETfold_pre2.0(20): 0.759 RDfolder: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.962 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs PETfold_pre2.0(20) Matthews Correlation Coefficient Fold: 0.862 PETfold_pre2.0(20): 0.854 Sensitivity Fold: 0.752 PETfold_pre2.0(20): 0.759 Positive Predictive Value Fold: 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 ContextFold: 0.759 Sensitivity PETfold_pre2.0(20): 0.759 ContextFold: 0.669 Positive Predictive Value PETfold_pre2.0(20): 0.962 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 MaxExpect: 0.783 Sensitivity PETfold_pre2.0(20): 0.759 MaxExpect: 0.677 Positive Predictive Value PETfold_pre2.0(20): 0.962 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Murlet(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Murlet(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Sfold: 0.721 Sensitivity PETfold_pre2.0(20): 0.759 Sfold: 0.624 Positive Predictive Value PETfold_pre2.0(20): 0.962 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 UNAFold: 0.649 Sensitivity PETfold_pre2.0(20): 0.759 UNAFold: 0.579 Positive Predictive Value PETfold_pre2.0(20): 0.962 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Vsfold4: 0.784 Sensitivity PETfold_pre2.0(20): 0.759 Vsfold4: 0.684 Positive Predictive Value PETfold_pre2.0(20): 0.962 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAshapes: 0.640 Sensitivity PETfold_pre2.0(20): 0.759 RNAshapes: 0.571 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAfold: 0.702 Sensitivity PETfold_pre2.0(20): 0.759 RNAfold: 0.617 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 MXScarna(seed): 0.827 Sensitivity PETfold_pre2.0(20): 0.750 MXScarna(seed): 0.713 Positive Predictive Value PETfold_pre2.0(20): 0.964 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAsubopt: 0.646 Sensitivity PETfold_pre2.0(20): 0.759 RNAsubopt: 0.579 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 RSpredict(seed): 0.602 Sensitivity PETfold_pre2.0(20): 0.750 RSpredict(seed): 0.435 Positive Predictive Value PETfold_pre2.0(20): 0.964 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CRWrnafold: 0.776 Sensitivity PETfold_pre2.0(20): 0.759 CRWrnafold: 0.684 Positive Predictive Value PETfold_pre2.0(20): 0.962 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 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	5 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAwolf: 0.661 Sensitivity PETfold_pre2.0(20): 0.759 RNAwolf: 0.647 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.873 Afold: 0.569 Sensitivity PETfold_pre2.0(20): 0.776 Afold: 0.500 Positive Predictive Value PETfold_pre2.0(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Alterna: 0.656 Sensitivity PETfold_pre2.0(20): 0.759 Alterna: 0.602 Positive Predictive Value PETfold_pre2.0(20): 0.962 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.849 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.750 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.964 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Mastr(20): 0.561 Sensitivity PETfold_pre2.0(20): 0.759 Mastr(20): 0.459 Positive Predictive Value PETfold_pre2.0(20): 0.962 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.876 NanoFolder: 0.144 Sensitivity PETfold_pre2.0(20): 0.788 NanoFolder: 0.173 Positive Predictive Value PETfold_pre2.0(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Carnac(20): 0.821 Sensitivity PETfold_pre2.0(20): 0.759 Carnac(20): 0.684 Positive Predictive Value PETfold_pre2.0(20): 0.962 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Multilign(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Multilign(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Multilign(20): 0.862 PETfold_pre2.0(20): 0.854 Sensitivity Multilign(20): 0.752 PETfold_pre2.0(20): 0.759 Positive Predictive Value Multilign(20): 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.857 PETfold_pre2.0(20): 0.854 Sensitivity TurboFold(20): 0.744 PETfold_pre2.0(20): 0.759 Positive Predictive Value TurboFold(20): 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNAalifold(20): 0.844 Sensitivity PETfold_pre2.0(20): 0.759 RNAalifold(20): 0.722 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RNASampler(20): 0.840 Sensitivity PETfold_pre2.0(20): 0.759 RNASampler(20): 0.714 Positive Predictive Value PETfold_pre2.0(20): 0.962 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 CMfinder(20): 0.779 Sensitivity PETfold_pre2.0(20): 0.759 CMfinder(20): 0.617 Positive Predictive Value PETfold_pre2.0(20): 0.962 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? PPfold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_pre2.0(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): 0.854 MXScarna(20): 0.837 Sensitivity PETfold_pre2.0(20): 0.759 MXScarna(20): 0.752 Positive Predictive Value PETfold_pre2.0(20): 0.962 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RSpredict(20): 0.672 Sensitivity PETfold_pre2.0(20): 0.759 RSpredict(20): 0.549 Positive Predictive Value PETfold_pre2.0(20): 0.962 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PETfold_pre2.0(20): 0.854 Sensitivity CentroidAlifold(20): 0.752 PETfold_pre2.0(20): 0.759 Positive Predictive Value CentroidAlifold(20): 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Murlet(20): 0.741 Sensitivity PETfold_pre2.0(20): 0.759 Murlet(20): 0.594 Positive Predictive Value PETfold_pre2.0(20): 0.962 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 PPfold(20): 0.840 Sensitivity PETfold_pre2.0(20): 0.759 PPfold(20): 0.737 Positive Predictive Value PETfold_pre2.0(20): 0.962 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 MCFold: 0.291 Sensitivity PETfold_pre2.0(20): 0.759 MCFold: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.962 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PPfold(seed)	7 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.943 PPfold(seed): 0.656 Sensitivity Cylofold: 0.935 PPfold(seed): 0.532 Positive Predictive Value Cylofold: 0.951 PPfold(seed): 0.815 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.932 PPfold(seed): 0.666 Sensitivity McQFold: 0.936 PPfold(seed): 0.536 Positive Predictive Value McQFold: 0.929 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.886 PPfold(seed): 0.666 Sensitivity Pknots: 0.893 PPfold(seed): 0.536 Positive Predictive Value Pknots: 0.880 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 PPfold(seed): 0.666 Sensitivity CentroidAlifold(seed): 0.536 PPfold(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.893 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.949 PPfold(seed): 0.666 Sensitivity PknotsRG: 0.943 PPfold(seed): 0.536 Positive Predictive Value PknotsRG: 0.957 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 PETfold_pre2.0(seed): 0.619 Sensitivity PPfold(seed): 0.536 PETfold_pre2.0(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 PETfold_pre2.0(seed): 0.721 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNASampler(seed): 0.569 Sensitivity PPfold(seed): 0.536 RNASampler(seed): 0.507 Positive Predictive Value PPfold(seed): 0.833 RNASampler(seed): 0.645 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.684 PPfold(seed): 0.666 Sensitivity IPknot: 0.586 PPfold(seed): 0.536 Positive Predictive Value IPknot: 0.804 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RNAalifold(seed): 0.644 Sensitivity PPfold(seed): 0.536 RNAalifold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 RNAalifold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidFold: 0.618 Sensitivity PPfold(seed): 0.536 CentroidFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 CentroidFold: 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): 0.666 CentroidHomfold‑LAST: 0.584 Sensitivity PPfold(seed): 0.536 CentroidHomfold‑LAST: 0.486 Positive Predictive Value PPfold(seed): 0.833 CentroidHomfold‑LAST: 0.708 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold5: 0.423 Sensitivity PPfold(seed): 0.536 Vsfold5: 0.407 Positive Predictive Value PPfold(seed): 0.833 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Carnac(seed): 0.625 Sensitivity PPfold(seed): 0.536 Carnac(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs ProbKnot Matthews Correlation Coefficient PPfold(seed): 0.666 ProbKnot: 0.539 Sensitivity PPfold(seed): 0.536 ProbKnot: 0.521 Positive Predictive Value PPfold(seed): 0.833 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.666 RNASLOpt: 0.588 Sensitivity PPfold(seed): 0.536 RNASLOpt: 0.514 Positive Predictive Value PPfold(seed): 0.833 RNASLOpt: 0.679 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): 0.666 Contrafold: 0.596 Sensitivity PPfold(seed): 0.536 Contrafold: 0.521 Positive Predictive Value PPfold(seed): 0.833 Contrafold: 0.689 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs HotKnots Matthews Correlation Coefficient PPfold(seed): 0.666 HotKnots: 0.566 Sensitivity PPfold(seed): 0.536 HotKnots: 0.586 Positive Predictive Value PPfold(seed): 0.833 HotKnots: 0.554 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RDfolder Matthews Correlation Coefficient PPfold(seed): 0.666 RDfolder: 0.593 Sensitivity PPfold(seed): 0.536 RDfolder: 0.486 Positive Predictive Value PPfold(seed): 0.833 RDfolder: 0.731 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Fold Matthews Correlation Coefficient PPfold(seed): 0.666 Fold: 0.457 Sensitivity PPfold(seed): 0.536 Fold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Fold: 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs ContextFold Matthews Correlation Coefficient PPfold(seed): 0.666 ContextFold: 0.566 Sensitivity PPfold(seed): 0.536 ContextFold: 0.514 Positive Predictive Value PPfold(seed): 0.833 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs MaxExpect Matthews Correlation Coefficient PPfold(seed): 0.666 MaxExpect: 0.553 Sensitivity PPfold(seed): 0.536 MaxExpect: 0.521 Positive Predictive Value PPfold(seed): 0.833 MaxExpect: 0.593 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Murlet(seed): 0.518 Sensitivity PPfold(seed): 0.536 Murlet(seed): 0.379 Positive Predictive Value PPfold(seed): 0.833 Murlet(seed): 0.716 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Sfold Matthews Correlation Coefficient PPfold(seed): 0.666 Sfold: 0.494 Sensitivity PPfold(seed): 0.536 Sfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 Sfold: 0.542 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs UNAFold Matthews Correlation Coefficient PPfold(seed): 0.666 UNAFold: 0.483 Sensitivity PPfold(seed): 0.536 UNAFold: 0.457 Positive Predictive Value PPfold(seed): 0.833 UNAFold: 0.520 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.666 Vsfold4: 0.260 Sensitivity PPfold(seed): 0.536 Vsfold4: 0.243 Positive Predictive Value PPfold(seed): 0.833 Vsfold4: 0.291 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): 0.666 RNAshapes: 0.481 Sensitivity PPfold(seed): 0.536 RNAshapes: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAshapes: 0.516 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAfold Matthews Correlation Coefficient PPfold(seed): 0.666 RNAfold: 0.472 Sensitivity PPfold(seed): 0.536 RNAfold: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAfold: 0.496 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 MXScarna(seed): 0.468 Sensitivity PPfold(seed): 0.536 MXScarna(seed): 0.464 Positive Predictive Value PPfold(seed): 0.833 MXScarna(seed): 0.481 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): 0.666 RNAsubopt: 0.478 Sensitivity PPfold(seed): 0.536 RNAsubopt: 0.457 Positive Predictive Value PPfold(seed): 0.833 RNAsubopt: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 RSpredict(seed): 0.437 Sensitivity PPfold(seed): 0.536 RSpredict(seed): 0.407 Positive Predictive Value PPfold(seed): 0.833 RSpredict(seed): 0.479 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.666 CRWrnafold: 0.400 Sensitivity PPfold(seed): 0.536 CRWrnafold: 0.386 Positive Predictive Value PPfold(seed): 0.833 CRWrnafold: 0.425 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.662 CMfinder(seed): 0.553 Sensitivity PPfold(seed): 0.529 CMfinder(seed): 0.404 Positive Predictive Value PPfold(seed): 0.833 CMfinder(seed): 0.764 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.666 RNAwolf: 0.455 Sensitivity PPfold(seed): 0.536 RNAwolf: 0.429 Positive Predictive Value PPfold(seed): 0.833 RNAwolf: 0.492 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.664 Afold: 0.480 Sensitivity PPfold(seed): 0.533 Afold: 0.443 Positive Predictive Value PPfold(seed): 0.833 Afold: 0.529 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Alterna Matthews Correlation Coefficient PPfold(seed): 0.666 Alterna: 0.414 Sensitivity PPfold(seed): 0.536 Alterna: 0.386 Positive Predictive Value PPfold(seed): 0.833 Alterna: 0.454 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Mastr(seed): 0.540 Sensitivity PPfold(seed): 0.536 Mastr(seed): 0.450 Positive Predictive Value PPfold(seed): 0.833 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): N/A PPfold(seed): N/A Sensitivity Mastr(20): N/A PPfold(seed): N/A Positive Predictive Value Mastr(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	3 PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.698 NanoFolder: 0.585 Sensitivity PPfold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value PPfold(seed): 0.879 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs Carnac(20) Matthews Correlation Coefficient PPfold(seed): N/A Carnac(20): N/A Sensitivity PPfold(seed): N/A Carnac(20): N/A Positive Predictive Value PPfold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 Multilign(seed): 0.575 Sensitivity PPfold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs Multilign(20) Matthews Correlation Coefficient PPfold(seed): N/A Multilign(20): N/A Sensitivity PPfold(seed): N/A Multilign(20): N/A Positive Predictive Value PPfold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): N/A PPfold(seed): N/A Sensitivity TurboFold(20): N/A PPfold(seed): N/A Positive Predictive Value TurboFold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): N/A PPfold(seed): N/A Sensitivity RNAalifold(20): N/A PPfold(seed): N/A Positive Predictive Value RNAalifold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): N/A PPfold(seed): N/A Sensitivity RNASampler(20): N/A PPfold(seed): N/A Positive Predictive Value RNASampler(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity PPfold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value PPfold(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PPfold(seed) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 TurboFold(seed): 0.644 Sensitivity PPfold(seed): 0.536 TurboFold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 TurboFold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs MXScarna(20) Matthews Correlation Coefficient PPfold(seed): N/A MXScarna(20): N/A Sensitivity PPfold(seed): N/A MXScarna(20): N/A Positive Predictive Value PPfold(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): N/A PPfold(seed): N/A Sensitivity RSpredict(20): N/A PPfold(seed): N/A Positive Predictive Value RSpredict(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(seed): N/A CentroidAlifold(20): N/A Sensitivity PPfold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value PPfold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Murlet(20) Matthews Correlation Coefficient PPfold(seed): N/A Murlet(20): N/A Sensitivity PPfold(seed): N/A Murlet(20): N/A Positive Predictive Value PPfold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): N/A PPfold(seed): N/A Sensitivity PPfold(20): N/A PPfold(seed): N/A Positive Predictive Value PPfold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs MCFold Matthews Correlation Coefficient PPfold(seed): 0.666 MCFold: 0.340 Sensitivity PPfold(seed): 0.536 MCFold: 0.407 Positive Predictive Value PPfold(seed): 0.833 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
TurboFold(seed)	8 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.911 TurboFold(seed): 0.587 Sensitivity Cylofold: 0.914 TurboFold(seed): 0.513 Positive Predictive Value Cylofold: 0.908 TurboFold(seed): 0.678 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 McQFold vs TurboFold(seed) Matthews Correlation Coefficient McQFold: 0.898 TurboFold(seed): 0.600 Sensitivity McQFold: 0.899 TurboFold(seed): 0.518 Positive Predictive Value McQFold: 0.899 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Pknots vs TurboFold(seed) Matthews Correlation Coefficient Pknots: 0.870 TurboFold(seed): 0.600 Sensitivity Pknots: 0.887 TurboFold(seed): 0.518 Positive Predictive Value Pknots: 0.856 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.706 TurboFold(seed): 0.600 Sensitivity CentroidAlifold(seed): 0.560 TurboFold(seed): 0.518 Positive Predictive Value CentroidAlifold(seed): 0.895 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.949 TurboFold(seed): 0.600 Sensitivity PknotsRG: 0.946 TurboFold(seed): 0.518 Positive Predictive Value PknotsRG: 0.952 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.638 TurboFold(seed): 0.600 Sensitivity PETfold_pre2.0(seed): 0.560 TurboFold(seed): 0.518 Positive Predictive Value PETfold_pre2.0(seed): 0.734 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.615 TurboFold(seed): 0.600 Sensitivity RNASampler(seed): 0.548 TurboFold(seed): 0.518 Positive Predictive Value RNASampler(seed): 0.697 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.677 TurboFold(seed): 0.600 Sensitivity IPknot: 0.595 TurboFold(seed): 0.518 Positive Predictive Value IPknot: 0.775 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.621 TurboFold(seed): 0.600 Sensitivity RNAalifold(seed): 0.500 TurboFold(seed): 0.518 Positive Predictive Value RNAalifold(seed): 0.778 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.621 TurboFold(seed): 0.600 Sensitivity CentroidFold: 0.536 TurboFold(seed): 0.518 Positive Predictive Value CentroidFold: 0.726 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.600 CentroidHomfold‑LAST: 0.593 Sensitivity TurboFold(seed): 0.518 CentroidHomfold‑LAST: 0.512 Positive Predictive Value TurboFold(seed): 0.702 CentroidHomfold‑LAST: 0.694 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.600 Vsfold5: 0.449 Sensitivity TurboFold(seed): 0.518 Vsfold5: 0.435 Positive Predictive Value TurboFold(seed): 0.702 Vsfold5: 0.474 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Carnac(seed): 0.571 Sensitivity TurboFold(seed): 0.518 Carnac(seed): 0.339 Positive Predictive Value TurboFold(seed): 0.702 Carnac(seed): 0.966 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.600 ProbKnot: 0.522 Sensitivity TurboFold(seed): 0.518 ProbKnot: 0.512 Positive Predictive Value TurboFold(seed): 0.702 ProbKnot: 0.541 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.600 RNASLOpt: 0.599 Sensitivity TurboFold(seed): 0.518 RNASLOpt: 0.536 Positive Predictive Value TurboFold(seed): 0.702 RNASLOpt: 0.677 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.600 Contrafold: 0.595 Sensitivity TurboFold(seed): 0.518 Contrafold: 0.542 Positive Predictive Value TurboFold(seed): 0.702 Contrafold: 0.659 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.600 HotKnots: 0.543 Sensitivity TurboFold(seed): 0.518 HotKnots: 0.560 Positive Predictive Value TurboFold(seed): 0.702 HotKnots: 0.534 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RDfolder vs TurboFold(seed) Matthews Correlation Coefficient RDfolder: 0.603 TurboFold(seed): 0.600 Sensitivity RDfolder: 0.512 TurboFold(seed): 0.518 Positive Predictive Value RDfolder: 0.717 TurboFold(seed): 0.702 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.600 Fold: 0.451 Sensitivity TurboFold(seed): 0.518 Fold: 0.440 Positive Predictive Value TurboFold(seed): 0.702 Fold: 0.471 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.600 ContextFold: 0.559 Sensitivity TurboFold(seed): 0.518 ContextFold: 0.500 Positive Predictive Value TurboFold(seed): 0.702 ContextFold: 0.632 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.600 MaxExpect: 0.526 Sensitivity TurboFold(seed): 0.518 MaxExpect: 0.506 Positive Predictive Value TurboFold(seed): 0.702 MaxExpect: 0.556 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Murlet(seed): 0.477 Sensitivity TurboFold(seed): 0.518 Murlet(seed): 0.333 Positive Predictive Value TurboFold(seed): 0.702 Murlet(seed): 0.691 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.600 Sfold: 0.476 Sensitivity TurboFold(seed): 0.518 Sfold: 0.446 Positive Predictive Value TurboFold(seed): 0.702 Sfold: 0.517 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.600 UNAFold: 0.475 Sensitivity TurboFold(seed): 0.518 UNAFold: 0.452 Positive Predictive Value TurboFold(seed): 0.702 UNAFold: 0.507 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.600 Vsfold4: 0.316 Sensitivity TurboFold(seed): 0.518 Vsfold4: 0.298 Positive Predictive Value TurboFold(seed): 0.702 Vsfold4: 0.347 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAshapes: 0.471 Sensitivity TurboFold(seed): 0.518 RNAshapes: 0.452 Positive Predictive Value TurboFold(seed): 0.702 RNAshapes: 0.500 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAfold: 0.464 Sensitivity TurboFold(seed): 0.518 RNAfold: 0.452 Positive Predictive Value TurboFold(seed): 0.702 RNAfold: 0.484 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 MXScarna(seed): 0.449 Sensitivity TurboFold(seed): 0.518 MXScarna(seed): 0.446 Positive Predictive Value TurboFold(seed): 0.702 MXScarna(seed): 0.460 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAsubopt: 0.468 Sensitivity TurboFold(seed): 0.518 RNAsubopt: 0.452 Positive Predictive Value TurboFold(seed): 0.702 RNAsubopt: 0.494 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 RSpredict(seed): 0.465 Sensitivity TurboFold(seed): 0.518 RSpredict(seed): 0.429 Positive Predictive Value TurboFold(seed): 0.702 RSpredict(seed): 0.514 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.600 CRWrnafold: 0.418 Sensitivity TurboFold(seed): 0.518 CRWrnafold: 0.405 Positive Predictive Value TurboFold(seed): 0.702 CRWrnafold: 0.442 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 CMfinder(seed) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(seed): 0.589 TurboFold(seed): 0.569 Sensitivity CMfinder(seed): 0.455 TurboFold(seed): 0.508 Positive Predictive Value CMfinder(seed): 0.769 TurboFold(seed): 0.644 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.600 RNAwolf: 0.444 Sensitivity TurboFold(seed): 0.518 RNAwolf: 0.423 Positive Predictive Value TurboFold(seed): 0.702 RNAwolf: 0.477 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.588 Afold: 0.469 Sensitivity TurboFold(seed): 0.513 Afold: 0.440 Positive Predictive Value TurboFold(seed): 0.681 Afold: 0.508 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.600 Alterna: 0.428 Sensitivity TurboFold(seed): 0.518 Alterna: 0.399 Positive Predictive Value TurboFold(seed): 0.702 Alterna: 0.469 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.600 Mastr(seed): 0.493 Sensitivity TurboFold(seed): 0.518 Mastr(seed): 0.375 Positive Predictive Value TurboFold(seed): 0.702 Mastr(seed): 0.656 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): N/A Mastr(20): N/A Sensitivity TurboFold(seed): N/A Mastr(20): N/A Positive Predictive Value TurboFold(seed): N/A Mastr(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	3 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.709 NanoFolder: 0.585 Sensitivity TurboFold(seed): 0.558 NanoFolder: 0.654 Positive Predictive Value TurboFold(seed): 0.906 NanoFolder: 0.531 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): N/A Carnac(20): N/A Sensitivity TurboFold(seed): N/A Carnac(20): N/A Positive Predictive Value TurboFold(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.644 Multilign(seed): 0.575 Sensitivity TurboFold(seed): 0.536 Multilign(seed): 0.536 Positive Predictive Value TurboFold(seed): 0.781 Multilign(seed): 0.625 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): N/A Multilign(20): N/A Sensitivity TurboFold(seed): N/A Multilign(20): N/A Positive Predictive Value TurboFold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs TurboFold(20) Matthews Correlation Coefficient TurboFold(seed): N/A TurboFold(20): N/A Sensitivity TurboFold(seed): N/A TurboFold(20): N/A Positive Predictive Value TurboFold(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A RNAalifold(20): N/A Sensitivity TurboFold(seed): N/A RNAalifold(20): N/A Positive Predictive Value TurboFold(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): N/A TurboFold(seed): N/A Sensitivity RNASampler(20): N/A TurboFold(seed): N/A Positive Predictive Value RNASampler(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): N/A PETfold_pre2.0(20): N/A Sensitivity TurboFold(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value TurboFold(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	8 PPfold(seed) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(seed): 0.666 TurboFold(seed): 0.644 Sensitivity PPfold(seed): 0.536 TurboFold(seed): 0.536 Positive Predictive Value PPfold(seed): 0.833 TurboFold(seed): 0.781 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): N/A MXScarna(20): N/A Sensitivity TurboFold(seed): N/A MXScarna(20): N/A Positive Predictive Value TurboFold(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs TurboFold(seed) Matthews Correlation Coefficient RSpredict(20): N/A TurboFold(seed): N/A Sensitivity RSpredict(20): N/A TurboFold(seed): N/A Positive Predictive Value RSpredict(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A CentroidAlifold(20): N/A Sensitivity TurboFold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value TurboFold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(20): N/A Sensitivity TurboFold(seed): N/A Murlet(20): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): N/A PPfold(20): N/A Sensitivity TurboFold(seed): N/A PPfold(20): N/A Positive Predictive Value TurboFold(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.600 MCFold: 0.343 Sensitivity TurboFold(seed): 0.518 MCFold: 0.405 Positive Predictive Value TurboFold(seed): 0.702 MCFold: 0.302 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
MXScarna(20)	5 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.837 Cylofold: 0.756 Sensitivity MXScarna(20): 0.752 Cylofold: 0.677 Positive Predictive Value MXScarna(20): 0.935 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.837 McQFold: 0.777 Sensitivity MXScarna(20): 0.752 McQFold: 0.692 Positive Predictive Value MXScarna(20): 0.935 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.837 Pknots: 0.723 Sensitivity MXScarna(20): 0.752 Pknots: 0.632 Positive Predictive Value MXScarna(20): 0.935 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 MXScarna(20): 0.855 Sensitivity CentroidAlifold(seed): 0.778 MXScarna(20): 0.769 Positive Predictive Value CentroidAlifold(seed): 1.000 MXScarna(20): 0.954 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.837 PknotsRG: 0.592 Sensitivity MXScarna(20): 0.752 PknotsRG: 0.526 Positive Predictive Value MXScarna(20): 0.935 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient MXScarna(20): 0.837 PETfold_pre2.0(seed): 0.835 Sensitivity MXScarna(20): 0.752 PETfold_pre2.0(seed): 0.774 Positive Predictive Value MXScarna(20): 0.935 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(20): N/A Sensitivity RNASampler(seed): N/A MXScarna(20): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.840 MXScarna(20): 0.837 Sensitivity IPknot: 0.737 MXScarna(20): 0.752 Positive Predictive Value IPknot: 0.961 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 RNAalifold(seed): 0.750 Sensitivity MXScarna(20): 0.769 RNAalifold(seed): 0.639 Positive Predictive Value MXScarna(20): 0.954 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs MXScarna(20) Matthews Correlation Coefficient CentroidFold: 0.849 MXScarna(20): 0.837 Sensitivity CentroidFold: 0.729 MXScarna(20): 0.752 Positive Predictive Value CentroidFold: 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 MXScarna(20): 0.837 Sensitivity CentroidHomfold‑LAST: 0.729 MXScarna(20): 0.752 Positive Predictive Value CentroidHomfold‑LAST: 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.837 Vsfold5: 0.774 Sensitivity MXScarna(20): 0.752 Vsfold5: 0.699 Positive Predictive Value MXScarna(20): 0.935 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): N/A Carnac(seed): N/A Sensitivity MXScarna(20): N/A Carnac(seed): N/A Positive Predictive Value MXScarna(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.837 ProbKnot: 0.803 Sensitivity MXScarna(20): 0.752 ProbKnot: 0.722 Positive Predictive Value MXScarna(20): 0.935 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.837 RNASLOpt: 0.792 Sensitivity MXScarna(20): 0.752 RNASLOpt: 0.692 Positive Predictive Value MXScarna(20): 0.935 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs MXScarna(20) Matthews Correlation Coefficient Contrafold: 0.854 MXScarna(20): 0.837 Sensitivity Contrafold: 0.759 MXScarna(20): 0.752 Positive Predictive Value Contrafold: 0.962 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.837 HotKnots: 0.717 Sensitivity MXScarna(20): 0.752 HotKnots: 0.639 Positive Predictive Value MXScarna(20): 0.935 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.837 RDfolder: 0.664 Sensitivity MXScarna(20): 0.752 RDfolder: 0.586 Positive Predictive Value MXScarna(20): 0.935 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs MXScarna(20) Matthews Correlation Coefficient Fold: 0.862 MXScarna(20): 0.837 Sensitivity Fold: 0.752 MXScarna(20): 0.752 Positive Predictive Value Fold: 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs ContextFold Matthews Correlation Coefficient MXScarna(20): 0.837 ContextFold: 0.759 Sensitivity MXScarna(20): 0.752 ContextFold: 0.669 Positive Predictive Value MXScarna(20): 0.935 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.837 MaxExpect: 0.783 Sensitivity MXScarna(20): 0.752 MaxExpect: 0.677 Positive Predictive Value MXScarna(20): 0.935 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Murlet(seed) vs MXScarna(20) Matthews Correlation Coefficient Murlet(seed): N/A MXScarna(20): N/A Sensitivity Murlet(seed): N/A MXScarna(20): N/A Positive Predictive Value Murlet(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.837 Sfold: 0.721 Sensitivity MXScarna(20): 0.752 Sfold: 0.624 Positive Predictive Value MXScarna(20): 0.935 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.837 UNAFold: 0.649 Sensitivity MXScarna(20): 0.752 UNAFold: 0.579 Positive Predictive Value MXScarna(20): 0.935 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.837 Vsfold4: 0.784 Sensitivity MXScarna(20): 0.752 Vsfold4: 0.684 Positive Predictive Value MXScarna(20): 0.935 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.837 RNAshapes: 0.640 Sensitivity MXScarna(20): 0.752 RNAshapes: 0.571 Positive Predictive Value MXScarna(20): 0.935 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.837 RNAfold: 0.702 Sensitivity MXScarna(20): 0.752 RNAfold: 0.617 Positive Predictive Value MXScarna(20): 0.935 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs MXScarna(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 MXScarna(seed): 0.827 Sensitivity MXScarna(20): 0.769 MXScarna(seed): 0.713 Positive Predictive Value MXScarna(20): 0.954 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.837 RNAsubopt: 0.646 Sensitivity MXScarna(20): 0.752 RNAsubopt: 0.579 Positive Predictive Value MXScarna(20): 0.935 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 RSpredict(seed): 0.602 Sensitivity MXScarna(20): 0.769 RSpredict(seed): 0.435 Positive Predictive Value MXScarna(20): 0.954 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.837 CRWrnafold: 0.776 Sensitivity MXScarna(20): 0.752 CRWrnafold: 0.684 Positive Predictive Value MXScarna(20): 0.935 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.837 RNAwolf: 0.661 Sensitivity MXScarna(20): 0.752 RNAwolf: 0.647 Positive Predictive Value MXScarna(20): 0.935 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.835 Afold: 0.569 Sensitivity MXScarna(20): 0.737 Afold: 0.500 Positive Predictive Value MXScarna(20): 0.949 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.837 Alterna: 0.656 Sensitivity MXScarna(20): 0.752 Alterna: 0.602 Positive Predictive Value MXScarna(20): 0.935 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.855 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.769 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.954 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.837 Mastr(20): 0.561 Sensitivity MXScarna(20): 0.752 Mastr(20): 0.459 Positive Predictive Value MXScarna(20): 0.935 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.810 NanoFolder: 0.144 Sensitivity MXScarna(20): 0.712 NanoFolder: 0.173 Positive Predictive Value MXScarna(20): 0.925 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.837 Carnac(20): 0.821 Sensitivity MXScarna(20): 0.752 Carnac(20): 0.684 Positive Predictive Value MXScarna(20): 0.935 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(20): N/A Sensitivity Multilign(seed): N/A MXScarna(20): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.862 MXScarna(20): 0.837 Sensitivity Multilign(20): 0.752 MXScarna(20): 0.752 Positive Predictive Value Multilign(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.857 MXScarna(20): 0.837 Sensitivity TurboFold(20): 0.744 MXScarna(20): 0.752 Positive Predictive Value TurboFold(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 MXScarna(20): 0.837 Sensitivity RNAalifold(20): 0.722 MXScarna(20): 0.752 Positive Predictive Value RNAalifold(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.840 MXScarna(20): 0.837 Sensitivity RNASampler(20): 0.714 MXScarna(20): 0.752 Positive Predictive Value RNASampler(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.837 CMfinder(20): 0.779 Sensitivity MXScarna(20): 0.752 CMfinder(20): 0.617 Positive Predictive Value MXScarna(20): 0.935 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 MXScarna(20): 0.837 Sensitivity PETfold_pre2.0(20): 0.759 MXScarna(20): 0.752 Positive Predictive Value PETfold_pre2.0(20): 0.962 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs MXScarna(20) Matthews Correlation Coefficient PPfold(seed): N/A MXScarna(20): N/A Sensitivity PPfold(seed): N/A MXScarna(20): N/A Positive Predictive Value PPfold(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): N/A MXScarna(20): N/A Sensitivity TurboFold(seed): N/A MXScarna(20): N/A Positive Predictive Value TurboFold(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.837 RSpredict(20): 0.672 Sensitivity MXScarna(20): 0.752 RSpredict(20): 0.549 Positive Predictive Value MXScarna(20): 0.935 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MXScarna(20): 0.837 Sensitivity CentroidAlifold(20): 0.752 MXScarna(20): 0.752 Positive Predictive Value CentroidAlifold(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.837 Murlet(20): 0.741 Sensitivity MXScarna(20): 0.752 Murlet(20): 0.594 Positive Predictive Value MXScarna(20): 0.935 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.840 MXScarna(20): 0.837 Sensitivity PPfold(20): 0.737 MXScarna(20): 0.752 Positive Predictive Value PPfold(20): 0.961 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.837 MCFold: 0.291 Sensitivity MXScarna(20): 0.752 MCFold: 0.323 Positive Predictive Value MXScarna(20): 0.935 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
RSpredict(20)	5 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.756 RSpredict(20): 0.672 Sensitivity Cylofold: 0.677 RSpredict(20): 0.549 Positive Predictive Value Cylofold: 0.849 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.777 RSpredict(20): 0.672 Sensitivity McQFold: 0.692 RSpredict(20): 0.549 Positive Predictive Value McQFold: 0.876 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Pknots vs RSpredict(20) Matthews Correlation Coefficient Pknots: 0.723 RSpredict(20): 0.672 Sensitivity Pknots: 0.632 RSpredict(20): 0.549 Positive Predictive Value Pknots: 0.832 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 RSpredict(20): 0.676 Sensitivity CentroidAlifold(seed): 0.778 RSpredict(20): 0.546 Positive Predictive Value CentroidAlifold(seed): 1.000 RSpredict(20): 0.843 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.672 PknotsRG: 0.592 Sensitivity RSpredict(20): 0.549 PknotsRG: 0.526 Positive Predictive Value RSpredict(20): 0.830 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RSpredict(20): 0.672 Sensitivity PETfold_pre2.0(seed): 0.774 RSpredict(20): 0.549 Positive Predictive Value PETfold_pre2.0(seed): 0.904 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): N/A RNASampler(seed): N/A Sensitivity RSpredict(20): N/A RNASampler(seed): N/A Positive Predictive Value RSpredict(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.840 RSpredict(20): 0.672 Sensitivity IPknot: 0.737 RSpredict(20): 0.549 Positive Predictive Value IPknot: 0.961 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.750 RSpredict(20): 0.676 Sensitivity RNAalifold(seed): 0.639 RSpredict(20): 0.546 Positive Predictive Value RNAalifold(seed): 0.885 RSpredict(20): 0.843 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.849 RSpredict(20): 0.672 Sensitivity CentroidFold: 0.729 RSpredict(20): 0.549 Positive Predictive Value CentroidFold: 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 RSpredict(20): 0.672 Sensitivity CentroidHomfold‑LAST: 0.729 RSpredict(20): 0.549 Positive Predictive Value CentroidHomfold‑LAST: 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Vsfold5 vs RSpredict(20) Matthews Correlation Coefficient Vsfold5: 0.774 RSpredict(20): 0.672 Sensitivity Vsfold5: 0.699 RSpredict(20): 0.549 Positive Predictive Value Vsfold5: 0.861 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): N/A Carnac(seed): N/A Sensitivity RSpredict(20): N/A Carnac(seed): N/A Positive Predictive Value RSpredict(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.803 RSpredict(20): 0.672 Sensitivity ProbKnot: 0.722 RSpredict(20): 0.549 Positive Predictive Value ProbKnot: 0.897 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.792 RSpredict(20): 0.672 Sensitivity RNASLOpt: 0.692 RSpredict(20): 0.549 Positive Predictive Value RNASLOpt: 0.911 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.854 RSpredict(20): 0.672 Sensitivity Contrafold: 0.759 RSpredict(20): 0.549 Positive Predictive Value Contrafold: 0.962 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.717 RSpredict(20): 0.672 Sensitivity HotKnots: 0.639 RSpredict(20): 0.549 Positive Predictive Value HotKnots: 0.810 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.672 RDfolder: 0.664 Sensitivity RSpredict(20): 0.549 RDfolder: 0.586 Positive Predictive Value RSpredict(20): 0.830 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.862 RSpredict(20): 0.672 Sensitivity Fold: 0.752 RSpredict(20): 0.549 Positive Predictive Value Fold: 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.759 RSpredict(20): 0.672 Sensitivity ContextFold: 0.669 RSpredict(20): 0.549 Positive Predictive Value ContextFold: 0.864 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.783 RSpredict(20): 0.672 Sensitivity MaxExpect: 0.677 RSpredict(20): 0.549 Positive Predictive Value MaxExpect: 0.909 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): N/A Murlet(seed): N/A Sensitivity RSpredict(20): N/A Murlet(seed): N/A Positive Predictive Value RSpredict(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.721 RSpredict(20): 0.672 Sensitivity Sfold: 0.624 RSpredict(20): 0.549 Positive Predictive Value Sfold: 0.838 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.672 UNAFold: 0.649 Sensitivity RSpredict(20): 0.549 UNAFold: 0.579 Positive Predictive Value RSpredict(20): 0.830 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Vsfold4 vs RSpredict(20) Matthews Correlation Coefficient Vsfold4: 0.784 RSpredict(20): 0.672 Sensitivity Vsfold4: 0.684 RSpredict(20): 0.549 Positive Predictive Value Vsfold4: 0.901 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.672 RNAshapes: 0.640 Sensitivity RSpredict(20): 0.549 RNAshapes: 0.571 Positive Predictive Value RSpredict(20): 0.830 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.702 RSpredict(20): 0.672 Sensitivity RNAfold: 0.617 RSpredict(20): 0.549 Positive Predictive Value RNAfold: 0.804 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 RSpredict(20): 0.676 Sensitivity MXScarna(seed): 0.713 RSpredict(20): 0.546 Positive Predictive Value MXScarna(seed): 0.963 RSpredict(20): 0.843 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.672 RNAsubopt: 0.646 Sensitivity RSpredict(20): 0.549 RNAsubopt: 0.579 Positive Predictive Value RSpredict(20): 0.830 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.676 RSpredict(seed): 0.602 Sensitivity RSpredict(20): 0.546 RSpredict(seed): 0.435 Positive Predictive Value RSpredict(20): 0.843 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.776 RSpredict(20): 0.672 Sensitivity CRWrnafold: 0.684 RSpredict(20): 0.549 Positive Predictive Value CRWrnafold: 0.883 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.672 RNAwolf: 0.661 Sensitivity RSpredict(20): 0.549 RNAwolf: 0.647 Positive Predictive Value RSpredict(20): 0.830 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.730 Afold: 0.569 Sensitivity RSpredict(20): 0.645 Afold: 0.500 Positive Predictive Value RSpredict(20): 0.831 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.672 Alterna: 0.656 Sensitivity RSpredict(20): 0.549 Alterna: 0.602 Positive Predictive Value RSpredict(20): 0.830 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.676 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.546 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.672 Mastr(20): 0.561 Sensitivity RSpredict(20): 0.549 Mastr(20): 0.459 Positive Predictive Value RSpredict(20): 0.830 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.744 NanoFolder: 0.144 Sensitivity RSpredict(20): 0.654 NanoFolder: 0.173 Positive Predictive Value RSpredict(20): 0.850 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.821 RSpredict(20): 0.672 Sensitivity Carnac(20): 0.684 RSpredict(20): 0.549 Positive Predictive Value Carnac(20): 0.989 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): N/A Multilign(seed): N/A Sensitivity RSpredict(20): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.862 RSpredict(20): 0.672 Sensitivity Multilign(20): 0.752 RSpredict(20): 0.549 Positive Predictive Value Multilign(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.857 RSpredict(20): 0.672 Sensitivity TurboFold(20): 0.744 RSpredict(20): 0.549 Positive Predictive Value TurboFold(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 RSpredict(20): 0.672 Sensitivity RNAalifold(20): 0.722 RSpredict(20): 0.549 Positive Predictive Value RNAalifold(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.840 RSpredict(20): 0.672 Sensitivity RNASampler(20): 0.714 RSpredict(20): 0.549 Positive Predictive Value RNASampler(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.779 RSpredict(20): 0.672 Sensitivity CMfinder(20): 0.617 RSpredict(20): 0.549 Positive Predictive Value CMfinder(20): 0.988 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 RSpredict(20): 0.672 Sensitivity PETfold_pre2.0(20): 0.759 RSpredict(20): 0.549 Positive Predictive Value PETfold_pre2.0(20): 0.962 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): N/A PPfold(seed): N/A Sensitivity RSpredict(20): N/A PPfold(seed): N/A Positive Predictive Value RSpredict(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs TurboFold(seed) Matthews Correlation Coefficient RSpredict(20): N/A TurboFold(seed): N/A Sensitivity RSpredict(20): N/A TurboFold(seed): N/A Positive Predictive Value RSpredict(20): N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.837 RSpredict(20): 0.672 Sensitivity MXScarna(20): 0.752 RSpredict(20): 0.549 Positive Predictive Value MXScarna(20): 0.935 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RSpredict(20): 0.672 Sensitivity CentroidAlifold(20): 0.752 RSpredict(20): 0.549 Positive Predictive Value CentroidAlifold(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.741 RSpredict(20): 0.672 Sensitivity Murlet(20): 0.594 RSpredict(20): 0.549 Positive Predictive Value Murlet(20): 0.929 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.840 RSpredict(20): 0.672 Sensitivity PPfold(20): 0.737 RSpredict(20): 0.549 Positive Predictive Value PPfold(20): 0.961 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.672 MCFold: 0.291 Sensitivity RSpredict(20): 0.549 MCFold: 0.323 Positive Predictive Value RSpredict(20): 0.830 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
CentroidAlifold(20)	5 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Cylofold: 0.756 Sensitivity CentroidAlifold(20): 0.752 Cylofold: 0.677 Positive Predictive Value CentroidAlifold(20): 0.990 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 McQFold: 0.777 Sensitivity CentroidAlifold(20): 0.752 McQFold: 0.692 Positive Predictive Value CentroidAlifold(20): 0.990 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Pknots: 0.723 Sensitivity CentroidAlifold(20): 0.752 Pknots: 0.632 Positive Predictive Value CentroidAlifold(20): 0.990 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 CentroidAlifold(20): 0.860 Sensitivity CentroidAlifold(seed): 0.778 CentroidAlifold(20): 0.741 Positive Predictive Value CentroidAlifold(seed): 1.000 CentroidAlifold(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PknotsRG: 0.592 Sensitivity CentroidAlifold(20): 0.752 PknotsRG: 0.526 Positive Predictive Value CentroidAlifold(20): 0.990 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PETfold_pre2.0(seed): 0.835 Sensitivity CentroidAlifold(20): 0.752 PETfold_pre2.0(seed): 0.774 Positive Predictive Value CentroidAlifold(20): 0.990 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(20): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.862 IPknot: 0.840 Sensitivity CentroidAlifold(20): 0.752 IPknot: 0.737 Positive Predictive Value CentroidAlifold(20): 0.990 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 RNAalifold(seed): 0.750 Sensitivity CentroidAlifold(20): 0.741 RNAalifold(seed): 0.639 Positive Predictive Value CentroidAlifold(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CentroidFold: 0.849 Sensitivity CentroidAlifold(20): 0.752 CentroidFold: 0.729 Positive Predictive Value CentroidAlifold(20): 0.990 CentroidFold: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CentroidHomfold‑LAST: 0.849 Sensitivity CentroidAlifold(20): 0.752 CentroidHomfold‑LAST: 0.729 Positive Predictive Value CentroidAlifold(20): 0.990 CentroidHomfold‑LAST: 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Vsfold5: 0.774 Sensitivity CentroidAlifold(20): 0.752 Vsfold5: 0.699 Positive Predictive Value CentroidAlifold(20): 0.990 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): N/A Carnac(seed): N/A Sensitivity CentroidAlifold(20): N/A Carnac(seed): N/A Positive Predictive Value CentroidAlifold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.862 ProbKnot: 0.803 Sensitivity CentroidAlifold(20): 0.752 ProbKnot: 0.722 Positive Predictive Value CentroidAlifold(20): 0.990 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNASLOpt: 0.792 Sensitivity CentroidAlifold(20): 0.752 RNASLOpt: 0.692 Positive Predictive Value CentroidAlifold(20): 0.990 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Contrafold: 0.854 Sensitivity CentroidAlifold(20): 0.752 Contrafold: 0.759 Positive Predictive Value CentroidAlifold(20): 0.990 Contrafold: 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.862 HotKnots: 0.717 Sensitivity CentroidAlifold(20): 0.752 HotKnots: 0.639 Positive Predictive Value CentroidAlifold(20): 0.990 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RDfolder: 0.664 Sensitivity CentroidAlifold(20): 0.752 RDfolder: 0.586 Positive Predictive Value CentroidAlifold(20): 0.990 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs CentroidAlifold(20) Matthews Correlation Coefficient Fold: 0.862 CentroidAlifold(20): 0.862 Sensitivity Fold: 0.752 CentroidAlifold(20): 0.752 Positive Predictive Value Fold: 0.990 CentroidAlifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 ContextFold: 0.759 Sensitivity CentroidAlifold(20): 0.752 ContextFold: 0.669 Positive Predictive Value CentroidAlifold(20): 0.990 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MaxExpect: 0.783 Sensitivity CentroidAlifold(20): 0.752 MaxExpect: 0.677 Positive Predictive Value CentroidAlifold(20): 0.990 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): N/A Murlet(seed): N/A Sensitivity CentroidAlifold(20): N/A Murlet(seed): N/A Positive Predictive Value CentroidAlifold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Sfold: 0.721 Sensitivity CentroidAlifold(20): 0.752 Sfold: 0.624 Positive Predictive Value CentroidAlifold(20): 0.990 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 UNAFold: 0.649 Sensitivity CentroidAlifold(20): 0.752 UNAFold: 0.579 Positive Predictive Value CentroidAlifold(20): 0.990 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Vsfold4: 0.784 Sensitivity CentroidAlifold(20): 0.752 Vsfold4: 0.684 Positive Predictive Value CentroidAlifold(20): 0.990 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAshapes: 0.640 Sensitivity CentroidAlifold(20): 0.752 RNAshapes: 0.571 Positive Predictive Value CentroidAlifold(20): 0.990 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAfold: 0.702 Sensitivity CentroidAlifold(20): 0.752 RNAfold: 0.617 Positive Predictive Value CentroidAlifold(20): 0.990 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 MXScarna(seed): 0.827 Sensitivity CentroidAlifold(20): 0.741 MXScarna(seed): 0.713 Positive Predictive Value CentroidAlifold(20): 1.000 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAsubopt: 0.646 Sensitivity CentroidAlifold(20): 0.752 RNAsubopt: 0.579 Positive Predictive Value CentroidAlifold(20): 0.990 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 RSpredict(seed): 0.602 Sensitivity CentroidAlifold(20): 0.741 RSpredict(seed): 0.435 Positive Predictive Value CentroidAlifold(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CRWrnafold: 0.776 Sensitivity CentroidAlifold(20): 0.752 CRWrnafold: 0.684 Positive Predictive Value CentroidAlifold(20): 0.990 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAwolf: 0.661 Sensitivity CentroidAlifold(20): 0.752 RNAwolf: 0.647 Positive Predictive Value CentroidAlifold(20): 0.990 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.873 Afold: 0.569 Sensitivity CentroidAlifold(20): 0.776 Afold: 0.500 Positive Predictive Value CentroidAlifold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Alterna: 0.656 Sensitivity CentroidAlifold(20): 0.752 Alterna: 0.602 Positive Predictive Value CentroidAlifold(20): 0.990 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.860 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.741 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Mastr(20): 0.561 Sensitivity CentroidAlifold(20): 0.752 Mastr(20): 0.459 Positive Predictive Value CentroidAlifold(20): 0.990 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.876 NanoFolder: 0.144 Sensitivity CentroidAlifold(20): 0.788 NanoFolder: 0.173 Positive Predictive Value CentroidAlifold(20): 0.976 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Carnac(20): 0.821 Sensitivity CentroidAlifold(20): 0.752 Carnac(20): 0.684 Positive Predictive Value CentroidAlifold(20): 0.990 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient Multilign(seed): N/A CentroidAlifold(20): N/A Sensitivity Multilign(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value Multilign(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Multilign(20): 0.862 Sensitivity CentroidAlifold(20): 0.752 Multilign(20): 0.752 Positive Predictive Value CentroidAlifold(20): 0.990 Multilign(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 TurboFold(20): 0.857 Sensitivity CentroidAlifold(20): 0.752 TurboFold(20): 0.744 Positive Predictive Value CentroidAlifold(20): 0.990 TurboFold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNAalifold(20): 0.844 Sensitivity CentroidAlifold(20): 0.752 RNAalifold(20): 0.722 Positive Predictive Value CentroidAlifold(20): 0.990 RNAalifold(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RNASampler(20): 0.840 Sensitivity CentroidAlifold(20): 0.752 RNASampler(20): 0.714 Positive Predictive Value CentroidAlifold(20): 0.990 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 CMfinder(20): 0.779 Sensitivity CentroidAlifold(20): 0.752 CMfinder(20): 0.617 Positive Predictive Value CentroidAlifold(20): 0.990 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PETfold_pre2.0(20): 0.854 Sensitivity CentroidAlifold(20): 0.752 PETfold_pre2.0(20): 0.759 Positive Predictive Value CentroidAlifold(20): 0.990 PETfold_pre2.0(20): 0.962 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(seed): N/A CentroidAlifold(20): N/A Sensitivity PPfold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value PPfold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): N/A CentroidAlifold(20): N/A Sensitivity TurboFold(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value TurboFold(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MXScarna(20): 0.837 Sensitivity CentroidAlifold(20): 0.752 MXScarna(20): 0.752 Positive Predictive Value CentroidAlifold(20): 0.990 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 RSpredict(20): 0.672 Sensitivity CentroidAlifold(20): 0.752 RSpredict(20): 0.549 Positive Predictive Value CentroidAlifold(20): 0.990 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Murlet(20): 0.741 Sensitivity CentroidAlifold(20): 0.752 Murlet(20): 0.594 Positive Predictive Value CentroidAlifold(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PPfold(20): 0.840 Sensitivity CentroidAlifold(20): 0.752 PPfold(20): 0.737 Positive Predictive Value CentroidAlifold(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MCFold: 0.291 Sensitivity CentroidAlifold(20): 0.752 MCFold: 0.323 Positive Predictive Value CentroidAlifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Murlet(20)	5 Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: 0.756 Murlet(20): 0.741 Sensitivity Cylofold: 0.677 Murlet(20): 0.594 Positive Predictive Value Cylofold: 0.849 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 McQFold vs Murlet(20) Matthews Correlation Coefficient McQFold: 0.777 Murlet(20): 0.741 Sensitivity McQFold: 0.692 Murlet(20): 0.594 Positive Predictive Value McQFold: 0.876 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.741 Pknots: 0.723 Sensitivity Murlet(20): 0.594 Pknots: 0.632 Positive Predictive Value Murlet(20): 0.929 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 Murlet(20): 0.780 Sensitivity CentroidAlifold(seed): 0.778 Murlet(20): 0.611 Positive Predictive Value CentroidAlifold(seed): 1.000 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.741 PknotsRG: 0.592 Sensitivity Murlet(20): 0.594 PknotsRG: 0.526 Positive Predictive Value Murlet(20): 0.929 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Murlet(20): 0.741 Sensitivity PETfold_pre2.0(seed): 0.774 Murlet(20): 0.594 Positive Predictive Value PETfold_pre2.0(seed): 0.904 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(20): N/A Sensitivity RNASampler(seed): N/A Murlet(20): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.840 Murlet(20): 0.741 Sensitivity IPknot: 0.737 Murlet(20): 0.594 Positive Predictive Value IPknot: 0.961 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.780 RNAalifold(seed): 0.750 Sensitivity Murlet(20): 0.611 RNAalifold(seed): 0.639 Positive Predictive Value Murlet(20): 1.000 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.849 Murlet(20): 0.741 Sensitivity CentroidFold: 0.729 Murlet(20): 0.594 Positive Predictive Value CentroidFold: 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 Murlet(20): 0.741 Sensitivity CentroidHomfold‑LAST: 0.729 Murlet(20): 0.594 Positive Predictive Value CentroidHomfold‑LAST: 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Vsfold5 vs Murlet(20) Matthews Correlation Coefficient Vsfold5: 0.774 Murlet(20): 0.741 Sensitivity Vsfold5: 0.699 Murlet(20): 0.594 Positive Predictive Value Vsfold5: 0.861 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): N/A Carnac(seed): N/A Sensitivity Murlet(20): N/A Carnac(seed): N/A Positive Predictive Value Murlet(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.803 Murlet(20): 0.741 Sensitivity ProbKnot: 0.722 Murlet(20): 0.594 Positive Predictive Value ProbKnot: 0.897 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs Murlet(20) Matthews Correlation Coefficient RNASLOpt: 0.792 Murlet(20): 0.741 Sensitivity RNASLOpt: 0.692 Murlet(20): 0.594 Positive Predictive Value RNASLOpt: 0.911 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs Murlet(20) Matthews Correlation Coefficient Contrafold: 0.854 Murlet(20): 0.741 Sensitivity Contrafold: 0.759 Murlet(20): 0.594 Positive Predictive Value Contrafold: 0.962 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.741 HotKnots: 0.717 Sensitivity Murlet(20): 0.594 HotKnots: 0.639 Positive Predictive Value Murlet(20): 0.929 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.741 RDfolder: 0.664 Sensitivity Murlet(20): 0.594 RDfolder: 0.586 Positive Predictive Value Murlet(20): 0.929 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.862 Murlet(20): 0.741 Sensitivity Fold: 0.752 Murlet(20): 0.594 Positive Predictive Value Fold: 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.759 Murlet(20): 0.741 Sensitivity ContextFold: 0.669 Murlet(20): 0.594 Positive Predictive Value ContextFold: 0.864 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.783 Murlet(20): 0.741 Sensitivity MaxExpect: 0.677 Murlet(20): 0.594 Positive Predictive Value MaxExpect: 0.909 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): N/A Murlet(seed): N/A Sensitivity Murlet(20): N/A Murlet(seed): N/A Positive Predictive Value Murlet(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.741 Sfold: 0.721 Sensitivity Murlet(20): 0.594 Sfold: 0.624 Positive Predictive Value Murlet(20): 0.929 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.741 UNAFold: 0.649 Sensitivity Murlet(20): 0.594 UNAFold: 0.579 Positive Predictive Value Murlet(20): 0.929 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Vsfold4 vs Murlet(20) Matthews Correlation Coefficient Vsfold4: 0.784 Murlet(20): 0.741 Sensitivity Vsfold4: 0.684 Murlet(20): 0.594 Positive Predictive Value Vsfold4: 0.901 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.741 RNAshapes: 0.640 Sensitivity Murlet(20): 0.594 RNAshapes: 0.571 Positive Predictive Value Murlet(20): 0.929 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.741 RNAfold: 0.702 Sensitivity Murlet(20): 0.594 RNAfold: 0.617 Positive Predictive Value Murlet(20): 0.929 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.827 Murlet(20): 0.780 Sensitivity MXScarna(seed): 0.713 Murlet(20): 0.611 Positive Predictive Value MXScarna(seed): 0.963 Murlet(20): 1.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.741 RNAsubopt: 0.646 Sensitivity Murlet(20): 0.594 RNAsubopt: 0.579 Positive Predictive Value Murlet(20): 0.929 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.780 RSpredict(seed): 0.602 Sensitivity Murlet(20): 0.611 RSpredict(seed): 0.435 Positive Predictive Value Murlet(20): 1.000 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CRWrnafold vs Murlet(20) Matthews Correlation Coefficient CRWrnafold: 0.776 Murlet(20): 0.741 Sensitivity CRWrnafold: 0.684 Murlet(20): 0.594 Positive Predictive Value CRWrnafold: 0.883 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	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	5 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.741 RNAwolf: 0.661 Sensitivity Murlet(20): 0.594 RNAwolf: 0.647 Positive Predictive Value Murlet(20): 0.929 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.747 Afold: 0.569 Sensitivity Murlet(20): 0.632 Afold: 0.500 Positive Predictive Value Murlet(20): 0.889 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.741 Alterna: 0.656 Sensitivity Murlet(20): 0.594 Alterna: 0.602 Positive Predictive Value Murlet(20): 0.929 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.780 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.611 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 1.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.741 Mastr(20): 0.561 Sensitivity Murlet(20): 0.594 Mastr(20): 0.459 Positive Predictive Value Murlet(20): 0.929 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.718 NanoFolder: 0.144 Sensitivity Murlet(20): 0.615 NanoFolder: 0.173 Positive Predictive Value Murlet(20): 0.842 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs Murlet(20) Matthews Correlation Coefficient Carnac(20): 0.821 Murlet(20): 0.741 Sensitivity Carnac(20): 0.684 Murlet(20): 0.594 Positive Predictive Value Carnac(20): 0.989 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): N/A Multilign(seed): N/A Sensitivity Murlet(20): N/A Multilign(seed): N/A Positive Predictive Value Murlet(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.862 Murlet(20): 0.741 Sensitivity Multilign(20): 0.752 Murlet(20): 0.594 Positive Predictive Value Multilign(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.857 Murlet(20): 0.741 Sensitivity TurboFold(20): 0.744 Murlet(20): 0.594 Positive Predictive Value TurboFold(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 Murlet(20): 0.741 Sensitivity RNAalifold(20): 0.722 Murlet(20): 0.594 Positive Predictive Value RNAalifold(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.840 Murlet(20): 0.741 Sensitivity RNASampler(20): 0.714 Murlet(20): 0.594 Positive Predictive Value RNASampler(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs Murlet(20) Matthews Correlation Coefficient CMfinder(20): 0.779 Murlet(20): 0.741 Sensitivity CMfinder(20): 0.617 Murlet(20): 0.594 Positive Predictive Value CMfinder(20): 0.988 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 Murlet(20): 0.741 Sensitivity PETfold_pre2.0(20): 0.759 Murlet(20): 0.594 Positive Predictive Value PETfold_pre2.0(20): 0.962 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PPfold(seed) vs Murlet(20) Matthews Correlation Coefficient PPfold(seed): N/A Murlet(20): N/A Sensitivity PPfold(seed): N/A Murlet(20): N/A Positive Predictive Value PPfold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(20): N/A Sensitivity TurboFold(seed): N/A Murlet(20): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.837 Murlet(20): 0.741 Sensitivity MXScarna(20): 0.752 Murlet(20): 0.594 Positive Predictive Value MXScarna(20): 0.935 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.741 RSpredict(20): 0.672 Sensitivity Murlet(20): 0.594 RSpredict(20): 0.549 Positive Predictive Value Murlet(20): 0.929 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 Murlet(20): 0.741 Sensitivity CentroidAlifold(20): 0.752 Murlet(20): 0.594 Positive Predictive Value CentroidAlifold(20): 0.990 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.840 Murlet(20): 0.741 Sensitivity PPfold(20): 0.737 Murlet(20): 0.594 Positive Predictive Value PPfold(20): 0.961 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.741 MCFold: 0.291 Sensitivity Murlet(20): 0.594 MCFold: 0.323 Positive Predictive Value Murlet(20): 0.929 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PPfold(20)	5 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.840 Cylofold: 0.756 Sensitivity PPfold(20): 0.737 Cylofold: 0.677 Positive Predictive Value PPfold(20): 0.961 Cylofold: 0.849 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.840 McQFold: 0.777 Sensitivity PPfold(20): 0.737 McQFold: 0.692 Positive Predictive Value PPfold(20): 0.961 McQFold: 0.876 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.840 Pknots: 0.723 Sensitivity PPfold(20): 0.737 Pknots: 0.632 Positive Predictive Value PPfold(20): 0.961 Pknots: 0.832 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.881 PPfold(20): 0.833 Sensitivity CentroidAlifold(seed): 0.778 PPfold(20): 0.722 Positive Predictive Value CentroidAlifold(seed): 1.000 PPfold(20): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.840 PknotsRG: 0.592 Sensitivity PPfold(20): 0.737 PknotsRG: 0.526 Positive Predictive Value PPfold(20): 0.961 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PPfold(20): 0.840 PETfold_pre2.0(seed): 0.835 Sensitivity PPfold(20): 0.737 PETfold_pre2.0(seed): 0.774 Positive Predictive Value PPfold(20): 0.961 PETfold_pre2.0(seed): 0.904 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(20): N/A Sensitivity RNASampler(seed): N/A PPfold(20): N/A Positive Predictive Value RNASampler(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.840 IPknot: 0.840 Sensitivity PPfold(20): 0.737 IPknot: 0.737 Positive Predictive Value PPfold(20): 0.961 IPknot: 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.833 RNAalifold(seed): 0.750 Sensitivity PPfold(20): 0.722 RNAalifold(seed): 0.639 Positive Predictive Value PPfold(20): 0.963 RNAalifold(seed): 0.885 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs PPfold(20) Matthews Correlation Coefficient CentroidFold: 0.849 PPfold(20): 0.840 Sensitivity CentroidFold: 0.729 PPfold(20): 0.737 Positive Predictive Value CentroidFold: 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.849 PPfold(20): 0.840 Sensitivity CentroidHomfold‑LAST: 0.729 PPfold(20): 0.737 Positive Predictive Value CentroidHomfold‑LAST: 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.840 Vsfold5: 0.774 Sensitivity PPfold(20): 0.737 Vsfold5: 0.699 Positive Predictive Value PPfold(20): 0.961 Vsfold5: 0.861 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): N/A Carnac(seed): N/A Sensitivity PPfold(20): N/A Carnac(seed): N/A Positive Predictive Value PPfold(20): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.840 ProbKnot: 0.803 Sensitivity PPfold(20): 0.737 ProbKnot: 0.722 Positive Predictive Value PPfold(20): 0.961 ProbKnot: 0.897 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.840 RNASLOpt: 0.792 Sensitivity PPfold(20): 0.737 RNASLOpt: 0.692 Positive Predictive Value PPfold(20): 0.961 RNASLOpt: 0.911 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs PPfold(20) Matthews Correlation Coefficient Contrafold: 0.854 PPfold(20): 0.840 Sensitivity Contrafold: 0.759 PPfold(20): 0.737 Positive Predictive Value Contrafold: 0.962 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.840 HotKnots: 0.717 Sensitivity PPfold(20): 0.737 HotKnots: 0.639 Positive Predictive Value PPfold(20): 0.961 HotKnots: 0.810 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.840 RDfolder: 0.664 Sensitivity PPfold(20): 0.737 RDfolder: 0.586 Positive Predictive Value PPfold(20): 0.961 RDfolder: 0.757 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Fold vs PPfold(20) Matthews Correlation Coefficient Fold: 0.862 PPfold(20): 0.840 Sensitivity Fold: 0.752 PPfold(20): 0.737 Positive Predictive Value Fold: 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.840 ContextFold: 0.759 Sensitivity PPfold(20): 0.737 ContextFold: 0.669 Positive Predictive Value PPfold(20): 0.961 ContextFold: 0.864 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.840 MaxExpect: 0.783 Sensitivity PPfold(20): 0.737 MaxExpect: 0.677 Positive Predictive Value PPfold(20): 0.961 MaxExpect: 0.909 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): N/A Murlet(seed): N/A Sensitivity PPfold(20): N/A Murlet(seed): N/A Positive Predictive Value PPfold(20): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.840 Sfold: 0.721 Sensitivity PPfold(20): 0.737 Sfold: 0.624 Positive Predictive Value PPfold(20): 0.961 Sfold: 0.838 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.840 UNAFold: 0.649 Sensitivity PPfold(20): 0.737 UNAFold: 0.579 Positive Predictive Value PPfold(20): 0.961 UNAFold: 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.840 Vsfold4: 0.784 Sensitivity PPfold(20): 0.737 Vsfold4: 0.684 Positive Predictive Value PPfold(20): 0.961 Vsfold4: 0.901 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.840 RNAshapes: 0.640 Sensitivity PPfold(20): 0.737 RNAshapes: 0.571 Positive Predictive Value PPfold(20): 0.961 RNAshapes: 0.724 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.840 RNAfold: 0.702 Sensitivity PPfold(20): 0.737 RNAfold: 0.617 Positive Predictive Value PPfold(20): 0.961 RNAfold: 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.833 MXScarna(seed): 0.827 Sensitivity PPfold(20): 0.722 MXScarna(seed): 0.713 Positive Predictive Value PPfold(20): 0.963 MXScarna(seed): 0.963 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.840 RNAsubopt: 0.646 Sensitivity PPfold(20): 0.737 RNAsubopt: 0.579 Positive Predictive Value PPfold(20): 0.961 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.833 RSpredict(seed): 0.602 Sensitivity PPfold(20): 0.722 RSpredict(seed): 0.435 Positive Predictive Value PPfold(20): 0.963 RSpredict(seed): 0.839 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.840 CRWrnafold: 0.776 Sensitivity PPfold(20): 0.737 CRWrnafold: 0.684 Positive Predictive Value PPfold(20): 0.961 CRWrnafold: 0.883 Number of pairs reference - predicted secondary structure: 5 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	5 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.840 RNAwolf: 0.661 Sensitivity PPfold(20): 0.737 RNAwolf: 0.647 Positive Predictive Value PPfold(20): 0.961 RNAwolf: 0.683 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.857 Afold: 0.569 Sensitivity PPfold(20): 0.750 Afold: 0.500 Positive Predictive Value PPfold(20): 0.983 Afold: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.840 Alterna: 0.656 Sensitivity PPfold(20): 0.737 Alterna: 0.602 Positive Predictive Value PPfold(20): 0.961 Alterna: 0.721 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.833 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.722 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.963 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.840 Mastr(20): 0.561 Sensitivity PPfold(20): 0.737 Mastr(20): 0.459 Positive Predictive Value PPfold(20): 0.961 Mastr(20): 0.693 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.854 NanoFolder: 0.144 Sensitivity PPfold(20): 0.750 NanoFolder: 0.173 Positive Predictive Value PPfold(20): 0.975 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.840 Carnac(20): 0.821 Sensitivity PPfold(20): 0.737 Carnac(20): 0.684 Positive Predictive Value PPfold(20): 0.961 Carnac(20): 0.989 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): N/A Multilign(seed): N/A Sensitivity PPfold(20): N/A Multilign(seed): N/A Positive Predictive Value PPfold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(20) vs PPfold(20) Matthews Correlation Coefficient Multilign(20): 0.862 PPfold(20): 0.840 Sensitivity Multilign(20): 0.752 PPfold(20): 0.737 Positive Predictive Value Multilign(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.857 PPfold(20): 0.840 Sensitivity TurboFold(20): 0.744 PPfold(20): 0.737 Positive Predictive Value TurboFold(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs PPfold(20) Matthews Correlation Coefficient RNAalifold(20): 0.844 PPfold(20): 0.840 Sensitivity RNAalifold(20): 0.722 PPfold(20): 0.737 Positive Predictive Value RNAalifold(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.840 RNASampler(20): 0.840 Sensitivity PPfold(20): 0.737 RNASampler(20): 0.714 Positive Predictive Value PPfold(20): 0.961 RNASampler(20): 0.990 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.840 CMfinder(20): 0.779 Sensitivity PPfold(20): 0.737 CMfinder(20): 0.617 Positive Predictive Value PPfold(20): 0.961 CMfinder(20): 0.988 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 PPfold(20): 0.840 Sensitivity PETfold_pre2.0(20): 0.759 PPfold(20): 0.737 Positive Predictive Value PETfold_pre2.0(20): 0.962 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): N/A PPfold(seed): N/A Sensitivity PPfold(20): N/A PPfold(seed): N/A Positive Predictive Value PPfold(20): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): N/A PPfold(20): N/A Sensitivity TurboFold(seed): N/A PPfold(20): N/A Positive Predictive Value TurboFold(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.840 MXScarna(20): 0.837 Sensitivity PPfold(20): 0.737 MXScarna(20): 0.752 Positive Predictive Value PPfold(20): 0.961 MXScarna(20): 0.935 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.840 RSpredict(20): 0.672 Sensitivity PPfold(20): 0.737 RSpredict(20): 0.549 Positive Predictive Value PPfold(20): 0.961 RSpredict(20): 0.830 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.862 PPfold(20): 0.840 Sensitivity CentroidAlifold(20): 0.752 PPfold(20): 0.737 Positive Predictive Value CentroidAlifold(20): 0.990 PPfold(20): 0.961 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.840 Murlet(20): 0.741 Sensitivity PPfold(20): 0.737 Murlet(20): 0.594 Positive Predictive Value PPfold(20): 0.961 Murlet(20): 0.929 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.840 MCFold: 0.291 Sensitivity PPfold(20): 0.737 MCFold: 0.323 Positive Predictive Value PPfold(20): 0.961 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
MCFold	44 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.771 MCFold: 0.294 Sensitivity Cylofold: 0.749 MCFold: 0.323 Positive Predictive Value Cylofold: 0.799 MCFold: 0.284 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.652 MCFold: 0.290 Sensitivity McQFold: 0.631 MCFold: 0.320 Positive Predictive Value McQFold: 0.681 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.707 MCFold: 0.296 Sensitivity Pknots: 0.676 MCFold: 0.325 Positive Predictive Value Pknots: 0.747 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.777 MCFold: 0.358 Sensitivity CentroidAlifold(seed): 0.642 MCFold: 0.409 Positive Predictive Value CentroidAlifold(seed): 0.944 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 4.63136857368e-09	48 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.537 MCFold: 0.290 Sensitivity PknotsRG: 0.522 MCFold: 0.320 Positive Predictive Value PknotsRG: 0.560 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.739 MCFold: 0.336 Sensitivity PETfold_pre2.0(seed): 0.663 MCFold: 0.387 Positive Predictive Value PETfold_pre2.0(seed): 0.829 MCFold: 0.303 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	11 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.621 MCFold: 0.354 Sensitivity RNASampler(seed): 0.546 MCFold: 0.415 Positive Predictive Value RNASampler(seed): 0.713 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	48 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.503 MCFold: 0.290 Sensitivity IPknot: 0.457 MCFold: 0.320 Positive Predictive Value IPknot: 0.562 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.664 MCFold: 0.358 Sensitivity RNAalifold(seed): 0.537 MCFold: 0.409 Positive Predictive Value RNAalifold(seed): 0.828 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.80908287419e-08	48 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.486 MCFold: 0.290 Sensitivity CentroidFold: 0.436 MCFold: 0.320 Positive Predictive Value CentroidFold: 0.550 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.487 MCFold: 0.290 Sensitivity CentroidHomfold‑LAST: 0.422 MCFold: 0.320 Positive Predictive Value CentroidHomfold‑LAST: 0.570 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.555 MCFold: 0.290 Sensitivity Vsfold5: 0.517 MCFold: 0.320 Positive Predictive Value Vsfold5: 0.604 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 Carnac(seed) vs MCFold Matthews Correlation Coefficient Carnac(seed): 0.566 MCFold: 0.354 Sensitivity Carnac(seed): 0.332 MCFold: 0.415 Positive Predictive Value Carnac(seed): 0.971 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.26545642304e-09	48 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.479 MCFold: 0.290 Sensitivity ProbKnot: 0.456 MCFold: 0.320 Positive Predictive Value ProbKnot: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.489 MCFold: 0.290 Sensitivity RNASLOpt: 0.442 MCFold: 0.320 Positive Predictive Value RNASLOpt: 0.549 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.471 MCFold: 0.290 Sensitivity Contrafold: 0.440 MCFold: 0.320 Positive Predictive Value Contrafold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.480 MCFold: 0.290 Sensitivity HotKnots: 0.464 MCFold: 0.320 Positive Predictive Value HotKnots: 0.506 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.505 MCFold: 0.296 Sensitivity RDfolder: 0.428 MCFold: 0.325 Positive Predictive Value RDfolder: 0.605 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.472 MCFold: 0.290 Sensitivity Fold: 0.443 MCFold: 0.320 Positive Predictive Value Fold: 0.513 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.449 MCFold: 0.290 Sensitivity ContextFold: 0.402 MCFold: 0.320 Positive Predictive Value ContextFold: 0.511 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.457 MCFold: 0.290 Sensitivity MaxExpect: 0.424 MCFold: 0.320 Positive Predictive Value MaxExpect: 0.502 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.456 MCFold: 0.354 Sensitivity Murlet(seed): 0.307 MCFold: 0.415 Positive Predictive Value Murlet(seed): 0.685 MCFold: 0.314 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	48 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.441 MCFold: 0.290 Sensitivity Sfold: 0.399 MCFold: 0.320 Positive Predictive Value Sfold: 0.497 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.423 MCFold: 0.290 Sensitivity UNAFold: 0.394 MCFold: 0.320 Positive Predictive Value UNAFold: 0.463 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.435 MCFold: 0.290 Sensitivity Vsfold4: 0.387 MCFold: 0.320 Positive Predictive Value Vsfold4: 0.498 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.438 MCFold: 0.290 Sensitivity RNAshapes: 0.408 MCFold: 0.320 Positive Predictive Value RNAshapes: 0.481 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.417 MCFold: 0.290 Sensitivity RNAfold: 0.391 MCFold: 0.320 Positive Predictive Value RNAfold: 0.455 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.538 MCFold: 0.358 Sensitivity MXScarna(seed): 0.502 MCFold: 0.409 Positive Predictive Value MXScarna(seed): 0.586 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 9.9460272886e-09	48 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.416 MCFold: 0.290 Sensitivity RNAsubopt: 0.393 MCFold: 0.320 Positive Predictive Value RNAsubopt: 0.451 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): 0.522 MCFold: 0.358 Sensitivity RSpredict(seed): 0.441 MCFold: 0.409 Positive Predictive Value RSpredict(seed): 0.627 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.12262428713e-08	48 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.411 MCFold: 0.290 Sensitivity CRWrnafold: 0.380 MCFold: 0.320 Positive Predictive Value CRWrnafold: 0.456 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.499 MCFold: 0.352 Sensitivity CMfinder(seed): 0.385 MCFold: 0.408 Positive Predictive Value CMfinder(seed): 0.657 MCFold: 0.315 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	48 RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.376 MCFold: 0.290 Sensitivity RNAwolf: 0.364 MCFold: 0.320 Positive Predictive Value RNAwolf: 0.400 MCFold: 0.276 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.280 MCFold: 0.263 Sensitivity Afold: 0.274 MCFold: 0.294 Positive Predictive Value Afold: 0.299 MCFold: 0.247 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 4.13872543599e-05	45 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.399 MCFold: 0.296 Sensitivity Alterna: 0.369 MCFold: 0.325 Positive Predictive Value Alterna: 0.444 MCFold: 0.285 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): 0.381 MCFold: 0.358 Sensitivity Mastr(seed): 0.220 MCFold: 0.409 Positive Predictive Value Mastr(seed): 0.670 MCFold: 0.325 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.81807643229e-05	5 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.561 MCFold: 0.291 Sensitivity Mastr(20): 0.459 MCFold: 0.323 Positive Predictive Value Mastr(20): 0.693 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	7 NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: 0.304 MCFold: 0.248 Sensitivity NanoFolder: 0.343 MCFold: 0.283 Positive Predictive Value NanoFolder: 0.281 MCFold: 0.229 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.821 MCFold: 0.291 Sensitivity Carnac(20): 0.684 MCFold: 0.323 Positive Predictive Value Carnac(20): 0.989 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.575 MCFold: 0.340 Sensitivity Multilign(seed): 0.536 MCFold: 0.407 Positive Predictive Value Multilign(seed): 0.625 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.862 MCFold: 0.291 Sensitivity Multilign(20): 0.752 MCFold: 0.323 Positive Predictive Value Multilign(20): 0.990 MCFold: 0.274 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): 0.857 MCFold: 0.291 Sensitivity TurboFold(20): 0.744 MCFold: 0.323 Positive Predictive Value TurboFold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.844 MCFold: 0.291 Sensitivity RNAalifold(20): 0.722 MCFold: 0.323 Positive Predictive Value RNAalifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.840 MCFold: 0.291 Sensitivity RNASampler(20): 0.714 MCFold: 0.323 Positive Predictive Value RNASampler(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.779 MCFold: 0.291 Sensitivity CMfinder(20): 0.617 MCFold: 0.323 Positive Predictive Value CMfinder(20): 0.988 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.854 MCFold: 0.291 Sensitivity PETfold_pre2.0(20): 0.759 MCFold: 0.323 Positive Predictive Value PETfold_pre2.0(20): 0.962 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PPfold(seed) vs MCFold Matthews Correlation Coefficient PPfold(seed): 0.666 MCFold: 0.340 Sensitivity PPfold(seed): 0.536 MCFold: 0.407 Positive Predictive Value PPfold(seed): 0.833 MCFold: 0.295 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.600 MCFold: 0.343 Sensitivity TurboFold(seed): 0.518 MCFold: 0.405 Positive Predictive Value TurboFold(seed): 0.702 MCFold: 0.302 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.837 MCFold: 0.291 Sensitivity MXScarna(20): 0.752 MCFold: 0.323 Positive Predictive Value MXScarna(20): 0.935 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.672 MCFold: 0.291 Sensitivity RSpredict(20): 0.549 MCFold: 0.323 Positive Predictive Value RSpredict(20): 0.830 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.862 MCFold: 0.291 Sensitivity CentroidAlifold(20): 0.752 MCFold: 0.323 Positive Predictive Value CentroidAlifold(20): 0.990 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.741 MCFold: 0.291 Sensitivity Murlet(20): 0.594 MCFold: 0.323 Positive Predictive Value Murlet(20): 0.929 MCFold: 0.274 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): 0.840 MCFold: 0.291 Sensitivity PPfold(20): 0.737 MCFold: 0.323 Positive Predictive Value PPfold(20): 0.961 MCFold: 0.274 Number of pairs reference - predicted secondary structure: 5 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).