CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Pseudoknotted medium-sized 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: 201, 800
Number of RNA sequences: 610
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	ContextFold	yes	42	0	0	11	610	610
2	PETfold_pre2.0(seed)	no	41	1	0	11	508	508
3	TurboFold(20)	no	38	2	0	13	204	204
4	PETfold_pre2.0(20)	no	36	3	1	13	204	204
4	PPfold(20)	yes	36	3	1	13	204	197
6	CentroidAlifold(20)	yes	35	5	0	13	204	204
7	CentroidAlifold(seed)	yes	35	6	0	12	508	277
8	CentroidHomfold‑LAST	yes	35	7	0	11	610	574
9	RNAalifold(20)	no	32	8	0	13	204	204
10	IPknot	yes	32	9	1	11	610	610
11	Multilign(20)	no	30	9	1	13	204	191
12	CentroidFold	yes	29	13	0	11	610	610
13	Contrafold	yes	28	14	0	11	610	610
14	MXScarna(20)	no	27	13	0	13	204	204
15	MXScarna(seed)	no	27	14	0	12	508	282
16	MaxExpect	yes	26	16	0	11	610	610
17	ProbKnot	yes	25	17	0	11	610	610
18	RNASampler(20)	no	23	11	0	19	204	45
19	Sfold	no	23	18	1	11	610	610
20	Fold	no	22	20	0	11	610	610
21	Murlet(20)	yes	21	18	1	13	204	145
22	PknotsRG	no	20	21	1	11	610	610
22	UNAFold	no	20	21	1	11	610	610
24	RNAfold	no	19	23	0	11	610	610
25	RNAsubopt	no	18	24	0	11	610	574
25	Afold	no	18	24	0	11	610	361
27	McQFold	yes	15	27	0	11	610	610
28	CMfinder(20)	yes	14	26	0	13	204	204
29	RNASLOpt	no	14	28	0	11	610	480
30	RNAalifold(seed)	no	12	29	0	12	508	278
31	CRWrnafold	yes	12	30	0	11	610	610
31	RNAshapes	no	12	30	0	11	610	526
33	RNAwolf	yes	9	33	0	11	610	610
33	Vsfold4	no	9	33	0	11	610	547
35	Vsfold5	no	7	34	1	11	610	538
36	CMfinder(seed)	yes	5	22	1	25	508	15
37	Carnac(20)	no	5	35	0	13	204	204
38	RSpredict(20)	no	4	36	0	13	204	204
39	NanoFolder	yes	3	36	0	14	610	105
40	RSpredict(seed)	no	3	38	0	12	508	280
41	Carnac(seed)	no	0	27	1	25	508	48
42	Mastr(20)	yes	0	39	1	13	204	204
43	Mastr(seed)	yes	0	39	2	12	508	258
N/A	Cylofold	no	0	0	0	53	610	2
N/A	MCFold	yes	0	0	0	53	610	0
N/A	RDfolder	no	0	0	0	53	610	0
N/A	HotKnots	no	0	0	0	53	610	0
N/A	Pknots	no	0	0	0	53	610	0
N/A	Alterna	no	0	0	0	53	610	0
N/A	TurboFold(seed)	no	0	0	0	53	508	1
N/A	Murlet(seed)	yes	0	0	0	53	508	0
N/A	Multilign(seed)	no	0	0	0	53	508	0
N/A	RNASampler(seed)	no	0	0	0	53	508	0
N/A	PPfold(seed)	yes	0	0	0	53	508	0

Detailed results of pairwise comparisons between methods

Legend:

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

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


ContextFold		+ ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.733 PETfold_pre2.0(seed): 0.681 Sensitivity ContextFold: 0.688 PETfold_pre2.0(seed): 0.590 Positive Predictive Value ContextFold: 0.781 PETfold_pre2.0(seed): 0.787 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.840 TurboFold(20): 0.740 Sensitivity ContextFold: 0.791 TurboFold(20): 0.685 Positive Predictive Value ContextFold: 0.892 TurboFold(20): 0.801 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.840 PETfold_pre2.0(20): 0.735 Sensitivity ContextFold: 0.791 PETfold_pre2.0(20): 0.652 Positive Predictive Value ContextFold: 0.892 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.840 PPfold(20): 0.734 Sensitivity ContextFold: 0.791 PPfold(20): 0.635 Positive Predictive Value ContextFold: 0.893 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.840 CentroidAlifold(20): 0.717 Sensitivity ContextFold: 0.791 CentroidAlifold(20): 0.561 Positive Predictive Value ContextFold: 0.892 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.813 CentroidAlifold(seed): 0.691 Sensitivity ContextFold: 0.765 CentroidAlifold(seed): 0.521 Positive Predictive Value ContextFold: 0.864 CentroidAlifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.731 CentroidHomfold‑LAST: 0.641 Sensitivity ContextFold: 0.689 CentroidHomfold‑LAST: 0.469 Positive Predictive Value ContextFold: 0.778 CentroidHomfold‑LAST: 0.877 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.840 RNAalifold(20): 0.660 Sensitivity ContextFold: 0.791 RNAalifold(20): 0.532 Positive Predictive Value ContextFold: 0.892 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.718 IPknot: 0.602 Sensitivity ContextFold: 0.677 IPknot: 0.545 Positive Predictive Value ContextFold: 0.763 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.842 Multilign(20): 0.649 Sensitivity ContextFold: 0.794 Multilign(20): 0.590 Positive Predictive Value ContextFold: 0.893 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.718 CentroidFold: 0.571 Sensitivity ContextFold: 0.677 CentroidFold: 0.516 Positive Predictive Value ContextFold: 0.763 CentroidFold: 0.635 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.718 Contrafold: 0.554 Sensitivity ContextFold: 0.677 Contrafold: 0.540 Positive Predictive Value ContextFold: 0.763 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.840 MXScarna(20): 0.626 Sensitivity ContextFold: 0.791 MXScarna(20): 0.551 Positive Predictive Value ContextFold: 0.892 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.812 MXScarna(seed): 0.595 Sensitivity ContextFold: 0.764 MXScarna(seed): 0.475 Positive Predictive Value ContextFold: 0.863 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.718 MaxExpect: 0.524 Sensitivity ContextFold: 0.677 MaxExpect: 0.511 Positive Predictive Value ContextFold: 0.763 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.718 ProbKnot: 0.522 Sensitivity ContextFold: 0.677 ProbKnot: 0.518 Positive Predictive Value ContextFold: 0.763 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.737 RNASampler(20): 0.543 Sensitivity ContextFold: 0.685 RNASampler(20): 0.425 Positive Predictive Value ContextFold: 0.793 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.718 Sfold: 0.514 Sensitivity ContextFold: 0.677 Sfold: 0.463 Positive Predictive Value ContextFold: 0.763 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.718 Fold: 0.495 Sensitivity ContextFold: 0.677 Fold: 0.498 Positive Predictive Value ContextFold: 0.763 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.823 Murlet(20): 0.548 Sensitivity ContextFold: 0.774 Murlet(20): 0.415 Positive Predictive Value ContextFold: 0.876 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.718 UNAFold: 0.475 Sensitivity ContextFold: 0.677 UNAFold: 0.473 Positive Predictive Value ContextFold: 0.763 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.718 PknotsRG: 0.476 Sensitivity ContextFold: 0.677 PknotsRG: 0.478 Positive Predictive Value ContextFold: 0.763 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.718 RNAfold: 0.474 Sensitivity ContextFold: 0.677 RNAfold: 0.477 Positive Predictive Value ContextFold: 0.763 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.752 Afold: 0.494 Sensitivity ContextFold: 0.710 Afold: 0.490 Positive Predictive Value ContextFold: 0.797 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.731 RNAsubopt: 0.475 Sensitivity ContextFold: 0.689 RNAsubopt: 0.482 Positive Predictive Value ContextFold: 0.778 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.718 McQFold: 0.450 Sensitivity ContextFold: 0.677 McQFold: 0.441 Positive Predictive Value ContextFold: 0.763 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.840 CMfinder(20): 0.479 Sensitivity ContextFold: 0.791 CMfinder(20): 0.308 Positive Predictive Value ContextFold: 0.892 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.736 RNASLOpt: 0.446 Sensitivity ContextFold: 0.692 RNASLOpt: 0.421 Positive Predictive Value ContextFold: 0.784 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.812 RNAalifold(seed): 0.469 Sensitivity ContextFold: 0.764 RNAalifold(seed): 0.272 Positive Predictive Value ContextFold: 0.864 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.736 RNAshapes: 0.408 Sensitivity ContextFold: 0.692 RNAshapes: 0.404 Positive Predictive Value ContextFold: 0.784 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.718 CRWrnafold: 0.417 Sensitivity ContextFold: 0.677 CRWrnafold: 0.421 Positive Predictive Value ContextFold: 0.763 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.732 Vsfold4: 0.335 Sensitivity ContextFold: 0.689 Vsfold4: 0.308 Positive Predictive Value ContextFold: 0.779 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.718 RNAwolf: 0.332 Sensitivity ContextFold: 0.677 RNAwolf: 0.347 Positive Predictive Value ContextFold: 0.763 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.735 Vsfold5: 0.329 Sensitivity ContextFold: 0.691 Vsfold5: 0.312 Positive Predictive Value ContextFold: 0.782 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.708 CMfinder(seed): 0.350 Sensitivity ContextFold: 0.665 CMfinder(seed): 0.159 Positive Predictive Value ContextFold: 0.756 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.840 Carnac(20): 0.360 Sensitivity ContextFold: 0.791 Carnac(20): 0.151 Positive Predictive Value ContextFold: 0.892 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.840 RSpredict(20): 0.347 Sensitivity ContextFold: 0.791 RSpredict(20): 0.220 Positive Predictive Value ContextFold: 0.892 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.757 NanoFolder: 0.172 Sensitivity ContextFold: 0.714 NanoFolder: 0.204 Positive Predictive Value ContextFold: 0.804 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.813 RSpredict(seed): 0.045 Sensitivity ContextFold: 0.765 RSpredict(seed): 0.011 Positive Predictive Value ContextFold: 0.864 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: N/A Murlet(seed): N/A Sensitivity ContextFold: N/A Murlet(seed): N/A Positive Predictive Value ContextFold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: N/A Multilign(seed): N/A Sensitivity ContextFold: N/A Multilign(seed): N/A Positive Predictive Value ContextFold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: N/A ContextFold: N/A Sensitivity HotKnots: N/A ContextFold: N/A Positive Predictive Value HotKnots: N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: N/A Pknots: N/A Sensitivity ContextFold: N/A Pknots: N/A Positive Predictive Value ContextFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.944 Cylofold: 0.271 Sensitivity ContextFold: 0.905 Cylofold: 0.241 Positive Predictive Value ContextFold: 0.984 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: N/A MCFold: N/A Sensitivity ContextFold: N/A MCFold: N/A Positive Predictive Value ContextFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs ContextFold Matthews Correlation Coefficient PPfold(seed): N/A ContextFold: N/A Sensitivity PPfold(seed): N/A ContextFold: N/A Positive Predictive Value PPfold(seed): N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: N/A ContextFold: N/A Sensitivity RDfolder: N/A ContextFold: N/A Positive Predictive Value RDfolder: N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.710 ContextFold: 0.703 Sensitivity TurboFold(seed): 0.677 ContextFold: 0.692 Positive Predictive Value TurboFold(seed): 0.746 ContextFold: 0.714 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): N/A ContextFold: N/A Sensitivity RNASampler(seed): N/A ContextFold: N/A Positive Predictive Value RNASampler(seed): N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: N/A Alterna: N/A Sensitivity ContextFold: N/A Alterna: N/A Positive Predictive Value ContextFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.659 Carnac(seed): 0.000 Sensitivity ContextFold: 0.623 Carnac(seed): 0.000 Positive Predictive Value ContextFold: 0.697 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.840 Mastr(20): 0.000 Sensitivity ContextFold: 0.791 Mastr(20): 0.000 Positive Predictive Value ContextFold: 0.892 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.804 Mastr(seed): 0.000 Sensitivity ContextFold: 0.757 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.854 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(seed)	508 ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.733 PETfold_pre2.0(seed): 0.681 Sensitivity ContextFold: 0.688 PETfold_pre2.0(seed): 0.590 Positive Predictive Value ContextFold: 0.781 PETfold_pre2.0(seed): 0.787 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 TurboFold(20): 0.740 Sensitivity PETfold_pre2.0(seed): 0.673 TurboFold(20): 0.685 Positive Predictive Value PETfold_pre2.0(seed): 0.845 TurboFold(20): 0.801 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 PETfold_pre2.0(20): 0.735 Sensitivity PETfold_pre2.0(seed): 0.673 PETfold_pre2.0(20): 0.652 Positive Predictive Value PETfold_pre2.0(seed): 0.845 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 PPfold(20): 0.734 Sensitivity PETfold_pre2.0(seed): 0.673 PPfold(20): 0.635 Positive Predictive Value PETfold_pre2.0(seed): 0.845 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 CentroidAlifold(20): 0.717 Sensitivity PETfold_pre2.0(seed): 0.673 CentroidAlifold(20): 0.561 Positive Predictive Value PETfold_pre2.0(seed): 0.845 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 CentroidAlifold(seed): 0.691 Sensitivity PETfold_pre2.0(seed): 0.632 CentroidAlifold(seed): 0.521 Positive Predictive Value PETfold_pre2.0(seed): 0.822 CentroidAlifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.682 CentroidHomfold‑LAST: 0.651 Sensitivity PETfold_pre2.0(seed): 0.592 CentroidHomfold‑LAST: 0.482 Positive Predictive Value PETfold_pre2.0(seed): 0.788 CentroidHomfold‑LAST: 0.880 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 RNAalifold(20): 0.660 Sensitivity PETfold_pre2.0(seed): 0.673 RNAalifold(20): 0.532 Positive Predictive Value PETfold_pre2.0(seed): 0.845 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 IPknot: 0.604 Sensitivity PETfold_pre2.0(seed): 0.590 IPknot: 0.543 Positive Predictive Value PETfold_pre2.0(seed): 0.787 IPknot: 0.673 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.753 Multilign(20): 0.649 Sensitivity PETfold_pre2.0(seed): 0.672 Multilign(20): 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.844 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 CentroidFold: 0.571 Sensitivity PETfold_pre2.0(seed): 0.590 CentroidFold: 0.514 Positive Predictive Value PETfold_pre2.0(seed): 0.787 CentroidFold: 0.636 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 Contrafold: 0.552 Sensitivity PETfold_pre2.0(seed): 0.590 Contrafold: 0.537 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 MXScarna(20): 0.626 Sensitivity PETfold_pre2.0(seed): 0.673 MXScarna(20): 0.551 Positive Predictive Value PETfold_pre2.0(seed): 0.845 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 MXScarna(seed): 0.595 Sensitivity PETfold_pre2.0(seed): 0.632 MXScarna(seed): 0.475 Positive Predictive Value PETfold_pre2.0(seed): 0.821 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 MaxExpect: 0.525 Sensitivity PETfold_pre2.0(seed): 0.590 MaxExpect: 0.510 Positive Predictive Value PETfold_pre2.0(seed): 0.787 MaxExpect: 0.542 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 ProbKnot: 0.524 Sensitivity PETfold_pre2.0(seed): 0.590 ProbKnot: 0.516 Positive Predictive Value PETfold_pre2.0(seed): 0.787 ProbKnot: 0.532 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.676 RNASampler(20): 0.543 Sensitivity PETfold_pre2.0(seed): 0.587 RNASampler(20): 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.779 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 Sfold: 0.510 Sensitivity PETfold_pre2.0(seed): 0.590 Sfold: 0.458 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Sfold: 0.570 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 Fold: 0.498 Sensitivity PETfold_pre2.0(seed): 0.590 Fold: 0.499 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Fold: 0.499 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.748 Murlet(20): 0.548 Sensitivity PETfold_pre2.0(seed): 0.668 Murlet(20): 0.415 Positive Predictive Value PETfold_pre2.0(seed): 0.837 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 UNAFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.590 UNAFold: 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.787 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 PknotsRG: 0.472 Sensitivity PETfold_pre2.0(seed): 0.590 PknotsRG: 0.472 Positive Predictive Value PETfold_pre2.0(seed): 0.787 PknotsRG: 0.473 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNAfold: 0.475 Sensitivity PETfold_pre2.0(seed): 0.590 RNAfold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAfold: 0.477 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.704 Afold: 0.501 Sensitivity PETfold_pre2.0(seed): 0.613 Afold: 0.493 Positive Predictive Value PETfold_pre2.0(seed): 0.810 Afold: 0.510 Number of pairs reference - predicted secondary structure: 281 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.682 RNAsubopt: 0.468 Sensitivity PETfold_pre2.0(seed): 0.592 RNAsubopt: 0.474 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RNAsubopt: 0.463 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 McQFold: 0.452 Sensitivity PETfold_pre2.0(seed): 0.590 McQFold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.787 McQFold: 0.465 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 CMfinder(20): 0.479 Sensitivity PETfold_pre2.0(seed): 0.673 CMfinder(20): 0.308 Positive Predictive Value PETfold_pre2.0(seed): 0.845 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.693 RNASLOpt: 0.447 Sensitivity PETfold_pre2.0(seed): 0.606 RNASLOpt: 0.422 Positive Predictive Value PETfold_pre2.0(seed): 0.794 RNASLOpt: 0.476 Number of pairs reference - predicted secondary structure: 438 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 RNAalifold(seed): 0.469 Sensitivity PETfold_pre2.0(seed): 0.632 RNAalifold(seed): 0.272 Positive Predictive Value PETfold_pre2.0(seed): 0.821 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 RNAshapes: 0.398 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.394 Positive Predictive Value PETfold_pre2.0(seed): 0.786 RNAshapes: 0.404 Number of pairs reference - predicted secondary structure: 476 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 CRWrnafold: 0.416 Sensitivity PETfold_pre2.0(seed): 0.590 CRWrnafold: 0.418 Positive Predictive Value PETfold_pre2.0(seed): 0.787 CRWrnafold: 0.417 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold4: 0.330 Sensitivity PETfold_pre2.0(seed): 0.594 Vsfold4: 0.304 Positive Predictive Value PETfold_pre2.0(seed): 0.786 Vsfold4: 0.362 Number of pairs reference - predicted secondary structure: 490 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNAwolf: 0.340 Sensitivity PETfold_pre2.0(seed): 0.590 RNAwolf: 0.355 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAwolf: 0.328 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold5: 0.324 Sensitivity PETfold_pre2.0(seed): 0.594 Vsfold5: 0.307 Positive Predictive Value PETfold_pre2.0(seed): 0.786 Vsfold5: 0.344 Number of pairs reference - predicted secondary structure: 484 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.413 CMfinder(seed): 0.350 Sensitivity PETfold_pre2.0(seed): 0.264 CMfinder(seed): 0.159 Positive Predictive Value PETfold_pre2.0(seed): 0.648 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 Carnac(20): 0.360 Sensitivity PETfold_pre2.0(seed): 0.673 Carnac(20): 0.151 Positive Predictive Value PETfold_pre2.0(seed): 0.845 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 RSpredict(20): 0.347 Sensitivity PETfold_pre2.0(seed): 0.673 RSpredict(20): 0.220 Positive Predictive Value PETfold_pre2.0(seed): 0.845 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.691 NanoFolder: 0.176 Sensitivity PETfold_pre2.0(seed): 0.597 NanoFolder: 0.208 Positive Predictive Value PETfold_pre2.0(seed): 0.800 NanoFolder: 0.151 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.721 RSpredict(seed): 0.045 Sensitivity PETfold_pre2.0(seed): 0.633 RSpredict(seed): 0.011 Positive Predictive Value PETfold_pre2.0(seed): 0.822 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity Murlet(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Murlet(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity Multilign(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Multilign(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient HotKnots: N/A PETfold_pre2.0(seed): N/A Sensitivity HotKnots: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value HotKnots: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(seed): N/A Sensitivity Pknots: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A MCFold: N/A Sensitivity PETfold_pre2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity PPfold(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value PPfold(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 PETfold_pre2.0(seed): 0.677 Sensitivity TurboFold(seed): 0.677 PETfold_pre2.0(seed): 0.646 Positive Predictive Value TurboFold(seed): 0.746 PETfold_pre2.0(seed): 0.712 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_pre2.0(seed): N/A Sensitivity Alterna: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.625 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.497 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.788 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(seed): 0.673 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.845 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.632 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.820 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(20)	204 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.840 TurboFold(20): 0.740 Sensitivity ContextFold: 0.791 TurboFold(20): 0.685 Positive Predictive Value ContextFold: 0.892 TurboFold(20): 0.801 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 TurboFold(20): 0.740 Sensitivity PETfold_pre2.0(seed): 0.673 TurboFold(20): 0.685 Positive Predictive Value PETfold_pre2.0(seed): 0.845 TurboFold(20): 0.801 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.740 PETfold_pre2.0(20): 0.735 Sensitivity TurboFold(20): 0.685 PETfold_pre2.0(20): 0.652 Positive Predictive Value TurboFold(20): 0.801 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.739 PPfold(20): 0.734 Sensitivity TurboFold(20): 0.684 PPfold(20): 0.635 Positive Predictive Value TurboFold(20): 0.800 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.740 CentroidAlifold(20): 0.717 Sensitivity TurboFold(20): 0.685 CentroidAlifold(20): 0.561 Positive Predictive Value TurboFold(20): 0.801 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 CentroidAlifold(seed): 0.722 Sensitivity TurboFold(20): 0.702 CentroidAlifold(seed): 0.548 Positive Predictive Value TurboFold(20): 0.823 CentroidAlifold(seed): 0.951 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.740 CentroidHomfold‑LAST: 0.702 Sensitivity TurboFold(20): 0.685 CentroidHomfold‑LAST: 0.551 Positive Predictive Value TurboFold(20): 0.801 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.740 RNAalifold(20): 0.660 Sensitivity TurboFold(20): 0.685 RNAalifold(20): 0.532 Positive Predictive Value TurboFold(20): 0.801 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.740 IPknot: 0.648 Sensitivity TurboFold(20): 0.685 IPknot: 0.574 Positive Predictive Value TurboFold(20): 0.801 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.739 Multilign(20): 0.649 Sensitivity TurboFold(20): 0.684 Multilign(20): 0.590 Positive Predictive Value TurboFold(20): 0.800 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.740 CentroidFold: 0.616 Sensitivity TurboFold(20): 0.685 CentroidFold: 0.547 Positive Predictive Value TurboFold(20): 0.801 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.740 Contrafold: 0.601 Sensitivity TurboFold(20): 0.685 Contrafold: 0.576 Positive Predictive Value TurboFold(20): 0.801 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.740 MXScarna(20): 0.626 Sensitivity TurboFold(20): 0.685 MXScarna(20): 0.551 Positive Predictive Value TurboFold(20): 0.801 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 MXScarna(seed): 0.655 Sensitivity TurboFold(20): 0.702 MXScarna(seed): 0.542 Positive Predictive Value TurboFold(20): 0.822 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.740 MaxExpect: 0.587 Sensitivity TurboFold(20): 0.685 MaxExpect: 0.561 Positive Predictive Value TurboFold(20): 0.801 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.740 ProbKnot: 0.586 Sensitivity TurboFold(20): 0.685 ProbKnot: 0.564 Positive Predictive Value TurboFold(20): 0.801 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.663 RNASampler(20): 0.543 Sensitivity TurboFold(20): 0.610 RNASampler(20): 0.425 Positive Predictive Value TurboFold(20): 0.720 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.740 Sfold: 0.568 Sensitivity TurboFold(20): 0.685 Sfold: 0.503 Positive Predictive Value TurboFold(20): 0.801 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.740 Fold: 0.550 Sensitivity TurboFold(20): 0.685 Fold: 0.541 Positive Predictive Value TurboFold(20): 0.801 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.729 Murlet(20): 0.548 Sensitivity TurboFold(20): 0.674 Murlet(20): 0.415 Positive Predictive Value TurboFold(20): 0.789 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.740 UNAFold: 0.531 Sensitivity TurboFold(20): 0.685 UNAFold: 0.519 Positive Predictive Value TurboFold(20): 0.801 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.740 PknotsRG: 0.512 Sensitivity TurboFold(20): 0.685 PknotsRG: 0.503 Positive Predictive Value TurboFold(20): 0.801 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.740 RNAfold: 0.527 Sensitivity TurboFold(20): 0.685 RNAfold: 0.518 Positive Predictive Value TurboFold(20): 0.801 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.756 Afold: 0.548 Sensitivity TurboFold(20): 0.699 Afold: 0.533 Positive Predictive Value TurboFold(20): 0.818 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.740 RNAsubopt: 0.519 Sensitivity TurboFold(20): 0.685 RNAsubopt: 0.518 Positive Predictive Value TurboFold(20): 0.801 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.740 McQFold: 0.452 Sensitivity TurboFold(20): 0.685 McQFold: 0.433 Positive Predictive Value TurboFold(20): 0.801 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.740 CMfinder(20): 0.479 Sensitivity TurboFold(20): 0.685 CMfinder(20): 0.308 Positive Predictive Value TurboFold(20): 0.801 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.735 RNASLOpt: 0.454 Sensitivity TurboFold(20): 0.680 RNASLOpt: 0.419 Positive Predictive Value TurboFold(20): 0.795 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RNAalifold(seed): 0.446 Sensitivity TurboFold(20): 0.702 RNAalifold(seed): 0.249 Positive Predictive Value TurboFold(20): 0.823 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.738 RNAshapes: 0.456 Sensitivity TurboFold(20): 0.682 RNAshapes: 0.441 Positive Predictive Value TurboFold(20): 0.799 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.740 CRWrnafold: 0.454 Sensitivity TurboFold(20): 0.685 CRWrnafold: 0.446 Positive Predictive Value TurboFold(20): 0.801 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.738 Vsfold4: 0.390 Sensitivity TurboFold(20): 0.683 Vsfold4: 0.352 Positive Predictive Value TurboFold(20): 0.799 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.740 RNAwolf: 0.367 Sensitivity TurboFold(20): 0.685 RNAwolf: 0.377 Positive Predictive Value TurboFold(20): 0.801 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.738 Vsfold5: 0.369 Sensitivity TurboFold(20): 0.682 Vsfold5: 0.342 Positive Predictive Value TurboFold(20): 0.798 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.740 Carnac(20): 0.360 Sensitivity TurboFold(20): 0.685 Carnac(20): 0.151 Positive Predictive Value TurboFold(20): 0.801 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.740 RSpredict(20): 0.347 Sensitivity TurboFold(20): 0.685 RSpredict(20): 0.220 Positive Predictive Value TurboFold(20): 0.801 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.728 NanoFolder: 0.152 Sensitivity TurboFold(20): 0.674 NanoFolder: 0.174 Positive Predictive Value TurboFold(20): 0.787 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RSpredict(seed): 0.054 Sensitivity TurboFold(20): 0.703 RSpredict(seed): 0.014 Positive Predictive Value TurboFold(20): 0.823 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: N/A TurboFold(20): N/A Sensitivity HotKnots: N/A TurboFold(20): N/A Positive Predictive Value HotKnots: 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 Pknots Matthews Correlation Coefficient TurboFold(20): N/A Pknots: N/A Sensitivity TurboFold(20): N/A Pknots: N/A Positive Predictive Value TurboFold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: N/A TurboFold(20): N/A Sensitivity Cylofold: N/A TurboFold(20): N/A Positive Predictive Value Cylofold: 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 MCFold Matthews Correlation Coefficient TurboFold(20): N/A MCFold: N/A Sensitivity TurboFold(20): N/A MCFold: N/A Positive Predictive Value TurboFold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RDfolder vs TurboFold(20) Matthews Correlation Coefficient RDfolder: N/A TurboFold(20): N/A Sensitivity RDfolder: N/A TurboFold(20): N/A Positive Predictive Value RDfolder: N/A TurboFold(20): 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	? 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	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): N/A Alterna: N/A Sensitivity TurboFold(20): N/A Alterna: N/A Positive Predictive Value TurboFold(20): N/A Alterna: 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): 0.781 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.777 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.786 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.740 Mastr(20): 0.000 Sensitivity TurboFold(20): 0.685 Mastr(20): 0.000 Positive Predictive Value TurboFold(20): 0.801 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.703 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.822 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(20)	204 ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.840 PETfold_pre2.0(20): 0.735 Sensitivity ContextFold: 0.791 PETfold_pre2.0(20): 0.652 Positive Predictive Value ContextFold: 0.892 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 PETfold_pre2.0(20): 0.735 Sensitivity PETfold_pre2.0(seed): 0.673 PETfold_pre2.0(20): 0.652 Positive Predictive Value PETfold_pre2.0(seed): 0.845 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.740 PETfold_pre2.0(20): 0.735 Sensitivity TurboFold(20): 0.685 PETfold_pre2.0(20): 0.652 Positive Predictive Value TurboFold(20): 0.801 PETfold_pre2.0(20): 0.829 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 4.48494289621e-08		= PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.734 PPfold(20): 0.734 Sensitivity PETfold_pre2.0(20): 0.652 PPfold(20): 0.635 Positive Predictive Value PETfold_pre2.0(20): 0.828 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 0.667107250991	+ PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidAlifold(20): 0.717 Sensitivity PETfold_pre2.0(20): 0.652 CentroidAlifold(20): 0.561 Positive Predictive Value PETfold_pre2.0(20): 0.829 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.754 CentroidAlifold(seed): 0.722 Sensitivity PETfold_pre2.0(20): 0.670 CentroidAlifold(seed): 0.548 Positive Predictive Value PETfold_pre2.0(20): 0.849 CentroidAlifold(seed): 0.951 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidHomfold‑LAST: 0.702 Sensitivity PETfold_pre2.0(20): 0.652 CentroidHomfold‑LAST: 0.551 Positive Predictive Value PETfold_pre2.0(20): 0.829 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAalifold(20): 0.660 Sensitivity PETfold_pre2.0(20): 0.652 RNAalifold(20): 0.532 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 IPknot: 0.648 Sensitivity PETfold_pre2.0(20): 0.652 IPknot: 0.574 Positive Predictive Value PETfold_pre2.0(20): 0.829 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Multilign(20): 0.649 Sensitivity PETfold_pre2.0(20): 0.652 Multilign(20): 0.590 Positive Predictive Value PETfold_pre2.0(20): 0.830 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidFold: 0.616 Sensitivity PETfold_pre2.0(20): 0.652 CentroidFold: 0.547 Positive Predictive Value PETfold_pre2.0(20): 0.829 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Contrafold: 0.601 Sensitivity PETfold_pre2.0(20): 0.652 Contrafold: 0.576 Positive Predictive Value PETfold_pre2.0(20): 0.829 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 MXScarna(20): 0.626 Sensitivity PETfold_pre2.0(20): 0.652 MXScarna(20): 0.551 Positive Predictive Value PETfold_pre2.0(20): 0.829 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.754 MXScarna(seed): 0.655 Sensitivity PETfold_pre2.0(20): 0.670 MXScarna(seed): 0.542 Positive Predictive Value PETfold_pre2.0(20): 0.850 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 MaxExpect: 0.587 Sensitivity PETfold_pre2.0(20): 0.652 MaxExpect: 0.561 Positive Predictive Value PETfold_pre2.0(20): 0.829 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 ProbKnot: 0.586 Sensitivity PETfold_pre2.0(20): 0.652 ProbKnot: 0.564 Positive Predictive Value PETfold_pre2.0(20): 0.829 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.650 RNASampler(20): 0.543 Sensitivity PETfold_pre2.0(20): 0.569 RNASampler(20): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.742 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Sfold: 0.568 Sensitivity PETfold_pre2.0(20): 0.652 Sfold: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.829 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Fold: 0.550 Sensitivity PETfold_pre2.0(20): 0.652 Fold: 0.541 Positive Predictive Value PETfold_pre2.0(20): 0.829 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.724 Murlet(20): 0.548 Sensitivity PETfold_pre2.0(20): 0.643 Murlet(20): 0.415 Positive Predictive Value PETfold_pre2.0(20): 0.815 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 UNAFold: 0.531 Sensitivity PETfold_pre2.0(20): 0.652 UNAFold: 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.829 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 PknotsRG: 0.512 Sensitivity PETfold_pre2.0(20): 0.652 PknotsRG: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.829 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAfold: 0.527 Sensitivity PETfold_pre2.0(20): 0.652 RNAfold: 0.518 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Afold: 0.548 Sensitivity PETfold_pre2.0(20): 0.662 Afold: 0.533 Positive Predictive Value PETfold_pre2.0(20): 0.844 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAsubopt: 0.519 Sensitivity PETfold_pre2.0(20): 0.652 RNAsubopt: 0.518 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 McQFold: 0.452 Sensitivity PETfold_pre2.0(20): 0.652 McQFold: 0.433 Positive Predictive Value PETfold_pre2.0(20): 0.829 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CMfinder(20): 0.479 Sensitivity PETfold_pre2.0(20): 0.652 CMfinder(20): 0.308 Positive Predictive Value PETfold_pre2.0(20): 0.829 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 RNASLOpt: 0.454 Sensitivity PETfold_pre2.0(20): 0.657 RNASLOpt: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.827 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.754 RNAalifold(seed): 0.446 Sensitivity PETfold_pre2.0(20): 0.670 RNAalifold(seed): 0.249 Positive Predictive Value PETfold_pre2.0(20): 0.849 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 RNAshapes: 0.456 Sensitivity PETfold_pre2.0(20): 0.655 RNAshapes: 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.831 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CRWrnafold: 0.454 Sensitivity PETfold_pre2.0(20): 0.652 CRWrnafold: 0.446 Positive Predictive Value PETfold_pre2.0(20): 0.829 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Vsfold4: 0.390 Sensitivity PETfold_pre2.0(20): 0.654 Vsfold4: 0.352 Positive Predictive Value PETfold_pre2.0(20): 0.829 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAwolf: 0.367 Sensitivity PETfold_pre2.0(20): 0.652 RNAwolf: 0.377 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Vsfold5: 0.369 Sensitivity PETfold_pre2.0(20): 0.655 Vsfold5: 0.342 Positive Predictive Value PETfold_pre2.0(20): 0.829 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Carnac(20): 0.360 Sensitivity PETfold_pre2.0(20): 0.652 Carnac(20): 0.151 Positive Predictive Value PETfold_pre2.0(20): 0.829 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RSpredict(20): 0.347 Sensitivity PETfold_pre2.0(20): 0.652 RSpredict(20): 0.220 Positive Predictive Value PETfold_pre2.0(20): 0.829 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.733 NanoFolder: 0.152 Sensitivity PETfold_pre2.0(20): 0.649 NanoFolder: 0.174 Positive Predictive Value PETfold_pre2.0(20): 0.829 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.755 RSpredict(seed): 0.054 Sensitivity PETfold_pre2.0(20): 0.671 RSpredict(seed): 0.014 Positive Predictive Value PETfold_pre2.0(20): 0.849 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs PETfold_pre2.0(20) Matthews Correlation Coefficient HotKnots: N/A PETfold_pre2.0(20): N/A Sensitivity HotKnots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value HotKnots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs PETfold_pre2.0(20) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(20): N/A Sensitivity Pknots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_pre2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(20): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Cylofold: 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 MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): N/A MCFold: N/A Sensitivity PETfold_pre2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RDfolder vs PETfold_pre2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(20): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(20): N/A Positive Predictive Value RDfolder: 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	? 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	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.818 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.760 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.881 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(20): 0.652 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.829 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.675 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.849 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(20)	197 ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.840 PPfold(20): 0.734 Sensitivity ContextFold: 0.791 PPfold(20): 0.635 Positive Predictive Value ContextFold: 0.893 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 PPfold(20): 0.734 Sensitivity PETfold_pre2.0(seed): 0.673 PPfold(20): 0.635 Positive Predictive Value PETfold_pre2.0(seed): 0.845 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.739 PPfold(20): 0.734 Sensitivity TurboFold(20): 0.684 PPfold(20): 0.635 Positive Predictive Value TurboFold(20): 0.800 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.734 PPfold(20): 0.734 Sensitivity PETfold_pre2.0(20): 0.652 PPfold(20): 0.635 Positive Predictive Value PETfold_pre2.0(20): 0.828 PPfold(20): 0.850 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 0.667107250991		+ PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.734 CentroidAlifold(20): 0.717 Sensitivity PPfold(20): 0.635 CentroidAlifold(20): 0.562 Positive Predictive Value PPfold(20): 0.850 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.752 CentroidAlifold(seed): 0.722 Sensitivity PPfold(20): 0.657 CentroidAlifold(seed): 0.549 Positive Predictive Value PPfold(20): 0.862 CentroidAlifold(seed): 0.952 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.734 CentroidHomfold‑LAST: 0.702 Sensitivity PPfold(20): 0.635 CentroidHomfold‑LAST: 0.550 Positive Predictive Value PPfold(20): 0.850 CentroidHomfold‑LAST: 0.897 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.734 RNAalifold(20): 0.661 Sensitivity PPfold(20): 0.635 RNAalifold(20): 0.534 Positive Predictive Value PPfold(20): 0.850 RNAalifold(20): 0.820 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.734 IPknot: 0.650 Sensitivity PPfold(20): 0.635 IPknot: 0.575 Positive Predictive Value PPfold(20): 0.850 IPknot: 0.736 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.735 Multilign(20): 0.650 Sensitivity PPfold(20): 0.635 Multilign(20): 0.590 Positive Predictive Value PPfold(20): 0.851 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.734 CentroidFold: 0.615 Sensitivity PPfold(20): 0.635 CentroidFold: 0.545 Positive Predictive Value PPfold(20): 0.850 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.734 Contrafold: 0.600 Sensitivity PPfold(20): 0.635 Contrafold: 0.575 Positive Predictive Value PPfold(20): 0.850 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.734 MXScarna(20): 0.626 Sensitivity PPfold(20): 0.635 MXScarna(20): 0.552 Positive Predictive Value PPfold(20): 0.850 MXScarna(20): 0.711 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.752 MXScarna(seed): 0.658 Sensitivity PPfold(20): 0.657 MXScarna(seed): 0.544 Positive Predictive Value PPfold(20): 0.862 MXScarna(seed): 0.797 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.734 MaxExpect: 0.584 Sensitivity PPfold(20): 0.635 MaxExpect: 0.559 Positive Predictive Value PPfold(20): 0.850 MaxExpect: 0.613 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.734 ProbKnot: 0.583 Sensitivity PPfold(20): 0.635 ProbKnot: 0.562 Positive Predictive Value PPfold(20): 0.850 ProbKnot: 0.607 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.656 RNASampler(20): 0.543 Sensitivity PPfold(20): 0.541 RNASampler(20): 0.425 Positive Predictive Value PPfold(20): 0.795 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.734 Sfold: 0.567 Sensitivity PPfold(20): 0.635 Sfold: 0.501 Positive Predictive Value PPfold(20): 0.850 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.734 Fold: 0.549 Sensitivity PPfold(20): 0.635 Fold: 0.540 Positive Predictive Value PPfold(20): 0.850 Fold: 0.560 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.725 Murlet(20): 0.552 Sensitivity PPfold(20): 0.626 Murlet(20): 0.419 Positive Predictive Value PPfold(20): 0.841 Murlet(20): 0.729 Number of pairs reference - predicted secondary structure: 143 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.734 UNAFold: 0.531 Sensitivity PPfold(20): 0.635 UNAFold: 0.519 Positive Predictive Value PPfold(20): 0.850 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.734 PknotsRG: 0.511 Sensitivity PPfold(20): 0.635 PknotsRG: 0.502 Positive Predictive Value PPfold(20): 0.850 PknotsRG: 0.522 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.734 RNAfold: 0.527 Sensitivity PPfold(20): 0.635 RNAfold: 0.518 Positive Predictive Value PPfold(20): 0.850 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.746 Afold: 0.549 Sensitivity PPfold(20): 0.648 Afold: 0.534 Positive Predictive Value PPfold(20): 0.859 Afold: 0.566 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.734 RNAsubopt: 0.519 Sensitivity PPfold(20): 0.635 RNAsubopt: 0.518 Positive Predictive Value PPfold(20): 0.850 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.734 McQFold: 0.452 Sensitivity PPfold(20): 0.635 McQFold: 0.433 Positive Predictive Value PPfold(20): 0.850 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.734 CMfinder(20): 0.480 Sensitivity PPfold(20): 0.635 CMfinder(20): 0.309 Positive Predictive Value PPfold(20): 0.850 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.737 RNASLOpt: 0.454 Sensitivity PPfold(20): 0.639 RNASLOpt: 0.420 Positive Predictive Value PPfold(20): 0.850 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 181 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.752 RNAalifold(seed): 0.445 Sensitivity PPfold(20): 0.657 RNAalifold(seed): 0.248 Positive Predictive Value PPfold(20): 0.862 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.738 RNAshapes: 0.455 Sensitivity PPfold(20): 0.638 RNAshapes: 0.440 Positive Predictive Value PPfold(20): 0.853 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 188 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.734 CRWrnafold: 0.454 Sensitivity PPfold(20): 0.635 CRWrnafold: 0.445 Positive Predictive Value PPfold(20): 0.850 CRWrnafold: 0.464 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.736 Vsfold4: 0.390 Sensitivity PPfold(20): 0.637 Vsfold4: 0.353 Positive Predictive Value PPfold(20): 0.851 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 193 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.734 RNAwolf: 0.368 Sensitivity PPfold(20): 0.635 RNAwolf: 0.378 Positive Predictive Value PPfold(20): 0.850 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.737 Vsfold5: 0.367 Sensitivity PPfold(20): 0.638 Vsfold5: 0.340 Positive Predictive Value PPfold(20): 0.851 Vsfold5: 0.399 Number of pairs reference - predicted secondary structure: 190 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.734 Carnac(20): 0.365 Sensitivity PPfold(20): 0.635 Carnac(20): 0.156 Positive Predictive Value PPfold(20): 0.850 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.734 RSpredict(20): 0.349 Sensitivity PPfold(20): 0.635 RSpredict(20): 0.222 Positive Predictive Value PPfold(20): 0.850 RSpredict(20): 0.551 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.732 NanoFolder: 0.155 Sensitivity PPfold(20): 0.632 NanoFolder: 0.178 Positive Predictive Value PPfold(20): 0.849 NanoFolder: 0.138 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.753 RSpredict(seed): 0.055 Sensitivity PPfold(20): 0.658 RSpredict(seed): 0.014 Positive Predictive Value PPfold(20): 0.862 RSpredict(seed): 0.219 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs PPfold(20) Matthews Correlation Coefficient HotKnots: N/A PPfold(20): N/A Sensitivity HotKnots: N/A PPfold(20): N/A Positive Predictive Value HotKnots: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): N/A Pknots: N/A Sensitivity PPfold(20): N/A Pknots: N/A Positive Predictive Value PPfold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PPfold(20) Matthews Correlation Coefficient Cylofold: N/A PPfold(20): N/A Sensitivity Cylofold: N/A PPfold(20): N/A Positive Predictive Value Cylofold: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): N/A MCFold: N/A Sensitivity PPfold(20): N/A MCFold: N/A Positive Predictive Value PPfold(20): N/A MCFold: 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(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): N/A RDfolder: N/A Sensitivity PPfold(20): N/A RDfolder: N/A Positive Predictive Value PPfold(20): N/A RDfolder: 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	? 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	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): N/A Alterna: N/A Sensitivity PPfold(20): N/A Alterna: N/A Positive Predictive Value PPfold(20): N/A Alterna: 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): 0.818 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.738 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.907 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.734 Mastr(20): 0.000 Sensitivity PPfold(20): 0.635 Mastr(20): 0.000 Positive Predictive Value PPfold(20): 0.850 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.755 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.660 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.863 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 142 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(20)	204 ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.840 CentroidAlifold(20): 0.717 Sensitivity ContextFold: 0.791 CentroidAlifold(20): 0.561 Positive Predictive Value ContextFold: 0.892 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 CentroidAlifold(20): 0.717 Sensitivity PETfold_pre2.0(seed): 0.673 CentroidAlifold(20): 0.561 Positive Predictive Value PETfold_pre2.0(seed): 0.845 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.740 CentroidAlifold(20): 0.717 Sensitivity TurboFold(20): 0.685 CentroidAlifold(20): 0.561 Positive Predictive Value TurboFold(20): 0.801 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidAlifold(20): 0.717 Sensitivity PETfold_pre2.0(20): 0.652 CentroidAlifold(20): 0.561 Positive Predictive Value PETfold_pre2.0(20): 0.829 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.734 CentroidAlifold(20): 0.717 Sensitivity PPfold(20): 0.635 CentroidAlifold(20): 0.562 Positive Predictive Value PPfold(20): 0.850 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 CentroidAlifold(seed): 0.722 Sensitivity CentroidAlifold(20): 0.562 CentroidAlifold(seed): 0.548 Positive Predictive Value CentroidAlifold(20): 0.933 CentroidAlifold(seed): 0.951 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CentroidHomfold‑LAST: 0.702 Sensitivity CentroidAlifold(20): 0.561 CentroidHomfold‑LAST: 0.551 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAalifold(20): 0.660 Sensitivity CentroidAlifold(20): 0.561 RNAalifold(20): 0.532 Positive Predictive Value CentroidAlifold(20): 0.916 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.717 IPknot: 0.648 Sensitivity CentroidAlifold(20): 0.561 IPknot: 0.574 Positive Predictive Value CentroidAlifold(20): 0.916 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.716 Multilign(20): 0.649 Sensitivity CentroidAlifold(20): 0.561 Multilign(20): 0.590 Positive Predictive Value CentroidAlifold(20): 0.916 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CentroidFold: 0.616 Sensitivity CentroidAlifold(20): 0.561 CentroidFold: 0.547 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Contrafold: 0.601 Sensitivity CentroidAlifold(20): 0.561 Contrafold: 0.576 Positive Predictive Value CentroidAlifold(20): 0.916 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 MXScarna(20): 0.626 Sensitivity CentroidAlifold(20): 0.561 MXScarna(20): 0.551 Positive Predictive Value CentroidAlifold(20): 0.916 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 MXScarna(seed): 0.655 Sensitivity CentroidAlifold(20): 0.562 MXScarna(seed): 0.542 Positive Predictive Value CentroidAlifold(20): 0.933 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.717 MaxExpect: 0.587 Sensitivity CentroidAlifold(20): 0.561 MaxExpect: 0.561 Positive Predictive Value CentroidAlifold(20): 0.916 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.717 ProbKnot: 0.586 Sensitivity CentroidAlifold(20): 0.561 ProbKnot: 0.564 Positive Predictive Value CentroidAlifold(20): 0.916 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.678 RNASampler(20): 0.543 Sensitivity CentroidAlifold(20): 0.540 RNASampler(20): 0.425 Positive Predictive Value CentroidAlifold(20): 0.853 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Sfold: 0.568 Sensitivity CentroidAlifold(20): 0.561 Sfold: 0.503 Positive Predictive Value CentroidAlifold(20): 0.916 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Fold: 0.550 Sensitivity CentroidAlifold(20): 0.561 Fold: 0.541 Positive Predictive Value CentroidAlifold(20): 0.916 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.716 Murlet(20): 0.548 Sensitivity CentroidAlifold(20): 0.566 Murlet(20): 0.415 Positive Predictive Value CentroidAlifold(20): 0.907 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 UNAFold: 0.531 Sensitivity CentroidAlifold(20): 0.561 UNAFold: 0.519 Positive Predictive Value CentroidAlifold(20): 0.916 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.717 PknotsRG: 0.512 Sensitivity CentroidAlifold(20): 0.561 PknotsRG: 0.503 Positive Predictive Value CentroidAlifold(20): 0.916 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAfold: 0.527 Sensitivity CentroidAlifold(20): 0.561 RNAfold: 0.518 Positive Predictive Value CentroidAlifold(20): 0.916 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.718 Afold: 0.548 Sensitivity CentroidAlifold(20): 0.557 Afold: 0.533 Positive Predictive Value CentroidAlifold(20): 0.927 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAsubopt: 0.519 Sensitivity CentroidAlifold(20): 0.561 RNAsubopt: 0.518 Positive Predictive Value CentroidAlifold(20): 0.916 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 McQFold: 0.452 Sensitivity CentroidAlifold(20): 0.561 McQFold: 0.433 Positive Predictive Value CentroidAlifold(20): 0.916 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CMfinder(20): 0.479 Sensitivity CentroidAlifold(20): 0.561 CMfinder(20): 0.308 Positive Predictive Value CentroidAlifold(20): 0.916 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNASLOpt: 0.454 Sensitivity CentroidAlifold(20): 0.563 RNASLOpt: 0.419 Positive Predictive Value CentroidAlifold(20): 0.914 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 RNAalifold(seed): 0.446 Sensitivity CentroidAlifold(20): 0.562 RNAalifold(seed): 0.249 Positive Predictive Value CentroidAlifold(20): 0.933 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAshapes: 0.456 Sensitivity CentroidAlifold(20): 0.561 RNAshapes: 0.441 Positive Predictive Value CentroidAlifold(20): 0.917 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CRWrnafold: 0.454 Sensitivity CentroidAlifold(20): 0.561 CRWrnafold: 0.446 Positive Predictive Value CentroidAlifold(20): 0.916 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Vsfold4: 0.390 Sensitivity CentroidAlifold(20): 0.562 Vsfold4: 0.352 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAwolf: 0.367 Sensitivity CentroidAlifold(20): 0.561 RNAwolf: 0.377 Positive Predictive Value CentroidAlifold(20): 0.916 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Vsfold5: 0.369 Sensitivity CentroidAlifold(20): 0.562 Vsfold5: 0.342 Positive Predictive Value CentroidAlifold(20): 0.917 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Carnac(20): 0.360 Sensitivity CentroidAlifold(20): 0.561 Carnac(20): 0.151 Positive Predictive Value CentroidAlifold(20): 0.916 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RSpredict(20): 0.347 Sensitivity CentroidAlifold(20): 0.561 RSpredict(20): 0.220 Positive Predictive Value CentroidAlifold(20): 0.916 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.711 NanoFolder: 0.152 Sensitivity CentroidAlifold(20): 0.560 NanoFolder: 0.174 Positive Predictive Value CentroidAlifold(20): 0.905 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 RSpredict(seed): 0.054 Sensitivity CentroidAlifold(20): 0.563 RSpredict(seed): 0.014 Positive Predictive Value CentroidAlifold(20): 0.933 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs CentroidAlifold(20) Matthews Correlation Coefficient HotKnots: N/A CentroidAlifold(20): N/A Sensitivity HotKnots: N/A CentroidAlifold(20): N/A Positive Predictive Value HotKnots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CentroidAlifold(20) Matthews Correlation Coefficient Pknots: N/A CentroidAlifold(20): N/A Sensitivity Pknots: N/A CentroidAlifold(20): N/A Positive Predictive Value Pknots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs CentroidAlifold(20) Matthews Correlation Coefficient Cylofold: N/A CentroidAlifold(20): N/A Sensitivity Cylofold: N/A CentroidAlifold(20): N/A Positive Predictive Value Cylofold: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): N/A MCFold: N/A Sensitivity CentroidAlifold(20): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(20): N/A MCFold: 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	? RDfolder vs CentroidAlifold(20) Matthews Correlation Coefficient RDfolder: N/A CentroidAlifold(20): N/A Sensitivity RDfolder: N/A CentroidAlifold(20): N/A Positive Predictive Value RDfolder: 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 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	? 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	? Alterna vs CentroidAlifold(20) Matthews Correlation Coefficient Alterna: N/A CentroidAlifold(20): N/A Sensitivity Alterna: N/A CentroidAlifold(20): N/A Positive Predictive Value Alterna: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.885 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.842 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.932 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Mastr(20): 0.000 Sensitivity CentroidAlifold(20): 0.561 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(20): 0.916 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.728 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.567 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.934 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	277 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.813 CentroidAlifold(seed): 0.691 Sensitivity ContextFold: 0.765 CentroidAlifold(seed): 0.521 Positive Predictive Value ContextFold: 0.864 CentroidAlifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 CentroidAlifold(seed): 0.691 Sensitivity PETfold_pre2.0(seed): 0.632 CentroidAlifold(seed): 0.521 Positive Predictive Value PETfold_pre2.0(seed): 0.822 CentroidAlifold(seed): 0.919 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 CentroidAlifold(seed): 0.722 Sensitivity TurboFold(20): 0.702 CentroidAlifold(seed): 0.548 Positive Predictive Value TurboFold(20): 0.823 CentroidAlifold(seed): 0.951 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.754 CentroidAlifold(seed): 0.722 Sensitivity PETfold_pre2.0(20): 0.670 CentroidAlifold(seed): 0.548 Positive Predictive Value PETfold_pre2.0(20): 0.849 CentroidAlifold(seed): 0.951 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	155 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.752 CentroidAlifold(seed): 0.722 Sensitivity PPfold(20): 0.657 CentroidAlifold(seed): 0.549 Positive Predictive Value PPfold(20): 0.862 CentroidAlifold(seed): 0.952 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 CentroidAlifold(seed): 0.722 Sensitivity CentroidAlifold(20): 0.562 CentroidAlifold(seed): 0.548 Positive Predictive Value CentroidAlifold(20): 0.933 CentroidAlifold(seed): 0.951 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.693 CentroidHomfold‑LAST: 0.675 Sensitivity CentroidAlifold(seed): 0.523 CentroidHomfold‑LAST: 0.507 Positive Predictive Value CentroidAlifold(seed): 0.920 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 RNAalifold(20): 0.668 Sensitivity CentroidAlifold(seed): 0.548 RNAalifold(20): 0.533 Positive Predictive Value CentroidAlifold(seed): 0.951 RNAalifold(20): 0.837 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 IPknot: 0.640 Sensitivity CentroidAlifold(seed): 0.521 IPknot: 0.568 Positive Predictive Value CentroidAlifold(seed): 0.919 IPknot: 0.722 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.720 Multilign(20): 0.657 Sensitivity CentroidAlifold(seed): 0.545 Multilign(20): 0.594 Positive Predictive Value CentroidAlifold(seed): 0.952 Multilign(20): 0.728 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 CentroidFold: 0.621 Sensitivity CentroidAlifold(seed): 0.521 CentroidFold: 0.554 Positive Predictive Value CentroidAlifold(seed): 0.919 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 Contrafold: 0.604 Sensitivity CentroidAlifold(seed): 0.521 Contrafold: 0.579 Positive Predictive Value CentroidAlifold(seed): 0.919 Contrafold: 0.631 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 MXScarna(20): 0.650 Sensitivity CentroidAlifold(seed): 0.548 MXScarna(20): 0.563 Positive Predictive Value CentroidAlifold(seed): 0.951 MXScarna(20): 0.752 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 MXScarna(seed): 0.594 Sensitivity CentroidAlifold(seed): 0.521 MXScarna(seed): 0.474 Positive Predictive Value CentroidAlifold(seed): 0.919 MXScarna(seed): 0.746 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 MaxExpect: 0.588 Sensitivity CentroidAlifold(seed): 0.521 MaxExpect: 0.563 Positive Predictive Value CentroidAlifold(seed): 0.919 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 ProbKnot: 0.587 Sensitivity CentroidAlifold(seed): 0.521 ProbKnot: 0.566 Positive Predictive Value CentroidAlifold(seed): 0.919 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.675 RNASampler(20): 0.480 Sensitivity CentroidAlifold(seed): 0.493 RNASampler(20): 0.343 Positive Predictive Value CentroidAlifold(seed): 0.927 RNASampler(20): 0.673 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 Sfold: 0.585 Sensitivity CentroidAlifold(seed): 0.521 Sfold: 0.520 Positive Predictive Value CentroidAlifold(seed): 0.919 Sfold: 0.659 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 Fold: 0.552 Sensitivity CentroidAlifold(seed): 0.521 Fold: 0.543 Positive Predictive Value CentroidAlifold(seed): 0.919 Fold: 0.563 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 Murlet(20): 0.533 Sensitivity CentroidAlifold(seed): 0.554 Murlet(20): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.951 Murlet(20): 0.732 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 UNAFold: 0.544 Sensitivity CentroidAlifold(seed): 0.521 UNAFold: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.919 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 PknotsRG: 0.527 Sensitivity CentroidAlifold(seed): 0.521 PknotsRG: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.919 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RNAfold: 0.535 Sensitivity CentroidAlifold(seed): 0.521 RNAfold: 0.524 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Afold: 0.530 Sensitivity CentroidAlifold(seed): 0.516 Afold: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.923 Afold: 0.544 Number of pairs reference - predicted secondary structure: 232 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.693 RNAsubopt: 0.533 Sensitivity CentroidAlifold(seed): 0.523 RNAsubopt: 0.531 Positive Predictive Value CentroidAlifold(seed): 0.920 RNAsubopt: 0.538 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 McQFold: 0.479 Sensitivity CentroidAlifold(seed): 0.521 McQFold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.919 McQFold: 0.502 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 CMfinder(20): 0.503 Sensitivity CentroidAlifold(seed): 0.548 CMfinder(20): 0.329 Positive Predictive Value CentroidAlifold(seed): 0.951 CMfinder(20): 0.769 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.708 RNASLOpt: 0.475 Sensitivity CentroidAlifold(seed): 0.538 RNASLOpt: 0.437 Positive Predictive Value CentroidAlifold(seed): 0.932 RNASLOpt: 0.518 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RNAalifold(seed): 0.469 Sensitivity CentroidAlifold(seed): 0.521 RNAalifold(seed): 0.271 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.696 RNAshapes: 0.486 Sensitivity CentroidAlifold(seed): 0.526 RNAshapes: 0.469 Positive Predictive Value CentroidAlifold(seed): 0.921 RNAshapes: 0.505 Number of pairs reference - predicted secondary structure: 253 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 CRWrnafold: 0.458 Sensitivity CentroidAlifold(seed): 0.521 CRWrnafold: 0.450 Positive Predictive Value CentroidAlifold(seed): 0.919 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 Vsfold4: 0.406 Sensitivity CentroidAlifold(seed): 0.528 Vsfold4: 0.365 Positive Predictive Value CentroidAlifold(seed): 0.921 Vsfold4: 0.452 Number of pairs reference - predicted secondary structure: 259 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RNAwolf: 0.372 Sensitivity CentroidAlifold(seed): 0.521 RNAwolf: 0.381 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAwolf: 0.366 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 Vsfold5: 0.378 Sensitivity CentroidAlifold(seed): 0.527 Vsfold5: 0.348 Positive Predictive Value CentroidAlifold(seed): 0.921 Vsfold5: 0.413 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.420 CMfinder(seed): 0.350 Sensitivity CentroidAlifold(seed): 0.246 CMfinder(seed): 0.159 Positive Predictive Value CentroidAlifold(seed): 0.717 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 Carnac(20): 0.332 Sensitivity CentroidAlifold(seed): 0.548 Carnac(20): 0.126 Positive Predictive Value CentroidAlifold(seed): 0.951 Carnac(20): 0.880 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 RSpredict(20): 0.306 Sensitivity CentroidAlifold(seed): 0.548 RSpredict(20): 0.174 Positive Predictive Value CentroidAlifold(seed): 0.951 RSpredict(20): 0.541 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 NanoFolder: 0.180 Sensitivity CentroidAlifold(seed): 0.512 NanoFolder: 0.206 Positive Predictive Value CentroidAlifold(seed): 0.912 NanoFolder: 0.161 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RSpredict(seed): 0.045 Sensitivity CentroidAlifold(seed): 0.521 RSpredict(seed): 0.011 Positive Predictive Value CentroidAlifold(seed): 0.919 RSpredict(seed): 0.186 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A Murlet(seed): N/A Sensitivity CentroidAlifold(seed): N/A Murlet(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A Multilign(seed): N/A Sensitivity CentroidAlifold(seed): N/A Multilign(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): N/A HotKnots: N/A Sensitivity CentroidAlifold(seed): N/A HotKnots: N/A Positive Predictive Value CentroidAlifold(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): N/A Pknots: N/A Sensitivity CentroidAlifold(seed): N/A Pknots: N/A Positive Predictive Value CentroidAlifold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): N/A Cylofold: N/A Sensitivity CentroidAlifold(seed): N/A Cylofold: N/A Positive Predictive Value CentroidAlifold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): N/A MCFold: N/A Sensitivity CentroidAlifold(seed): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A PPfold(seed): N/A Sensitivity CentroidAlifold(seed): N/A PPfold(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): N/A RDfolder: N/A Sensitivity CentroidAlifold(seed): N/A RDfolder: N/A Positive Predictive Value CentroidAlifold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.744 TurboFold(seed): 0.710 Sensitivity CentroidAlifold(seed): 0.646 TurboFold(seed): 0.677 Positive Predictive Value CentroidAlifold(seed): 0.857 TurboFold(seed): 0.746 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(seed): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(seed): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): N/A Alterna: N/A Sensitivity CentroidAlifold(seed): N/A Alterna: N/A Positive Predictive Value CentroidAlifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.650 Carnac(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.475 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.891 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 Mastr(20): 0.000 Sensitivity CentroidAlifold(seed): 0.548 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.951 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.692 Mastr(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.523 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.918 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 250 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidHomfold‑LAST	574 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.731 CentroidHomfold‑LAST: 0.641 Sensitivity ContextFold: 0.689 CentroidHomfold‑LAST: 0.469 Positive Predictive Value ContextFold: 0.778 CentroidHomfold‑LAST: 0.877 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.682 CentroidHomfold‑LAST: 0.651 Sensitivity PETfold_pre2.0(seed): 0.592 CentroidHomfold‑LAST: 0.482 Positive Predictive Value PETfold_pre2.0(seed): 0.788 CentroidHomfold‑LAST: 0.880 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.740 CentroidHomfold‑LAST: 0.702 Sensitivity TurboFold(20): 0.685 CentroidHomfold‑LAST: 0.551 Positive Predictive Value TurboFold(20): 0.801 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidHomfold‑LAST: 0.702 Sensitivity PETfold_pre2.0(20): 0.652 CentroidHomfold‑LAST: 0.551 Positive Predictive Value PETfold_pre2.0(20): 0.829 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.734 CentroidHomfold‑LAST: 0.702 Sensitivity PPfold(20): 0.635 CentroidHomfold‑LAST: 0.550 Positive Predictive Value PPfold(20): 0.850 CentroidHomfold‑LAST: 0.897 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CentroidHomfold‑LAST: 0.702 Sensitivity CentroidAlifold(20): 0.561 CentroidHomfold‑LAST: 0.551 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidHomfold‑LAST: 0.896 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	273 CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.693 CentroidHomfold‑LAST: 0.675 Sensitivity CentroidAlifold(seed): 0.523 CentroidHomfold‑LAST: 0.507 Positive Predictive Value CentroidAlifold(seed): 0.920 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 RNAalifold(20): 0.660 Sensitivity CentroidHomfold‑LAST: 0.551 RNAalifold(20): 0.532 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 IPknot: 0.605 Sensitivity CentroidHomfold‑LAST: 0.469 IPknot: 0.548 Positive Predictive Value CentroidHomfold‑LAST: 0.877 IPknot: 0.670 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.700 Multilign(20): 0.649 Sensitivity CentroidHomfold‑LAST: 0.548 Multilign(20): 0.590 Positive Predictive Value CentroidHomfold‑LAST: 0.894 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 CentroidFold: 0.575 Sensitivity CentroidHomfold‑LAST: 0.469 CentroidFold: 0.520 Positive Predictive Value CentroidHomfold‑LAST: 0.877 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Contrafold: 0.557 Sensitivity CentroidHomfold‑LAST: 0.469 Contrafold: 0.543 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 MXScarna(20): 0.626 Sensitivity CentroidHomfold‑LAST: 0.551 MXScarna(20): 0.551 Positive Predictive Value CentroidHomfold‑LAST: 0.896 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 MXScarna(seed): 0.599 Sensitivity CentroidHomfold‑LAST: 0.508 MXScarna(seed): 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.899 MXScarna(seed): 0.750 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 MaxExpect: 0.527 Sensitivity CentroidHomfold‑LAST: 0.469 MaxExpect: 0.513 Positive Predictive Value CentroidHomfold‑LAST: 0.877 MaxExpect: 0.542 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 ProbKnot: 0.526 Sensitivity CentroidHomfold‑LAST: 0.469 ProbKnot: 0.520 Positive Predictive Value CentroidHomfold‑LAST: 0.877 ProbKnot: 0.532 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 RNASampler(20): 0.543 Sensitivity CentroidHomfold‑LAST: 0.532 RNASampler(20): 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.861 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Sfold: 0.517 Sensitivity CentroidHomfold‑LAST: 0.469 Sfold: 0.466 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Sfold: 0.575 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Fold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.469 Fold: 0.502 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Fold: 0.499 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.695 Murlet(20): 0.548 Sensitivity CentroidHomfold‑LAST: 0.545 Murlet(20): 0.415 Positive Predictive Value CentroidHomfold‑LAST: 0.887 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 UNAFold: 0.479 Sensitivity CentroidHomfold‑LAST: 0.469 UNAFold: 0.476 Positive Predictive Value CentroidHomfold‑LAST: 0.877 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 PknotsRG: 0.478 Sensitivity CentroidHomfold‑LAST: 0.469 PknotsRG: 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.877 PknotsRG: 0.479 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAfold: 0.480 Sensitivity CentroidHomfold‑LAST: 0.469 RNAfold: 0.481 Positive Predictive Value CentroidHomfold‑LAST: 0.877 RNAfold: 0.480 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.656 Afold: 0.503 Sensitivity CentroidHomfold‑LAST: 0.488 Afold: 0.497 Positive Predictive Value CentroidHomfold‑LAST: 0.884 Afold: 0.511 Number of pairs reference - predicted secondary structure: 329 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAsubopt: 0.475 Sensitivity CentroidHomfold‑LAST: 0.469 RNAsubopt: 0.482 Positive Predictive Value CentroidHomfold‑LAST: 0.877 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 McQFold: 0.456 Sensitivity CentroidHomfold‑LAST: 0.469 McQFold: 0.446 Positive Predictive Value CentroidHomfold‑LAST: 0.877 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 CMfinder(20): 0.479 Sensitivity CentroidHomfold‑LAST: 0.551 CMfinder(20): 0.308 Positive Predictive Value CentroidHomfold‑LAST: 0.896 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.648 RNASLOpt: 0.446 Sensitivity CentroidHomfold‑LAST: 0.481 RNASLOpt: 0.421 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 RNAalifold(seed): 0.470 Sensitivity CentroidHomfold‑LAST: 0.507 RNAalifold(seed): 0.272 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 274 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RNAshapes: 0.408 Sensitivity CentroidHomfold‑LAST: 0.475 RNAshapes: 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.876 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 CRWrnafold: 0.423 Sensitivity CentroidHomfold‑LAST: 0.469 CRWrnafold: 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.877 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Vsfold4: 0.335 Sensitivity CentroidHomfold‑LAST: 0.475 Vsfold4: 0.308 Positive Predictive Value CentroidHomfold‑LAST: 0.876 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAwolf: 0.338 Sensitivity CentroidHomfold‑LAST: 0.469 RNAwolf: 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.877 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Vsfold5: 0.329 Sensitivity CentroidHomfold‑LAST: 0.475 Vsfold5: 0.312 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.667 CMfinder(seed): 0.350 Sensitivity CentroidHomfold‑LAST: 0.490 CMfinder(seed): 0.159 Positive Predictive Value CentroidHomfold‑LAST: 0.909 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 Carnac(20): 0.360 Sensitivity CentroidHomfold‑LAST: 0.551 Carnac(20): 0.151 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 RSpredict(20): 0.347 Sensitivity CentroidHomfold‑LAST: 0.551 RSpredict(20): 0.220 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.647 NanoFolder: 0.174 Sensitivity CentroidHomfold‑LAST: 0.478 NanoFolder: 0.207 Positive Predictive Value CentroidHomfold‑LAST: 0.877 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 RSpredict(seed): 0.046 Sensitivity CentroidHomfold‑LAST: 0.508 RSpredict(seed): 0.011 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RSpredict(seed): 0.194 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Murlet(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity Murlet(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Murlet(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Multilign(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity Multilign(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Multilign(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: N/A CentroidHomfold‑LAST: N/A Sensitivity HotKnots: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value HotKnots: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: N/A CentroidHomfold‑LAST: N/A Sensitivity Pknots: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Pknots: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Cylofold: 0.271 Sensitivity CentroidHomfold‑LAST: 0.613 Cylofold: 0.241 Positive Predictive Value CentroidHomfold‑LAST: 0.808 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A MCFold: N/A Sensitivity CentroidHomfold‑LAST: N/A MCFold: N/A Positive Predictive Value CentroidHomfold‑LAST: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity PPfold(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value PPfold(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CentroidHomfold‑LAST Matthews Correlation Coefficient RDfolder: N/A CentroidHomfold‑LAST: N/A Sensitivity RDfolder: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value RDfolder: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.789 TurboFold(seed): 0.710 Sensitivity CentroidHomfold‑LAST: 0.692 TurboFold(seed): 0.677 Positive Predictive Value CentroidHomfold‑LAST: 0.900 TurboFold(seed): 0.746 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity RNASampler(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value RNASampler(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CentroidHomfold‑LAST Matthews Correlation Coefficient Alterna: N/A CentroidHomfold‑LAST: N/A Sensitivity Alterna: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Alterna: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.636 Carnac(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.463 Carnac(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.874 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 Mastr(20): 0.000 Sensitivity CentroidHomfold‑LAST: 0.551 Mastr(20): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.511 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(20)	204 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.840 RNAalifold(20): 0.660 Sensitivity ContextFold: 0.791 RNAalifold(20): 0.532 Positive Predictive Value ContextFold: 0.892 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 RNAalifold(20): 0.660 Sensitivity PETfold_pre2.0(seed): 0.673 RNAalifold(20): 0.532 Positive Predictive Value PETfold_pre2.0(seed): 0.845 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.740 RNAalifold(20): 0.660 Sensitivity TurboFold(20): 0.685 RNAalifold(20): 0.532 Positive Predictive Value TurboFold(20): 0.801 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAalifold(20): 0.660 Sensitivity PETfold_pre2.0(20): 0.652 RNAalifold(20): 0.532 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.734 RNAalifold(20): 0.661 Sensitivity PPfold(20): 0.635 RNAalifold(20): 0.534 Positive Predictive Value PPfold(20): 0.850 RNAalifold(20): 0.820 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAalifold(20): 0.660 Sensitivity CentroidAlifold(20): 0.561 RNAalifold(20): 0.532 Positive Predictive Value CentroidAlifold(20): 0.916 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 RNAalifold(20): 0.668 Sensitivity CentroidAlifold(seed): 0.548 RNAalifold(20): 0.533 Positive Predictive Value CentroidAlifold(seed): 0.951 RNAalifold(20): 0.837 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 RNAalifold(20): 0.660 Sensitivity CentroidHomfold‑LAST: 0.551 RNAalifold(20): 0.532 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RNAalifold(20): 0.819 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.660 IPknot: 0.648 Sensitivity RNAalifold(20): 0.532 IPknot: 0.574 Positive Predictive Value RNAalifold(20): 0.819 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Multilign(20): 0.649 Sensitivity RNAalifold(20): 0.531 Multilign(20): 0.590 Positive Predictive Value RNAalifold(20): 0.819 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.660 CentroidFold: 0.616 Sensitivity RNAalifold(20): 0.532 CentroidFold: 0.547 Positive Predictive Value RNAalifold(20): 0.819 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.660 Contrafold: 0.601 Sensitivity RNAalifold(20): 0.532 Contrafold: 0.576 Positive Predictive Value RNAalifold(20): 0.819 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 MXScarna(20): 0.626 Sensitivity RNAalifold(20): 0.532 MXScarna(20): 0.551 Positive Predictive Value RNAalifold(20): 0.819 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.667 MXScarna(seed): 0.655 Sensitivity RNAalifold(20): 0.532 MXScarna(seed): 0.542 Positive Predictive Value RNAalifold(20): 0.837 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.660 MaxExpect: 0.587 Sensitivity RNAalifold(20): 0.532 MaxExpect: 0.561 Positive Predictive Value RNAalifold(20): 0.819 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.660 ProbKnot: 0.586 Sensitivity RNAalifold(20): 0.532 ProbKnot: 0.564 Positive Predictive Value RNAalifold(20): 0.819 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.625 RNASampler(20): 0.543 Sensitivity RNAalifold(20): 0.520 RNASampler(20): 0.425 Positive Predictive Value RNAalifold(20): 0.753 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.660 Sfold: 0.568 Sensitivity RNAalifold(20): 0.532 Sfold: 0.503 Positive Predictive Value RNAalifold(20): 0.819 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.660 Fold: 0.550 Sensitivity RNAalifold(20): 0.532 Fold: 0.541 Positive Predictive Value RNAalifold(20): 0.819 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.663 Murlet(20): 0.548 Sensitivity RNAalifold(20): 0.542 Murlet(20): 0.415 Positive Predictive Value RNAalifold(20): 0.814 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.660 UNAFold: 0.531 Sensitivity RNAalifold(20): 0.532 UNAFold: 0.519 Positive Predictive Value RNAalifold(20): 0.819 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.660 PknotsRG: 0.512 Sensitivity RNAalifold(20): 0.532 PknotsRG: 0.503 Positive Predictive Value RNAalifold(20): 0.819 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.660 RNAfold: 0.527 Sensitivity RNAalifold(20): 0.532 RNAfold: 0.518 Positive Predictive Value RNAalifold(20): 0.819 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.661 Afold: 0.548 Sensitivity RNAalifold(20): 0.527 Afold: 0.533 Positive Predictive Value RNAalifold(20): 0.831 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.660 RNAsubopt: 0.519 Sensitivity RNAalifold(20): 0.532 RNAsubopt: 0.518 Positive Predictive Value RNAalifold(20): 0.819 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.660 McQFold: 0.452 Sensitivity RNAalifold(20): 0.532 McQFold: 0.433 Positive Predictive Value RNAalifold(20): 0.819 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 CMfinder(20): 0.479 Sensitivity RNAalifold(20): 0.532 CMfinder(20): 0.308 Positive Predictive Value RNAalifold(20): 0.819 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.662 RNASLOpt: 0.454 Sensitivity RNAalifold(20): 0.536 RNASLOpt: 0.419 Positive Predictive Value RNAalifold(20): 0.818 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAalifold(seed): 0.446 Sensitivity RNAalifold(20): 0.533 RNAalifold(seed): 0.249 Positive Predictive Value RNAalifold(20): 0.837 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.662 RNAshapes: 0.456 Sensitivity RNAalifold(20): 0.534 RNAshapes: 0.441 Positive Predictive Value RNAalifold(20): 0.822 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.660 CRWrnafold: 0.454 Sensitivity RNAalifold(20): 0.532 CRWrnafold: 0.446 Positive Predictive Value RNAalifold(20): 0.819 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.661 Vsfold4: 0.390 Sensitivity RNAalifold(20): 0.534 Vsfold4: 0.352 Positive Predictive Value RNAalifold(20): 0.820 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.660 RNAwolf: 0.367 Sensitivity RNAalifold(20): 0.532 RNAwolf: 0.377 Positive Predictive Value RNAalifold(20): 0.819 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.662 Vsfold5: 0.369 Sensitivity RNAalifold(20): 0.534 Vsfold5: 0.342 Positive Predictive Value RNAalifold(20): 0.820 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Carnac(20): 0.360 Sensitivity RNAalifold(20): 0.532 Carnac(20): 0.151 Positive Predictive Value RNAalifold(20): 0.819 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 RSpredict(20): 0.347 Sensitivity RNAalifold(20): 0.532 RSpredict(20): 0.220 Positive Predictive Value RNAalifold(20): 0.819 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.658 NanoFolder: 0.152 Sensitivity RNAalifold(20): 0.536 NanoFolder: 0.174 Positive Predictive Value RNAalifold(20): 0.810 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.668 RSpredict(seed): 0.054 Sensitivity RNAalifold(20): 0.534 RSpredict(seed): 0.014 Positive Predictive Value RNAalifold(20): 0.838 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs RNAalifold(20) Matthews Correlation Coefficient HotKnots: N/A RNAalifold(20): N/A Sensitivity HotKnots: N/A RNAalifold(20): N/A Positive Predictive Value HotKnots: 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 Pknots Matthews Correlation Coefficient RNAalifold(20): N/A Pknots: N/A Sensitivity RNAalifold(20): N/A Pknots: N/A Positive Predictive Value RNAalifold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs RNAalifold(20) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(20): N/A Sensitivity Cylofold: N/A RNAalifold(20): N/A Positive Predictive Value Cylofold: 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 MCFold Matthews Correlation Coefficient RNAalifold(20): N/A MCFold: N/A Sensitivity RNAalifold(20): N/A MCFold: N/A Positive Predictive Value RNAalifold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RDfolder vs RNAalifold(20) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(20): N/A Sensitivity RDfolder: N/A RNAalifold(20): N/A Positive Predictive Value RDfolder: N/A RNAalifold(20): 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	? 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	? RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): N/A Alterna: N/A Sensitivity RNAalifold(20): N/A Alterna: N/A Positive Predictive Value RNAalifold(20): N/A Alterna: 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): 0.716 Carnac(seed): 0.000 Sensitivity RNAalifold(20): 0.616 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.833 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Mastr(20): 0.000 Sensitivity RNAalifold(20): 0.532 Mastr(20): 0.000 Positive Predictive Value RNAalifold(20): 0.819 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.669 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.536 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.836 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
IPknot	610 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.718 IPknot: 0.602 Sensitivity ContextFold: 0.677 IPknot: 0.545 Positive Predictive Value ContextFold: 0.763 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 IPknot: 0.604 Sensitivity PETfold_pre2.0(seed): 0.590 IPknot: 0.543 Positive Predictive Value PETfold_pre2.0(seed): 0.787 IPknot: 0.673 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.740 IPknot: 0.648 Sensitivity TurboFold(20): 0.685 IPknot: 0.574 Positive Predictive Value TurboFold(20): 0.801 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 IPknot: 0.648 Sensitivity PETfold_pre2.0(20): 0.652 IPknot: 0.574 Positive Predictive Value PETfold_pre2.0(20): 0.829 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.734 IPknot: 0.650 Sensitivity PPfold(20): 0.635 IPknot: 0.575 Positive Predictive Value PPfold(20): 0.850 IPknot: 0.736 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.717 IPknot: 0.648 Sensitivity CentroidAlifold(20): 0.561 IPknot: 0.574 Positive Predictive Value CentroidAlifold(20): 0.916 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 IPknot: 0.640 Sensitivity CentroidAlifold(seed): 0.521 IPknot: 0.568 Positive Predictive Value CentroidAlifold(seed): 0.919 IPknot: 0.722 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 IPknot: 0.605 Sensitivity CentroidHomfold‑LAST: 0.469 IPknot: 0.548 Positive Predictive Value CentroidHomfold‑LAST: 0.877 IPknot: 0.670 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.660 IPknot: 0.648 Sensitivity RNAalifold(20): 0.532 IPknot: 0.574 Positive Predictive Value RNAalifold(20): 0.819 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08		= Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.649 IPknot: 0.648 Sensitivity Multilign(20): 0.590 IPknot: 0.575 Positive Predictive Value Multilign(20): 0.717 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 0.0144324399527	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.602 CentroidFold: 0.571 Sensitivity IPknot: 0.545 CentroidFold: 0.516 Positive Predictive Value IPknot: 0.667 CentroidFold: 0.635 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.602 Contrafold: 0.554 Sensitivity IPknot: 0.545 Contrafold: 0.540 Positive Predictive Value IPknot: 0.667 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.648 MXScarna(20): 0.626 Sensitivity IPknot: 0.574 MXScarna(20): 0.551 Positive Predictive Value IPknot: 0.733 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.640 MXScarna(seed): 0.595 Sensitivity IPknot: 0.568 MXScarna(seed): 0.475 Positive Predictive Value IPknot: 0.723 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.602 MaxExpect: 0.524 Sensitivity IPknot: 0.545 MaxExpect: 0.511 Positive Predictive Value IPknot: 0.667 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.602 ProbKnot: 0.522 Sensitivity IPknot: 0.545 ProbKnot: 0.518 Positive Predictive Value IPknot: 0.667 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.582 RNASampler(20): 0.543 Sensitivity IPknot: 0.514 RNASampler(20): 0.425 Positive Predictive Value IPknot: 0.659 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.602 Sfold: 0.514 Sensitivity IPknot: 0.545 Sfold: 0.463 Positive Predictive Value IPknot: 0.667 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.602 Fold: 0.495 Sensitivity IPknot: 0.545 Fold: 0.498 Positive Predictive Value IPknot: 0.667 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.644 Murlet(20): 0.548 Sensitivity IPknot: 0.570 Murlet(20): 0.415 Positive Predictive Value IPknot: 0.730 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.602 UNAFold: 0.475 Sensitivity IPknot: 0.545 UNAFold: 0.473 Positive Predictive Value IPknot: 0.667 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.602 PknotsRG: 0.476 Sensitivity IPknot: 0.545 PknotsRG: 0.478 Positive Predictive Value IPknot: 0.667 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.602 RNAfold: 0.474 Sensitivity IPknot: 0.545 RNAfold: 0.477 Positive Predictive Value IPknot: 0.667 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.620 Afold: 0.494 Sensitivity IPknot: 0.558 Afold: 0.490 Positive Predictive Value IPknot: 0.689 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.605 RNAsubopt: 0.475 Sensitivity IPknot: 0.548 RNAsubopt: 0.482 Positive Predictive Value IPknot: 0.670 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.602 McQFold: 0.450 Sensitivity IPknot: 0.545 McQFold: 0.441 Positive Predictive Value IPknot: 0.667 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.648 CMfinder(20): 0.479 Sensitivity IPknot: 0.574 CMfinder(20): 0.308 Positive Predictive Value IPknot: 0.733 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.603 RNASLOpt: 0.446 Sensitivity IPknot: 0.544 RNASLOpt: 0.421 Positive Predictive Value IPknot: 0.669 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.640 RNAalifold(seed): 0.469 Sensitivity IPknot: 0.567 RNAalifold(seed): 0.272 Positive Predictive Value IPknot: 0.722 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.604 RNAshapes: 0.408 Sensitivity IPknot: 0.545 RNAshapes: 0.404 Positive Predictive Value IPknot: 0.671 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.602 CRWrnafold: 0.417 Sensitivity IPknot: 0.545 CRWrnafold: 0.421 Positive Predictive Value IPknot: 0.667 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.603 Vsfold4: 0.335 Sensitivity IPknot: 0.545 Vsfold4: 0.308 Positive Predictive Value IPknot: 0.668 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.602 RNAwolf: 0.332 Sensitivity IPknot: 0.545 RNAwolf: 0.347 Positive Predictive Value IPknot: 0.667 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.603 Vsfold5: 0.329 Sensitivity IPknot: 0.545 Vsfold5: 0.312 Positive Predictive Value IPknot: 0.669 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.632 CMfinder(seed): 0.350 Sensitivity IPknot: 0.573 CMfinder(seed): 0.159 Positive Predictive Value IPknot: 0.698 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.648 Carnac(20): 0.360 Sensitivity IPknot: 0.574 Carnac(20): 0.151 Positive Predictive Value IPknot: 0.733 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.648 RSpredict(20): 0.347 Sensitivity IPknot: 0.574 RSpredict(20): 0.220 Positive Predictive Value IPknot: 0.733 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.627 NanoFolder: 0.172 Sensitivity IPknot: 0.564 NanoFolder: 0.204 Positive Predictive Value IPknot: 0.699 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.640 RSpredict(seed): 0.045 Sensitivity IPknot: 0.567 RSpredict(seed): 0.011 Positive Predictive Value IPknot: 0.723 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs IPknot Matthews Correlation Coefficient Murlet(seed): N/A IPknot: N/A Sensitivity Murlet(seed): N/A IPknot: N/A Positive Predictive Value Murlet(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs IPknot Matthews Correlation Coefficient Multilign(seed): N/A IPknot: N/A Sensitivity Multilign(seed): N/A IPknot: N/A Positive Predictive Value Multilign(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs IPknot Matthews Correlation Coefficient HotKnots: N/A IPknot: N/A Sensitivity HotKnots: N/A IPknot: N/A Positive Predictive Value HotKnots: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs IPknot Matthews Correlation Coefficient Pknots: N/A IPknot: N/A Sensitivity Pknots: N/A IPknot: N/A Positive Predictive Value Pknots: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.648 Cylofold: 0.271 Sensitivity IPknot: 0.584 Cylofold: 0.241 Positive Predictive Value IPknot: 0.721 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MCFold vs IPknot Matthews Correlation Coefficient MCFold: N/A IPknot: N/A Sensitivity MCFold: N/A IPknot: N/A Positive Predictive Value MCFold: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs IPknot Matthews Correlation Coefficient PPfold(seed): N/A IPknot: N/A Sensitivity PPfold(seed): N/A IPknot: N/A Positive Predictive Value PPfold(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs IPknot Matthews Correlation Coefficient RDfolder: N/A IPknot: N/A Sensitivity RDfolder: N/A IPknot: N/A Positive Predictive Value RDfolder: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.710 IPknot: 0.579 Sensitivity TurboFold(seed): 0.677 IPknot: 0.585 Positive Predictive Value TurboFold(seed): 0.746 IPknot: 0.576 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): N/A IPknot: N/A Sensitivity RNASampler(seed): N/A IPknot: N/A Positive Predictive Value RNASampler(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs IPknot Matthews Correlation Coefficient Alterna: N/A IPknot: N/A Sensitivity Alterna: N/A IPknot: N/A Positive Predictive Value Alterna: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.563 Carnac(seed): 0.000 Sensitivity IPknot: 0.516 Carnac(seed): 0.000 Positive Predictive Value IPknot: 0.615 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.648 Mastr(20): 0.000 Sensitivity IPknot: 0.574 Mastr(20): 0.000 Positive Predictive Value IPknot: 0.733 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.637 Mastr(seed): 0.000 Sensitivity IPknot: 0.566 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.717 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(20)	191 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.842 Multilign(20): 0.649 Sensitivity ContextFold: 0.794 Multilign(20): 0.590 Positive Predictive Value ContextFold: 0.893 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.753 Multilign(20): 0.649 Sensitivity PETfold_pre2.0(seed): 0.672 Multilign(20): 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.844 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.739 Multilign(20): 0.649 Sensitivity TurboFold(20): 0.684 Multilign(20): 0.590 Positive Predictive Value TurboFold(20): 0.800 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Multilign(20): 0.649 Sensitivity PETfold_pre2.0(20): 0.652 Multilign(20): 0.590 Positive Predictive Value PETfold_pre2.0(20): 0.830 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.735 Multilign(20): 0.650 Sensitivity PPfold(20): 0.635 Multilign(20): 0.590 Positive Predictive Value PPfold(20): 0.851 Multilign(20): 0.718 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.716 Multilign(20): 0.649 Sensitivity CentroidAlifold(20): 0.561 Multilign(20): 0.590 Positive Predictive Value CentroidAlifold(20): 0.916 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.720 Multilign(20): 0.657 Sensitivity CentroidAlifold(seed): 0.545 Multilign(20): 0.594 Positive Predictive Value CentroidAlifold(seed): 0.952 Multilign(20): 0.728 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.700 Multilign(20): 0.649 Sensitivity CentroidHomfold‑LAST: 0.548 Multilign(20): 0.590 Positive Predictive Value CentroidHomfold‑LAST: 0.894 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.659 Multilign(20): 0.649 Sensitivity RNAalifold(20): 0.531 Multilign(20): 0.590 Positive Predictive Value RNAalifold(20): 0.819 Multilign(20): 0.717 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.649 IPknot: 0.648 Sensitivity Multilign(20): 0.590 IPknot: 0.575 Positive Predictive Value Multilign(20): 0.717 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 0.0144324399527		+ Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.649 CentroidFold: 0.617 Sensitivity Multilign(20): 0.590 CentroidFold: 0.548 Positive Predictive Value Multilign(20): 0.717 CentroidFold: 0.696 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.649 Contrafold: 0.601 Sensitivity Multilign(20): 0.590 Contrafold: 0.576 Positive Predictive Value Multilign(20): 0.717 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.649 MXScarna(20): 0.622 Sensitivity Multilign(20): 0.590 MXScarna(20): 0.547 Positive Predictive Value Multilign(20): 0.717 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(20): 0.657 MXScarna(seed): 0.654 Sensitivity Multilign(20): 0.594 MXScarna(seed): 0.539 Positive Predictive Value Multilign(20): 0.728 MXScarna(seed): 0.795 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 6.06606238843e-08	+ Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.649 MaxExpect: 0.587 Sensitivity Multilign(20): 0.590 MaxExpect: 0.561 Positive Predictive Value Multilign(20): 0.717 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.649 ProbKnot: 0.586 Sensitivity Multilign(20): 0.590 ProbKnot: 0.564 Positive Predictive Value Multilign(20): 0.717 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.602 RNASampler(20): 0.546 Sensitivity Multilign(20): 0.551 RNASampler(20): 0.427 Positive Predictive Value Multilign(20): 0.660 RNASampler(20): 0.697 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.649 Sfold: 0.566 Sensitivity Multilign(20): 0.590 Sfold: 0.502 Positive Predictive Value Multilign(20): 0.717 Sfold: 0.641 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.649 Fold: 0.550 Sensitivity Multilign(20): 0.590 Fold: 0.541 Positive Predictive Value Multilign(20): 0.717 Fold: 0.561 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.651 Murlet(20): 0.545 Sensitivity Multilign(20): 0.593 Murlet(20): 0.412 Positive Predictive Value Multilign(20): 0.717 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.649 UNAFold: 0.532 Sensitivity Multilign(20): 0.590 UNAFold: 0.520 Positive Predictive Value Multilign(20): 0.717 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.649 PknotsRG: 0.510 Sensitivity Multilign(20): 0.590 PknotsRG: 0.501 Positive Predictive Value Multilign(20): 0.717 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.649 RNAfold: 0.527 Sensitivity Multilign(20): 0.590 RNAfold: 0.519 Positive Predictive Value Multilign(20): 0.717 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.653 Afold: 0.545 Sensitivity Multilign(20): 0.591 Afold: 0.531 Positive Predictive Value Multilign(20): 0.723 Afold: 0.562 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.649 RNAsubopt: 0.517 Sensitivity Multilign(20): 0.590 RNAsubopt: 0.516 Positive Predictive Value Multilign(20): 0.717 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.649 McQFold: 0.451 Sensitivity Multilign(20): 0.590 McQFold: 0.431 Positive Predictive Value Multilign(20): 0.717 McQFold: 0.473 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.649 CMfinder(20): 0.481 Sensitivity Multilign(20): 0.590 CMfinder(20): 0.310 Positive Predictive Value Multilign(20): 0.717 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.654 RNASLOpt: 0.454 Sensitivity Multilign(20): 0.596 RNASLOpt: 0.419 Positive Predictive Value Multilign(20): 0.718 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 177 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.657 RNAalifold(seed): 0.435 Sensitivity Multilign(20): 0.594 RNAalifold(seed): 0.239 Positive Predictive Value Multilign(20): 0.728 RNAalifold(seed): 0.792 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.650 RNAshapes: 0.453 Sensitivity Multilign(20): 0.590 RNAshapes: 0.439 Positive Predictive Value Multilign(20): 0.716 RNAshapes: 0.470 Number of pairs reference - predicted secondary structure: 182 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.649 CRWrnafold: 0.452 Sensitivity Multilign(20): 0.590 CRWrnafold: 0.443 Positive Predictive Value Multilign(20): 0.717 CRWrnafold: 0.462 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.648 Vsfold4: 0.392 Sensitivity Multilign(20): 0.589 Vsfold4: 0.355 Positive Predictive Value Multilign(20): 0.714 Vsfold4: 0.435 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.649 RNAwolf: 0.364 Sensitivity Multilign(20): 0.590 RNAwolf: 0.374 Positive Predictive Value Multilign(20): 0.717 RNAwolf: 0.357 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.649 Vsfold5: 0.370 Sensitivity Multilign(20): 0.590 Vsfold5: 0.343 Positive Predictive Value Multilign(20): 0.715 Vsfold5: 0.402 Number of pairs reference - predicted secondary structure: 184 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.649 Carnac(20): 0.346 Sensitivity Multilign(20): 0.590 Carnac(20): 0.140 Positive Predictive Value Multilign(20): 0.717 Carnac(20): 0.854 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.649 RSpredict(20): 0.332 Sensitivity Multilign(20): 0.590 RSpredict(20): 0.207 Positive Predictive Value Multilign(20): 0.717 RSpredict(20): 0.533 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.633 NanoFolder: 0.160 Sensitivity Multilign(20): 0.577 NanoFolder: 0.182 Positive Predictive Value Multilign(20): 0.696 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.657 RSpredict(seed): 0.057 Sensitivity Multilign(20): 0.594 RSpredict(seed): 0.014 Positive Predictive Value Multilign(20): 0.728 RSpredict(seed): 0.228 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: N/A Multilign(20): N/A Sensitivity HotKnots: N/A Multilign(20): N/A Positive Predictive Value HotKnots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Multilign(20) Matthews Correlation Coefficient Pknots: N/A Multilign(20): N/A Sensitivity Pknots: N/A Multilign(20): N/A Positive Predictive Value Pknots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: N/A Multilign(20): N/A Sensitivity Cylofold: N/A Multilign(20): N/A Positive Predictive Value Cylofold: 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 MCFold Matthews Correlation Coefficient Multilign(20): N/A MCFold: N/A Sensitivity Multilign(20): N/A MCFold: N/A Positive Predictive Value Multilign(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RDfolder vs Multilign(20) Matthews Correlation Coefficient RDfolder: N/A Multilign(20): N/A Sensitivity RDfolder: N/A Multilign(20): N/A Positive Predictive Value RDfolder: 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	? 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	? Alterna vs Multilign(20) Matthews Correlation Coefficient Alterna: N/A Multilign(20): N/A Sensitivity Alterna: N/A Multilign(20): N/A Positive Predictive Value Alterna: 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 Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.644 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.627 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.662 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.649 Mastr(20): 0.000 Sensitivity Multilign(20): 0.590 Mastr(20): 0.000 Positive Predictive Value Multilign(20): 0.717 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.660 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.598 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.729 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidFold	610 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.718 CentroidFold: 0.571 Sensitivity ContextFold: 0.677 CentroidFold: 0.516 Positive Predictive Value ContextFold: 0.763 CentroidFold: 0.635 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 CentroidFold: 0.571 Sensitivity PETfold_pre2.0(seed): 0.590 CentroidFold: 0.514 Positive Predictive Value PETfold_pre2.0(seed): 0.787 CentroidFold: 0.636 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.740 CentroidFold: 0.616 Sensitivity TurboFold(20): 0.685 CentroidFold: 0.547 Positive Predictive Value TurboFold(20): 0.801 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CentroidFold: 0.616 Sensitivity PETfold_pre2.0(20): 0.652 CentroidFold: 0.547 Positive Predictive Value PETfold_pre2.0(20): 0.829 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.734 CentroidFold: 0.615 Sensitivity PPfold(20): 0.635 CentroidFold: 0.545 Positive Predictive Value PPfold(20): 0.850 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CentroidFold: 0.616 Sensitivity CentroidAlifold(20): 0.561 CentroidFold: 0.547 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 CentroidFold: 0.621 Sensitivity CentroidAlifold(seed): 0.521 CentroidFold: 0.554 Positive Predictive Value CentroidAlifold(seed): 0.919 CentroidFold: 0.698 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 CentroidFold: 0.575 Sensitivity CentroidHomfold‑LAST: 0.469 CentroidFold: 0.520 Positive Predictive Value CentroidHomfold‑LAST: 0.877 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.660 CentroidFold: 0.616 Sensitivity RNAalifold(20): 0.532 CentroidFold: 0.547 Positive Predictive Value RNAalifold(20): 0.819 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.602 CentroidFold: 0.571 Sensitivity IPknot: 0.545 CentroidFold: 0.516 Positive Predictive Value IPknot: 0.667 CentroidFold: 0.635 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.649 CentroidFold: 0.617 Sensitivity Multilign(20): 0.590 CentroidFold: 0.548 Positive Predictive Value Multilign(20): 0.717 CentroidFold: 0.696 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.571 Contrafold: 0.554 Sensitivity CentroidFold: 0.516 Contrafold: 0.540 Positive Predictive Value CentroidFold: 0.635 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.626 CentroidFold: 0.616 Sensitivity MXScarna(20): 0.551 CentroidFold: 0.547 Positive Predictive Value MXScarna(20): 0.712 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MXScarna(seed) Matthews Correlation Coefficient CentroidFold: 0.622 MXScarna(seed): 0.595 Sensitivity CentroidFold: 0.554 MXScarna(seed): 0.475 Positive Predictive Value CentroidFold: 0.699 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.571 MaxExpect: 0.524 Sensitivity CentroidFold: 0.516 MaxExpect: 0.511 Positive Predictive Value CentroidFold: 0.635 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.571 ProbKnot: 0.522 Sensitivity CentroidFold: 0.516 ProbKnot: 0.518 Positive Predictive Value CentroidFold: 0.635 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.543 CentroidFold: 0.500 Sensitivity RNASampler(20): 0.425 CentroidFold: 0.437 Positive Predictive Value RNASampler(20): 0.695 CentroidFold: 0.574 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.571 Sfold: 0.514 Sensitivity CentroidFold: 0.516 Sfold: 0.463 Positive Predictive Value CentroidFold: 0.635 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.571 Fold: 0.495 Sensitivity CentroidFold: 0.516 Fold: 0.498 Positive Predictive Value CentroidFold: 0.635 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.604 Murlet(20): 0.548 Sensitivity CentroidFold: 0.536 Murlet(20): 0.415 Positive Predictive Value CentroidFold: 0.682 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.571 UNAFold: 0.475 Sensitivity CentroidFold: 0.516 UNAFold: 0.473 Positive Predictive Value CentroidFold: 0.635 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.571 PknotsRG: 0.476 Sensitivity CentroidFold: 0.516 PknotsRG: 0.478 Positive Predictive Value CentroidFold: 0.635 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.571 RNAfold: 0.474 Sensitivity CentroidFold: 0.516 RNAfold: 0.477 Positive Predictive Value CentroidFold: 0.635 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.596 Afold: 0.494 Sensitivity CentroidFold: 0.537 Afold: 0.490 Positive Predictive Value CentroidFold: 0.663 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.575 RNAsubopt: 0.475 Sensitivity CentroidFold: 0.520 RNAsubopt: 0.482 Positive Predictive Value CentroidFold: 0.638 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.571 McQFold: 0.450 Sensitivity CentroidFold: 0.516 McQFold: 0.441 Positive Predictive Value CentroidFold: 0.635 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.616 CMfinder(20): 0.479 Sensitivity CentroidFold: 0.547 CMfinder(20): 0.308 Positive Predictive Value CentroidFold: 0.695 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.568 RNASLOpt: 0.446 Sensitivity CentroidFold: 0.511 RNASLOpt: 0.421 Positive Predictive Value CentroidFold: 0.633 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.621 RNAalifold(seed): 0.469 Sensitivity CentroidFold: 0.553 RNAalifold(seed): 0.272 Positive Predictive Value CentroidFold: 0.698 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.571 RNAshapes: 0.408 Sensitivity CentroidFold: 0.515 RNAshapes: 0.404 Positive Predictive Value CentroidFold: 0.635 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.571 CRWrnafold: 0.417 Sensitivity CentroidFold: 0.516 CRWrnafold: 0.421 Positive Predictive Value CentroidFold: 0.635 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.570 Vsfold4: 0.335 Sensitivity CentroidFold: 0.514 Vsfold4: 0.308 Positive Predictive Value CentroidFold: 0.633 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.571 RNAwolf: 0.332 Sensitivity CentroidFold: 0.516 RNAwolf: 0.347 Positive Predictive Value CentroidFold: 0.635 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.570 Vsfold5: 0.329 Sensitivity CentroidFold: 0.514 Vsfold5: 0.312 Positive Predictive Value CentroidFold: 0.633 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.592 CMfinder(seed): 0.350 Sensitivity CentroidFold: 0.519 CMfinder(seed): 0.159 Positive Predictive Value CentroidFold: 0.675 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.616 Carnac(20): 0.360 Sensitivity CentroidFold: 0.547 Carnac(20): 0.151 Positive Predictive Value CentroidFold: 0.695 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.616 RSpredict(20): 0.347 Sensitivity CentroidFold: 0.547 RSpredict(20): 0.220 Positive Predictive Value CentroidFold: 0.695 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.585 NanoFolder: 0.172 Sensitivity CentroidFold: 0.527 NanoFolder: 0.204 Positive Predictive Value CentroidFold: 0.651 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.621 RSpredict(seed): 0.045 Sensitivity CentroidFold: 0.553 RSpredict(seed): 0.011 Positive Predictive Value CentroidFold: 0.698 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: N/A Murlet(seed): N/A Sensitivity CentroidFold: N/A Murlet(seed): N/A Positive Predictive Value CentroidFold: 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 CentroidFold Matthews Correlation Coefficient Multilign(seed): N/A CentroidFold: N/A Sensitivity Multilign(seed): N/A CentroidFold: N/A Positive Predictive Value Multilign(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs CentroidFold Matthews Correlation Coefficient HotKnots: N/A CentroidFold: N/A Sensitivity HotKnots: N/A CentroidFold: N/A Positive Predictive Value HotKnots: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: N/A CentroidFold: N/A Sensitivity Pknots: N/A CentroidFold: N/A Positive Predictive Value Pknots: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.626 Cylofold: 0.271 Sensitivity CentroidFold: 0.584 Cylofold: 0.241 Positive Predictive Value CentroidFold: 0.672 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: N/A MCFold: N/A Sensitivity CentroidFold: N/A MCFold: N/A Positive Predictive Value CentroidFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): N/A CentroidFold: N/A Sensitivity PPfold(seed): N/A CentroidFold: N/A Positive Predictive Value PPfold(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CentroidFold Matthews Correlation Coefficient RDfolder: N/A CentroidFold: N/A Sensitivity RDfolder: N/A CentroidFold: N/A Positive Predictive Value RDfolder: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.710 CentroidFold: 0.645 Sensitivity TurboFold(seed): 0.677 CentroidFold: 0.646 Positive Predictive Value TurboFold(seed): 0.746 CentroidFold: 0.646 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): N/A CentroidFold: N/A Sensitivity RNASampler(seed): N/A CentroidFold: N/A Positive Predictive Value RNASampler(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CentroidFold Matthews Correlation Coefficient Alterna: N/A CentroidFold: N/A Sensitivity Alterna: N/A CentroidFold: N/A Positive Predictive Value Alterna: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.565 Carnac(seed): 0.000 Sensitivity CentroidFold: 0.517 Carnac(seed): 0.000 Positive Predictive Value CentroidFold: 0.618 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.616 Mastr(20): 0.000 Sensitivity CentroidFold: 0.547 Mastr(20): 0.000 Positive Predictive Value CentroidFold: 0.695 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.619 Mastr(seed): 0.000 Sensitivity CentroidFold: 0.553 Mastr(seed): 0.000 Positive Predictive Value CentroidFold: 0.694 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
Contrafold	610 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.718 Contrafold: 0.554 Sensitivity ContextFold: 0.677 Contrafold: 0.540 Positive Predictive Value ContextFold: 0.763 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 Contrafold: 0.552 Sensitivity PETfold_pre2.0(seed): 0.590 Contrafold: 0.537 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.740 Contrafold: 0.601 Sensitivity TurboFold(20): 0.685 Contrafold: 0.576 Positive Predictive Value TurboFold(20): 0.801 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Contrafold: 0.601 Sensitivity PETfold_pre2.0(20): 0.652 Contrafold: 0.576 Positive Predictive Value PETfold_pre2.0(20): 0.829 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.734 Contrafold: 0.600 Sensitivity PPfold(20): 0.635 Contrafold: 0.575 Positive Predictive Value PPfold(20): 0.850 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Contrafold: 0.601 Sensitivity CentroidAlifold(20): 0.561 Contrafold: 0.576 Positive Predictive Value CentroidAlifold(20): 0.916 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 Contrafold: 0.604 Sensitivity CentroidAlifold(seed): 0.521 Contrafold: 0.579 Positive Predictive Value CentroidAlifold(seed): 0.919 Contrafold: 0.631 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Contrafold: 0.557 Sensitivity CentroidHomfold‑LAST: 0.469 Contrafold: 0.543 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Contrafold: 0.572 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.660 Contrafold: 0.601 Sensitivity RNAalifold(20): 0.532 Contrafold: 0.576 Positive Predictive Value RNAalifold(20): 0.819 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.602 Contrafold: 0.554 Sensitivity IPknot: 0.545 Contrafold: 0.540 Positive Predictive Value IPknot: 0.667 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.649 Contrafold: 0.601 Sensitivity Multilign(20): 0.590 Contrafold: 0.576 Positive Predictive Value Multilign(20): 0.717 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.571 Contrafold: 0.554 Sensitivity CentroidFold: 0.516 Contrafold: 0.540 Positive Predictive Value CentroidFold: 0.635 Contrafold: 0.569 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08		- MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.626 Contrafold: 0.601 Sensitivity MXScarna(20): 0.551 Contrafold: 0.576 Positive Predictive Value MXScarna(20): 0.712 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MXScarna(seed) Matthews Correlation Coefficient Contrafold: 0.604 MXScarna(seed): 0.595 Sensitivity Contrafold: 0.580 MXScarna(seed): 0.475 Positive Predictive Value Contrafold: 0.631 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.554 MaxExpect: 0.524 Sensitivity Contrafold: 0.540 MaxExpect: 0.511 Positive Predictive Value Contrafold: 0.569 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.554 ProbKnot: 0.522 Sensitivity Contrafold: 0.540 ProbKnot: 0.518 Positive Predictive Value Contrafold: 0.569 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.543 Contrafold: 0.482 Sensitivity RNASampler(20): 0.425 Contrafold: 0.465 Positive Predictive Value RNASampler(20): 0.695 Contrafold: 0.502 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.554 Sfold: 0.514 Sensitivity Contrafold: 0.540 Sfold: 0.463 Positive Predictive Value Contrafold: 0.569 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.554 Fold: 0.495 Sensitivity Contrafold: 0.540 Fold: 0.498 Positive Predictive Value Contrafold: 0.569 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(20) Matthews Correlation Coefficient Contrafold: 0.587 Murlet(20): 0.548 Sensitivity Contrafold: 0.564 Murlet(20): 0.415 Positive Predictive Value Contrafold: 0.613 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.554 UNAFold: 0.475 Sensitivity Contrafold: 0.540 UNAFold: 0.473 Positive Predictive Value Contrafold: 0.569 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.554 PknotsRG: 0.476 Sensitivity Contrafold: 0.540 PknotsRG: 0.478 Positive Predictive Value Contrafold: 0.569 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.554 RNAfold: 0.474 Sensitivity Contrafold: 0.540 RNAfold: 0.477 Positive Predictive Value Contrafold: 0.569 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.581 Afold: 0.494 Sensitivity Contrafold: 0.563 Afold: 0.490 Positive Predictive Value Contrafold: 0.600 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.557 RNAsubopt: 0.475 Sensitivity Contrafold: 0.543 RNAsubopt: 0.482 Positive Predictive Value Contrafold: 0.572 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.554 McQFold: 0.450 Sensitivity Contrafold: 0.540 McQFold: 0.441 Positive Predictive Value Contrafold: 0.569 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.601 CMfinder(20): 0.479 Sensitivity Contrafold: 0.576 CMfinder(20): 0.308 Positive Predictive Value Contrafold: 0.628 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.549 RNASLOpt: 0.446 Sensitivity Contrafold: 0.535 RNASLOpt: 0.421 Positive Predictive Value Contrafold: 0.566 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.604 RNAalifold(seed): 0.469 Sensitivity Contrafold: 0.579 RNAalifold(seed): 0.272 Positive Predictive Value Contrafold: 0.631 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.552 RNAshapes: 0.408 Sensitivity Contrafold: 0.538 RNAshapes: 0.404 Positive Predictive Value Contrafold: 0.569 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.554 CRWrnafold: 0.417 Sensitivity Contrafold: 0.540 CRWrnafold: 0.421 Positive Predictive Value Contrafold: 0.569 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.551 Vsfold4: 0.335 Sensitivity Contrafold: 0.537 Vsfold4: 0.308 Positive Predictive Value Contrafold: 0.567 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.554 RNAwolf: 0.332 Sensitivity Contrafold: 0.540 RNAwolf: 0.347 Positive Predictive Value Contrafold: 0.569 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.551 Vsfold5: 0.329 Sensitivity Contrafold: 0.537 Vsfold5: 0.312 Positive Predictive Value Contrafold: 0.567 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.576 CMfinder(seed): 0.350 Sensitivity Contrafold: 0.556 CMfinder(seed): 0.159 Positive Predictive Value Contrafold: 0.597 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.601 Carnac(20): 0.360 Sensitivity Contrafold: 0.576 Carnac(20): 0.151 Positive Predictive Value Contrafold: 0.628 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.601 RSpredict(20): 0.347 Sensitivity Contrafold: 0.576 RSpredict(20): 0.220 Positive Predictive Value Contrafold: 0.628 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.563 NanoFolder: 0.172 Sensitivity Contrafold: 0.549 NanoFolder: 0.204 Positive Predictive Value Contrafold: 0.580 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.604 RSpredict(seed): 0.045 Sensitivity Contrafold: 0.579 RSpredict(seed): 0.011 Positive Predictive Value Contrafold: 0.631 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: N/A Murlet(seed): N/A Sensitivity Contrafold: N/A Murlet(seed): N/A Positive Predictive Value Contrafold: 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 Contrafold Matthews Correlation Coefficient Multilign(seed): N/A Contrafold: N/A Sensitivity Multilign(seed): N/A Contrafold: N/A Positive Predictive Value Multilign(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: N/A Contrafold: N/A Sensitivity HotKnots: N/A Contrafold: N/A Positive Predictive Value HotKnots: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Contrafold Matthews Correlation Coefficient Pknots: N/A Contrafold: N/A Sensitivity Pknots: N/A Contrafold: N/A Positive Predictive Value Pknots: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.616 Cylofold: 0.271 Sensitivity Contrafold: 0.591 Cylofold: 0.241 Positive Predictive Value Contrafold: 0.643 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: N/A MCFold: N/A Sensitivity Contrafold: N/A MCFold: N/A Positive Predictive Value Contrafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): N/A Contrafold: N/A Sensitivity PPfold(seed): N/A Contrafold: N/A Positive Predictive Value PPfold(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Contrafold Matthews Correlation Coefficient RDfolder: N/A Contrafold: N/A Sensitivity RDfolder: N/A Contrafold: N/A Positive Predictive Value RDfolder: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.710 Contrafold: 0.581 Sensitivity TurboFold(seed): 0.677 Contrafold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 Contrafold: 0.565 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): N/A Contrafold: N/A Sensitivity RNASampler(seed): N/A Contrafold: N/A Positive Predictive Value RNASampler(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: N/A Alterna: N/A Sensitivity Contrafold: N/A Alterna: N/A Positive Predictive Value Contrafold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.546 Carnac(seed): 0.000 Sensitivity Contrafold: 0.537 Carnac(seed): 0.000 Positive Predictive Value Contrafold: 0.556 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.601 Mastr(20): 0.000 Sensitivity Contrafold: 0.576 Mastr(20): 0.000 Positive Predictive Value Contrafold: 0.628 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.602 Mastr(seed): 0.000 Sensitivity Contrafold: 0.578 Mastr(seed): 0.000 Positive Predictive Value Contrafold: 0.627 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(20)	204 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.840 MXScarna(20): 0.626 Sensitivity ContextFold: 0.791 MXScarna(20): 0.551 Positive Predictive Value ContextFold: 0.892 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 MXScarna(20): 0.626 Sensitivity PETfold_pre2.0(seed): 0.673 MXScarna(20): 0.551 Positive Predictive Value PETfold_pre2.0(seed): 0.845 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.740 MXScarna(20): 0.626 Sensitivity TurboFold(20): 0.685 MXScarna(20): 0.551 Positive Predictive Value TurboFold(20): 0.801 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 MXScarna(20): 0.626 Sensitivity PETfold_pre2.0(20): 0.652 MXScarna(20): 0.551 Positive Predictive Value PETfold_pre2.0(20): 0.829 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.734 MXScarna(20): 0.626 Sensitivity PPfold(20): 0.635 MXScarna(20): 0.552 Positive Predictive Value PPfold(20): 0.850 MXScarna(20): 0.711 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 MXScarna(20): 0.626 Sensitivity CentroidAlifold(20): 0.561 MXScarna(20): 0.551 Positive Predictive Value CentroidAlifold(20): 0.916 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 MXScarna(20): 0.650 Sensitivity CentroidAlifold(seed): 0.548 MXScarna(20): 0.563 Positive Predictive Value CentroidAlifold(seed): 0.951 MXScarna(20): 0.752 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 MXScarna(20): 0.626 Sensitivity CentroidHomfold‑LAST: 0.551 MXScarna(20): 0.551 Positive Predictive Value CentroidHomfold‑LAST: 0.896 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 MXScarna(20): 0.626 Sensitivity RNAalifold(20): 0.532 MXScarna(20): 0.551 Positive Predictive Value RNAalifold(20): 0.819 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.648 MXScarna(20): 0.626 Sensitivity IPknot: 0.574 MXScarna(20): 0.551 Positive Predictive Value IPknot: 0.733 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.649 MXScarna(20): 0.622 Sensitivity Multilign(20): 0.590 MXScarna(20): 0.547 Positive Predictive Value Multilign(20): 0.717 MXScarna(20): 0.710 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.626 CentroidFold: 0.616 Sensitivity MXScarna(20): 0.551 CentroidFold: 0.547 Positive Predictive Value MXScarna(20): 0.712 CentroidFold: 0.695 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.626 Contrafold: 0.601 Sensitivity MXScarna(20): 0.551 Contrafold: 0.576 Positive Predictive Value MXScarna(20): 0.712 Contrafold: 0.628 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08		- MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 MXScarna(20): 0.651 Sensitivity MXScarna(seed): 0.542 MXScarna(20): 0.563 Positive Predictive Value MXScarna(seed): 0.793 MXScarna(20): 0.752 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.626 MaxExpect: 0.587 Sensitivity MXScarna(20): 0.551 MaxExpect: 0.561 Positive Predictive Value MXScarna(20): 0.712 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.626 ProbKnot: 0.586 Sensitivity MXScarna(20): 0.551 ProbKnot: 0.564 Positive Predictive Value MXScarna(20): 0.712 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.543 MXScarna(20): 0.519 Sensitivity RNASampler(20): 0.425 MXScarna(20): 0.480 Positive Predictive Value RNASampler(20): 0.695 MXScarna(20): 0.562 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.626 Sfold: 0.568 Sensitivity MXScarna(20): 0.551 Sfold: 0.503 Positive Predictive Value MXScarna(20): 0.712 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.626 Fold: 0.550 Sensitivity MXScarna(20): 0.551 Fold: 0.541 Positive Predictive Value MXScarna(20): 0.712 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.610 Murlet(20): 0.548 Sensitivity MXScarna(20): 0.543 Murlet(20): 0.415 Positive Predictive Value MXScarna(20): 0.688 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.626 UNAFold: 0.531 Sensitivity MXScarna(20): 0.551 UNAFold: 0.519 Positive Predictive Value MXScarna(20): 0.712 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.626 PknotsRG: 0.512 Sensitivity MXScarna(20): 0.551 PknotsRG: 0.503 Positive Predictive Value MXScarna(20): 0.712 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.626 RNAfold: 0.527 Sensitivity MXScarna(20): 0.551 RNAfold: 0.518 Positive Predictive Value MXScarna(20): 0.712 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.641 Afold: 0.548 Sensitivity MXScarna(20): 0.554 Afold: 0.533 Positive Predictive Value MXScarna(20): 0.743 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.626 RNAsubopt: 0.519 Sensitivity MXScarna(20): 0.551 RNAsubopt: 0.518 Positive Predictive Value MXScarna(20): 0.712 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.626 McQFold: 0.452 Sensitivity MXScarna(20): 0.551 McQFold: 0.433 Positive Predictive Value MXScarna(20): 0.712 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.626 CMfinder(20): 0.479 Sensitivity MXScarna(20): 0.551 CMfinder(20): 0.308 Positive Predictive Value MXScarna(20): 0.712 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.618 RNASLOpt: 0.454 Sensitivity MXScarna(20): 0.545 RNASLOpt: 0.419 Positive Predictive Value MXScarna(20): 0.703 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.650 RNAalifold(seed): 0.446 Sensitivity MXScarna(20): 0.563 RNAalifold(seed): 0.249 Positive Predictive Value MXScarna(20): 0.752 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.621 RNAshapes: 0.456 Sensitivity MXScarna(20): 0.547 RNAshapes: 0.441 Positive Predictive Value MXScarna(20): 0.707 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.626 CRWrnafold: 0.454 Sensitivity MXScarna(20): 0.551 CRWrnafold: 0.446 Positive Predictive Value MXScarna(20): 0.712 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.625 Vsfold4: 0.390 Sensitivity MXScarna(20): 0.550 Vsfold4: 0.352 Positive Predictive Value MXScarna(20): 0.710 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.626 RNAwolf: 0.367 Sensitivity MXScarna(20): 0.551 RNAwolf: 0.377 Positive Predictive Value MXScarna(20): 0.712 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.621 Vsfold5: 0.369 Sensitivity MXScarna(20): 0.547 Vsfold5: 0.342 Positive Predictive Value MXScarna(20): 0.707 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.626 Carnac(20): 0.360 Sensitivity MXScarna(20): 0.551 Carnac(20): 0.151 Positive Predictive Value MXScarna(20): 0.712 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.626 RSpredict(20): 0.347 Sensitivity MXScarna(20): 0.551 RSpredict(20): 0.220 Positive Predictive Value MXScarna(20): 0.712 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.629 NanoFolder: 0.152 Sensitivity MXScarna(20): 0.554 NanoFolder: 0.174 Positive Predictive Value MXScarna(20): 0.716 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.651 RSpredict(seed): 0.054 Sensitivity MXScarna(20): 0.564 RSpredict(seed): 0.014 Positive Predictive Value MXScarna(20): 0.753 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs MXScarna(20) Matthews Correlation Coefficient HotKnots: N/A MXScarna(20): N/A Sensitivity HotKnots: N/A MXScarna(20): N/A Positive Predictive Value HotKnots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs MXScarna(20) Matthews Correlation Coefficient Pknots: N/A MXScarna(20): N/A Sensitivity Pknots: N/A MXScarna(20): N/A Positive Predictive Value Pknots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs MXScarna(20) Matthews Correlation Coefficient Cylofold: N/A MXScarna(20): N/A Sensitivity Cylofold: N/A MXScarna(20): N/A Positive Predictive Value Cylofold: 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 MCFold Matthews Correlation Coefficient MXScarna(20): N/A MCFold: N/A Sensitivity MXScarna(20): N/A MCFold: N/A Positive Predictive Value MXScarna(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RDfolder vs MXScarna(20) Matthews Correlation Coefficient RDfolder: N/A MXScarna(20): N/A Sensitivity RDfolder: N/A MXScarna(20): N/A Positive Predictive Value RDfolder: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? 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	? Alterna vs MXScarna(20) Matthews Correlation Coefficient Alterna: N/A MXScarna(20): N/A Sensitivity Alterna: N/A MXScarna(20): N/A Positive Predictive Value Alterna: 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 Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.695 Carnac(seed): 0.000 Sensitivity MXScarna(20): 0.680 Carnac(seed): 0.000 Positive Predictive Value MXScarna(20): 0.712 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.626 Mastr(20): 0.000 Sensitivity MXScarna(20): 0.551 Mastr(20): 0.000 Positive Predictive Value MXScarna(20): 0.712 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.659 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.573 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.759 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(seed)	282 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.812 MXScarna(seed): 0.595 Sensitivity ContextFold: 0.764 MXScarna(seed): 0.475 Positive Predictive Value ContextFold: 0.863 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 MXScarna(seed): 0.595 Sensitivity PETfold_pre2.0(seed): 0.632 MXScarna(seed): 0.475 Positive Predictive Value PETfold_pre2.0(seed): 0.821 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 MXScarna(seed): 0.655 Sensitivity TurboFold(20): 0.702 MXScarna(seed): 0.542 Positive Predictive Value TurboFold(20): 0.822 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.754 MXScarna(seed): 0.655 Sensitivity PETfold_pre2.0(20): 0.670 MXScarna(seed): 0.542 Positive Predictive Value PETfold_pre2.0(20): 0.850 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	157 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.752 MXScarna(seed): 0.658 Sensitivity PPfold(20): 0.657 MXScarna(seed): 0.544 Positive Predictive Value PPfold(20): 0.862 MXScarna(seed): 0.797 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 MXScarna(seed): 0.655 Sensitivity CentroidAlifold(20): 0.562 MXScarna(seed): 0.542 Positive Predictive Value CentroidAlifold(20): 0.933 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 MXScarna(seed): 0.594 Sensitivity CentroidAlifold(seed): 0.521 MXScarna(seed): 0.474 Positive Predictive Value CentroidAlifold(seed): 0.919 MXScarna(seed): 0.746 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 MXScarna(seed): 0.599 Sensitivity CentroidHomfold‑LAST: 0.508 MXScarna(seed): 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.899 MXScarna(seed): 0.750 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 RNAalifold(20) vs MXScarna(seed) Matthews Correlation Coefficient RNAalifold(20): 0.667 MXScarna(seed): 0.655 Sensitivity RNAalifold(20): 0.532 MXScarna(seed): 0.542 Positive Predictive Value RNAalifold(20): 0.837 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.640 MXScarna(seed): 0.595 Sensitivity IPknot: 0.568 MXScarna(seed): 0.475 Positive Predictive Value IPknot: 0.723 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 Multilign(20) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(20): 0.657 MXScarna(seed): 0.654 Sensitivity Multilign(20): 0.594 MXScarna(seed): 0.539 Positive Predictive Value Multilign(20): 0.728 MXScarna(seed): 0.795 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 6.06606238843e-08	282 CentroidFold vs MXScarna(seed) Matthews Correlation Coefficient CentroidFold: 0.622 MXScarna(seed): 0.595 Sensitivity CentroidFold: 0.554 MXScarna(seed): 0.475 Positive Predictive Value CentroidFold: 0.699 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 Contrafold vs MXScarna(seed) Matthews Correlation Coefficient Contrafold: 0.604 MXScarna(seed): 0.595 Sensitivity Contrafold: 0.580 MXScarna(seed): 0.475 Positive Predictive Value Contrafold: 0.631 MXScarna(seed): 0.747 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 4.1569883686e-08	164 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 MXScarna(20): 0.651 Sensitivity MXScarna(seed): 0.542 MXScarna(20): 0.563 Positive Predictive Value MXScarna(seed): 0.793 MXScarna(20): 0.752 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.85233844192e-08		+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.595 MaxExpect: 0.588 Sensitivity MXScarna(seed): 0.475 MaxExpect: 0.563 Positive Predictive Value MXScarna(seed): 0.747 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.595 ProbKnot: 0.587 Sensitivity MXScarna(seed): 0.475 ProbKnot: 0.567 Positive Predictive Value MXScarna(seed): 0.747 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.85233844192e-08	? MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.574 RNASampler(20): 0.480 Sensitivity MXScarna(seed): 0.455 RNASampler(20): 0.343 Positive Predictive Value MXScarna(seed): 0.725 RNASampler(20): 0.673 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.595 Sfold: 0.586 Sensitivity MXScarna(seed): 0.475 Sfold: 0.521 Positive Predictive Value MXScarna(seed): 0.747 Sfold: 0.660 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.595 Fold: 0.552 Sensitivity MXScarna(seed): 0.475 Fold: 0.543 Positive Predictive Value MXScarna(seed): 0.747 Fold: 0.563 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 Murlet(20): 0.533 Sensitivity MXScarna(seed): 0.553 Murlet(20): 0.389 Positive Predictive Value MXScarna(seed): 0.793 Murlet(20): 0.732 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.595 UNAFold: 0.544 Sensitivity MXScarna(seed): 0.475 UNAFold: 0.530 Positive Predictive Value MXScarna(seed): 0.747 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.595 PknotsRG: 0.527 Sensitivity MXScarna(seed): 0.475 PknotsRG: 0.517 Positive Predictive Value MXScarna(seed): 0.747 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.595 RNAfold: 0.536 Sensitivity MXScarna(seed): 0.475 RNAfold: 0.525 Positive Predictive Value MXScarna(seed): 0.747 RNAfold: 0.548 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.591 Afold: 0.531 Sensitivity MXScarna(seed): 0.469 Afold: 0.518 Positive Predictive Value MXScarna(seed): 0.746 Afold: 0.545 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.599 RNAsubopt: 0.535 Sensitivity MXScarna(seed): 0.479 RNAsubopt: 0.532 Positive Predictive Value MXScarna(seed): 0.750 RNAsubopt: 0.539 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.595 McQFold: 0.481 Sensitivity MXScarna(seed): 0.475 McQFold: 0.460 Positive Predictive Value MXScarna(seed): 0.747 McQFold: 0.504 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 CMfinder(20): 0.503 Sensitivity MXScarna(seed): 0.542 CMfinder(20): 0.330 Positive Predictive Value MXScarna(seed): 0.793 CMfinder(20): 0.769 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.618 RNASLOpt: 0.475 Sensitivity MXScarna(seed): 0.500 RNASLOpt: 0.438 Positive Predictive Value MXScarna(seed): 0.767 RNASLOpt: 0.518 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.594 RNAalifold(seed): 0.469 Sensitivity MXScarna(seed): 0.474 RNAalifold(seed): 0.272 Positive Predictive Value MXScarna(seed): 0.746 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.604 RNAshapes: 0.486 Sensitivity MXScarna(seed): 0.485 RNAshapes: 0.469 Positive Predictive Value MXScarna(seed): 0.754 RNAshapes: 0.504 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.595 CRWrnafold: 0.459 Sensitivity MXScarna(seed): 0.475 CRWrnafold: 0.451 Positive Predictive Value MXScarna(seed): 0.747 CRWrnafold: 0.468 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.606 Vsfold4: 0.406 Sensitivity MXScarna(seed): 0.487 Vsfold4: 0.366 Positive Predictive Value MXScarna(seed): 0.755 Vsfold4: 0.453 Number of pairs reference - predicted secondary structure: 264 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.595 RNAwolf: 0.372 Sensitivity MXScarna(seed): 0.475 RNAwolf: 0.381 Positive Predictive Value MXScarna(seed): 0.747 RNAwolf: 0.366 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.604 Vsfold5: 0.380 Sensitivity MXScarna(seed): 0.485 Vsfold5: 0.350 Positive Predictive Value MXScarna(seed): 0.754 Vsfold5: 0.415 Number of pairs reference - predicted secondary structure: 260 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 MXScarna(seed): 0.283 Sensitivity CMfinder(seed): 0.159 MXScarna(seed): 0.165 Positive Predictive Value CMfinder(seed): 0.770 MXScarna(seed): 0.490 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 Carnac(20): 0.331 Sensitivity MXScarna(seed): 0.542 Carnac(20): 0.125 Positive Predictive Value MXScarna(seed): 0.793 Carnac(20): 0.878 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 RSpredict(20): 0.304 Sensitivity MXScarna(seed): 0.542 RSpredict(20): 0.172 Positive Predictive Value MXScarna(seed): 0.793 RSpredict(20): 0.538 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.587 NanoFolder: 0.180 Sensitivity MXScarna(seed): 0.470 NanoFolder: 0.206 Positive Predictive Value MXScarna(seed): 0.734 NanoFolder: 0.161 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.595 RSpredict(seed): 0.045 Sensitivity MXScarna(seed): 0.475 RSpredict(seed): 0.011 Positive Predictive Value MXScarna(seed): 0.746 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 279 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs MXScarna(seed) Matthews Correlation Coefficient Murlet(seed): N/A MXScarna(seed): N/A Sensitivity Murlet(seed): N/A MXScarna(seed): N/A Positive Predictive Value Murlet(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(seed): N/A Sensitivity Multilign(seed): N/A MXScarna(seed): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: N/A MXScarna(seed): N/A Sensitivity HotKnots: N/A MXScarna(seed): N/A Positive Predictive Value HotKnots: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: N/A MXScarna(seed): N/A Sensitivity Pknots: N/A MXScarna(seed): N/A Positive Predictive Value Pknots: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: N/A MXScarna(seed): N/A Sensitivity Cylofold: N/A MXScarna(seed): N/A Positive Predictive Value Cylofold: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): N/A MCFold: N/A Sensitivity MXScarna(seed): N/A MCFold: N/A Positive Predictive Value MXScarna(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): N/A MXScarna(seed): N/A Sensitivity PPfold(seed): N/A MXScarna(seed): N/A Positive Predictive Value PPfold(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: N/A MXScarna(seed): N/A Sensitivity RDfolder: N/A MXScarna(seed): N/A Positive Predictive Value RDfolder: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 MXScarna(seed): 0.695 Sensitivity TurboFold(seed): 0.677 MXScarna(seed): 0.538 Positive Predictive Value TurboFold(seed): 0.746 MXScarna(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(seed): N/A Sensitivity RNASampler(seed): N/A MXScarna(seed): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs MXScarna(seed) Matthews Correlation Coefficient Alterna: N/A MXScarna(seed): N/A Sensitivity Alterna: N/A MXScarna(seed): N/A Positive Predictive Value Alterna: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.504 Carnac(seed): 0.000 Sensitivity MXScarna(seed): 0.364 Carnac(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.700 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 Mastr(20): 0.000 Sensitivity MXScarna(seed): 0.542 Mastr(20): 0.000 Positive Predictive Value MXScarna(seed): 0.793 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.596 Mastr(seed): 0.000 Sensitivity MXScarna(seed): 0.476 Mastr(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.747 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08
MaxExpect	610 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.718 MaxExpect: 0.524 Sensitivity ContextFold: 0.677 MaxExpect: 0.511 Positive Predictive Value ContextFold: 0.763 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 MaxExpect: 0.525 Sensitivity PETfold_pre2.0(seed): 0.590 MaxExpect: 0.510 Positive Predictive Value PETfold_pre2.0(seed): 0.787 MaxExpect: 0.542 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.740 MaxExpect: 0.587 Sensitivity TurboFold(20): 0.685 MaxExpect: 0.561 Positive Predictive Value TurboFold(20): 0.801 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 MaxExpect: 0.587 Sensitivity PETfold_pre2.0(20): 0.652 MaxExpect: 0.561 Positive Predictive Value PETfold_pre2.0(20): 0.829 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.734 MaxExpect: 0.584 Sensitivity PPfold(20): 0.635 MaxExpect: 0.559 Positive Predictive Value PPfold(20): 0.850 MaxExpect: 0.613 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.717 MaxExpect: 0.587 Sensitivity CentroidAlifold(20): 0.561 MaxExpect: 0.561 Positive Predictive Value CentroidAlifold(20): 0.916 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 MaxExpect: 0.588 Sensitivity CentroidAlifold(seed): 0.521 MaxExpect: 0.563 Positive Predictive Value CentroidAlifold(seed): 0.919 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 MaxExpect: 0.527 Sensitivity CentroidHomfold‑LAST: 0.469 MaxExpect: 0.513 Positive Predictive Value CentroidHomfold‑LAST: 0.877 MaxExpect: 0.542 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.660 MaxExpect: 0.587 Sensitivity RNAalifold(20): 0.532 MaxExpect: 0.561 Positive Predictive Value RNAalifold(20): 0.819 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.602 MaxExpect: 0.524 Sensitivity IPknot: 0.545 MaxExpect: 0.511 Positive Predictive Value IPknot: 0.667 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.649 MaxExpect: 0.587 Sensitivity Multilign(20): 0.590 MaxExpect: 0.561 Positive Predictive Value Multilign(20): 0.717 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.571 MaxExpect: 0.524 Sensitivity CentroidFold: 0.516 MaxExpect: 0.511 Positive Predictive Value CentroidFold: 0.635 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.554 MaxExpect: 0.524 Sensitivity Contrafold: 0.540 MaxExpect: 0.511 Positive Predictive Value Contrafold: 0.569 MaxExpect: 0.538 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.626 MaxExpect: 0.587 Sensitivity MXScarna(20): 0.551 MaxExpect: 0.561 Positive Predictive Value MXScarna(20): 0.712 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.595 MaxExpect: 0.588 Sensitivity MXScarna(seed): 0.475 MaxExpect: 0.563 Positive Predictive Value MXScarna(seed): 0.747 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 5.62644058675e-08		+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.524 ProbKnot: 0.522 Sensitivity MaxExpect: 0.511 ProbKnot: 0.518 Positive Predictive Value MaxExpect: 0.538 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.543 MaxExpect: 0.460 Sensitivity RNASampler(20): 0.425 MaxExpect: 0.448 Positive Predictive Value RNASampler(20): 0.695 MaxExpect: 0.474 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.524 Sfold: 0.514 Sensitivity MaxExpect: 0.511 Sfold: 0.463 Positive Predictive Value MaxExpect: 0.538 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.524 Fold: 0.495 Sensitivity MaxExpect: 0.511 Fold: 0.498 Positive Predictive Value MaxExpect: 0.538 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.574 Murlet(20): 0.548 Sensitivity MaxExpect: 0.551 Murlet(20): 0.415 Positive Predictive Value MaxExpect: 0.601 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.524 UNAFold: 0.475 Sensitivity MaxExpect: 0.511 UNAFold: 0.473 Positive Predictive Value MaxExpect: 0.538 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.524 PknotsRG: 0.476 Sensitivity MaxExpect: 0.511 PknotsRG: 0.478 Positive Predictive Value MaxExpect: 0.538 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.524 RNAfold: 0.474 Sensitivity MaxExpect: 0.511 RNAfold: 0.477 Positive Predictive Value MaxExpect: 0.538 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.553 Afold: 0.494 Sensitivity MaxExpect: 0.537 Afold: 0.490 Positive Predictive Value MaxExpect: 0.570 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.527 RNAsubopt: 0.475 Sensitivity MaxExpect: 0.513 RNAsubopt: 0.482 Positive Predictive Value MaxExpect: 0.542 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.524 McQFold: 0.450 Sensitivity MaxExpect: 0.511 McQFold: 0.441 Positive Predictive Value MaxExpect: 0.538 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.587 CMfinder(20): 0.479 Sensitivity MaxExpect: 0.561 CMfinder(20): 0.308 Positive Predictive Value MaxExpect: 0.615 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.524 RNASLOpt: 0.446 Sensitivity MaxExpect: 0.510 RNASLOpt: 0.421 Positive Predictive Value MaxExpect: 0.540 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAalifold(seed) Matthews Correlation Coefficient MaxExpect: 0.587 RNAalifold(seed): 0.469 Sensitivity MaxExpect: 0.562 RNAalifold(seed): 0.272 Positive Predictive Value MaxExpect: 0.615 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.526 RNAshapes: 0.408 Sensitivity MaxExpect: 0.512 RNAshapes: 0.404 Positive Predictive Value MaxExpect: 0.543 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.524 CRWrnafold: 0.417 Sensitivity MaxExpect: 0.511 CRWrnafold: 0.421 Positive Predictive Value MaxExpect: 0.538 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.523 Vsfold4: 0.335 Sensitivity MaxExpect: 0.510 Vsfold4: 0.308 Positive Predictive Value MaxExpect: 0.539 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.524 RNAwolf: 0.332 Sensitivity MaxExpect: 0.511 RNAwolf: 0.347 Positive Predictive Value MaxExpect: 0.538 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.525 Vsfold5: 0.329 Sensitivity MaxExpect: 0.511 Vsfold5: 0.312 Positive Predictive Value MaxExpect: 0.541 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.559 CMfinder(seed): 0.350 Sensitivity MaxExpect: 0.543 CMfinder(seed): 0.159 Positive Predictive Value MaxExpect: 0.576 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.587 Carnac(20): 0.360 Sensitivity MaxExpect: 0.561 Carnac(20): 0.151 Positive Predictive Value MaxExpect: 0.615 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.587 RSpredict(20): 0.347 Sensitivity MaxExpect: 0.561 RSpredict(20): 0.220 Positive Predictive Value MaxExpect: 0.615 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.549 NanoFolder: 0.172 Sensitivity MaxExpect: 0.532 NanoFolder: 0.204 Positive Predictive Value MaxExpect: 0.568 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.589 RSpredict(seed): 0.045 Sensitivity MaxExpect: 0.564 RSpredict(seed): 0.011 Positive Predictive Value MaxExpect: 0.617 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: N/A Murlet(seed): N/A Sensitivity MaxExpect: N/A Murlet(seed): N/A Positive Predictive Value MaxExpect: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: N/A Multilign(seed): N/A Sensitivity MaxExpect: N/A Multilign(seed): N/A Positive Predictive Value MaxExpect: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: N/A HotKnots: N/A Sensitivity MaxExpect: N/A HotKnots: N/A Positive Predictive Value MaxExpect: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: N/A Pknots: N/A Sensitivity MaxExpect: N/A Pknots: N/A Positive Predictive Value MaxExpect: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.631 Cylofold: 0.271 Sensitivity MaxExpect: 0.620 Cylofold: 0.241 Positive Predictive Value MaxExpect: 0.644 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: N/A MCFold: N/A Sensitivity MaxExpect: N/A MCFold: N/A Positive Predictive Value MaxExpect: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: N/A PPfold(seed): N/A Sensitivity MaxExpect: N/A PPfold(seed): N/A Positive Predictive Value MaxExpect: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: N/A RDfolder: N/A Sensitivity MaxExpect: N/A RDfolder: N/A Positive Predictive Value MaxExpect: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.710 MaxExpect: 0.651 Sensitivity TurboFold(seed): 0.677 MaxExpect: 0.662 Positive Predictive Value TurboFold(seed): 0.746 MaxExpect: 0.642 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: N/A RNASampler(seed): N/A Sensitivity MaxExpect: N/A RNASampler(seed): N/A Positive Predictive Value MaxExpect: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: N/A Alterna: N/A Sensitivity MaxExpect: N/A Alterna: N/A Positive Predictive Value MaxExpect: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.516 Carnac(seed): 0.000 Sensitivity MaxExpect: 0.509 Carnac(seed): 0.000 Positive Predictive Value MaxExpect: 0.525 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.587 Mastr(20): 0.000 Sensitivity MaxExpect: 0.561 Mastr(20): 0.000 Positive Predictive Value MaxExpect: 0.615 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.585 Mastr(seed): 0.000 Sensitivity MaxExpect: 0.561 Mastr(seed): 0.000 Positive Predictive Value MaxExpect: 0.612 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	610 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.718 ProbKnot: 0.522 Sensitivity ContextFold: 0.677 ProbKnot: 0.518 Positive Predictive Value ContextFold: 0.763 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 ProbKnot: 0.524 Sensitivity PETfold_pre2.0(seed): 0.590 ProbKnot: 0.516 Positive Predictive Value PETfold_pre2.0(seed): 0.787 ProbKnot: 0.532 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.740 ProbKnot: 0.586 Sensitivity TurboFold(20): 0.685 ProbKnot: 0.564 Positive Predictive Value TurboFold(20): 0.801 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 ProbKnot: 0.586 Sensitivity PETfold_pre2.0(20): 0.652 ProbKnot: 0.564 Positive Predictive Value PETfold_pre2.0(20): 0.829 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.734 ProbKnot: 0.583 Sensitivity PPfold(20): 0.635 ProbKnot: 0.562 Positive Predictive Value PPfold(20): 0.850 ProbKnot: 0.607 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.717 ProbKnot: 0.586 Sensitivity CentroidAlifold(20): 0.561 ProbKnot: 0.564 Positive Predictive Value CentroidAlifold(20): 0.916 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 ProbKnot: 0.587 Sensitivity CentroidAlifold(seed): 0.521 ProbKnot: 0.566 Positive Predictive Value CentroidAlifold(seed): 0.919 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 ProbKnot: 0.526 Sensitivity CentroidHomfold‑LAST: 0.469 ProbKnot: 0.520 Positive Predictive Value CentroidHomfold‑LAST: 0.877 ProbKnot: 0.532 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.660 ProbKnot: 0.586 Sensitivity RNAalifold(20): 0.532 ProbKnot: 0.564 Positive Predictive Value RNAalifold(20): 0.819 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.602 ProbKnot: 0.522 Sensitivity IPknot: 0.545 ProbKnot: 0.518 Positive Predictive Value IPknot: 0.667 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.649 ProbKnot: 0.586 Sensitivity Multilign(20): 0.590 ProbKnot: 0.564 Positive Predictive Value Multilign(20): 0.717 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.571 ProbKnot: 0.522 Sensitivity CentroidFold: 0.516 ProbKnot: 0.518 Positive Predictive Value CentroidFold: 0.635 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.554 ProbKnot: 0.522 Sensitivity Contrafold: 0.540 ProbKnot: 0.518 Positive Predictive Value Contrafold: 0.569 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.626 ProbKnot: 0.586 Sensitivity MXScarna(20): 0.551 ProbKnot: 0.564 Positive Predictive Value MXScarna(20): 0.712 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.595 ProbKnot: 0.587 Sensitivity MXScarna(seed): 0.475 ProbKnot: 0.567 Positive Predictive Value MXScarna(seed): 0.747 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.85233844192e-08	610 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.524 ProbKnot: 0.522 Sensitivity MaxExpect: 0.511 ProbKnot: 0.518 Positive Predictive Value MaxExpect: 0.538 ProbKnot: 0.527 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.543 ProbKnot: 0.461 Sensitivity RNASampler(20): 0.425 ProbKnot: 0.460 Positive Predictive Value RNASampler(20): 0.695 ProbKnot: 0.463 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Sfold Matthews Correlation Coefficient ProbKnot: 0.522 Sfold: 0.514 Sensitivity ProbKnot: 0.518 Sfold: 0.463 Positive Predictive Value ProbKnot: 0.527 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.522 Fold: 0.495 Sensitivity ProbKnot: 0.518 Fold: 0.498 Positive Predictive Value ProbKnot: 0.527 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.573 Murlet(20): 0.548 Sensitivity ProbKnot: 0.555 Murlet(20): 0.415 Positive Predictive Value ProbKnot: 0.593 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.522 UNAFold: 0.475 Sensitivity ProbKnot: 0.518 UNAFold: 0.473 Positive Predictive Value ProbKnot: 0.527 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.522 PknotsRG: 0.476 Sensitivity ProbKnot: 0.518 PknotsRG: 0.478 Positive Predictive Value ProbKnot: 0.527 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.522 RNAfold: 0.474 Sensitivity ProbKnot: 0.518 RNAfold: 0.477 Positive Predictive Value ProbKnot: 0.527 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.550 Afold: 0.494 Sensitivity ProbKnot: 0.541 Afold: 0.490 Positive Predictive Value ProbKnot: 0.559 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.526 RNAsubopt: 0.475 Sensitivity ProbKnot: 0.520 RNAsubopt: 0.482 Positive Predictive Value ProbKnot: 0.532 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.522 McQFold: 0.450 Sensitivity ProbKnot: 0.518 McQFold: 0.441 Positive Predictive Value ProbKnot: 0.527 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.586 CMfinder(20): 0.479 Sensitivity ProbKnot: 0.564 CMfinder(20): 0.308 Positive Predictive Value ProbKnot: 0.610 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.523 RNASLOpt: 0.446 Sensitivity ProbKnot: 0.517 RNASLOpt: 0.421 Positive Predictive Value ProbKnot: 0.530 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.587 RNAalifold(seed): 0.469 Sensitivity ProbKnot: 0.566 RNAalifold(seed): 0.272 Positive Predictive Value ProbKnot: 0.610 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.525 RNAshapes: 0.408 Sensitivity ProbKnot: 0.519 RNAshapes: 0.404 Positive Predictive Value ProbKnot: 0.533 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.522 CRWrnafold: 0.417 Sensitivity ProbKnot: 0.518 CRWrnafold: 0.421 Positive Predictive Value ProbKnot: 0.527 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.522 Vsfold4: 0.335 Sensitivity ProbKnot: 0.517 Vsfold4: 0.308 Positive Predictive Value ProbKnot: 0.529 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.522 RNAwolf: 0.332 Sensitivity ProbKnot: 0.518 RNAwolf: 0.347 Positive Predictive Value ProbKnot: 0.527 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.524 Vsfold5: 0.329 Sensitivity ProbKnot: 0.518 Vsfold5: 0.312 Positive Predictive Value ProbKnot: 0.530 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.554 CMfinder(seed): 0.350 Sensitivity ProbKnot: 0.550 CMfinder(seed): 0.159 Positive Predictive Value ProbKnot: 0.560 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.586 Carnac(20): 0.360 Sensitivity ProbKnot: 0.564 Carnac(20): 0.151 Positive Predictive Value ProbKnot: 0.610 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.586 RSpredict(20): 0.347 Sensitivity ProbKnot: 0.564 RSpredict(20): 0.220 Positive Predictive Value ProbKnot: 0.610 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.547 NanoFolder: 0.172 Sensitivity ProbKnot: 0.539 NanoFolder: 0.204 Positive Predictive Value ProbKnot: 0.557 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.588 RSpredict(seed): 0.045 Sensitivity ProbKnot: 0.567 RSpredict(seed): 0.011 Positive Predictive Value ProbKnot: 0.611 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: N/A Murlet(seed): N/A Sensitivity ProbKnot: N/A Murlet(seed): N/A Positive Predictive Value ProbKnot: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: N/A Multilign(seed): N/A Sensitivity ProbKnot: N/A Multilign(seed): N/A Positive Predictive Value ProbKnot: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: N/A ProbKnot: N/A Sensitivity HotKnots: N/A ProbKnot: N/A Positive Predictive Value HotKnots: N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: N/A Pknots: N/A Sensitivity ProbKnot: N/A Pknots: N/A Positive Predictive Value ProbKnot: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.634 Cylofold: 0.271 Sensitivity ProbKnot: 0.620 Cylofold: 0.241 Positive Predictive Value ProbKnot: 0.649 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: N/A MCFold: N/A Sensitivity ProbKnot: N/A MCFold: N/A Positive Predictive Value ProbKnot: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: N/A PPfold(seed): N/A Sensitivity ProbKnot: N/A PPfold(seed): N/A Positive Predictive Value ProbKnot: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs ProbKnot Matthews Correlation Coefficient RDfolder: N/A ProbKnot: N/A Sensitivity RDfolder: N/A ProbKnot: N/A Positive Predictive Value RDfolder: N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.710 ProbKnot: 0.641 Sensitivity TurboFold(seed): 0.677 ProbKnot: 0.662 Positive Predictive Value TurboFold(seed): 0.746 ProbKnot: 0.623 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): N/A ProbKnot: N/A Sensitivity RNASampler(seed): N/A ProbKnot: N/A Positive Predictive Value RNASampler(seed): N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: N/A Alterna: N/A Sensitivity ProbKnot: N/A Alterna: N/A Positive Predictive Value ProbKnot: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.513 Carnac(seed): 0.000 Sensitivity ProbKnot: 0.509 Carnac(seed): 0.000 Positive Predictive Value ProbKnot: 0.519 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.586 Mastr(20): 0.000 Sensitivity ProbKnot: 0.564 Mastr(20): 0.000 Positive Predictive Value ProbKnot: 0.610 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.585 Mastr(seed): 0.000 Sensitivity ProbKnot: 0.566 Mastr(seed): 0.000 Positive Predictive Value ProbKnot: 0.606 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(20)	45 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.737 RNASampler(20): 0.543 Sensitivity ContextFold: 0.685 RNASampler(20): 0.425 Positive Predictive Value ContextFold: 0.793 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.676 RNASampler(20): 0.543 Sensitivity PETfold_pre2.0(seed): 0.587 RNASampler(20): 0.425 Positive Predictive Value PETfold_pre2.0(seed): 0.779 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.663 RNASampler(20): 0.543 Sensitivity TurboFold(20): 0.610 RNASampler(20): 0.425 Positive Predictive Value TurboFold(20): 0.720 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.650 RNASampler(20): 0.543 Sensitivity PETfold_pre2.0(20): 0.569 RNASampler(20): 0.425 Positive Predictive Value PETfold_pre2.0(20): 0.742 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.656 RNASampler(20): 0.543 Sensitivity PPfold(20): 0.541 RNASampler(20): 0.425 Positive Predictive Value PPfold(20): 0.795 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.678 RNASampler(20): 0.543 Sensitivity CentroidAlifold(20): 0.540 RNASampler(20): 0.425 Positive Predictive Value CentroidAlifold(20): 0.853 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.675 RNASampler(20): 0.480 Sensitivity CentroidAlifold(seed): 0.493 RNASampler(20): 0.343 Positive Predictive Value CentroidAlifold(seed): 0.927 RNASampler(20): 0.673 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	45 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 RNASampler(20): 0.543 Sensitivity CentroidHomfold‑LAST: 0.532 RNASampler(20): 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.861 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.625 RNASampler(20): 0.543 Sensitivity RNAalifold(20): 0.520 RNASampler(20): 0.425 Positive Predictive Value RNAalifold(20): 0.753 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.582 RNASampler(20): 0.543 Sensitivity IPknot: 0.514 RNASampler(20): 0.425 Positive Predictive Value IPknot: 0.659 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.602 RNASampler(20): 0.546 Sensitivity Multilign(20): 0.551 RNASampler(20): 0.427 Positive Predictive Value Multilign(20): 0.660 RNASampler(20): 0.697 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.543 CentroidFold: 0.500 Sensitivity RNASampler(20): 0.425 CentroidFold: 0.437 Positive Predictive Value RNASampler(20): 0.695 CentroidFold: 0.574 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.543 Contrafold: 0.482 Sensitivity RNASampler(20): 0.425 Contrafold: 0.465 Positive Predictive Value RNASampler(20): 0.695 Contrafold: 0.502 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.543 MXScarna(20): 0.519 Sensitivity RNASampler(20): 0.425 MXScarna(20): 0.480 Positive Predictive Value RNASampler(20): 0.695 MXScarna(20): 0.562 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.574 RNASampler(20): 0.480 Sensitivity MXScarna(seed): 0.455 RNASampler(20): 0.343 Positive Predictive Value MXScarna(seed): 0.725 RNASampler(20): 0.673 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	45 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.543 MaxExpect: 0.460 Sensitivity RNASampler(20): 0.425 MaxExpect: 0.448 Positive Predictive Value RNASampler(20): 0.695 MaxExpect: 0.474 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.543 ProbKnot: 0.461 Sensitivity RNASampler(20): 0.425 ProbKnot: 0.460 Positive Predictive Value RNASampler(20): 0.695 ProbKnot: 0.463 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.543 Sfold: 0.400 Sensitivity RNASampler(20): 0.425 Sfold: 0.345 Positive Predictive Value RNASampler(20): 0.695 Sfold: 0.465 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.543 Fold: 0.451 Sensitivity RNASampler(20): 0.425 Fold: 0.454 Positive Predictive Value RNASampler(20): 0.695 Fold: 0.450 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.575 RNASampler(20): 0.545 Sensitivity Murlet(20): 0.471 RNASampler(20): 0.429 Positive Predictive Value Murlet(20): 0.702 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.543 UNAFold: 0.370 Sensitivity RNASampler(20): 0.425 UNAFold: 0.372 Positive Predictive Value RNASampler(20): 0.695 UNAFold: 0.370 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.543 PknotsRG: 0.389 Sensitivity RNASampler(20): 0.425 PknotsRG: 0.395 Positive Predictive Value RNASampler(20): 0.695 PknotsRG: 0.385 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.543 RNAfold: 0.390 Sensitivity RNASampler(20): 0.425 RNAfold: 0.397 Positive Predictive Value RNASampler(20): 0.695 RNAfold: 0.386 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.518 Afold: 0.485 Sensitivity RNASampler(20): 0.388 Afold: 0.480 Positive Predictive Value RNASampler(20): 0.691 Afold: 0.491 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.3551590886e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.543 RNAsubopt: 0.362 Sensitivity RNASampler(20): 0.425 RNAsubopt: 0.371 Positive Predictive Value RNASampler(20): 0.695 RNAsubopt: 0.354 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.543 McQFold: 0.387 Sensitivity RNASampler(20): 0.425 McQFold: 0.380 Positive Predictive Value RNASampler(20): 0.695 McQFold: 0.396 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.543 CMfinder(20): 0.370 Sensitivity RNASampler(20): 0.425 CMfinder(20): 0.220 Positive Predictive Value RNASampler(20): 0.695 CMfinder(20): 0.625 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.543 RNASLOpt: 0.374 Sensitivity RNASampler(20): 0.425 RNASLOpt: 0.356 Positive Predictive Value RNASampler(20): 0.695 RNASLOpt: 0.396 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.480 RNAalifold(seed): 0.439 Sensitivity RNASampler(20): 0.343 RNAalifold(seed): 0.245 Positive Predictive Value RNASampler(20): 0.673 RNAalifold(seed): 0.791 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.543 RNAshapes: 0.306 Sensitivity RNASampler(20): 0.425 RNAshapes: 0.306 Positive Predictive Value RNASampler(20): 0.697 RNAshapes: 0.308 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.543 CRWrnafold: 0.369 Sensitivity RNASampler(20): 0.425 CRWrnafold: 0.374 Positive Predictive Value RNASampler(20): 0.695 CRWrnafold: 0.366 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.543 Vsfold4: 0.245 Sensitivity RNASampler(20): 0.425 Vsfold4: 0.229 Positive Predictive Value RNASampler(20): 0.695 Vsfold4: 0.265 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.543 RNAwolf: 0.286 Sensitivity RNASampler(20): 0.425 RNAwolf: 0.305 Positive Predictive Value RNASampler(20): 0.695 RNAwolf: 0.271 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.543 Vsfold5: 0.244 Sensitivity RNASampler(20): 0.425 Vsfold5: 0.234 Positive Predictive Value RNASampler(20): 0.695 Vsfold5: 0.256 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.543 Carnac(20): 0.453 Sensitivity RNASampler(20): 0.425 Carnac(20): 0.249 Positive Predictive Value RNASampler(20): 0.695 Carnac(20): 0.827 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.543 RSpredict(20): 0.477 Sensitivity RNASampler(20): 0.425 RSpredict(20): 0.406 Positive Predictive Value RNASampler(20): 0.695 RSpredict(20): 0.561 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.618 NanoFolder: 0.097 Sensitivity RNASampler(20): 0.506 NanoFolder: 0.120 Positive Predictive Value RNASampler(20): 0.755 NanoFolder: 0.081 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.480 RSpredict(seed): 0.006 Sensitivity RNASampler(20): 0.343 RSpredict(seed): 0.001 Positive Predictive Value RNASampler(20): 0.673 RSpredict(seed): 0.030 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 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	? 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	? RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): N/A HotKnots: N/A Sensitivity RNASampler(20): N/A HotKnots: N/A Positive Predictive Value RNASampler(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): N/A Pknots: N/A Sensitivity RNASampler(20): N/A Pknots: N/A Positive Predictive Value RNASampler(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): N/A Cylofold: N/A Sensitivity RNASampler(20): N/A Cylofold: N/A Positive Predictive Value RNASampler(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): N/A MCFold: N/A Sensitivity RNASampler(20): N/A MCFold: N/A Positive Predictive Value RNASampler(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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 RDfolder Matthews Correlation Coefficient RNASampler(20): N/A RDfolder: N/A Sensitivity RNASampler(20): N/A RDfolder: N/A Positive Predictive Value RNASampler(20): N/A RDfolder: 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 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(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): N/A Alterna: N/A Sensitivity RNASampler(20): N/A Alterna: N/A Positive Predictive Value RNASampler(20): N/A Alterna: 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	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.543 Mastr(20): 0.000 Sensitivity RNASampler(20): 0.425 Mastr(20): 0.000 Positive Predictive Value RNASampler(20): 0.695 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.480 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.343 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.673 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Sfold	610 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.718 Sfold: 0.514 Sensitivity ContextFold: 0.677 Sfold: 0.463 Positive Predictive Value ContextFold: 0.763 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 Sfold: 0.510 Sensitivity PETfold_pre2.0(seed): 0.590 Sfold: 0.458 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Sfold: 0.570 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.740 Sfold: 0.568 Sensitivity TurboFold(20): 0.685 Sfold: 0.503 Positive Predictive Value TurboFold(20): 0.801 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Sfold: 0.568 Sensitivity PETfold_pre2.0(20): 0.652 Sfold: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.829 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.734 Sfold: 0.567 Sensitivity PPfold(20): 0.635 Sfold: 0.501 Positive Predictive Value PPfold(20): 0.850 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Sfold: 0.568 Sensitivity CentroidAlifold(20): 0.561 Sfold: 0.503 Positive Predictive Value CentroidAlifold(20): 0.916 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 Sfold: 0.585 Sensitivity CentroidAlifold(seed): 0.521 Sfold: 0.520 Positive Predictive Value CentroidAlifold(seed): 0.919 Sfold: 0.659 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Sfold: 0.517 Sensitivity CentroidHomfold‑LAST: 0.469 Sfold: 0.466 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Sfold: 0.575 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.660 Sfold: 0.568 Sensitivity RNAalifold(20): 0.532 Sfold: 0.503 Positive Predictive Value RNAalifold(20): 0.819 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.602 Sfold: 0.514 Sensitivity IPknot: 0.545 Sfold: 0.463 Positive Predictive Value IPknot: 0.667 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.649 Sfold: 0.566 Sensitivity Multilign(20): 0.590 Sfold: 0.502 Positive Predictive Value Multilign(20): 0.717 Sfold: 0.641 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.571 Sfold: 0.514 Sensitivity CentroidFold: 0.516 Sfold: 0.463 Positive Predictive Value CentroidFold: 0.635 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.554 Sfold: 0.514 Sensitivity Contrafold: 0.540 Sfold: 0.463 Positive Predictive Value Contrafold: 0.569 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.626 Sfold: 0.568 Sensitivity MXScarna(20): 0.551 Sfold: 0.503 Positive Predictive Value MXScarna(20): 0.712 Sfold: 0.643 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.595 Sfold: 0.586 Sensitivity MXScarna(seed): 0.475 Sfold: 0.521 Positive Predictive Value MXScarna(seed): 0.747 Sfold: 0.660 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.524 Sfold: 0.514 Sensitivity MaxExpect: 0.511 Sfold: 0.463 Positive Predictive Value MaxExpect: 0.538 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs Sfold Matthews Correlation Coefficient ProbKnot: 0.522 Sfold: 0.514 Sensitivity ProbKnot: 0.518 Sfold: 0.463 Positive Predictive Value ProbKnot: 0.527 Sfold: 0.571 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.543 Sfold: 0.400 Sensitivity RNASampler(20): 0.425 Sfold: 0.345 Positive Predictive Value RNASampler(20): 0.695 Sfold: 0.465 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.514 Fold: 0.495 Sensitivity Sfold: 0.463 Fold: 0.498 Positive Predictive Value Sfold: 0.571 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.550 Murlet(20): 0.548 Sensitivity Sfold: 0.483 Murlet(20): 0.415 Positive Predictive Value Sfold: 0.628 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 0.0265675133358	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.514 UNAFold: 0.475 Sensitivity Sfold: 0.463 UNAFold: 0.473 Positive Predictive Value Sfold: 0.571 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.514 PknotsRG: 0.476 Sensitivity Sfold: 0.463 PknotsRG: 0.478 Positive Predictive Value Sfold: 0.571 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.514 RNAfold: 0.474 Sensitivity Sfold: 0.463 RNAfold: 0.477 Positive Predictive Value Sfold: 0.571 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.552 Afold: 0.494 Sensitivity Sfold: 0.496 Afold: 0.490 Positive Predictive Value Sfold: 0.616 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.517 RNAsubopt: 0.475 Sensitivity Sfold: 0.466 RNAsubopt: 0.482 Positive Predictive Value Sfold: 0.575 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.514 McQFold: 0.450 Sensitivity Sfold: 0.463 McQFold: 0.441 Positive Predictive Value Sfold: 0.571 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.568 CMfinder(20): 0.479 Sensitivity Sfold: 0.503 CMfinder(20): 0.308 Positive Predictive Value Sfold: 0.643 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.509 RNASLOpt: 0.446 Sensitivity Sfold: 0.458 RNASLOpt: 0.421 Positive Predictive Value Sfold: 0.567 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.585 RNAalifold(seed): 0.469 Sensitivity Sfold: 0.519 RNAalifold(seed): 0.272 Positive Predictive Value Sfold: 0.659 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.513 RNAshapes: 0.408 Sensitivity Sfold: 0.462 RNAshapes: 0.404 Positive Predictive Value Sfold: 0.572 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.514 CRWrnafold: 0.417 Sensitivity Sfold: 0.463 CRWrnafold: 0.421 Positive Predictive Value Sfold: 0.571 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.512 Vsfold4: 0.335 Sensitivity Sfold: 0.461 Vsfold4: 0.308 Positive Predictive Value Sfold: 0.570 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.514 RNAwolf: 0.332 Sensitivity Sfold: 0.463 RNAwolf: 0.347 Positive Predictive Value Sfold: 0.571 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.511 Vsfold5: 0.329 Sensitivity Sfold: 0.461 Vsfold5: 0.312 Positive Predictive Value Sfold: 0.569 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.601 CMfinder(seed): 0.350 Sensitivity Sfold: 0.529 CMfinder(seed): 0.159 Positive Predictive Value Sfold: 0.684 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.568 Carnac(20): 0.360 Sensitivity Sfold: 0.503 Carnac(20): 0.151 Positive Predictive Value Sfold: 0.643 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.568 RSpredict(20): 0.347 Sensitivity Sfold: 0.503 RSpredict(20): 0.220 Positive Predictive Value Sfold: 0.643 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.540 NanoFolder: 0.172 Sensitivity Sfold: 0.483 NanoFolder: 0.204 Positive Predictive Value Sfold: 0.605 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.585 RSpredict(seed): 0.045 Sensitivity Sfold: 0.520 RSpredict(seed): 0.011 Positive Predictive Value Sfold: 0.660 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs Sfold Matthews Correlation Coefficient Murlet(seed): N/A Sfold: N/A Sensitivity Murlet(seed): N/A Sfold: N/A Positive Predictive Value Murlet(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): N/A Sfold: N/A Sensitivity Multilign(seed): N/A Sfold: N/A Positive Predictive Value Multilign(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: N/A Sfold: N/A Sensitivity HotKnots: N/A Sfold: N/A Positive Predictive Value HotKnots: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Sfold Matthews Correlation Coefficient Pknots: N/A Sfold: N/A Sensitivity Pknots: N/A Sfold: N/A Positive Predictive Value Pknots: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.657 Cylofold: 0.271 Sensitivity Sfold: 0.562 Cylofold: 0.241 Positive Predictive Value Sfold: 0.770 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Sfold vs MCFold Matthews Correlation Coefficient Sfold: N/A MCFold: N/A Sensitivity Sfold: N/A MCFold: N/A Positive Predictive Value Sfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Sfold Matthews Correlation Coefficient PPfold(seed): N/A Sfold: N/A Sensitivity PPfold(seed): N/A Sfold: N/A Positive Predictive Value PPfold(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: N/A Sfold: N/A Sensitivity RDfolder: N/A Sfold: N/A Positive Predictive Value RDfolder: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.710 Sfold: 0.594 Sensitivity TurboFold(seed): 0.677 Sfold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): N/A Sfold: N/A Sensitivity RNASampler(seed): N/A Sfold: N/A Positive Predictive Value RNASampler(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Sfold Matthews Correlation Coefficient Alterna: N/A Sfold: N/A Sensitivity Alterna: N/A Sfold: N/A Positive Predictive Value Alterna: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.544 Carnac(seed): 0.000 Sensitivity Sfold: 0.487 Carnac(seed): 0.000 Positive Predictive Value Sfold: 0.609 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.568 Mastr(20): 0.000 Sensitivity Sfold: 0.503 Mastr(20): 0.000 Positive Predictive Value Sfold: 0.643 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.581 Mastr(seed): 0.000 Sensitivity Sfold: 0.518 Mastr(seed): 0.000 Positive Predictive Value Sfold: 0.653 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	610 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.718 Fold: 0.495 Sensitivity ContextFold: 0.677 Fold: 0.498 Positive Predictive Value ContextFold: 0.763 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 Fold: 0.498 Sensitivity PETfold_pre2.0(seed): 0.590 Fold: 0.499 Positive Predictive Value PETfold_pre2.0(seed): 0.787 Fold: 0.499 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.740 Fold: 0.550 Sensitivity TurboFold(20): 0.685 Fold: 0.541 Positive Predictive Value TurboFold(20): 0.801 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Fold: 0.550 Sensitivity PETfold_pre2.0(20): 0.652 Fold: 0.541 Positive Predictive Value PETfold_pre2.0(20): 0.829 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.734 Fold: 0.549 Sensitivity PPfold(20): 0.635 Fold: 0.540 Positive Predictive Value PPfold(20): 0.850 Fold: 0.560 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Fold: 0.550 Sensitivity CentroidAlifold(20): 0.561 Fold: 0.541 Positive Predictive Value CentroidAlifold(20): 0.916 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 Fold: 0.552 Sensitivity CentroidAlifold(seed): 0.521 Fold: 0.543 Positive Predictive Value CentroidAlifold(seed): 0.919 Fold: 0.563 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 Fold: 0.499 Sensitivity CentroidHomfold‑LAST: 0.469 Fold: 0.502 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Fold: 0.499 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.660 Fold: 0.550 Sensitivity RNAalifold(20): 0.532 Fold: 0.541 Positive Predictive Value RNAalifold(20): 0.819 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.602 Fold: 0.495 Sensitivity IPknot: 0.545 Fold: 0.498 Positive Predictive Value IPknot: 0.667 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.649 Fold: 0.550 Sensitivity Multilign(20): 0.590 Fold: 0.541 Positive Predictive Value Multilign(20): 0.717 Fold: 0.561 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.571 Fold: 0.495 Sensitivity CentroidFold: 0.516 Fold: 0.498 Positive Predictive Value CentroidFold: 0.635 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.554 Fold: 0.495 Sensitivity Contrafold: 0.540 Fold: 0.498 Positive Predictive Value Contrafold: 0.569 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.626 Fold: 0.550 Sensitivity MXScarna(20): 0.551 Fold: 0.541 Positive Predictive Value MXScarna(20): 0.712 Fold: 0.560 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.595 Fold: 0.552 Sensitivity MXScarna(seed): 0.475 Fold: 0.543 Positive Predictive Value MXScarna(seed): 0.747 Fold: 0.563 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.524 Fold: 0.495 Sensitivity MaxExpect: 0.511 Fold: 0.498 Positive Predictive Value MaxExpect: 0.538 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.522 Fold: 0.495 Sensitivity ProbKnot: 0.518 Fold: 0.498 Positive Predictive Value ProbKnot: 0.527 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.543 Fold: 0.451 Sensitivity RNASampler(20): 0.425 Fold: 0.454 Positive Predictive Value RNASampler(20): 0.695 Fold: 0.450 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.514 Fold: 0.495 Sensitivity Sfold: 0.463 Fold: 0.498 Positive Predictive Value Sfold: 0.571 Fold: 0.493 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.548 Fold: 0.543 Sensitivity Murlet(20): 0.415 Fold: 0.536 Positive Predictive Value Murlet(20): 0.725 Fold: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 6.93152570412e-05	+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.495 UNAFold: 0.475 Sensitivity Fold: 0.498 UNAFold: 0.473 Positive Predictive Value Fold: 0.493 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.495 PknotsRG: 0.476 Sensitivity Fold: 0.498 PknotsRG: 0.478 Positive Predictive Value Fold: 0.493 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.495 RNAfold: 0.474 Sensitivity Fold: 0.498 RNAfold: 0.477 Positive Predictive Value Fold: 0.493 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.518 Afold: 0.494 Sensitivity Fold: 0.517 Afold: 0.490 Positive Predictive Value Fold: 0.520 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.499 RNAsubopt: 0.475 Sensitivity Fold: 0.502 RNAsubopt: 0.482 Positive Predictive Value Fold: 0.499 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.495 McQFold: 0.450 Sensitivity Fold: 0.498 McQFold: 0.441 Positive Predictive Value Fold: 0.493 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.550 CMfinder(20): 0.479 Sensitivity Fold: 0.541 CMfinder(20): 0.308 Positive Predictive Value Fold: 0.560 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.495 RNASLOpt: 0.446 Sensitivity Fold: 0.497 RNASLOpt: 0.421 Positive Predictive Value Fold: 0.496 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.551 RNAalifold(seed): 0.469 Sensitivity Fold: 0.542 RNAalifold(seed): 0.272 Positive Predictive Value Fold: 0.562 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.498 RNAshapes: 0.408 Sensitivity Fold: 0.500 RNAshapes: 0.404 Positive Predictive Value Fold: 0.498 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.495 CRWrnafold: 0.417 Sensitivity Fold: 0.498 CRWrnafold: 0.421 Positive Predictive Value Fold: 0.493 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.496 Vsfold4: 0.335 Sensitivity Fold: 0.498 Vsfold4: 0.308 Positive Predictive Value Fold: 0.496 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.495 RNAwolf: 0.332 Sensitivity Fold: 0.498 RNAwolf: 0.347 Positive Predictive Value Fold: 0.493 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.498 Vsfold5: 0.329 Sensitivity Fold: 0.499 Vsfold5: 0.312 Positive Predictive Value Fold: 0.497 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.510 CMfinder(seed): 0.350 Sensitivity Fold: 0.516 CMfinder(seed): 0.159 Positive Predictive Value Fold: 0.505 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.550 Carnac(20): 0.360 Sensitivity Fold: 0.541 Carnac(20): 0.151 Positive Predictive Value Fold: 0.560 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.550 RSpredict(20): 0.347 Sensitivity Fold: 0.541 RSpredict(20): 0.220 Positive Predictive Value Fold: 0.560 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.511 NanoFolder: 0.172 Sensitivity Fold: 0.511 NanoFolder: 0.204 Positive Predictive Value Fold: 0.512 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.552 RSpredict(seed): 0.045 Sensitivity Fold: 0.543 RSpredict(seed): 0.011 Positive Predictive Value Fold: 0.563 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: N/A Murlet(seed): N/A Sensitivity Fold: N/A Murlet(seed): N/A Positive Predictive Value Fold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs Multilign(seed) Matthews Correlation Coefficient Fold: N/A Multilign(seed): N/A Sensitivity Fold: N/A Multilign(seed): N/A Positive Predictive Value Fold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs HotKnots Matthews Correlation Coefficient Fold: N/A HotKnots: N/A Sensitivity Fold: N/A HotKnots: N/A Positive Predictive Value Fold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs Pknots Matthews Correlation Coefficient Fold: N/A Pknots: N/A Sensitivity Fold: N/A Pknots: N/A Positive Predictive Value Fold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.597 Cylofold: 0.271 Sensitivity Fold: 0.591 Cylofold: 0.241 Positive Predictive Value Fold: 0.604 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Fold vs MCFold Matthews Correlation Coefficient Fold: N/A MCFold: N/A Sensitivity Fold: N/A MCFold: N/A Positive Predictive Value Fold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: N/A PPfold(seed): N/A Sensitivity Fold: N/A PPfold(seed): N/A Positive Predictive Value Fold: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs RDfolder Matthews Correlation Coefficient Fold: N/A RDfolder: N/A Sensitivity Fold: N/A RDfolder: N/A Positive Predictive Value Fold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.710 Fold: 0.651 Sensitivity TurboFold(seed): 0.677 Fold: 0.662 Positive Predictive Value TurboFold(seed): 0.746 Fold: 0.642 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Fold vs RNASampler(seed) Matthews Correlation Coefficient Fold: N/A RNASampler(seed): N/A Sensitivity Fold: N/A RNASampler(seed): N/A Positive Predictive Value Fold: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs Alterna Matthews Correlation Coefficient Fold: N/A Alterna: N/A Sensitivity Fold: N/A Alterna: N/A Positive Predictive Value Fold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.488 Carnac(seed): 0.000 Sensitivity Fold: 0.493 Carnac(seed): 0.000 Positive Predictive Value Fold: 0.484 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.550 Mastr(20): 0.000 Sensitivity Fold: 0.541 Mastr(20): 0.000 Positive Predictive Value Fold: 0.560 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.550 Mastr(seed): 0.000 Sensitivity Fold: 0.542 Mastr(seed): 0.000 Positive Predictive Value Fold: 0.559 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(20)	145 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.823 Murlet(20): 0.548 Sensitivity ContextFold: 0.774 Murlet(20): 0.415 Positive Predictive Value ContextFold: 0.876 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.748 Murlet(20): 0.548 Sensitivity PETfold_pre2.0(seed): 0.668 Murlet(20): 0.415 Positive Predictive Value PETfold_pre2.0(seed): 0.837 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.729 Murlet(20): 0.548 Sensitivity TurboFold(20): 0.674 Murlet(20): 0.415 Positive Predictive Value TurboFold(20): 0.789 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.724 Murlet(20): 0.548 Sensitivity PETfold_pre2.0(20): 0.643 Murlet(20): 0.415 Positive Predictive Value PETfold_pre2.0(20): 0.815 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	143 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.725 Murlet(20): 0.552 Sensitivity PPfold(20): 0.626 Murlet(20): 0.419 Positive Predictive Value PPfold(20): 0.841 Murlet(20): 0.729 Number of pairs reference - predicted secondary structure: 143 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.716 Murlet(20): 0.548 Sensitivity CentroidAlifold(20): 0.566 Murlet(20): 0.415 Positive Predictive Value CentroidAlifold(20): 0.907 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 Murlet(20): 0.533 Sensitivity CentroidAlifold(seed): 0.554 Murlet(20): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.951 Murlet(20): 0.732 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.695 Murlet(20): 0.548 Sensitivity CentroidHomfold‑LAST: 0.545 Murlet(20): 0.415 Positive Predictive Value CentroidHomfold‑LAST: 0.887 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.663 Murlet(20): 0.548 Sensitivity RNAalifold(20): 0.542 Murlet(20): 0.415 Positive Predictive Value RNAalifold(20): 0.814 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.644 Murlet(20): 0.548 Sensitivity IPknot: 0.570 Murlet(20): 0.415 Positive Predictive Value IPknot: 0.730 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	133 Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.651 Murlet(20): 0.545 Sensitivity Multilign(20): 0.593 Murlet(20): 0.412 Positive Predictive Value Multilign(20): 0.717 Murlet(20): 0.722 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.604 Murlet(20): 0.548 Sensitivity CentroidFold: 0.536 Murlet(20): 0.415 Positive Predictive Value CentroidFold: 0.682 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Contrafold vs Murlet(20) Matthews Correlation Coefficient Contrafold: 0.587 Murlet(20): 0.548 Sensitivity Contrafold: 0.564 Murlet(20): 0.415 Positive Predictive Value Contrafold: 0.613 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.610 Murlet(20): 0.548 Sensitivity MXScarna(20): 0.543 Murlet(20): 0.415 Positive Predictive Value MXScarna(20): 0.688 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.661 Murlet(20): 0.533 Sensitivity MXScarna(seed): 0.553 Murlet(20): 0.389 Positive Predictive Value MXScarna(seed): 0.793 Murlet(20): 0.732 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.574 Murlet(20): 0.548 Sensitivity MaxExpect: 0.551 Murlet(20): 0.415 Positive Predictive Value MaxExpect: 0.601 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.573 Murlet(20): 0.548 Sensitivity ProbKnot: 0.555 Murlet(20): 0.415 Positive Predictive Value ProbKnot: 0.593 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.575 RNASampler(20): 0.545 Sensitivity Murlet(20): 0.471 RNASampler(20): 0.429 Positive Predictive Value Murlet(20): 0.702 RNASampler(20): 0.695 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 5.23657817852e-08	145 Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.550 Murlet(20): 0.548 Sensitivity Sfold: 0.483 Murlet(20): 0.415 Positive Predictive Value Sfold: 0.628 Murlet(20): 0.725 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 0.0265675133358	145 Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.548 Fold: 0.543 Sensitivity Murlet(20): 0.415 Fold: 0.536 Positive Predictive Value Murlet(20): 0.725 Fold: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 6.93152570412e-05		+ Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.548 UNAFold: 0.512 Sensitivity Murlet(20): 0.415 UNAFold: 0.503 Positive Predictive Value Murlet(20): 0.725 UNAFold: 0.523 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.548 PknotsRG: 0.494 Sensitivity Murlet(20): 0.415 PknotsRG: 0.487 Positive Predictive Value Murlet(20): 0.725 PknotsRG: 0.502 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.548 RNAfold: 0.511 Sensitivity Murlet(20): 0.415 RNAfold: 0.505 Positive Predictive Value Murlet(20): 0.725 RNAfold: 0.519 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Afold vs Murlet(20) Matthews Correlation Coefficient Afold: 0.540 Murlet(20): 0.523 Sensitivity Afold: 0.527 Murlet(20): 0.382 Positive Predictive Value Afold: 0.556 Murlet(20): 0.717 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.548 RNAsubopt: 0.499 Sensitivity Murlet(20): 0.415 RNAsubopt: 0.499 Positive Predictive Value Murlet(20): 0.725 RNAsubopt: 0.501 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.548 McQFold: 0.437 Sensitivity Murlet(20): 0.415 McQFold: 0.421 Positive Predictive Value Murlet(20): 0.725 McQFold: 0.456 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.548 CMfinder(20): 0.462 Sensitivity Murlet(20): 0.415 CMfinder(20): 0.294 Positive Predictive Value Murlet(20): 0.725 CMfinder(20): 0.729 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.555 RNASLOpt: 0.434 Sensitivity Murlet(20): 0.424 RNASLOpt: 0.403 Positive Predictive Value Murlet(20): 0.727 RNASLOpt: 0.470 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.533 RNAalifold(seed): 0.456 Sensitivity Murlet(20): 0.389 RNAalifold(seed): 0.260 Positive Predictive Value Murlet(20): 0.732 RNAalifold(seed): 0.802 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.553 RNAshapes: 0.431 Sensitivity Murlet(20): 0.419 RNAshapes: 0.419 Positive Predictive Value Murlet(20): 0.732 RNAshapes: 0.446 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.548 CRWrnafold: 0.434 Sensitivity Murlet(20): 0.415 CRWrnafold: 0.428 Positive Predictive Value Murlet(20): 0.725 CRWrnafold: 0.443 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.551 Vsfold4: 0.371 Sensitivity Murlet(20): 0.419 Vsfold4: 0.337 Positive Predictive Value Murlet(20): 0.728 Vsfold4: 0.412 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.548 RNAwolf: 0.352 Sensitivity Murlet(20): 0.415 RNAwolf: 0.364 Positive Predictive Value Murlet(20): 0.725 RNAwolf: 0.343 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.553 Vsfold5: 0.350 Sensitivity Murlet(20): 0.420 Vsfold5: 0.325 Positive Predictive Value Murlet(20): 0.729 Vsfold5: 0.379 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.548 Carnac(20): 0.387 Sensitivity Murlet(20): 0.415 Carnac(20): 0.175 Positive Predictive Value Murlet(20): 0.725 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.548 RSpredict(20): 0.378 Sensitivity Murlet(20): 0.415 RSpredict(20): 0.254 Positive Predictive Value Murlet(20): 0.725 RSpredict(20): 0.565 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.539 NanoFolder: 0.151 Sensitivity Murlet(20): 0.402 NanoFolder: 0.174 Positive Predictive Value Murlet(20): 0.723 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.533 RSpredict(seed): 0.059 Sensitivity Murlet(20): 0.389 RSpredict(seed): 0.015 Positive Predictive Value Murlet(20): 0.732 RSpredict(seed): 0.233 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs Murlet(20) Matthews Correlation Coefficient HotKnots: N/A Murlet(20): N/A Sensitivity HotKnots: N/A Murlet(20): N/A Positive Predictive Value HotKnots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Murlet(20) Matthews Correlation Coefficient Pknots: N/A Murlet(20): N/A Sensitivity Pknots: N/A Murlet(20): N/A Positive Predictive Value Pknots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: N/A Murlet(20): N/A Sensitivity Cylofold: N/A Murlet(20): N/A Positive Predictive Value Cylofold: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): N/A MCFold: N/A Sensitivity Murlet(20): N/A MCFold: N/A Positive Predictive Value Murlet(20): N/A MCFold: 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	? RDfolder vs Murlet(20) Matthews Correlation Coefficient RDfolder: N/A Murlet(20): N/A Sensitivity RDfolder: N/A Murlet(20): N/A Positive Predictive Value RDfolder: 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 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	? 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	? Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): N/A Alterna: N/A Sensitivity Murlet(20): N/A Alterna: N/A Positive Predictive Value Murlet(20): N/A Alterna: 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): 0.333 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.243 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.456 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.548 Mastr(20): 0.000 Sensitivity Murlet(20): 0.415 Mastr(20): 0.000 Positive Predictive Value Murlet(20): 0.725 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.537 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.394 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.734 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08
UNAFold	610 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.718 UNAFold: 0.475 Sensitivity ContextFold: 0.677 UNAFold: 0.473 Positive Predictive Value ContextFold: 0.763 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 UNAFold: 0.474 Sensitivity PETfold_pre2.0(seed): 0.590 UNAFold: 0.470 Positive Predictive Value PETfold_pre2.0(seed): 0.787 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.740 UNAFold: 0.531 Sensitivity TurboFold(20): 0.685 UNAFold: 0.519 Positive Predictive Value TurboFold(20): 0.801 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 UNAFold: 0.531 Sensitivity PETfold_pre2.0(20): 0.652 UNAFold: 0.519 Positive Predictive Value PETfold_pre2.0(20): 0.829 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.734 UNAFold: 0.531 Sensitivity PPfold(20): 0.635 UNAFold: 0.519 Positive Predictive Value PPfold(20): 0.850 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 UNAFold: 0.531 Sensitivity CentroidAlifold(20): 0.561 UNAFold: 0.519 Positive Predictive Value CentroidAlifold(20): 0.916 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 UNAFold: 0.544 Sensitivity CentroidAlifold(seed): 0.521 UNAFold: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.919 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 UNAFold: 0.479 Sensitivity CentroidHomfold‑LAST: 0.469 UNAFold: 0.476 Positive Predictive Value CentroidHomfold‑LAST: 0.877 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.660 UNAFold: 0.531 Sensitivity RNAalifold(20): 0.532 UNAFold: 0.519 Positive Predictive Value RNAalifold(20): 0.819 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.602 UNAFold: 0.475 Sensitivity IPknot: 0.545 UNAFold: 0.473 Positive Predictive Value IPknot: 0.667 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.649 UNAFold: 0.532 Sensitivity Multilign(20): 0.590 UNAFold: 0.520 Positive Predictive Value Multilign(20): 0.717 UNAFold: 0.546 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.571 UNAFold: 0.475 Sensitivity CentroidFold: 0.516 UNAFold: 0.473 Positive Predictive Value CentroidFold: 0.635 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.554 UNAFold: 0.475 Sensitivity Contrafold: 0.540 UNAFold: 0.473 Positive Predictive Value Contrafold: 0.569 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.626 UNAFold: 0.531 Sensitivity MXScarna(20): 0.551 UNAFold: 0.519 Positive Predictive Value MXScarna(20): 0.712 UNAFold: 0.545 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.595 UNAFold: 0.544 Sensitivity MXScarna(seed): 0.475 UNAFold: 0.530 Positive Predictive Value MXScarna(seed): 0.747 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.524 UNAFold: 0.475 Sensitivity MaxExpect: 0.511 UNAFold: 0.473 Positive Predictive Value MaxExpect: 0.538 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.522 UNAFold: 0.475 Sensitivity ProbKnot: 0.518 UNAFold: 0.473 Positive Predictive Value ProbKnot: 0.527 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.543 UNAFold: 0.370 Sensitivity RNASampler(20): 0.425 UNAFold: 0.372 Positive Predictive Value RNASampler(20): 0.695 UNAFold: 0.370 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.514 UNAFold: 0.475 Sensitivity Sfold: 0.463 UNAFold: 0.473 Positive Predictive Value Sfold: 0.571 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.495 UNAFold: 0.475 Sensitivity Fold: 0.498 UNAFold: 0.473 Positive Predictive Value Fold: 0.493 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.548 UNAFold: 0.512 Sensitivity Murlet(20): 0.415 UNAFold: 0.503 Positive Predictive Value Murlet(20): 0.725 UNAFold: 0.523 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08		= PknotsRG vs UNAFold Matthews Correlation Coefficient PknotsRG: 0.476 UNAFold: 0.475 Sensitivity PknotsRG: 0.478 UNAFold: 0.473 Positive Predictive Value PknotsRG: 0.475 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 0.00353686086758	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.475 RNAfold: 0.474 Sensitivity UNAFold: 0.473 RNAfold: 0.477 Positive Predictive Value UNAFold: 0.479 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.5012140095e-07	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.511 Afold: 0.494 Sensitivity UNAFold: 0.505 Afold: 0.490 Positive Predictive Value UNAFold: 0.518 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.479 RNAsubopt: 0.475 Sensitivity UNAFold: 0.476 RNAsubopt: 0.482 Positive Predictive Value UNAFold: 0.484 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.475 McQFold: 0.450 Sensitivity UNAFold: 0.473 McQFold: 0.441 Positive Predictive Value UNAFold: 0.479 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.531 CMfinder(20): 0.479 Sensitivity UNAFold: 0.519 CMfinder(20): 0.308 Positive Predictive Value UNAFold: 0.545 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.470 RNASLOpt: 0.446 Sensitivity UNAFold: 0.467 RNASLOpt: 0.421 Positive Predictive Value UNAFold: 0.475 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.544 RNAalifold(seed): 0.469 Sensitivity UNAFold: 0.530 RNAalifold(seed): 0.272 Positive Predictive Value UNAFold: 0.560 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.475 RNAshapes: 0.408 Sensitivity UNAFold: 0.472 RNAshapes: 0.404 Positive Predictive Value UNAFold: 0.480 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.475 CRWrnafold: 0.417 Sensitivity UNAFold: 0.473 CRWrnafold: 0.421 Positive Predictive Value UNAFold: 0.479 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.474 Vsfold4: 0.335 Sensitivity UNAFold: 0.471 Vsfold4: 0.308 Positive Predictive Value UNAFold: 0.479 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.475 RNAwolf: 0.332 Sensitivity UNAFold: 0.473 RNAwolf: 0.347 Positive Predictive Value UNAFold: 0.479 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.474 Vsfold5: 0.329 Sensitivity UNAFold: 0.470 Vsfold5: 0.312 Positive Predictive Value UNAFold: 0.479 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.487 CMfinder(seed): 0.350 Sensitivity UNAFold: 0.480 CMfinder(seed): 0.159 Positive Predictive Value UNAFold: 0.495 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.531 Carnac(20): 0.360 Sensitivity UNAFold: 0.519 Carnac(20): 0.151 Positive Predictive Value UNAFold: 0.545 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.531 RSpredict(20): 0.347 Sensitivity UNAFold: 0.519 RSpredict(20): 0.220 Positive Predictive Value UNAFold: 0.545 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.498 NanoFolder: 0.172 Sensitivity UNAFold: 0.493 NanoFolder: 0.204 Positive Predictive Value UNAFold: 0.505 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.544 RSpredict(seed): 0.045 Sensitivity UNAFold: 0.531 RSpredict(seed): 0.011 Positive Predictive Value UNAFold: 0.560 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: N/A Murlet(seed): N/A Sensitivity UNAFold: N/A Murlet(seed): N/A Positive Predictive Value UNAFold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs Multilign(seed) Matthews Correlation Coefficient UNAFold: N/A Multilign(seed): N/A Sensitivity UNAFold: N/A Multilign(seed): N/A Positive Predictive Value UNAFold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: N/A HotKnots: N/A Sensitivity UNAFold: N/A HotKnots: N/A Positive Predictive Value UNAFold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: N/A Pknots: N/A Sensitivity UNAFold: N/A Pknots: N/A Positive Predictive Value UNAFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.443 Cylofold: 0.271 Sensitivity UNAFold: 0.431 Cylofold: 0.241 Positive Predictive Value UNAFold: 0.457 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: N/A MCFold: N/A Sensitivity UNAFold: N/A MCFold: N/A Positive Predictive Value UNAFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: N/A PPfold(seed): N/A Sensitivity UNAFold: N/A PPfold(seed): N/A Positive Predictive Value UNAFold: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: N/A RDfolder: N/A Sensitivity UNAFold: N/A RDfolder: N/A Positive Predictive Value UNAFold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.710 UNAFold: 0.594 Sensitivity TurboFold(seed): 0.677 UNAFold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 UNAFold: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: N/A RNASampler(seed): N/A Sensitivity UNAFold: N/A RNASampler(seed): N/A Positive Predictive Value UNAFold: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: N/A Alterna: N/A Sensitivity UNAFold: N/A Alterna: N/A Positive Predictive Value UNAFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.486 Carnac(seed): 0.000 Sensitivity UNAFold: 0.486 Carnac(seed): 0.000 Positive Predictive Value UNAFold: 0.488 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.531 Mastr(20): 0.000 Sensitivity UNAFold: 0.519 Mastr(20): 0.000 Positive Predictive Value UNAFold: 0.545 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.540 Mastr(seed): 0.000 Sensitivity UNAFold: 0.528 Mastr(seed): 0.000 Positive Predictive Value UNAFold: 0.554 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	610 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.718 PknotsRG: 0.476 Sensitivity ContextFold: 0.677 PknotsRG: 0.478 Positive Predictive Value ContextFold: 0.763 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 PknotsRG: 0.472 Sensitivity PETfold_pre2.0(seed): 0.590 PknotsRG: 0.472 Positive Predictive Value PETfold_pre2.0(seed): 0.787 PknotsRG: 0.473 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.740 PknotsRG: 0.512 Sensitivity TurboFold(20): 0.685 PknotsRG: 0.503 Positive Predictive Value TurboFold(20): 0.801 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 PknotsRG: 0.512 Sensitivity PETfold_pre2.0(20): 0.652 PknotsRG: 0.503 Positive Predictive Value PETfold_pre2.0(20): 0.829 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.734 PknotsRG: 0.511 Sensitivity PPfold(20): 0.635 PknotsRG: 0.502 Positive Predictive Value PPfold(20): 0.850 PknotsRG: 0.522 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.717 PknotsRG: 0.512 Sensitivity CentroidAlifold(20): 0.561 PknotsRG: 0.503 Positive Predictive Value CentroidAlifold(20): 0.916 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 PknotsRG: 0.527 Sensitivity CentroidAlifold(seed): 0.521 PknotsRG: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.919 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 PknotsRG: 0.478 Sensitivity CentroidHomfold‑LAST: 0.469 PknotsRG: 0.479 Positive Predictive Value CentroidHomfold‑LAST: 0.877 PknotsRG: 0.479 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.660 PknotsRG: 0.512 Sensitivity RNAalifold(20): 0.532 PknotsRG: 0.503 Positive Predictive Value RNAalifold(20): 0.819 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.602 PknotsRG: 0.476 Sensitivity IPknot: 0.545 PknotsRG: 0.478 Positive Predictive Value IPknot: 0.667 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.649 PknotsRG: 0.510 Sensitivity Multilign(20): 0.590 PknotsRG: 0.501 Positive Predictive Value Multilign(20): 0.717 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.571 PknotsRG: 0.476 Sensitivity CentroidFold: 0.516 PknotsRG: 0.478 Positive Predictive Value CentroidFold: 0.635 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.554 PknotsRG: 0.476 Sensitivity Contrafold: 0.540 PknotsRG: 0.478 Positive Predictive Value Contrafold: 0.569 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.626 PknotsRG: 0.512 Sensitivity MXScarna(20): 0.551 PknotsRG: 0.503 Positive Predictive Value MXScarna(20): 0.712 PknotsRG: 0.523 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.595 PknotsRG: 0.527 Sensitivity MXScarna(seed): 0.475 PknotsRG: 0.517 Positive Predictive Value MXScarna(seed): 0.747 PknotsRG: 0.539 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.524 PknotsRG: 0.476 Sensitivity MaxExpect: 0.511 PknotsRG: 0.478 Positive Predictive Value MaxExpect: 0.538 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.522 PknotsRG: 0.476 Sensitivity ProbKnot: 0.518 PknotsRG: 0.478 Positive Predictive Value ProbKnot: 0.527 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.543 PknotsRG: 0.389 Sensitivity RNASampler(20): 0.425 PknotsRG: 0.395 Positive Predictive Value RNASampler(20): 0.695 PknotsRG: 0.385 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.514 PknotsRG: 0.476 Sensitivity Sfold: 0.463 PknotsRG: 0.478 Positive Predictive Value Sfold: 0.571 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.495 PknotsRG: 0.476 Sensitivity Fold: 0.498 PknotsRG: 0.478 Positive Predictive Value Fold: 0.493 PknotsRG: 0.475 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.548 PknotsRG: 0.494 Sensitivity Murlet(20): 0.415 PknotsRG: 0.487 Positive Predictive Value Murlet(20): 0.725 PknotsRG: 0.502 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 PknotsRG vs UNAFold Matthews Correlation Coefficient PknotsRG: 0.476 UNAFold: 0.475 Sensitivity PknotsRG: 0.478 UNAFold: 0.473 Positive Predictive Value PknotsRG: 0.475 UNAFold: 0.479 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 0.00353686086758		+ PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.476 RNAfold: 0.474 Sensitivity PknotsRG: 0.478 RNAfold: 0.477 Positive Predictive Value PknotsRG: 0.475 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 9.49173053431e-08	+ PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.502 Afold: 0.494 Sensitivity PknotsRG: 0.500 Afold: 0.490 Positive Predictive Value PknotsRG: 0.506 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.478 RNAsubopt: 0.475 Sensitivity PknotsRG: 0.479 RNAsubopt: 0.482 Positive Predictive Value PknotsRG: 0.479 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.476 McQFold: 0.450 Sensitivity PknotsRG: 0.478 McQFold: 0.441 Positive Predictive Value PknotsRG: 0.475 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.512 CMfinder(20): 0.479 Sensitivity PknotsRG: 0.503 CMfinder(20): 0.308 Positive Predictive Value PknotsRG: 0.523 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.467 RNASLOpt: 0.446 Sensitivity PknotsRG: 0.468 RNASLOpt: 0.421 Positive Predictive Value PknotsRG: 0.468 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.527 RNAalifold(seed): 0.469 Sensitivity PknotsRG: 0.516 RNAalifold(seed): 0.272 Positive Predictive Value PknotsRG: 0.539 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.474 RNAshapes: 0.408 Sensitivity PknotsRG: 0.475 RNAshapes: 0.404 Positive Predictive Value PknotsRG: 0.476 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.476 CRWrnafold: 0.417 Sensitivity PknotsRG: 0.478 CRWrnafold: 0.421 Positive Predictive Value PknotsRG: 0.475 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.473 Vsfold4: 0.335 Sensitivity PknotsRG: 0.474 Vsfold4: 0.308 Positive Predictive Value PknotsRG: 0.474 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.476 RNAwolf: 0.332 Sensitivity PknotsRG: 0.478 RNAwolf: 0.347 Positive Predictive Value PknotsRG: 0.475 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.473 Vsfold5: 0.329 Sensitivity PknotsRG: 0.473 Vsfold5: 0.312 Positive Predictive Value PknotsRG: 0.473 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.503 CMfinder(seed): 0.350 Sensitivity PknotsRG: 0.510 CMfinder(seed): 0.159 Positive Predictive Value PknotsRG: 0.496 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.512 Carnac(20): 0.360 Sensitivity PknotsRG: 0.503 Carnac(20): 0.151 Positive Predictive Value PknotsRG: 0.523 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.512 RSpredict(20): 0.347 Sensitivity PknotsRG: 0.503 RSpredict(20): 0.220 Positive Predictive Value PknotsRG: 0.523 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.488 NanoFolder: 0.172 Sensitivity PknotsRG: 0.488 NanoFolder: 0.204 Positive Predictive Value PknotsRG: 0.490 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.527 RSpredict(seed): 0.045 Sensitivity PknotsRG: 0.517 RSpredict(seed): 0.011 Positive Predictive Value PknotsRG: 0.539 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: N/A Murlet(seed): N/A Sensitivity PknotsRG: N/A Murlet(seed): N/A Positive Predictive Value PknotsRG: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: N/A Multilign(seed): N/A Sensitivity PknotsRG: N/A Multilign(seed): N/A Positive Predictive Value PknotsRG: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: N/A HotKnots: N/A Sensitivity PknotsRG: N/A HotKnots: N/A Positive Predictive Value PknotsRG: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: N/A Pknots: N/A Sensitivity PknotsRG: N/A Pknots: N/A Positive Predictive Value PknotsRG: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.437 Cylofold: 0.271 Sensitivity PknotsRG: 0.438 Cylofold: 0.241 Positive Predictive Value PknotsRG: 0.438 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: N/A MCFold: N/A Sensitivity PknotsRG: N/A MCFold: N/A Positive Predictive Value PknotsRG: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: N/A PPfold(seed): N/A Sensitivity PknotsRG: N/A PPfold(seed): N/A Positive Predictive Value PknotsRG: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: N/A RDfolder: N/A Sensitivity PknotsRG: N/A RDfolder: N/A Positive Predictive Value PknotsRG: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs PknotsRG Matthews Correlation Coefficient TurboFold(seed): 0.710 PknotsRG: 0.594 Sensitivity TurboFold(seed): 0.677 PknotsRG: 0.600 Positive Predictive Value TurboFold(seed): 0.746 PknotsRG: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: N/A RNASampler(seed): N/A Sensitivity PknotsRG: N/A RNASampler(seed): N/A Positive Predictive Value PknotsRG: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: N/A Alterna: N/A Sensitivity PknotsRG: N/A Alterna: N/A Positive Predictive Value PknotsRG: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.487 Carnac(seed): 0.000 Sensitivity PknotsRG: 0.493 Carnac(seed): 0.000 Positive Predictive Value PknotsRG: 0.483 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.512 Mastr(20): 0.000 Sensitivity PknotsRG: 0.503 Mastr(20): 0.000 Positive Predictive Value PknotsRG: 0.523 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.523 Mastr(seed): 0.000 Sensitivity PknotsRG: 0.515 Mastr(seed): 0.000 Positive Predictive Value PknotsRG: 0.533 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	610 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.718 RNAfold: 0.474 Sensitivity ContextFold: 0.677 RNAfold: 0.477 Positive Predictive Value ContextFold: 0.763 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNAfold: 0.475 Sensitivity PETfold_pre2.0(seed): 0.590 RNAfold: 0.476 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAfold: 0.477 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.740 RNAfold: 0.527 Sensitivity TurboFold(20): 0.685 RNAfold: 0.518 Positive Predictive Value TurboFold(20): 0.801 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAfold: 0.527 Sensitivity PETfold_pre2.0(20): 0.652 RNAfold: 0.518 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.734 RNAfold: 0.527 Sensitivity PPfold(20): 0.635 RNAfold: 0.518 Positive Predictive Value PPfold(20): 0.850 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAfold: 0.527 Sensitivity CentroidAlifold(20): 0.561 RNAfold: 0.518 Positive Predictive Value CentroidAlifold(20): 0.916 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RNAfold: 0.535 Sensitivity CentroidAlifold(seed): 0.521 RNAfold: 0.524 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAfold: 0.480 Sensitivity CentroidHomfold‑LAST: 0.469 RNAfold: 0.481 Positive Predictive Value CentroidHomfold‑LAST: 0.877 RNAfold: 0.480 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.660 RNAfold: 0.527 Sensitivity RNAalifold(20): 0.532 RNAfold: 0.518 Positive Predictive Value RNAalifold(20): 0.819 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.602 RNAfold: 0.474 Sensitivity IPknot: 0.545 RNAfold: 0.477 Positive Predictive Value IPknot: 0.667 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.649 RNAfold: 0.527 Sensitivity Multilign(20): 0.590 RNAfold: 0.519 Positive Predictive Value Multilign(20): 0.717 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.571 RNAfold: 0.474 Sensitivity CentroidFold: 0.516 RNAfold: 0.477 Positive Predictive Value CentroidFold: 0.635 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.554 RNAfold: 0.474 Sensitivity Contrafold: 0.540 RNAfold: 0.477 Positive Predictive Value Contrafold: 0.569 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.626 RNAfold: 0.527 Sensitivity MXScarna(20): 0.551 RNAfold: 0.518 Positive Predictive Value MXScarna(20): 0.712 RNAfold: 0.537 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.595 RNAfold: 0.536 Sensitivity MXScarna(seed): 0.475 RNAfold: 0.525 Positive Predictive Value MXScarna(seed): 0.747 RNAfold: 0.548 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.524 RNAfold: 0.474 Sensitivity MaxExpect: 0.511 RNAfold: 0.477 Positive Predictive Value MaxExpect: 0.538 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.522 RNAfold: 0.474 Sensitivity ProbKnot: 0.518 RNAfold: 0.477 Positive Predictive Value ProbKnot: 0.527 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.543 RNAfold: 0.390 Sensitivity RNASampler(20): 0.425 RNAfold: 0.397 Positive Predictive Value RNASampler(20): 0.695 RNAfold: 0.386 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.514 RNAfold: 0.474 Sensitivity Sfold: 0.463 RNAfold: 0.477 Positive Predictive Value Sfold: 0.571 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.495 RNAfold: 0.474 Sensitivity Fold: 0.498 RNAfold: 0.477 Positive Predictive Value Fold: 0.493 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.548 RNAfold: 0.511 Sensitivity Murlet(20): 0.415 RNAfold: 0.505 Positive Predictive Value Murlet(20): 0.725 RNAfold: 0.519 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.475 RNAfold: 0.474 Sensitivity UNAFold: 0.473 RNAfold: 0.477 Positive Predictive Value UNAFold: 0.479 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.5012140095e-07	610 PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.476 RNAfold: 0.474 Sensitivity PknotsRG: 0.478 RNAfold: 0.477 Positive Predictive Value PknotsRG: 0.475 RNAfold: 0.473 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 9.49173053431e-08		+ RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.505 Afold: 0.494 Sensitivity RNAfold: 0.503 Afold: 0.490 Positive Predictive Value RNAfold: 0.509 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.480 RNAsubopt: 0.475 Sensitivity RNAfold: 0.481 RNAsubopt: 0.482 Positive Predictive Value RNAfold: 0.480 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.474 McQFold: 0.450 Sensitivity RNAfold: 0.477 McQFold: 0.441 Positive Predictive Value RNAfold: 0.473 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.527 CMfinder(20): 0.479 Sensitivity RNAfold: 0.518 CMfinder(20): 0.308 Positive Predictive Value RNAfold: 0.537 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.472 RNASLOpt: 0.446 Sensitivity RNAfold: 0.473 RNASLOpt: 0.421 Positive Predictive Value RNAfold: 0.473 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.534 RNAalifold(seed): 0.469 Sensitivity RNAfold: 0.523 RNAalifold(seed): 0.272 Positive Predictive Value RNAfold: 0.547 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.476 RNAshapes: 0.408 Sensitivity RNAfold: 0.477 RNAshapes: 0.404 Positive Predictive Value RNAfold: 0.477 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.474 CRWrnafold: 0.417 Sensitivity RNAfold: 0.477 CRWrnafold: 0.421 Positive Predictive Value RNAfold: 0.473 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.475 Vsfold4: 0.335 Sensitivity RNAfold: 0.476 Vsfold4: 0.308 Positive Predictive Value RNAfold: 0.476 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.474 RNAwolf: 0.332 Sensitivity RNAfold: 0.477 RNAwolf: 0.347 Positive Predictive Value RNAfold: 0.473 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.474 Vsfold5: 0.329 Sensitivity RNAfold: 0.475 Vsfold5: 0.312 Positive Predictive Value RNAfold: 0.475 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.466 CMfinder(seed): 0.350 Sensitivity RNAfold: 0.468 CMfinder(seed): 0.159 Positive Predictive Value RNAfold: 0.465 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ RNAfold vs Carnac(20) Matthews Correlation Coefficient RNAfold: 0.527 Carnac(20): 0.360 Sensitivity RNAfold: 0.518 Carnac(20): 0.151 Positive Predictive Value RNAfold: 0.537 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.527 RSpredict(20): 0.347 Sensitivity RNAfold: 0.518 RSpredict(20): 0.220 Positive Predictive Value RNAfold: 0.537 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.493 NanoFolder: 0.172 Sensitivity RNAfold: 0.492 NanoFolder: 0.204 Positive Predictive Value RNAfold: 0.497 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.535 RSpredict(seed): 0.045 Sensitivity RNAfold: 0.525 RSpredict(seed): 0.011 Positive Predictive Value RNAfold: 0.548 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs RNAfold Matthews Correlation Coefficient Murlet(seed): N/A RNAfold: N/A Sensitivity Murlet(seed): N/A RNAfold: N/A Positive Predictive Value Murlet(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): N/A RNAfold: N/A Sensitivity Multilign(seed): N/A RNAfold: N/A Positive Predictive Value Multilign(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: N/A RNAfold: N/A Sensitivity HotKnots: N/A RNAfold: N/A Positive Predictive Value HotKnots: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs RNAfold Matthews Correlation Coefficient Pknots: N/A RNAfold: N/A Sensitivity Pknots: N/A RNAfold: N/A Positive Predictive Value Pknots: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.446 Cylofold: 0.271 Sensitivity RNAfold: 0.431 Cylofold: 0.241 Positive Predictive Value RNAfold: 0.465 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: N/A MCFold: N/A Sensitivity RNAfold: N/A MCFold: N/A Positive Predictive Value RNAfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs RNAfold Matthews Correlation Coefficient PPfold(seed): N/A RNAfold: N/A Sensitivity PPfold(seed): N/A RNAfold: N/A Positive Predictive Value PPfold(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: N/A RNAfold: N/A Sensitivity RDfolder: N/A RNAfold: N/A Positive Predictive Value RDfolder: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAfold: 0.594 Sensitivity TurboFold(seed): 0.677 RNAfold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 RNAfold: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): N/A RNAfold: N/A Sensitivity RNASampler(seed): N/A RNAfold: N/A Positive Predictive Value RNASampler(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAfold Matthews Correlation Coefficient Alterna: N/A RNAfold: N/A Sensitivity Alterna: N/A RNAfold: N/A Positive Predictive Value Alterna: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.475 Carnac(seed): 0.000 Sensitivity RNAfold: 0.479 Carnac(seed): 0.000 Positive Predictive Value RNAfold: 0.472 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.527 Mastr(20): 0.000 Sensitivity RNAfold: 0.518 Mastr(20): 0.000 Positive Predictive Value RNAfold: 0.537 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.532 Mastr(seed): 0.000 Sensitivity RNAfold: 0.523 Mastr(seed): 0.000 Positive Predictive Value RNAfold: 0.543 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
Afold	361 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.752 Afold: 0.494 Sensitivity ContextFold: 0.710 Afold: 0.490 Positive Predictive Value ContextFold: 0.797 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	281 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.704 Afold: 0.501 Sensitivity PETfold_pre2.0(seed): 0.613 Afold: 0.493 Positive Predictive Value PETfold_pre2.0(seed): 0.810 Afold: 0.510 Number of pairs reference - predicted secondary structure: 281 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.756 Afold: 0.548 Sensitivity TurboFold(20): 0.699 Afold: 0.533 Positive Predictive Value TurboFold(20): 0.818 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Afold: 0.548 Sensitivity PETfold_pre2.0(20): 0.662 Afold: 0.533 Positive Predictive Value PETfold_pre2.0(20): 0.844 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.746 Afold: 0.549 Sensitivity PPfold(20): 0.648 Afold: 0.534 Positive Predictive Value PPfold(20): 0.859 Afold: 0.566 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.718 Afold: 0.548 Sensitivity CentroidAlifold(20): 0.557 Afold: 0.533 Positive Predictive Value CentroidAlifold(20): 0.927 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	232 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Afold: 0.530 Sensitivity CentroidAlifold(seed): 0.516 Afold: 0.517 Positive Predictive Value CentroidAlifold(seed): 0.923 Afold: 0.544 Number of pairs reference - predicted secondary structure: 232 Wilcoxon single-rank test P-value: 3.56938820447e-08	329 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.656 Afold: 0.503 Sensitivity CentroidHomfold‑LAST: 0.488 Afold: 0.497 Positive Predictive Value CentroidHomfold‑LAST: 0.884 Afold: 0.511 Number of pairs reference - predicted secondary structure: 329 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.661 Afold: 0.548 Sensitivity RNAalifold(20): 0.527 Afold: 0.533 Positive Predictive Value RNAalifold(20): 0.831 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.620 Afold: 0.494 Sensitivity IPknot: 0.558 Afold: 0.490 Positive Predictive Value IPknot: 0.689 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	146 Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.653 Afold: 0.545 Sensitivity Multilign(20): 0.591 Afold: 0.531 Positive Predictive Value Multilign(20): 0.723 Afold: 0.562 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.596 Afold: 0.494 Sensitivity CentroidFold: 0.537 Afold: 0.490 Positive Predictive Value CentroidFold: 0.663 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.581 Afold: 0.494 Sensitivity Contrafold: 0.563 Afold: 0.490 Positive Predictive Value Contrafold: 0.600 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.641 Afold: 0.548 Sensitivity MXScarna(20): 0.554 Afold: 0.533 Positive Predictive Value MXScarna(20): 0.743 Afold: 0.564 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.591 Afold: 0.531 Sensitivity MXScarna(seed): 0.469 Afold: 0.518 Positive Predictive Value MXScarna(seed): 0.746 Afold: 0.545 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.553 Afold: 0.494 Sensitivity MaxExpect: 0.537 Afold: 0.490 Positive Predictive Value MaxExpect: 0.570 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.550 Afold: 0.494 Sensitivity ProbKnot: 0.541 Afold: 0.490 Positive Predictive Value ProbKnot: 0.559 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.518 Afold: 0.485 Sensitivity RNASampler(20): 0.388 Afold: 0.480 Positive Predictive Value RNASampler(20): 0.691 Afold: 0.491 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.3551590886e-08	361 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.552 Afold: 0.494 Sensitivity Sfold: 0.496 Afold: 0.490 Positive Predictive Value Sfold: 0.616 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 Fold vs Afold Matthews Correlation Coefficient Fold: 0.518 Afold: 0.494 Sensitivity Fold: 0.517 Afold: 0.490 Positive Predictive Value Fold: 0.520 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	97 Afold vs Murlet(20) Matthews Correlation Coefficient Afold: 0.540 Murlet(20): 0.523 Sensitivity Afold: 0.527 Murlet(20): 0.382 Positive Predictive Value Afold: 0.556 Murlet(20): 0.717 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.511 Afold: 0.494 Sensitivity UNAFold: 0.505 Afold: 0.490 Positive Predictive Value UNAFold: 0.518 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.502 Afold: 0.494 Sensitivity PknotsRG: 0.500 Afold: 0.490 Positive Predictive Value PknotsRG: 0.506 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.505 Afold: 0.494 Sensitivity RNAfold: 0.503 Afold: 0.490 Positive Predictive Value RNAfold: 0.509 Afold: 0.499 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.517 Afold: 0.503 Sensitivity RNAsubopt: 0.520 Afold: 0.497 Positive Predictive Value RNAsubopt: 0.517 Afold: 0.511 Number of pairs reference - predicted secondary structure: 329 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.494 McQFold: 0.459 Sensitivity Afold: 0.490 McQFold: 0.446 Positive Predictive Value Afold: 0.499 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.548 CMfinder(20): 0.497 Sensitivity Afold: 0.533 CMfinder(20): 0.325 Positive Predictive Value Afold: 0.564 CMfinder(20): 0.762 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.500 RNASLOpt: 0.467 Sensitivity Afold: 0.493 RNASLOpt: 0.434 Positive Predictive Value Afold: 0.509 RNASLOpt: 0.503 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.530 RNAalifold(seed): 0.462 Sensitivity Afold: 0.517 RNAalifold(seed): 0.264 Positive Predictive Value Afold: 0.544 RNAalifold(seed): 0.810 Number of pairs reference - predicted secondary structure: 232 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.503 RNAshapes: 0.461 Sensitivity Afold: 0.496 RNAshapes: 0.451 Positive Predictive Value Afold: 0.512 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 298 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.494 CRWrnafold: 0.436 Sensitivity Afold: 0.490 CRWrnafold: 0.436 Positive Predictive Value Afold: 0.499 CRWrnafold: 0.438 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.499 Vsfold4: 0.377 Sensitivity Afold: 0.493 Vsfold4: 0.343 Positive Predictive Value Afold: 0.508 Vsfold4: 0.416 Number of pairs reference - predicted secondary structure: 307 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.494 RNAwolf: 0.344 Sensitivity Afold: 0.490 RNAwolf: 0.356 Positive Predictive Value Afold: 0.499 RNAwolf: 0.334 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.501 Vsfold5: 0.364 Sensitivity Afold: 0.494 Vsfold5: 0.340 Positive Predictive Value Afold: 0.510 Vsfold5: 0.392 Number of pairs reference - predicted secondary structure: 301 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.534 CMfinder(seed): 0.346 Sensitivity Afold: 0.528 CMfinder(seed): 0.160 Positive Predictive Value Afold: 0.543 CMfinder(seed): 0.753 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.5677163434e-08	+ Afold vs Carnac(20) Matthews Correlation Coefficient Afold: 0.548 Carnac(20): 0.317 Sensitivity Afold: 0.533 Carnac(20): 0.114 Positive Predictive Value Afold: 0.564 Carnac(20): 0.879 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.548 RSpredict(20): 0.297 Sensitivity Afold: 0.533 RSpredict(20): 0.170 Positive Predictive Value Afold: 0.564 RSpredict(20): 0.523 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.525 NanoFolder: 0.169 Sensitivity Afold: 0.516 NanoFolder: 0.195 Positive Predictive Value Afold: 0.535 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.531 RSpredict(seed): 0.042 Sensitivity Afold: 0.518 RSpredict(seed): 0.010 Positive Predictive Value Afold: 0.545 RSpredict(seed): 0.179 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: N/A Murlet(seed): N/A Sensitivity Afold: N/A Murlet(seed): N/A Positive Predictive Value Afold: 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 Afold Matthews Correlation Coefficient Multilign(seed): N/A Afold: N/A Sensitivity Multilign(seed): N/A Afold: N/A Positive Predictive Value Multilign(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Afold Matthews Correlation Coefficient HotKnots: N/A Afold: N/A Sensitivity HotKnots: N/A Afold: N/A Positive Predictive Value HotKnots: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Afold Matthews Correlation Coefficient Pknots: N/A Afold: N/A Sensitivity Pknots: N/A Afold: N/A Positive Predictive Value Pknots: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.460 Cylofold: 0.271 Sensitivity Afold: 0.460 Cylofold: 0.241 Positive Predictive Value Afold: 0.463 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Afold vs MCFold Matthews Correlation Coefficient Afold: N/A MCFold: N/A Sensitivity Afold: N/A MCFold: N/A Positive Predictive Value Afold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): N/A Afold: N/A Sensitivity PPfold(seed): N/A Afold: N/A Positive Predictive Value PPfold(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Afold Matthews Correlation Coefficient RDfolder: N/A Afold: N/A Sensitivity RDfolder: N/A Afold: N/A Positive Predictive Value RDfolder: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.710 Afold: 0.605 Sensitivity TurboFold(seed): 0.677 Afold: 0.615 Positive Predictive Value TurboFold(seed): 0.746 Afold: 0.597 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): N/A Afold: N/A Sensitivity RNASampler(seed): N/A Afold: N/A Positive Predictive Value RNASampler(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Afold Matthews Correlation Coefficient Alterna: N/A Afold: N/A Sensitivity Alterna: N/A Afold: N/A Positive Predictive Value Alterna: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.472 Carnac(seed): 0.000 Sensitivity Afold: 0.474 Carnac(seed): 0.000 Positive Predictive Value Afold: 0.472 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.548 Mastr(20): 0.000 Sensitivity Afold: 0.533 Mastr(20): 0.000 Positive Predictive Value Afold: 0.564 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.527 Mastr(seed): 0.000 Sensitivity Afold: 0.516 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.539 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAsubopt	574 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.731 RNAsubopt: 0.475 Sensitivity ContextFold: 0.689 RNAsubopt: 0.482 Positive Predictive Value ContextFold: 0.778 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	504 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.682 RNAsubopt: 0.468 Sensitivity PETfold_pre2.0(seed): 0.592 RNAsubopt: 0.474 Positive Predictive Value PETfold_pre2.0(seed): 0.788 RNAsubopt: 0.463 Number of pairs reference - predicted secondary structure: 504 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.740 RNAsubopt: 0.519 Sensitivity TurboFold(20): 0.685 RNAsubopt: 0.518 Positive Predictive Value TurboFold(20): 0.801 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAsubopt: 0.519 Sensitivity PETfold_pre2.0(20): 0.652 RNAsubopt: 0.518 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.734 RNAsubopt: 0.519 Sensitivity PPfold(20): 0.635 RNAsubopt: 0.518 Positive Predictive Value PPfold(20): 0.850 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAsubopt: 0.519 Sensitivity CentroidAlifold(20): 0.561 RNAsubopt: 0.518 Positive Predictive Value CentroidAlifold(20): 0.916 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	273 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.693 RNAsubopt: 0.533 Sensitivity CentroidAlifold(seed): 0.523 RNAsubopt: 0.531 Positive Predictive Value CentroidAlifold(seed): 0.920 RNAsubopt: 0.538 Number of pairs reference - predicted secondary structure: 273 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAsubopt: 0.475 Sensitivity CentroidHomfold‑LAST: 0.469 RNAsubopt: 0.482 Positive Predictive Value CentroidHomfold‑LAST: 0.877 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.660 RNAsubopt: 0.519 Sensitivity RNAalifold(20): 0.532 RNAsubopt: 0.518 Positive Predictive Value RNAalifold(20): 0.819 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.605 RNAsubopt: 0.475 Sensitivity IPknot: 0.548 RNAsubopt: 0.482 Positive Predictive Value IPknot: 0.670 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.649 RNAsubopt: 0.517 Sensitivity Multilign(20): 0.590 RNAsubopt: 0.516 Positive Predictive Value Multilign(20): 0.717 RNAsubopt: 0.520 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.575 RNAsubopt: 0.475 Sensitivity CentroidFold: 0.520 RNAsubopt: 0.482 Positive Predictive Value CentroidFold: 0.638 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.557 RNAsubopt: 0.475 Sensitivity Contrafold: 0.543 RNAsubopt: 0.482 Positive Predictive Value Contrafold: 0.572 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.626 RNAsubopt: 0.519 Sensitivity MXScarna(20): 0.551 RNAsubopt: 0.518 Positive Predictive Value MXScarna(20): 0.712 RNAsubopt: 0.522 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.599 RNAsubopt: 0.535 Sensitivity MXScarna(seed): 0.479 RNAsubopt: 0.532 Positive Predictive Value MXScarna(seed): 0.750 RNAsubopt: 0.539 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.527 RNAsubopt: 0.475 Sensitivity MaxExpect: 0.513 RNAsubopt: 0.482 Positive Predictive Value MaxExpect: 0.542 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.526 RNAsubopt: 0.475 Sensitivity ProbKnot: 0.520 RNAsubopt: 0.482 Positive Predictive Value ProbKnot: 0.532 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.543 RNAsubopt: 0.362 Sensitivity RNASampler(20): 0.425 RNAsubopt: 0.371 Positive Predictive Value RNASampler(20): 0.695 RNAsubopt: 0.354 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.517 RNAsubopt: 0.475 Sensitivity Sfold: 0.466 RNAsubopt: 0.482 Positive Predictive Value Sfold: 0.575 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.499 RNAsubopt: 0.475 Sensitivity Fold: 0.502 RNAsubopt: 0.482 Positive Predictive Value Fold: 0.499 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.548 RNAsubopt: 0.499 Sensitivity Murlet(20): 0.415 RNAsubopt: 0.499 Positive Predictive Value Murlet(20): 0.725 RNAsubopt: 0.501 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.479 RNAsubopt: 0.475 Sensitivity UNAFold: 0.476 RNAsubopt: 0.482 Positive Predictive Value UNAFold: 0.484 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.478 RNAsubopt: 0.475 Sensitivity PknotsRG: 0.479 RNAsubopt: 0.482 Positive Predictive Value PknotsRG: 0.479 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 4.48494289621e-08	574 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.480 RNAsubopt: 0.475 Sensitivity RNAfold: 0.481 RNAsubopt: 0.482 Positive Predictive Value RNAfold: 0.480 RNAsubopt: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	329 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.517 Afold: 0.503 Sensitivity RNAsubopt: 0.520 Afold: 0.497 Positive Predictive Value RNAsubopt: 0.517 Afold: 0.511 Number of pairs reference - predicted secondary structure: 329 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.475 McQFold: 0.456 Sensitivity RNAsubopt: 0.482 McQFold: 0.446 Positive Predictive Value RNAsubopt: 0.469 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.519 CMfinder(20): 0.479 Sensitivity RNAsubopt: 0.518 CMfinder(20): 0.308 Positive Predictive Value RNAsubopt: 0.522 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.468 RNASLOpt: 0.446 Sensitivity RNAsubopt: 0.475 RNASLOpt: 0.421 Positive Predictive Value RNAsubopt: 0.463 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.533 RNAalifold(seed): 0.470 Sensitivity RNAsubopt: 0.530 RNAalifold(seed): 0.272 Positive Predictive Value RNAsubopt: 0.537 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 274 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.472 RNAshapes: 0.408 Sensitivity RNAsubopt: 0.479 RNAshapes: 0.404 Positive Predictive Value RNAsubopt: 0.467 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.475 CRWrnafold: 0.423 Sensitivity RNAsubopt: 0.482 CRWrnafold: 0.425 Positive Predictive Value RNAsubopt: 0.469 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.470 Vsfold4: 0.335 Sensitivity RNAsubopt: 0.478 Vsfold4: 0.308 Positive Predictive Value RNAsubopt: 0.465 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.475 RNAwolf: 0.338 Sensitivity RNAsubopt: 0.482 RNAwolf: 0.354 Positive Predictive Value RNAsubopt: 0.469 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.470 Vsfold5: 0.329 Sensitivity RNAsubopt: 0.477 Vsfold5: 0.312 Positive Predictive Value RNAsubopt: 0.465 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.496 CMfinder(seed): 0.350 Sensitivity RNAsubopt: 0.505 CMfinder(seed): 0.159 Positive Predictive Value RNAsubopt: 0.488 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.42071836373e-08	+ RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.519 Carnac(20): 0.360 Sensitivity RNAsubopt: 0.518 Carnac(20): 0.151 Positive Predictive Value RNAsubopt: 0.522 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.519 RSpredict(20): 0.347 Sensitivity RNAsubopt: 0.518 RSpredict(20): 0.220 Positive Predictive Value RNAsubopt: 0.522 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.505 NanoFolder: 0.174 Sensitivity RNAsubopt: 0.510 NanoFolder: 0.207 Positive Predictive Value RNAsubopt: 0.501 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.534 RSpredict(seed): 0.046 Sensitivity RNAsubopt: 0.531 RSpredict(seed): 0.011 Positive Predictive Value RNAsubopt: 0.538 RSpredict(seed): 0.194 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs RNAsubopt Matthews Correlation Coefficient Murlet(seed): N/A RNAsubopt: N/A Sensitivity Murlet(seed): N/A RNAsubopt: N/A Positive Predictive Value Murlet(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): N/A RNAsubopt: N/A Sensitivity Multilign(seed): N/A RNAsubopt: N/A Positive Predictive Value Multilign(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: N/A RNAsubopt: N/A Sensitivity HotKnots: N/A RNAsubopt: N/A Positive Predictive Value HotKnots: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: N/A RNAsubopt: N/A Sensitivity Pknots: N/A RNAsubopt: N/A Positive Predictive Value Pknots: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.437 Cylofold: 0.271 Sensitivity RNAsubopt: 0.431 Cylofold: 0.241 Positive Predictive Value RNAsubopt: 0.447 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: N/A MCFold: N/A Sensitivity RNAsubopt: N/A MCFold: N/A Positive Predictive Value RNAsubopt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): N/A RNAsubopt: N/A Sensitivity PPfold(seed): N/A RNAsubopt: N/A Positive Predictive Value PPfold(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: N/A RNAsubopt: N/A Sensitivity RDfolder: N/A RNAsubopt: N/A Positive Predictive Value RDfolder: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAsubopt: 0.472 Sensitivity TurboFold(seed): 0.677 RNAsubopt: 0.477 Positive Predictive Value TurboFold(seed): 0.746 RNAsubopt: 0.470 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): N/A RNAsubopt: N/A Sensitivity RNASampler(seed): N/A RNAsubopt: N/A Positive Predictive Value RNASampler(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAsubopt Matthews Correlation Coefficient Alterna: N/A RNAsubopt: N/A Sensitivity Alterna: N/A RNAsubopt: N/A Positive Predictive Value Alterna: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.488 Carnac(seed): 0.000 Sensitivity RNAsubopt: 0.498 Carnac(seed): 0.000 Positive Predictive Value RNAsubopt: 0.481 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.519 Mastr(20): 0.000 Sensitivity RNAsubopt: 0.518 Mastr(20): 0.000 Positive Predictive Value RNAsubopt: 0.522 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.534 Mastr(seed): 0.000 Sensitivity RNAsubopt: 0.533 Mastr(seed): 0.000 Positive Predictive Value RNAsubopt: 0.537 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08
McQFold	610 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.718 McQFold: 0.450 Sensitivity ContextFold: 0.677 McQFold: 0.441 Positive Predictive Value ContextFold: 0.763 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 McQFold: 0.452 Sensitivity PETfold_pre2.0(seed): 0.590 McQFold: 0.441 Positive Predictive Value PETfold_pre2.0(seed): 0.787 McQFold: 0.465 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.740 McQFold: 0.452 Sensitivity TurboFold(20): 0.685 McQFold: 0.433 Positive Predictive Value TurboFold(20): 0.801 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 McQFold: 0.452 Sensitivity PETfold_pre2.0(20): 0.652 McQFold: 0.433 Positive Predictive Value PETfold_pre2.0(20): 0.829 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.734 McQFold: 0.452 Sensitivity PPfold(20): 0.635 McQFold: 0.433 Positive Predictive Value PPfold(20): 0.850 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 McQFold: 0.452 Sensitivity CentroidAlifold(20): 0.561 McQFold: 0.433 Positive Predictive Value CentroidAlifold(20): 0.916 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 McQFold: 0.479 Sensitivity CentroidAlifold(seed): 0.521 McQFold: 0.458 Positive Predictive Value CentroidAlifold(seed): 0.919 McQFold: 0.502 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 McQFold: 0.456 Sensitivity CentroidHomfold‑LAST: 0.469 McQFold: 0.446 Positive Predictive Value CentroidHomfold‑LAST: 0.877 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.660 McQFold: 0.452 Sensitivity RNAalifold(20): 0.532 McQFold: 0.433 Positive Predictive Value RNAalifold(20): 0.819 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.602 McQFold: 0.450 Sensitivity IPknot: 0.545 McQFold: 0.441 Positive Predictive Value IPknot: 0.667 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.649 McQFold: 0.451 Sensitivity Multilign(20): 0.590 McQFold: 0.431 Positive Predictive Value Multilign(20): 0.717 McQFold: 0.473 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.571 McQFold: 0.450 Sensitivity CentroidFold: 0.516 McQFold: 0.441 Positive Predictive Value CentroidFold: 0.635 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.554 McQFold: 0.450 Sensitivity Contrafold: 0.540 McQFold: 0.441 Positive Predictive Value Contrafold: 0.569 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.626 McQFold: 0.452 Sensitivity MXScarna(20): 0.551 McQFold: 0.433 Positive Predictive Value MXScarna(20): 0.712 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.595 McQFold: 0.481 Sensitivity MXScarna(seed): 0.475 McQFold: 0.460 Positive Predictive Value MXScarna(seed): 0.747 McQFold: 0.504 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.524 McQFold: 0.450 Sensitivity MaxExpect: 0.511 McQFold: 0.441 Positive Predictive Value MaxExpect: 0.538 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.522 McQFold: 0.450 Sensitivity ProbKnot: 0.518 McQFold: 0.441 Positive Predictive Value ProbKnot: 0.527 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.543 McQFold: 0.387 Sensitivity RNASampler(20): 0.425 McQFold: 0.380 Positive Predictive Value RNASampler(20): 0.695 McQFold: 0.396 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.514 McQFold: 0.450 Sensitivity Sfold: 0.463 McQFold: 0.441 Positive Predictive Value Sfold: 0.571 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.495 McQFold: 0.450 Sensitivity Fold: 0.498 McQFold: 0.441 Positive Predictive Value Fold: 0.493 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.548 McQFold: 0.437 Sensitivity Murlet(20): 0.415 McQFold: 0.421 Positive Predictive Value Murlet(20): 0.725 McQFold: 0.456 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.475 McQFold: 0.450 Sensitivity UNAFold: 0.473 McQFold: 0.441 Positive Predictive Value UNAFold: 0.479 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.476 McQFold: 0.450 Sensitivity PknotsRG: 0.478 McQFold: 0.441 Positive Predictive Value PknotsRG: 0.475 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.474 McQFold: 0.450 Sensitivity RNAfold: 0.477 McQFold: 0.441 Positive Predictive Value RNAfold: 0.473 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.494 McQFold: 0.459 Sensitivity Afold: 0.490 McQFold: 0.446 Positive Predictive Value Afold: 0.499 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.475 McQFold: 0.456 Sensitivity RNAsubopt: 0.482 McQFold: 0.446 Positive Predictive Value RNAsubopt: 0.469 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.479 McQFold: 0.452 Sensitivity CMfinder(20): 0.308 McQFold: 0.433 Positive Predictive Value CMfinder(20): 0.747 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.455 RNASLOpt: 0.446 Sensitivity McQFold: 0.444 RNASLOpt: 0.421 Positive Predictive Value McQFold: 0.468 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAalifold(seed) Matthews Correlation Coefficient McQFold: 0.479 RNAalifold(seed): 0.469 Sensitivity McQFold: 0.458 RNAalifold(seed): 0.272 Positive Predictive Value McQFold: 0.502 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.458 RNAshapes: 0.408 Sensitivity McQFold: 0.447 RNAshapes: 0.404 Positive Predictive Value McQFold: 0.472 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.450 CRWrnafold: 0.417 Sensitivity McQFold: 0.441 CRWrnafold: 0.421 Positive Predictive Value McQFold: 0.461 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.456 Vsfold4: 0.335 Sensitivity McQFold: 0.445 Vsfold4: 0.308 Positive Predictive Value McQFold: 0.469 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.450 RNAwolf: 0.332 Sensitivity McQFold: 0.441 RNAwolf: 0.347 Positive Predictive Value McQFold: 0.461 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.457 Vsfold5: 0.329 Sensitivity McQFold: 0.446 Vsfold5: 0.312 Positive Predictive Value McQFold: 0.470 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.472 CMfinder(seed): 0.350 Sensitivity McQFold: 0.456 CMfinder(seed): 0.159 Positive Predictive Value McQFold: 0.489 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.452 Carnac(20): 0.360 Sensitivity McQFold: 0.433 Carnac(20): 0.151 Positive Predictive Value McQFold: 0.474 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.452 RSpredict(20): 0.347 Sensitivity McQFold: 0.433 RSpredict(20): 0.220 Positive Predictive Value McQFold: 0.474 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.443 NanoFolder: 0.172 Sensitivity McQFold: 0.431 NanoFolder: 0.204 Positive Predictive Value McQFold: 0.457 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.479 RSpredict(seed): 0.045 Sensitivity McQFold: 0.458 RSpredict(seed): 0.011 Positive Predictive Value McQFold: 0.503 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: N/A Murlet(seed): N/A Sensitivity McQFold: N/A Murlet(seed): N/A Positive Predictive Value McQFold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: N/A Multilign(seed): N/A Sensitivity McQFold: N/A Multilign(seed): N/A Positive Predictive Value McQFold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: N/A McQFold: N/A Sensitivity HotKnots: N/A McQFold: N/A Positive Predictive Value HotKnots: N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? McQFold vs Pknots Matthews Correlation Coefficient McQFold: N/A Pknots: N/A Sensitivity McQFold: N/A Pknots: N/A Positive Predictive Value McQFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.526 Cylofold: 0.271 Sensitivity McQFold: 0.489 Cylofold: 0.241 Positive Predictive Value McQFold: 0.568 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? McQFold vs MCFold Matthews Correlation Coefficient McQFold: N/A MCFold: N/A Sensitivity McQFold: N/A MCFold: N/A Positive Predictive Value McQFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs McQFold Matthews Correlation Coefficient PPfold(seed): N/A McQFold: N/A Sensitivity PPfold(seed): N/A McQFold: N/A Positive Predictive Value PPfold(seed): N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs McQFold Matthews Correlation Coefficient RDfolder: N/A McQFold: N/A Sensitivity RDfolder: N/A McQFold: N/A Positive Predictive Value RDfolder: N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.710 McQFold: 0.566 Sensitivity TurboFold(seed): 0.677 McQFold: 0.554 Positive Predictive Value TurboFold(seed): 0.746 McQFold: 0.581 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): N/A McQFold: N/A Sensitivity RNASampler(seed): N/A McQFold: N/A Positive Predictive Value RNASampler(seed): N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? McQFold vs Alterna Matthews Correlation Coefficient McQFold: N/A Alterna: N/A Sensitivity McQFold: N/A Alterna: N/A Positive Predictive Value McQFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.448 Carnac(seed): 0.000 Sensitivity McQFold: 0.441 Carnac(seed): 0.000 Positive Predictive Value McQFold: 0.457 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.452 Mastr(20): 0.000 Sensitivity McQFold: 0.433 Mastr(20): 0.000 Positive Predictive Value McQFold: 0.474 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.483 Mastr(seed): 0.000 Sensitivity McQFold: 0.463 Mastr(seed): 0.000 Positive Predictive Value McQFold: 0.505 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(20)	204 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.840 CMfinder(20): 0.479 Sensitivity ContextFold: 0.791 CMfinder(20): 0.308 Positive Predictive Value ContextFold: 0.892 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 CMfinder(20): 0.479 Sensitivity PETfold_pre2.0(seed): 0.673 CMfinder(20): 0.308 Positive Predictive Value PETfold_pre2.0(seed): 0.845 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.740 CMfinder(20): 0.479 Sensitivity TurboFold(20): 0.685 CMfinder(20): 0.308 Positive Predictive Value TurboFold(20): 0.801 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CMfinder(20): 0.479 Sensitivity PETfold_pre2.0(20): 0.652 CMfinder(20): 0.308 Positive Predictive Value PETfold_pre2.0(20): 0.829 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.734 CMfinder(20): 0.480 Sensitivity PPfold(20): 0.635 CMfinder(20): 0.309 Positive Predictive Value PPfold(20): 0.850 CMfinder(20): 0.748 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CMfinder(20): 0.479 Sensitivity CentroidAlifold(20): 0.561 CMfinder(20): 0.308 Positive Predictive Value CentroidAlifold(20): 0.916 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 CMfinder(20): 0.503 Sensitivity CentroidAlifold(seed): 0.548 CMfinder(20): 0.329 Positive Predictive Value CentroidAlifold(seed): 0.951 CMfinder(20): 0.769 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 CMfinder(20): 0.479 Sensitivity CentroidHomfold‑LAST: 0.551 CMfinder(20): 0.308 Positive Predictive Value CentroidHomfold‑LAST: 0.896 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 CMfinder(20): 0.479 Sensitivity RNAalifold(20): 0.532 CMfinder(20): 0.308 Positive Predictive Value RNAalifold(20): 0.819 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.648 CMfinder(20): 0.479 Sensitivity IPknot: 0.574 CMfinder(20): 0.308 Positive Predictive Value IPknot: 0.733 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.649 CMfinder(20): 0.481 Sensitivity Multilign(20): 0.590 CMfinder(20): 0.310 Positive Predictive Value Multilign(20): 0.717 CMfinder(20): 0.749 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.616 CMfinder(20): 0.479 Sensitivity CentroidFold: 0.547 CMfinder(20): 0.308 Positive Predictive Value CentroidFold: 0.695 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.601 CMfinder(20): 0.479 Sensitivity Contrafold: 0.576 CMfinder(20): 0.308 Positive Predictive Value Contrafold: 0.628 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.626 CMfinder(20): 0.479 Sensitivity MXScarna(20): 0.551 CMfinder(20): 0.308 Positive Predictive Value MXScarna(20): 0.712 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 CMfinder(20): 0.503 Sensitivity MXScarna(seed): 0.542 CMfinder(20): 0.330 Positive Predictive Value MXScarna(seed): 0.793 CMfinder(20): 0.769 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.587 CMfinder(20): 0.479 Sensitivity MaxExpect: 0.561 CMfinder(20): 0.308 Positive Predictive Value MaxExpect: 0.615 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.586 CMfinder(20): 0.479 Sensitivity ProbKnot: 0.564 CMfinder(20): 0.308 Positive Predictive Value ProbKnot: 0.610 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.543 CMfinder(20): 0.370 Sensitivity RNASampler(20): 0.425 CMfinder(20): 0.220 Positive Predictive Value RNASampler(20): 0.695 CMfinder(20): 0.625 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.568 CMfinder(20): 0.479 Sensitivity Sfold: 0.503 CMfinder(20): 0.308 Positive Predictive Value Sfold: 0.643 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.550 CMfinder(20): 0.479 Sensitivity Fold: 0.541 CMfinder(20): 0.308 Positive Predictive Value Fold: 0.560 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.548 CMfinder(20): 0.462 Sensitivity Murlet(20): 0.415 CMfinder(20): 0.294 Positive Predictive Value Murlet(20): 0.725 CMfinder(20): 0.729 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.531 CMfinder(20): 0.479 Sensitivity UNAFold: 0.519 CMfinder(20): 0.308 Positive Predictive Value UNAFold: 0.545 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.512 CMfinder(20): 0.479 Sensitivity PknotsRG: 0.503 CMfinder(20): 0.308 Positive Predictive Value PknotsRG: 0.523 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.527 CMfinder(20): 0.479 Sensitivity RNAfold: 0.518 CMfinder(20): 0.308 Positive Predictive Value RNAfold: 0.537 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.548 CMfinder(20): 0.497 Sensitivity Afold: 0.533 CMfinder(20): 0.325 Positive Predictive Value Afold: 0.564 CMfinder(20): 0.762 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.519 CMfinder(20): 0.479 Sensitivity RNAsubopt: 0.518 CMfinder(20): 0.308 Positive Predictive Value RNAsubopt: 0.522 CMfinder(20): 0.747 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.479 McQFold: 0.452 Sensitivity CMfinder(20): 0.308 McQFold: 0.433 Positive Predictive Value CMfinder(20): 0.747 McQFold: 0.474 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.490 RNASLOpt: 0.454 Sensitivity CMfinder(20): 0.319 RNASLOpt: 0.419 Positive Predictive Value CMfinder(20): 0.754 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.503 RNAalifold(seed): 0.446 Sensitivity CMfinder(20): 0.329 RNAalifold(seed): 0.249 Positive Predictive Value CMfinder(20): 0.769 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.488 RNAshapes: 0.456 Sensitivity CMfinder(20): 0.317 RNAshapes: 0.441 Positive Predictive Value CMfinder(20): 0.755 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.479 CRWrnafold: 0.454 Sensitivity CMfinder(20): 0.308 CRWrnafold: 0.446 Positive Predictive Value CMfinder(20): 0.747 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.485 Vsfold4: 0.390 Sensitivity CMfinder(20): 0.314 Vsfold4: 0.352 Positive Predictive Value CMfinder(20): 0.752 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.479 RNAwolf: 0.367 Sensitivity CMfinder(20): 0.308 RNAwolf: 0.377 Positive Predictive Value CMfinder(20): 0.747 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.488 Vsfold5: 0.369 Sensitivity CMfinder(20): 0.316 Vsfold5: 0.342 Positive Predictive Value CMfinder(20): 0.754 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.479 Carnac(20): 0.360 Sensitivity CMfinder(20): 0.308 Carnac(20): 0.151 Positive Predictive Value CMfinder(20): 0.747 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.479 RSpredict(20): 0.347 Sensitivity CMfinder(20): 0.308 RSpredict(20): 0.220 Positive Predictive Value CMfinder(20): 0.747 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.482 NanoFolder: 0.152 Sensitivity CMfinder(20): 0.306 NanoFolder: 0.174 Positive Predictive Value CMfinder(20): 0.762 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.504 RSpredict(seed): 0.054 Sensitivity CMfinder(20): 0.331 RSpredict(seed): 0.014 Positive Predictive Value CMfinder(20): 0.769 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.140 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.085 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.232 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.479 Mastr(20): 0.000 Sensitivity CMfinder(20): 0.308 Mastr(20): 0.000 Positive Predictive Value CMfinder(20): 0.747 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.503 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.332 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.764 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASLOpt	480 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.736 RNASLOpt: 0.446 Sensitivity ContextFold: 0.692 RNASLOpt: 0.421 Positive Predictive Value ContextFold: 0.784 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	438 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.693 RNASLOpt: 0.447 Sensitivity PETfold_pre2.0(seed): 0.606 RNASLOpt: 0.422 Positive Predictive Value PETfold_pre2.0(seed): 0.794 RNASLOpt: 0.476 Number of pairs reference - predicted secondary structure: 438 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.735 RNASLOpt: 0.454 Sensitivity TurboFold(20): 0.680 RNASLOpt: 0.419 Positive Predictive Value TurboFold(20): 0.795 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 RNASLOpt: 0.454 Sensitivity PETfold_pre2.0(20): 0.657 RNASLOpt: 0.419 Positive Predictive Value PETfold_pre2.0(20): 0.827 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	181 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.737 RNASLOpt: 0.454 Sensitivity PPfold(20): 0.639 RNASLOpt: 0.420 Positive Predictive Value PPfold(20): 0.850 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 181 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNASLOpt: 0.454 Sensitivity CentroidAlifold(20): 0.563 RNASLOpt: 0.419 Positive Predictive Value CentroidAlifold(20): 0.914 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	228 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.708 RNASLOpt: 0.475 Sensitivity CentroidAlifold(seed): 0.538 RNASLOpt: 0.437 Positive Predictive Value CentroidAlifold(seed): 0.932 RNASLOpt: 0.518 Number of pairs reference - predicted secondary structure: 228 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.648 RNASLOpt: 0.446 Sensitivity CentroidHomfold‑LAST: 0.481 RNASLOpt: 0.421 Positive Predictive Value CentroidHomfold‑LAST: 0.873 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.662 RNASLOpt: 0.454 Sensitivity RNAalifold(20): 0.536 RNASLOpt: 0.419 Positive Predictive Value RNAalifold(20): 0.818 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.603 RNASLOpt: 0.446 Sensitivity IPknot: 0.544 RNASLOpt: 0.421 Positive Predictive Value IPknot: 0.669 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	177 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.654 RNASLOpt: 0.454 Sensitivity Multilign(20): 0.596 RNASLOpt: 0.419 Positive Predictive Value Multilign(20): 0.718 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 177 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.568 RNASLOpt: 0.446 Sensitivity CentroidFold: 0.511 RNASLOpt: 0.421 Positive Predictive Value CentroidFold: 0.633 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.549 RNASLOpt: 0.446 Sensitivity Contrafold: 0.535 RNASLOpt: 0.421 Positive Predictive Value Contrafold: 0.566 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.618 RNASLOpt: 0.454 Sensitivity MXScarna(20): 0.545 RNASLOpt: 0.419 Positive Predictive Value MXScarna(20): 0.703 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.618 RNASLOpt: 0.475 Sensitivity MXScarna(seed): 0.500 RNASLOpt: 0.438 Positive Predictive Value MXScarna(seed): 0.767 RNASLOpt: 0.518 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.524 RNASLOpt: 0.446 Sensitivity MaxExpect: 0.510 RNASLOpt: 0.421 Positive Predictive Value MaxExpect: 0.540 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.523 RNASLOpt: 0.446 Sensitivity ProbKnot: 0.517 RNASLOpt: 0.421 Positive Predictive Value ProbKnot: 0.530 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.543 RNASLOpt: 0.374 Sensitivity RNASampler(20): 0.425 RNASLOpt: 0.356 Positive Predictive Value RNASampler(20): 0.695 RNASLOpt: 0.396 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.509 RNASLOpt: 0.446 Sensitivity Sfold: 0.458 RNASLOpt: 0.421 Positive Predictive Value Sfold: 0.567 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.495 RNASLOpt: 0.446 Sensitivity Fold: 0.497 RNASLOpt: 0.421 Positive Predictive Value Fold: 0.496 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.555 RNASLOpt: 0.434 Sensitivity Murlet(20): 0.424 RNASLOpt: 0.403 Positive Predictive Value Murlet(20): 0.727 RNASLOpt: 0.470 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.470 RNASLOpt: 0.446 Sensitivity UNAFold: 0.467 RNASLOpt: 0.421 Positive Predictive Value UNAFold: 0.475 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.467 RNASLOpt: 0.446 Sensitivity PknotsRG: 0.468 RNASLOpt: 0.421 Positive Predictive Value PknotsRG: 0.468 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.472 RNASLOpt: 0.446 Sensitivity RNAfold: 0.473 RNASLOpt: 0.421 Positive Predictive Value RNAfold: 0.473 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	275 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.500 RNASLOpt: 0.467 Sensitivity Afold: 0.493 RNASLOpt: 0.434 Positive Predictive Value Afold: 0.509 RNASLOpt: 0.503 Number of pairs reference - predicted secondary structure: 275 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.468 RNASLOpt: 0.446 Sensitivity RNAsubopt: 0.475 RNASLOpt: 0.421 Positive Predictive Value RNAsubopt: 0.463 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.455 RNASLOpt: 0.446 Sensitivity McQFold: 0.444 RNASLOpt: 0.421 Positive Predictive Value McQFold: 0.468 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.490 RNASLOpt: 0.454 Sensitivity CMfinder(20): 0.319 RNASLOpt: 0.419 Positive Predictive Value CMfinder(20): 0.754 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASLOpt vs RNAalifold(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 RNAalifold(seed): 0.466 Sensitivity RNASLOpt: 0.436 RNAalifold(seed): 0.268 Positive Predictive Value RNASLOpt: 0.517 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 229 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.446 RNAshapes: 0.402 Sensitivity RNASLOpt: 0.421 RNAshapes: 0.398 Positive Predictive Value RNASLOpt: 0.474 RNAshapes: 0.408 Number of pairs reference - predicted secondary structure: 474 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs CRWrnafold Matthews Correlation Coefficient RNASLOpt: 0.446 CRWrnafold: 0.419 Sensitivity RNASLOpt: 0.421 CRWrnafold: 0.421 Positive Predictive Value RNASLOpt: 0.473 CRWrnafold: 0.419 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold4: 0.338 Sensitivity RNASLOpt: 0.421 Vsfold4: 0.311 Positive Predictive Value RNASLOpt: 0.473 Vsfold4: 0.369 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.446 RNAwolf: 0.337 Sensitivity RNASLOpt: 0.421 RNAwolf: 0.352 Positive Predictive Value RNASLOpt: 0.473 RNAwolf: 0.324 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold5: 0.332 Sensitivity RNASLOpt: 0.421 Vsfold5: 0.316 Positive Predictive Value RNASLOpt: 0.473 Vsfold5: 0.350 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.450 CMfinder(seed): 0.356 Sensitivity RNASLOpt: 0.424 CMfinder(seed): 0.168 Positive Predictive Value RNASLOpt: 0.480 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.22797000563e-08	+ RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.454 Carnac(20): 0.353 Sensitivity RNASLOpt: 0.419 Carnac(20): 0.146 Positive Predictive Value RNASLOpt: 0.494 Carnac(20): 0.854 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.454 RSpredict(20): 0.352 Sensitivity RNASLOpt: 0.419 RSpredict(20): 0.224 Positive Predictive Value RNASLOpt: 0.494 RSpredict(20): 0.554 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.460 NanoFolder: 0.179 Sensitivity RNASLOpt: 0.428 NanoFolder: 0.210 Positive Predictive Value RNASLOpt: 0.496 NanoFolder: 0.155 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.475 RSpredict(seed): 0.036 Sensitivity RNASLOpt: 0.437 RSpredict(seed): 0.008 Positive Predictive Value RNASLOpt: 0.518 RSpredict(seed): 0.159 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): N/A RNASLOpt: N/A Sensitivity Murlet(seed): N/A RNASLOpt: N/A Positive Predictive Value Murlet(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): N/A RNASLOpt: N/A Sensitivity Multilign(seed): N/A RNASLOpt: N/A Positive Predictive Value Multilign(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: N/A RNASLOpt: N/A Sensitivity HotKnots: N/A RNASLOpt: N/A Positive Predictive Value HotKnots: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: N/A RNASLOpt: N/A Sensitivity Pknots: N/A RNASLOpt: N/A Positive Predictive Value Pknots: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.382 Cylofold: 0.271 Sensitivity RNASLOpt: 0.358 Cylofold: 0.241 Positive Predictive Value RNASLOpt: 0.412 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: N/A MCFold: N/A Sensitivity RNASLOpt: N/A MCFold: N/A Positive Predictive Value RNASLOpt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): N/A RNASLOpt: N/A Sensitivity PPfold(seed): N/A RNASLOpt: N/A Positive Predictive Value PPfold(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNASLOpt Matthews Correlation Coefficient RDfolder: N/A RNASLOpt: N/A Sensitivity RDfolder: N/A RNASLOpt: N/A Positive Predictive Value RDfolder: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.710 RNASLOpt: 0.357 Sensitivity TurboFold(seed): 0.677 RNASLOpt: 0.338 Positive Predictive Value TurboFold(seed): 0.746 RNASLOpt: 0.379 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): N/A RNASLOpt: N/A Sensitivity RNASampler(seed): N/A RNASLOpt: N/A Positive Predictive Value RNASampler(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: N/A RNASLOpt: N/A Sensitivity Alterna: N/A RNASLOpt: N/A Positive Predictive Value Alterna: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.449 Carnac(seed): 0.000 Sensitivity RNASLOpt: 0.414 Carnac(seed): 0.000 Positive Predictive Value RNASLOpt: 0.488 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.454 Mastr(20): 0.000 Sensitivity RNASLOpt: 0.419 Mastr(20): 0.000 Positive Predictive Value RNASLOpt: 0.494 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.473 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.436 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.515 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(seed)	278 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.812 RNAalifold(seed): 0.469 Sensitivity ContextFold: 0.764 RNAalifold(seed): 0.272 Positive Predictive Value ContextFold: 0.864 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 RNAalifold(seed): 0.469 Sensitivity PETfold_pre2.0(seed): 0.632 RNAalifold(seed): 0.272 Positive Predictive Value PETfold_pre2.0(seed): 0.821 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RNAalifold(seed): 0.446 Sensitivity TurboFold(20): 0.702 RNAalifold(seed): 0.249 Positive Predictive Value TurboFold(20): 0.823 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.754 RNAalifold(seed): 0.446 Sensitivity PETfold_pre2.0(20): 0.670 RNAalifold(seed): 0.249 Positive Predictive Value PETfold_pre2.0(20): 0.849 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	155 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.752 RNAalifold(seed): 0.445 Sensitivity PPfold(20): 0.657 RNAalifold(seed): 0.248 Positive Predictive Value PPfold(20): 0.862 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 RNAalifold(seed): 0.446 Sensitivity CentroidAlifold(20): 0.562 RNAalifold(seed): 0.249 Positive Predictive Value CentroidAlifold(20): 0.933 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RNAalifold(seed): 0.469 Sensitivity CentroidAlifold(seed): 0.521 RNAalifold(seed): 0.271 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	274 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 RNAalifold(seed): 0.470 Sensitivity CentroidHomfold‑LAST: 0.507 RNAalifold(seed): 0.272 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 274 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAalifold(seed): 0.446 Sensitivity RNAalifold(20): 0.533 RNAalifold(seed): 0.249 Positive Predictive Value RNAalifold(20): 0.837 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.640 RNAalifold(seed): 0.469 Sensitivity IPknot: 0.567 RNAalifold(seed): 0.272 Positive Predictive Value IPknot: 0.722 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.657 RNAalifold(seed): 0.435 Sensitivity Multilign(20): 0.594 RNAalifold(seed): 0.239 Positive Predictive Value Multilign(20): 0.728 RNAalifold(seed): 0.792 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.621 RNAalifold(seed): 0.469 Sensitivity CentroidFold: 0.553 RNAalifold(seed): 0.272 Positive Predictive Value CentroidFold: 0.698 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.604 RNAalifold(seed): 0.469 Sensitivity Contrafold: 0.579 RNAalifold(seed): 0.272 Positive Predictive Value Contrafold: 0.631 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.650 RNAalifold(seed): 0.446 Sensitivity MXScarna(20): 0.563 RNAalifold(seed): 0.249 Positive Predictive Value MXScarna(20): 0.752 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.594 RNAalifold(seed): 0.469 Sensitivity MXScarna(seed): 0.474 RNAalifold(seed): 0.272 Positive Predictive Value MXScarna(seed): 0.746 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 MaxExpect vs RNAalifold(seed) Matthews Correlation Coefficient MaxExpect: 0.587 RNAalifold(seed): 0.469 Sensitivity MaxExpect: 0.562 RNAalifold(seed): 0.272 Positive Predictive Value MaxExpect: 0.615 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.587 RNAalifold(seed): 0.469 Sensitivity ProbKnot: 0.566 RNAalifold(seed): 0.272 Positive Predictive Value ProbKnot: 0.610 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.480 RNAalifold(seed): 0.439 Sensitivity RNASampler(20): 0.343 RNAalifold(seed): 0.245 Positive Predictive Value RNASampler(20): 0.673 RNAalifold(seed): 0.791 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	278 Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.585 RNAalifold(seed): 0.469 Sensitivity Sfold: 0.519 RNAalifold(seed): 0.272 Positive Predictive Value Sfold: 0.659 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.551 RNAalifold(seed): 0.469 Sensitivity Fold: 0.542 RNAalifold(seed): 0.272 Positive Predictive Value Fold: 0.562 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.533 RNAalifold(seed): 0.456 Sensitivity Murlet(20): 0.389 RNAalifold(seed): 0.260 Positive Predictive Value Murlet(20): 0.732 RNAalifold(seed): 0.802 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.544 RNAalifold(seed): 0.469 Sensitivity UNAFold: 0.530 RNAalifold(seed): 0.272 Positive Predictive Value UNAFold: 0.560 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.527 RNAalifold(seed): 0.469 Sensitivity PknotsRG: 0.516 RNAalifold(seed): 0.272 Positive Predictive Value PknotsRG: 0.539 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.534 RNAalifold(seed): 0.469 Sensitivity RNAfold: 0.523 RNAalifold(seed): 0.272 Positive Predictive Value RNAfold: 0.547 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	232 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.530 RNAalifold(seed): 0.462 Sensitivity Afold: 0.517 RNAalifold(seed): 0.264 Positive Predictive Value Afold: 0.544 RNAalifold(seed): 0.810 Number of pairs reference - predicted secondary structure: 232 Wilcoxon single-rank test P-value: 3.56938820447e-08	274 RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.533 RNAalifold(seed): 0.470 Sensitivity RNAsubopt: 0.530 RNAalifold(seed): 0.272 Positive Predictive Value RNAsubopt: 0.537 RNAalifold(seed): 0.813 Number of pairs reference - predicted secondary structure: 274 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 McQFold vs RNAalifold(seed) Matthews Correlation Coefficient McQFold: 0.479 RNAalifold(seed): 0.469 Sensitivity McQFold: 0.458 RNAalifold(seed): 0.272 Positive Predictive Value McQFold: 0.502 RNAalifold(seed): 0.811 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.503 RNAalifold(seed): 0.446 Sensitivity CMfinder(20): 0.329 RNAalifold(seed): 0.249 Positive Predictive Value CMfinder(20): 0.769 RNAalifold(seed): 0.799 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	229 RNASLOpt vs RNAalifold(seed) Matthews Correlation Coefficient RNASLOpt: 0.474 RNAalifold(seed): 0.466 Sensitivity RNASLOpt: 0.436 RNAalifold(seed): 0.268 Positive Predictive Value RNASLOpt: 0.517 RNAalifold(seed): 0.812 Number of pairs reference - predicted secondary structure: 229 Wilcoxon single-rank test P-value: 5.21776328505e-08		- RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.485 RNAalifold(seed): 0.463 Sensitivity RNAshapes: 0.469 RNAalifold(seed): 0.266 Positive Predictive Value RNAshapes: 0.504 RNAalifold(seed): 0.807 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.469 CRWrnafold: 0.457 Sensitivity RNAalifold(seed): 0.272 CRWrnafold: 0.449 Positive Predictive Value RNAalifold(seed): 0.811 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.467 Vsfold4: 0.405 Sensitivity RNAalifold(seed): 0.270 Vsfold4: 0.365 Positive Predictive Value RNAalifold(seed): 0.809 Vsfold4: 0.452 Number of pairs reference - predicted secondary structure: 260 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.469 RNAwolf: 0.372 Sensitivity RNAalifold(seed): 0.272 RNAwolf: 0.380 Positive Predictive Value RNAalifold(seed): 0.811 RNAwolf: 0.365 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.464 Vsfold5: 0.379 Sensitivity RNAalifold(seed): 0.267 Vsfold5: 0.348 Positive Predictive Value RNAalifold(seed): 0.808 Vsfold5: 0.413 Number of pairs reference - predicted secondary structure: 256 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.416 CMfinder(seed): 0.350 Sensitivity RNAalifold(seed): 0.219 CMfinder(seed): 0.159 Positive Predictive Value RNAalifold(seed): 0.791 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.446 Carnac(20): 0.332 Sensitivity RNAalifold(seed): 0.249 Carnac(20): 0.126 Positive Predictive Value RNAalifold(seed): 0.799 Carnac(20): 0.880 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.446 RSpredict(20): 0.306 Sensitivity RNAalifold(seed): 0.249 RSpredict(20): 0.174 Positive Predictive Value RNAalifold(seed): 0.799 RSpredict(20): 0.541 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.454 NanoFolder: 0.180 Sensitivity RNAalifold(seed): 0.257 NanoFolder: 0.206 Positive Predictive Value RNAalifold(seed): 0.801 NanoFolder: 0.161 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.469 RSpredict(seed): 0.045 Sensitivity RNAalifold(seed): 0.272 RSpredict(seed): 0.011 Positive Predictive Value RNAalifold(seed): 0.811 RSpredict(seed): 0.187 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A Murlet(seed): N/A Sensitivity RNAalifold(seed): N/A Murlet(seed): N/A Positive Predictive Value RNAalifold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A Multilign(seed): N/A Sensitivity RNAalifold(seed): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: N/A RNAalifold(seed): N/A Sensitivity HotKnots: N/A RNAalifold(seed): N/A Positive Predictive Value HotKnots: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: N/A RNAalifold(seed): N/A Sensitivity Pknots: N/A RNAalifold(seed): N/A Positive Predictive Value Pknots: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(seed): N/A Sensitivity Cylofold: N/A RNAalifold(seed): N/A Positive Predictive Value Cylofold: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): N/A MCFold: N/A Sensitivity RNAalifold(seed): N/A MCFold: N/A Positive Predictive Value RNAalifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): N/A RNAalifold(seed): N/A Sensitivity PPfold(seed): N/A RNAalifold(seed): N/A Positive Predictive Value PPfold(seed): N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAalifold(seed) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(seed): N/A Sensitivity RDfolder: N/A RNAalifold(seed): N/A Positive Predictive Value RDfolder: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAalifold(seed): 0.680 Sensitivity TurboFold(seed): 0.677 RNAalifold(seed): 0.554 Positive Predictive Value TurboFold(seed): 0.746 RNAalifold(seed): 0.837 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(seed): N/A Sensitivity RNASampler(seed): N/A RNAalifold(seed): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): N/A Alterna: N/A Sensitivity RNAalifold(seed): N/A Alterna: N/A Positive Predictive Value RNAalifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.619 Carnac(seed): 0.000 Sensitivity RNAalifold(seed): 0.427 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.899 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.446 Mastr(20): 0.000 Sensitivity RNAalifold(seed): 0.249 Mastr(20): 0.000 Positive Predictive Value RNAalifold(seed): 0.799 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.475 Mastr(seed): 0.000 Sensitivity RNAalifold(seed): 0.278 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.814 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAshapes	526 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.736 RNAshapes: 0.408 Sensitivity ContextFold: 0.692 RNAshapes: 0.404 Positive Predictive Value ContextFold: 0.784 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	476 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 RNAshapes: 0.398 Sensitivity PETfold_pre2.0(seed): 0.595 RNAshapes: 0.394 Positive Predictive Value PETfold_pre2.0(seed): 0.786 RNAshapes: 0.404 Number of pairs reference - predicted secondary structure: 476 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.738 RNAshapes: 0.456 Sensitivity TurboFold(20): 0.682 RNAshapes: 0.441 Positive Predictive Value TurboFold(20): 0.799 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.737 RNAshapes: 0.456 Sensitivity PETfold_pre2.0(20): 0.655 RNAshapes: 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.831 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	188 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.738 RNAshapes: 0.455 Sensitivity PPfold(20): 0.638 RNAshapes: 0.440 Positive Predictive Value PPfold(20): 0.853 RNAshapes: 0.471 Number of pairs reference - predicted secondary structure: 188 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAshapes: 0.456 Sensitivity CentroidAlifold(20): 0.561 RNAshapes: 0.441 Positive Predictive Value CentroidAlifold(20): 0.917 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	253 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.696 RNAshapes: 0.486 Sensitivity CentroidAlifold(seed): 0.526 RNAshapes: 0.469 Positive Predictive Value CentroidAlifold(seed): 0.921 RNAshapes: 0.505 Number of pairs reference - predicted secondary structure: 253 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 RNAshapes: 0.408 Sensitivity CentroidHomfold‑LAST: 0.475 RNAshapes: 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.876 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.662 RNAshapes: 0.456 Sensitivity RNAalifold(20): 0.534 RNAshapes: 0.441 Positive Predictive Value RNAalifold(20): 0.822 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.604 RNAshapes: 0.408 Sensitivity IPknot: 0.545 RNAshapes: 0.404 Positive Predictive Value IPknot: 0.671 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	182 Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.650 RNAshapes: 0.453 Sensitivity Multilign(20): 0.590 RNAshapes: 0.439 Positive Predictive Value Multilign(20): 0.716 RNAshapes: 0.470 Number of pairs reference - predicted secondary structure: 182 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.571 RNAshapes: 0.408 Sensitivity CentroidFold: 0.515 RNAshapes: 0.404 Positive Predictive Value CentroidFold: 0.635 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.552 RNAshapes: 0.408 Sensitivity Contrafold: 0.538 RNAshapes: 0.404 Positive Predictive Value Contrafold: 0.569 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.621 RNAshapes: 0.456 Sensitivity MXScarna(20): 0.547 RNAshapes: 0.441 Positive Predictive Value MXScarna(20): 0.707 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.604 RNAshapes: 0.486 Sensitivity MXScarna(seed): 0.485 RNAshapes: 0.469 Positive Predictive Value MXScarna(seed): 0.754 RNAshapes: 0.504 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.526 RNAshapes: 0.408 Sensitivity MaxExpect: 0.512 RNAshapes: 0.404 Positive Predictive Value MaxExpect: 0.543 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.525 RNAshapes: 0.408 Sensitivity ProbKnot: 0.519 RNAshapes: 0.404 Positive Predictive Value ProbKnot: 0.533 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.543 RNAshapes: 0.306 Sensitivity RNASampler(20): 0.425 RNAshapes: 0.306 Positive Predictive Value RNASampler(20): 0.697 RNAshapes: 0.308 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.513 RNAshapes: 0.408 Sensitivity Sfold: 0.462 RNAshapes: 0.404 Positive Predictive Value Sfold: 0.572 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.498 RNAshapes: 0.408 Sensitivity Fold: 0.500 RNAshapes: 0.404 Positive Predictive Value Fold: 0.498 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.553 RNAshapes: 0.431 Sensitivity Murlet(20): 0.419 RNAshapes: 0.419 Positive Predictive Value Murlet(20): 0.732 RNAshapes: 0.446 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.475 RNAshapes: 0.408 Sensitivity UNAFold: 0.472 RNAshapes: 0.404 Positive Predictive Value UNAFold: 0.480 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.474 RNAshapes: 0.408 Sensitivity PknotsRG: 0.475 RNAshapes: 0.404 Positive Predictive Value PknotsRG: 0.476 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.476 RNAshapes: 0.408 Sensitivity RNAfold: 0.477 RNAshapes: 0.404 Positive Predictive Value RNAfold: 0.477 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	298 Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.503 RNAshapes: 0.461 Sensitivity Afold: 0.496 RNAshapes: 0.451 Positive Predictive Value Afold: 0.512 RNAshapes: 0.474 Number of pairs reference - predicted secondary structure: 298 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.472 RNAshapes: 0.408 Sensitivity RNAsubopt: 0.479 RNAshapes: 0.404 Positive Predictive Value RNAsubopt: 0.467 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.458 RNAshapes: 0.408 Sensitivity McQFold: 0.447 RNAshapes: 0.404 Positive Predictive Value McQFold: 0.472 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.488 RNAshapes: 0.456 Sensitivity CMfinder(20): 0.317 RNAshapes: 0.441 Positive Predictive Value CMfinder(20): 0.755 RNAshapes: 0.473 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	474 RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.446 RNAshapes: 0.402 Sensitivity RNASLOpt: 0.421 RNAshapes: 0.398 Positive Predictive Value RNASLOpt: 0.474 RNAshapes: 0.408 Number of pairs reference - predicted secondary structure: 474 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.485 RNAalifold(seed): 0.463 Sensitivity RNAshapes: 0.469 RNAalifold(seed): 0.266 Positive Predictive Value RNAshapes: 0.504 RNAalifold(seed): 0.807 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.421 RNAshapes: 0.408 Sensitivity CRWrnafold: 0.423 RNAshapes: 0.404 Positive Predictive Value CRWrnafold: 0.422 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.406 Vsfold4: 0.338 Sensitivity RNAshapes: 0.402 Vsfold4: 0.311 Positive Predictive Value RNAshapes: 0.412 Vsfold4: 0.369 Number of pairs reference - predicted secondary structure: 523 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.408 RNAwolf: 0.340 Sensitivity RNAshapes: 0.404 RNAwolf: 0.355 Positive Predictive Value RNAshapes: 0.414 RNAwolf: 0.328 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.405 Vsfold5: 0.330 Sensitivity RNAshapes: 0.402 Vsfold5: 0.314 Positive Predictive Value RNAshapes: 0.411 Vsfold5: 0.350 Number of pairs reference - predicted secondary structure: 522 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.559 CMfinder(seed): 0.343 Sensitivity RNAshapes: 0.552 CMfinder(seed): 0.157 Positive Predictive Value RNAshapes: 0.568 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.39162260866e-08	+ RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.456 Carnac(20): 0.359 Sensitivity RNAshapes: 0.441 Carnac(20): 0.150 Positive Predictive Value RNAshapes: 0.473 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.456 RSpredict(20): 0.352 Sensitivity RNAshapes: 0.441 RSpredict(20): 0.224 Positive Predictive Value RNAshapes: 0.473 RSpredict(20): 0.556 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.433 NanoFolder: 0.175 Sensitivity RNAshapes: 0.426 NanoFolder: 0.207 Positive Predictive Value RNAshapes: 0.443 NanoFolder: 0.151 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.485 RSpredict(seed): 0.039 Sensitivity RNAshapes: 0.469 RSpredict(seed): 0.009 Positive Predictive Value RNAshapes: 0.504 RSpredict(seed): 0.166 Number of pairs reference - predicted secondary structure: 256 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): N/A RNAshapes: N/A Sensitivity Murlet(seed): N/A RNAshapes: N/A Positive Predictive Value Murlet(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): N/A RNAshapes: N/A Sensitivity Multilign(seed): N/A RNAshapes: N/A Positive Predictive Value Multilign(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: N/A RNAshapes: N/A Sensitivity HotKnots: N/A RNAshapes: N/A Positive Predictive Value HotKnots: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: N/A RNAshapes: N/A Sensitivity Pknots: N/A RNAshapes: N/A Positive Predictive Value Pknots: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.455 Cylofold: 0.271 Sensitivity RNAshapes: 0.453 Cylofold: 0.241 Positive Predictive Value RNAshapes: 0.459 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: N/A MCFold: N/A Sensitivity RNAshapes: N/A MCFold: N/A Positive Predictive Value RNAshapes: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): N/A RNAshapes: N/A Sensitivity PPfold(seed): N/A RNAshapes: N/A Positive Predictive Value PPfold(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: N/A RNAshapes: N/A Sensitivity RDfolder: N/A RNAshapes: N/A Positive Predictive Value RDfolder: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAshapes: 0.553 Sensitivity TurboFold(seed): 0.677 RNAshapes: 0.554 Positive Predictive Value TurboFold(seed): 0.746 RNAshapes: 0.554 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): N/A RNAshapes: N/A Sensitivity RNASampler(seed): N/A RNAshapes: N/A Positive Predictive Value RNASampler(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAshapes Matthews Correlation Coefficient Alterna: N/A RNAshapes: N/A Sensitivity Alterna: N/A RNAshapes: N/A Positive Predictive Value Alterna: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.469 Carnac(seed): 0.000 Sensitivity RNAshapes: 0.460 Carnac(seed): 0.000 Positive Predictive Value RNAshapes: 0.479 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.456 Mastr(20): 0.000 Sensitivity RNAshapes: 0.441 Mastr(20): 0.000 Positive Predictive Value RNAshapes: 0.473 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.482 Mastr(seed): 0.000 Sensitivity RNAshapes: 0.466 Mastr(seed): 0.000 Positive Predictive Value RNAshapes: 0.499 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08
CRWrnafold	610 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.718 CRWrnafold: 0.417 Sensitivity ContextFold: 0.677 CRWrnafold: 0.421 Positive Predictive Value ContextFold: 0.763 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 CRWrnafold: 0.416 Sensitivity PETfold_pre2.0(seed): 0.590 CRWrnafold: 0.418 Positive Predictive Value PETfold_pre2.0(seed): 0.787 CRWrnafold: 0.417 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.740 CRWrnafold: 0.454 Sensitivity TurboFold(20): 0.685 CRWrnafold: 0.446 Positive Predictive Value TurboFold(20): 0.801 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 CRWrnafold: 0.454 Sensitivity PETfold_pre2.0(20): 0.652 CRWrnafold: 0.446 Positive Predictive Value PETfold_pre2.0(20): 0.829 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.734 CRWrnafold: 0.454 Sensitivity PPfold(20): 0.635 CRWrnafold: 0.445 Positive Predictive Value PPfold(20): 0.850 CRWrnafold: 0.464 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.717 CRWrnafold: 0.454 Sensitivity CentroidAlifold(20): 0.561 CRWrnafold: 0.446 Positive Predictive Value CentroidAlifold(20): 0.916 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 CRWrnafold: 0.458 Sensitivity CentroidAlifold(seed): 0.521 CRWrnafold: 0.450 Positive Predictive Value CentroidAlifold(seed): 0.919 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 CRWrnafold: 0.423 Sensitivity CentroidHomfold‑LAST: 0.469 CRWrnafold: 0.425 Positive Predictive Value CentroidHomfold‑LAST: 0.877 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.660 CRWrnafold: 0.454 Sensitivity RNAalifold(20): 0.532 CRWrnafold: 0.446 Positive Predictive Value RNAalifold(20): 0.819 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.602 CRWrnafold: 0.417 Sensitivity IPknot: 0.545 CRWrnafold: 0.421 Positive Predictive Value IPknot: 0.667 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.649 CRWrnafold: 0.452 Sensitivity Multilign(20): 0.590 CRWrnafold: 0.443 Positive Predictive Value Multilign(20): 0.717 CRWrnafold: 0.462 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.571 CRWrnafold: 0.417 Sensitivity CentroidFold: 0.516 CRWrnafold: 0.421 Positive Predictive Value CentroidFold: 0.635 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.554 CRWrnafold: 0.417 Sensitivity Contrafold: 0.540 CRWrnafold: 0.421 Positive Predictive Value Contrafold: 0.569 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.626 CRWrnafold: 0.454 Sensitivity MXScarna(20): 0.551 CRWrnafold: 0.446 Positive Predictive Value MXScarna(20): 0.712 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.595 CRWrnafold: 0.459 Sensitivity MXScarna(seed): 0.475 CRWrnafold: 0.451 Positive Predictive Value MXScarna(seed): 0.747 CRWrnafold: 0.468 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.524 CRWrnafold: 0.417 Sensitivity MaxExpect: 0.511 CRWrnafold: 0.421 Positive Predictive Value MaxExpect: 0.538 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.522 CRWrnafold: 0.417 Sensitivity ProbKnot: 0.518 CRWrnafold: 0.421 Positive Predictive Value ProbKnot: 0.527 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.543 CRWrnafold: 0.369 Sensitivity RNASampler(20): 0.425 CRWrnafold: 0.374 Positive Predictive Value RNASampler(20): 0.695 CRWrnafold: 0.366 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.514 CRWrnafold: 0.417 Sensitivity Sfold: 0.463 CRWrnafold: 0.421 Positive Predictive Value Sfold: 0.571 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.495 CRWrnafold: 0.417 Sensitivity Fold: 0.498 CRWrnafold: 0.421 Positive Predictive Value Fold: 0.493 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.548 CRWrnafold: 0.434 Sensitivity Murlet(20): 0.415 CRWrnafold: 0.428 Positive Predictive Value Murlet(20): 0.725 CRWrnafold: 0.443 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.475 CRWrnafold: 0.417 Sensitivity UNAFold: 0.473 CRWrnafold: 0.421 Positive Predictive Value UNAFold: 0.479 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.476 CRWrnafold: 0.417 Sensitivity PknotsRG: 0.478 CRWrnafold: 0.421 Positive Predictive Value PknotsRG: 0.475 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.474 CRWrnafold: 0.417 Sensitivity RNAfold: 0.477 CRWrnafold: 0.421 Positive Predictive Value RNAfold: 0.473 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.494 CRWrnafold: 0.436 Sensitivity Afold: 0.490 CRWrnafold: 0.436 Positive Predictive Value Afold: 0.499 CRWrnafold: 0.438 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.475 CRWrnafold: 0.423 Sensitivity RNAsubopt: 0.482 CRWrnafold: 0.425 Positive Predictive Value RNAsubopt: 0.469 CRWrnafold: 0.422 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.450 CRWrnafold: 0.417 Sensitivity McQFold: 0.441 CRWrnafold: 0.421 Positive Predictive Value McQFold: 0.461 CRWrnafold: 0.415 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.479 CRWrnafold: 0.454 Sensitivity CMfinder(20): 0.308 CRWrnafold: 0.446 Positive Predictive Value CMfinder(20): 0.747 CRWrnafold: 0.465 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 RNASLOpt vs CRWrnafold Matthews Correlation Coefficient RNASLOpt: 0.446 CRWrnafold: 0.419 Sensitivity RNASLOpt: 0.421 CRWrnafold: 0.421 Positive Predictive Value RNASLOpt: 0.473 CRWrnafold: 0.419 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.469 CRWrnafold: 0.457 Sensitivity RNAalifold(seed): 0.272 CRWrnafold: 0.449 Positive Predictive Value RNAalifold(seed): 0.811 CRWrnafold: 0.467 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.421 RNAshapes: 0.408 Sensitivity CRWrnafold: 0.423 RNAshapes: 0.404 Positive Predictive Value CRWrnafold: 0.422 RNAshapes: 0.414 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.420 Vsfold4: 0.335 Sensitivity CRWrnafold: 0.422 Vsfold4: 0.308 Positive Predictive Value CRWrnafold: 0.420 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.417 RNAwolf: 0.332 Sensitivity CRWrnafold: 0.421 RNAwolf: 0.347 Positive Predictive Value CRWrnafold: 0.415 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.420 Vsfold5: 0.329 Sensitivity CRWrnafold: 0.422 Vsfold5: 0.312 Positive Predictive Value CRWrnafold: 0.420 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.472 CMfinder(seed): 0.350 Sensitivity CRWrnafold: 0.482 CMfinder(seed): 0.159 Positive Predictive Value CRWrnafold: 0.465 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.454 Carnac(20): 0.360 Sensitivity CRWrnafold: 0.446 Carnac(20): 0.151 Positive Predictive Value CRWrnafold: 0.465 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.454 RSpredict(20): 0.347 Sensitivity CRWrnafold: 0.446 RSpredict(20): 0.220 Positive Predictive Value CRWrnafold: 0.465 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.442 NanoFolder: 0.172 Sensitivity CRWrnafold: 0.443 NanoFolder: 0.204 Positive Predictive Value CRWrnafold: 0.443 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.457 RSpredict(seed): 0.045 Sensitivity CRWrnafold: 0.449 RSpredict(seed): 0.011 Positive Predictive Value CRWrnafold: 0.467 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): N/A CRWrnafold: N/A Sensitivity Murlet(seed): N/A CRWrnafold: N/A Positive Predictive Value Murlet(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): N/A CRWrnafold: N/A Sensitivity Multilign(seed): N/A CRWrnafold: N/A Positive Predictive Value Multilign(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: N/A CRWrnafold: N/A Sensitivity HotKnots: N/A CRWrnafold: N/A Positive Predictive Value HotKnots: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: N/A CRWrnafold: N/A Sensitivity Pknots: N/A CRWrnafold: N/A Positive Predictive Value Pknots: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.470 Cylofold: 0.271 Sensitivity CRWrnafold: 0.474 Cylofold: 0.241 Positive Predictive Value CRWrnafold: 0.468 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: N/A MCFold: N/A Sensitivity CRWrnafold: N/A MCFold: N/A Positive Predictive Value CRWrnafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): N/A CRWrnafold: N/A Sensitivity PPfold(seed): N/A CRWrnafold: N/A Positive Predictive Value PPfold(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: N/A CRWrnafold: N/A Sensitivity RDfolder: N/A CRWrnafold: N/A Positive Predictive Value RDfolder: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.710 CRWrnafold: 0.483 Sensitivity TurboFold(seed): 0.677 CRWrnafold: 0.477 Positive Predictive Value TurboFold(seed): 0.746 CRWrnafold: 0.492 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): N/A CRWrnafold: N/A Sensitivity RNASampler(seed): N/A CRWrnafold: N/A Positive Predictive Value RNASampler(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CRWrnafold Matthews Correlation Coefficient Alterna: N/A CRWrnafold: N/A Sensitivity Alterna: N/A CRWrnafold: N/A Positive Predictive Value Alterna: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.436 Carnac(seed): 0.000 Sensitivity CRWrnafold: 0.444 Carnac(seed): 0.000 Positive Predictive Value CRWrnafold: 0.430 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.454 Mastr(20): 0.000 Sensitivity CRWrnafold: 0.446 Mastr(20): 0.000 Positive Predictive Value CRWrnafold: 0.465 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.455 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.449 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.464 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold4	547 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.732 Vsfold4: 0.335 Sensitivity ContextFold: 0.689 Vsfold4: 0.308 Positive Predictive Value ContextFold: 0.779 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	490 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold4: 0.330 Sensitivity PETfold_pre2.0(seed): 0.594 Vsfold4: 0.304 Positive Predictive Value PETfold_pre2.0(seed): 0.786 Vsfold4: 0.362 Number of pairs reference - predicted secondary structure: 490 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.738 Vsfold4: 0.390 Sensitivity TurboFold(20): 0.683 Vsfold4: 0.352 Positive Predictive Value TurboFold(20): 0.799 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Vsfold4: 0.390 Sensitivity PETfold_pre2.0(20): 0.654 Vsfold4: 0.352 Positive Predictive Value PETfold_pre2.0(20): 0.829 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	193 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.736 Vsfold4: 0.390 Sensitivity PPfold(20): 0.637 Vsfold4: 0.353 Positive Predictive Value PPfold(20): 0.851 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 193 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Vsfold4: 0.390 Sensitivity CentroidAlifold(20): 0.562 Vsfold4: 0.352 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	259 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 Vsfold4: 0.406 Sensitivity CentroidAlifold(seed): 0.528 Vsfold4: 0.365 Positive Predictive Value CentroidAlifold(seed): 0.921 Vsfold4: 0.452 Number of pairs reference - predicted secondary structure: 259 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Vsfold4: 0.335 Sensitivity CentroidHomfold‑LAST: 0.475 Vsfold4: 0.308 Positive Predictive Value CentroidHomfold‑LAST: 0.876 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.661 Vsfold4: 0.390 Sensitivity RNAalifold(20): 0.534 Vsfold4: 0.352 Positive Predictive Value RNAalifold(20): 0.820 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.603 Vsfold4: 0.335 Sensitivity IPknot: 0.545 Vsfold4: 0.308 Positive Predictive Value IPknot: 0.668 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	187 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.648 Vsfold4: 0.392 Sensitivity Multilign(20): 0.589 Vsfold4: 0.355 Positive Predictive Value Multilign(20): 0.714 Vsfold4: 0.435 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.570 Vsfold4: 0.335 Sensitivity CentroidFold: 0.514 Vsfold4: 0.308 Positive Predictive Value CentroidFold: 0.633 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.551 Vsfold4: 0.335 Sensitivity Contrafold: 0.537 Vsfold4: 0.308 Positive Predictive Value Contrafold: 0.567 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.625 Vsfold4: 0.390 Sensitivity MXScarna(20): 0.550 Vsfold4: 0.352 Positive Predictive Value MXScarna(20): 0.710 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	264 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.606 Vsfold4: 0.406 Sensitivity MXScarna(seed): 0.487 Vsfold4: 0.366 Positive Predictive Value MXScarna(seed): 0.755 Vsfold4: 0.453 Number of pairs reference - predicted secondary structure: 264 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.523 Vsfold4: 0.335 Sensitivity MaxExpect: 0.510 Vsfold4: 0.308 Positive Predictive Value MaxExpect: 0.539 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.522 Vsfold4: 0.335 Sensitivity ProbKnot: 0.517 Vsfold4: 0.308 Positive Predictive Value ProbKnot: 0.529 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.543 Vsfold4: 0.245 Sensitivity RNASampler(20): 0.425 Vsfold4: 0.229 Positive Predictive Value RNASampler(20): 0.695 Vsfold4: 0.265 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.512 Vsfold4: 0.335 Sensitivity Sfold: 0.461 Vsfold4: 0.308 Positive Predictive Value Sfold: 0.570 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.496 Vsfold4: 0.335 Sensitivity Fold: 0.498 Vsfold4: 0.308 Positive Predictive Value Fold: 0.496 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.551 Vsfold4: 0.371 Sensitivity Murlet(20): 0.419 Vsfold4: 0.337 Positive Predictive Value Murlet(20): 0.728 Vsfold4: 0.412 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.474 Vsfold4: 0.335 Sensitivity UNAFold: 0.471 Vsfold4: 0.308 Positive Predictive Value UNAFold: 0.479 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.473 Vsfold4: 0.335 Sensitivity PknotsRG: 0.474 Vsfold4: 0.308 Positive Predictive Value PknotsRG: 0.474 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.475 Vsfold4: 0.335 Sensitivity RNAfold: 0.476 Vsfold4: 0.308 Positive Predictive Value RNAfold: 0.476 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	307 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.499 Vsfold4: 0.377 Sensitivity Afold: 0.493 Vsfold4: 0.343 Positive Predictive Value Afold: 0.508 Vsfold4: 0.416 Number of pairs reference - predicted secondary structure: 307 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.470 Vsfold4: 0.335 Sensitivity RNAsubopt: 0.478 Vsfold4: 0.308 Positive Predictive Value RNAsubopt: 0.465 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.456 Vsfold4: 0.335 Sensitivity McQFold: 0.445 Vsfold4: 0.308 Positive Predictive Value McQFold: 0.469 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.485 Vsfold4: 0.390 Sensitivity CMfinder(20): 0.314 Vsfold4: 0.352 Positive Predictive Value CMfinder(20): 0.752 Vsfold4: 0.433 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold4: 0.338 Sensitivity RNASLOpt: 0.421 Vsfold4: 0.311 Positive Predictive Value RNASLOpt: 0.473 Vsfold4: 0.369 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	260 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.467 Vsfold4: 0.405 Sensitivity RNAalifold(seed): 0.270 Vsfold4: 0.365 Positive Predictive Value RNAalifold(seed): 0.809 Vsfold4: 0.452 Number of pairs reference - predicted secondary structure: 260 Wilcoxon single-rank test P-value: 3.56938820447e-08	523 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.406 Vsfold4: 0.338 Sensitivity RNAshapes: 0.402 Vsfold4: 0.311 Positive Predictive Value RNAshapes: 0.412 Vsfold4: 0.369 Number of pairs reference - predicted secondary structure: 523 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.420 Vsfold4: 0.335 Sensitivity CRWrnafold: 0.422 Vsfold4: 0.308 Positive Predictive Value CRWrnafold: 0.420 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.339 Vsfold4: 0.335 Sensitivity RNAwolf: 0.354 Vsfold4: 0.308 Positive Predictive Value RNAwolf: 0.327 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.336 Vsfold5: 0.329 Sensitivity Vsfold4: 0.309 Vsfold5: 0.312 Positive Predictive Value Vsfold4: 0.367 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: 0.392 CMfinder(seed): 0.343 Sensitivity Vsfold4: 0.361 CMfinder(seed): 0.157 Positive Predictive Value Vsfold4: 0.429 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ Vsfold4 vs Carnac(20) Matthews Correlation Coefficient Vsfold4: 0.390 Carnac(20): 0.358 Sensitivity Vsfold4: 0.352 Carnac(20): 0.150 Positive Predictive Value Vsfold4: 0.433 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(20) Matthews Correlation Coefficient Vsfold4: 0.390 RSpredict(20): 0.350 Sensitivity Vsfold4: 0.352 RSpredict(20): 0.223 Positive Predictive Value Vsfold4: 0.433 RSpredict(20): 0.553 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.360 NanoFolder: 0.175 Sensitivity Vsfold4: 0.328 NanoFolder: 0.208 Positive Predictive Value Vsfold4: 0.396 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.406 RSpredict(seed): 0.044 Sensitivity Vsfold4: 0.366 RSpredict(seed): 0.011 Positive Predictive Value Vsfold4: 0.453 RSpredict(seed): 0.186 Number of pairs reference - predicted secondary structure: 262 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: N/A Murlet(seed): N/A Sensitivity Vsfold4: N/A Murlet(seed): N/A Positive Predictive Value Vsfold4: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold4 vs Multilign(seed) Matthews Correlation Coefficient Vsfold4: N/A Multilign(seed): N/A Sensitivity Vsfold4: N/A Multilign(seed): N/A Positive Predictive Value Vsfold4: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: N/A Vsfold4: N/A Sensitivity HotKnots: N/A Vsfold4: N/A Positive Predictive Value HotKnots: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: N/A Vsfold4: N/A Sensitivity Pknots: N/A Vsfold4: N/A Positive Predictive Value Pknots: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.271 Vsfold4: 0.267 Sensitivity Cylofold: 0.241 Vsfold4: 0.241 Positive Predictive Value Cylofold: 0.308 Vsfold4: 0.300 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: N/A MCFold: N/A Sensitivity Vsfold4: N/A MCFold: N/A Positive Predictive Value Vsfold4: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): N/A Vsfold4: N/A Sensitivity PPfold(seed): N/A Vsfold4: N/A Positive Predictive Value PPfold(seed): N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: N/A Vsfold4: N/A Sensitivity RDfolder: N/A Vsfold4: N/A Positive Predictive Value RDfolder: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.710 Vsfold4: 0.099 Sensitivity TurboFold(seed): 0.677 Vsfold4: 0.092 Positive Predictive Value TurboFold(seed): 0.746 Vsfold4: 0.111 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): N/A Vsfold4: N/A Sensitivity RNASampler(seed): N/A Vsfold4: N/A Positive Predictive Value RNASampler(seed): N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: N/A Alterna: N/A Sensitivity Vsfold4: N/A Alterna: N/A Positive Predictive Value Vsfold4: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.310 Carnac(seed): 0.000 Sensitivity Vsfold4: 0.286 Carnac(seed): 0.000 Positive Predictive Value Vsfold4: 0.340 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.390 Mastr(20): 0.000 Sensitivity Vsfold4: 0.352 Mastr(20): 0.000 Positive Predictive Value Vsfold4: 0.433 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.400 Mastr(seed): 0.000 Sensitivity Vsfold4: 0.361 Mastr(seed): 0.000 Positive Predictive Value Vsfold4: 0.445 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAwolf	610 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.718 RNAwolf: 0.332 Sensitivity ContextFold: 0.677 RNAwolf: 0.347 Positive Predictive Value ContextFold: 0.763 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	508 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.681 RNAwolf: 0.340 Sensitivity PETfold_pre2.0(seed): 0.590 RNAwolf: 0.355 Positive Predictive Value PETfold_pre2.0(seed): 0.787 RNAwolf: 0.328 Number of pairs reference - predicted secondary structure: 508 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.740 RNAwolf: 0.367 Sensitivity TurboFold(20): 0.685 RNAwolf: 0.377 Positive Predictive Value TurboFold(20): 0.801 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNAwolf: 0.367 Sensitivity PETfold_pre2.0(20): 0.652 RNAwolf: 0.377 Positive Predictive Value PETfold_pre2.0(20): 0.829 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.734 RNAwolf: 0.368 Sensitivity PPfold(20): 0.635 RNAwolf: 0.378 Positive Predictive Value PPfold(20): 0.850 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RNAwolf: 0.367 Sensitivity CentroidAlifold(20): 0.561 RNAwolf: 0.377 Positive Predictive Value CentroidAlifold(20): 0.916 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RNAwolf: 0.372 Sensitivity CentroidAlifold(seed): 0.521 RNAwolf: 0.381 Positive Predictive Value CentroidAlifold(seed): 0.919 RNAwolf: 0.366 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.641 RNAwolf: 0.338 Sensitivity CentroidHomfold‑LAST: 0.469 RNAwolf: 0.354 Positive Predictive Value CentroidHomfold‑LAST: 0.877 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.660 RNAwolf: 0.367 Sensitivity RNAalifold(20): 0.532 RNAwolf: 0.377 Positive Predictive Value RNAalifold(20): 0.819 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.602 RNAwolf: 0.332 Sensitivity IPknot: 0.545 RNAwolf: 0.347 Positive Predictive Value IPknot: 0.667 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.649 RNAwolf: 0.364 Sensitivity Multilign(20): 0.590 RNAwolf: 0.374 Positive Predictive Value Multilign(20): 0.717 RNAwolf: 0.357 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.571 RNAwolf: 0.332 Sensitivity CentroidFold: 0.516 RNAwolf: 0.347 Positive Predictive Value CentroidFold: 0.635 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.554 RNAwolf: 0.332 Sensitivity Contrafold: 0.540 RNAwolf: 0.347 Positive Predictive Value Contrafold: 0.569 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.626 RNAwolf: 0.367 Sensitivity MXScarna(20): 0.551 RNAwolf: 0.377 Positive Predictive Value MXScarna(20): 0.712 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	282 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.595 RNAwolf: 0.372 Sensitivity MXScarna(seed): 0.475 RNAwolf: 0.381 Positive Predictive Value MXScarna(seed): 0.747 RNAwolf: 0.366 Number of pairs reference - predicted secondary structure: 282 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.524 RNAwolf: 0.332 Sensitivity MaxExpect: 0.511 RNAwolf: 0.347 Positive Predictive Value MaxExpect: 0.538 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.522 RNAwolf: 0.332 Sensitivity ProbKnot: 0.518 RNAwolf: 0.347 Positive Predictive Value ProbKnot: 0.527 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.543 RNAwolf: 0.286 Sensitivity RNASampler(20): 0.425 RNAwolf: 0.305 Positive Predictive Value RNASampler(20): 0.695 RNAwolf: 0.271 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.514 RNAwolf: 0.332 Sensitivity Sfold: 0.463 RNAwolf: 0.347 Positive Predictive Value Sfold: 0.571 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.495 RNAwolf: 0.332 Sensitivity Fold: 0.498 RNAwolf: 0.347 Positive Predictive Value Fold: 0.493 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.548 RNAwolf: 0.352 Sensitivity Murlet(20): 0.415 RNAwolf: 0.364 Positive Predictive Value Murlet(20): 0.725 RNAwolf: 0.343 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.475 RNAwolf: 0.332 Sensitivity UNAFold: 0.473 RNAwolf: 0.347 Positive Predictive Value UNAFold: 0.479 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.476 RNAwolf: 0.332 Sensitivity PknotsRG: 0.478 RNAwolf: 0.347 Positive Predictive Value PknotsRG: 0.475 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.474 RNAwolf: 0.332 Sensitivity RNAfold: 0.477 RNAwolf: 0.347 Positive Predictive Value RNAfold: 0.473 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	361 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.494 RNAwolf: 0.344 Sensitivity Afold: 0.490 RNAwolf: 0.356 Positive Predictive Value Afold: 0.499 RNAwolf: 0.334 Number of pairs reference - predicted secondary structure: 361 Wilcoxon single-rank test P-value: 3.56938820447e-08	574 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.475 RNAwolf: 0.338 Sensitivity RNAsubopt: 0.482 RNAwolf: 0.354 Positive Predictive Value RNAsubopt: 0.469 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 574 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.450 RNAwolf: 0.332 Sensitivity McQFold: 0.441 RNAwolf: 0.347 Positive Predictive Value McQFold: 0.461 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.479 RNAwolf: 0.367 Sensitivity CMfinder(20): 0.308 RNAwolf: 0.377 Positive Predictive Value CMfinder(20): 0.747 RNAwolf: 0.359 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.446 RNAwolf: 0.337 Sensitivity RNASLOpt: 0.421 RNAwolf: 0.352 Positive Predictive Value RNASLOpt: 0.473 RNAwolf: 0.324 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.469 RNAwolf: 0.372 Sensitivity RNAalifold(seed): 0.272 RNAwolf: 0.380 Positive Predictive Value RNAalifold(seed): 0.811 RNAwolf: 0.365 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.408 RNAwolf: 0.340 Sensitivity RNAshapes: 0.404 RNAwolf: 0.355 Positive Predictive Value RNAshapes: 0.414 RNAwolf: 0.328 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	610 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.417 RNAwolf: 0.332 Sensitivity CRWrnafold: 0.421 RNAwolf: 0.347 Positive Predictive Value CRWrnafold: 0.415 RNAwolf: 0.319 Number of pairs reference - predicted secondary structure: 610 Wilcoxon single-rank test P-value: 3.56938820447e-08	547 RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.339 Vsfold4: 0.335 Sensitivity RNAwolf: 0.354 Vsfold4: 0.308 Positive Predictive Value RNAwolf: 0.327 Vsfold4: 0.365 Number of pairs reference - predicted secondary structure: 547 Wilcoxon single-rank test P-value: 5.21776328505e-08		+ RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.339 Vsfold5: 0.329 Sensitivity RNAwolf: 0.354 Vsfold5: 0.312 Positive Predictive Value RNAwolf: 0.327 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.350 RNAwolf: 0.237 Sensitivity CMfinder(seed): 0.159 RNAwolf: 0.248 Positive Predictive Value CMfinder(seed): 0.770 RNAwolf: 0.229 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ RNAwolf vs Carnac(20) Matthews Correlation Coefficient RNAwolf: 0.367 Carnac(20): 0.360 Sensitivity RNAwolf: 0.377 Carnac(20): 0.151 Positive Predictive Value RNAwolf: 0.359 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 8.81311508309e-08	+ RNAwolf vs RSpredict(20) Matthews Correlation Coefficient RNAwolf: 0.367 RSpredict(20): 0.347 Sensitivity RNAwolf: 0.377 RSpredict(20): 0.220 Positive Predictive Value RNAwolf: 0.359 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.334 NanoFolder: 0.172 Sensitivity RNAwolf: 0.346 NanoFolder: 0.204 Positive Predictive Value RNAwolf: 0.324 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.372 RSpredict(seed): 0.045 Sensitivity RNAwolf: 0.380 RSpredict(seed): 0.011 Positive Predictive Value RNAwolf: 0.365 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): N/A RNAwolf: N/A Sensitivity Murlet(seed): N/A RNAwolf: N/A Positive Predictive Value Murlet(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): N/A RNAwolf: N/A Sensitivity Multilign(seed): N/A RNAwolf: N/A Positive Predictive Value Multilign(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: N/A RNAwolf: N/A Sensitivity HotKnots: N/A RNAwolf: N/A Positive Predictive Value HotKnots: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: N/A RNAwolf: N/A Sensitivity Pknots: N/A RNAwolf: N/A Positive Predictive Value Pknots: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAwolf vs Cylofold Matthews Correlation Coefficient RNAwolf: 0.339 Cylofold: 0.271 Sensitivity RNAwolf: 0.350 Cylofold: 0.241 Positive Predictive Value RNAwolf: 0.331 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: N/A MCFold: N/A Sensitivity RNAwolf: N/A MCFold: N/A Positive Predictive Value RNAwolf: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): N/A RNAwolf: N/A Sensitivity PPfold(seed): N/A RNAwolf: N/A Positive Predictive Value PPfold(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: N/A RNAwolf: N/A Sensitivity RDfolder: N/A RNAwolf: N/A Positive Predictive Value RDfolder: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAwolf: 0.620 Sensitivity TurboFold(seed): 0.677 RNAwolf: 0.631 Positive Predictive Value TurboFold(seed): 0.746 RNAwolf: 0.612 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): N/A RNAwolf: N/A Sensitivity RNASampler(seed): N/A RNAwolf: N/A Positive Predictive Value RNASampler(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: N/A RNAwolf: N/A Sensitivity Alterna: N/A RNAwolf: N/A Positive Predictive Value Alterna: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.290 Carnac(seed): 0.000 Sensitivity RNAwolf: 0.306 Carnac(seed): 0.000 Positive Predictive Value RNAwolf: 0.277 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.367 Mastr(20): 0.000 Sensitivity RNAwolf: 0.377 Mastr(20): 0.000 Positive Predictive Value RNAwolf: 0.359 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.368 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.377 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.361 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold5	538 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.735 Vsfold5: 0.329 Sensitivity ContextFold: 0.691 Vsfold5: 0.312 Positive Predictive Value ContextFold: 0.782 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	484 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.683 Vsfold5: 0.324 Sensitivity PETfold_pre2.0(seed): 0.594 Vsfold5: 0.307 Positive Predictive Value PETfold_pre2.0(seed): 0.786 Vsfold5: 0.344 Number of pairs reference - predicted secondary structure: 484 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.738 Vsfold5: 0.369 Sensitivity TurboFold(20): 0.682 Vsfold5: 0.342 Positive Predictive Value TurboFold(20): 0.798 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Vsfold5: 0.369 Sensitivity PETfold_pre2.0(20): 0.655 Vsfold5: 0.342 Positive Predictive Value PETfold_pre2.0(20): 0.829 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	190 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.737 Vsfold5: 0.367 Sensitivity PPfold(20): 0.638 Vsfold5: 0.340 Positive Predictive Value PPfold(20): 0.851 Vsfold5: 0.399 Number of pairs reference - predicted secondary structure: 190 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Vsfold5: 0.369 Sensitivity CentroidAlifold(20): 0.562 Vsfold5: 0.342 Positive Predictive Value CentroidAlifold(20): 0.917 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.697 Vsfold5: 0.378 Sensitivity CentroidAlifold(seed): 0.527 Vsfold5: 0.348 Positive Predictive Value CentroidAlifold(seed): 0.921 Vsfold5: 0.413 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.645 Vsfold5: 0.329 Sensitivity CentroidHomfold‑LAST: 0.475 Vsfold5: 0.312 Positive Predictive Value CentroidHomfold‑LAST: 0.877 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.662 Vsfold5: 0.369 Sensitivity RNAalifold(20): 0.534 Vsfold5: 0.342 Positive Predictive Value RNAalifold(20): 0.820 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.603 Vsfold5: 0.329 Sensitivity IPknot: 0.545 Vsfold5: 0.312 Positive Predictive Value IPknot: 0.669 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	184 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.649 Vsfold5: 0.370 Sensitivity Multilign(20): 0.590 Vsfold5: 0.343 Positive Predictive Value Multilign(20): 0.715 Vsfold5: 0.402 Number of pairs reference - predicted secondary structure: 184 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.570 Vsfold5: 0.329 Sensitivity CentroidFold: 0.514 Vsfold5: 0.312 Positive Predictive Value CentroidFold: 0.633 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.551 Vsfold5: 0.329 Sensitivity Contrafold: 0.537 Vsfold5: 0.312 Positive Predictive Value Contrafold: 0.567 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.621 Vsfold5: 0.369 Sensitivity MXScarna(20): 0.547 Vsfold5: 0.342 Positive Predictive Value MXScarna(20): 0.707 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	260 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.604 Vsfold5: 0.380 Sensitivity MXScarna(seed): 0.485 Vsfold5: 0.350 Positive Predictive Value MXScarna(seed): 0.754 Vsfold5: 0.415 Number of pairs reference - predicted secondary structure: 260 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.525 Vsfold5: 0.329 Sensitivity MaxExpect: 0.511 Vsfold5: 0.312 Positive Predictive Value MaxExpect: 0.541 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.524 Vsfold5: 0.329 Sensitivity ProbKnot: 0.518 Vsfold5: 0.312 Positive Predictive Value ProbKnot: 0.530 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.543 Vsfold5: 0.244 Sensitivity RNASampler(20): 0.425 Vsfold5: 0.234 Positive Predictive Value RNASampler(20): 0.695 Vsfold5: 0.256 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.511 Vsfold5: 0.329 Sensitivity Sfold: 0.461 Vsfold5: 0.312 Positive Predictive Value Sfold: 0.569 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.498 Vsfold5: 0.329 Sensitivity Fold: 0.499 Vsfold5: 0.312 Positive Predictive Value Fold: 0.497 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	139 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.553 Vsfold5: 0.350 Sensitivity Murlet(20): 0.420 Vsfold5: 0.325 Positive Predictive Value Murlet(20): 0.729 Vsfold5: 0.379 Number of pairs reference - predicted secondary structure: 139 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.474 Vsfold5: 0.329 Sensitivity UNAFold: 0.470 Vsfold5: 0.312 Positive Predictive Value UNAFold: 0.479 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.473 Vsfold5: 0.329 Sensitivity PknotsRG: 0.473 Vsfold5: 0.312 Positive Predictive Value PknotsRG: 0.473 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.474 Vsfold5: 0.329 Sensitivity RNAfold: 0.475 Vsfold5: 0.312 Positive Predictive Value RNAfold: 0.475 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	301 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.501 Vsfold5: 0.364 Sensitivity Afold: 0.494 Vsfold5: 0.340 Positive Predictive Value Afold: 0.510 Vsfold5: 0.392 Number of pairs reference - predicted secondary structure: 301 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.470 Vsfold5: 0.329 Sensitivity RNAsubopt: 0.477 Vsfold5: 0.312 Positive Predictive Value RNAsubopt: 0.465 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.457 Vsfold5: 0.329 Sensitivity McQFold: 0.446 Vsfold5: 0.312 Positive Predictive Value McQFold: 0.470 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.488 Vsfold5: 0.369 Sensitivity CMfinder(20): 0.316 Vsfold5: 0.342 Positive Predictive Value CMfinder(20): 0.754 Vsfold5: 0.400 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	480 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.446 Vsfold5: 0.332 Sensitivity RNASLOpt: 0.421 Vsfold5: 0.316 Positive Predictive Value RNASLOpt: 0.473 Vsfold5: 0.350 Number of pairs reference - predicted secondary structure: 480 Wilcoxon single-rank test P-value: 3.56938820447e-08	256 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.464 Vsfold5: 0.379 Sensitivity RNAalifold(seed): 0.267 Vsfold5: 0.348 Positive Predictive Value RNAalifold(seed): 0.808 Vsfold5: 0.413 Number of pairs reference - predicted secondary structure: 256 Wilcoxon single-rank test P-value: 3.56938820447e-08	522 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.405 Vsfold5: 0.330 Sensitivity RNAshapes: 0.402 Vsfold5: 0.314 Positive Predictive Value RNAshapes: 0.411 Vsfold5: 0.350 Number of pairs reference - predicted secondary structure: 522 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.420 Vsfold5: 0.329 Sensitivity CRWrnafold: 0.422 Vsfold5: 0.312 Positive Predictive Value CRWrnafold: 0.420 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.336 Vsfold5: 0.329 Sensitivity Vsfold4: 0.309 Vsfold5: 0.312 Positive Predictive Value Vsfold4: 0.367 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08	538 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.339 Vsfold5: 0.329 Sensitivity RNAwolf: 0.354 Vsfold5: 0.312 Positive Predictive Value RNAwolf: 0.327 Vsfold5: 0.348 Number of pairs reference - predicted secondary structure: 538 Wilcoxon single-rank test P-value: 3.56938820447e-08		= Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: 0.346 CMfinder(seed): 0.343 Sensitivity Vsfold5: 0.322 CMfinder(seed): 0.157 Positive Predictive Value Vsfold5: 0.374 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0869137492703	+ Vsfold5 vs Carnac(20) Matthews Correlation Coefficient Vsfold5: 0.369 Carnac(20): 0.359 Sensitivity Vsfold5: 0.342 Carnac(20): 0.150 Positive Predictive Value Vsfold5: 0.400 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ Vsfold5 vs RSpredict(20) Matthews Correlation Coefficient Vsfold5: 0.369 RSpredict(20): 0.351 Sensitivity Vsfold5: 0.342 RSpredict(20): 0.224 Positive Predictive Value Vsfold5: 0.400 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.340 NanoFolder: 0.176 Sensitivity Vsfold5: 0.319 NanoFolder: 0.208 Positive Predictive Value Vsfold5: 0.366 NanoFolder: 0.151 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.379 RSpredict(seed): 0.038 Sensitivity Vsfold5: 0.349 RSpredict(seed): 0.009 Positive Predictive Value Vsfold5: 0.414 RSpredict(seed): 0.164 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold5 vs Murlet(seed) Matthews Correlation Coefficient Vsfold5: N/A Murlet(seed): N/A Sensitivity Vsfold5: N/A Murlet(seed): N/A Positive Predictive Value Vsfold5: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold5 vs Multilign(seed) Matthews Correlation Coefficient Vsfold5: N/A Multilign(seed): N/A Sensitivity Vsfold5: N/A Multilign(seed): N/A Positive Predictive Value Vsfold5: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: N/A Vsfold5: N/A Sensitivity HotKnots: N/A Vsfold5: N/A Positive Predictive Value HotKnots: N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold5 vs Pknots Matthews Correlation Coefficient Vsfold5: N/A Pknots: N/A Sensitivity Vsfold5: N/A Pknots: N/A Positive Predictive Value Vsfold5: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold5 vs Cylofold Matthews Correlation Coefficient Vsfold5: 0.357 Cylofold: 0.271 Sensitivity Vsfold5: 0.336 Cylofold: 0.241 Positive Predictive Value Vsfold5: 0.383 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: N/A MCFold: N/A Sensitivity Vsfold5: N/A MCFold: N/A Positive Predictive Value Vsfold5: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: N/A PPfold(seed): N/A Sensitivity Vsfold5: N/A PPfold(seed): N/A Positive Predictive Value Vsfold5: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Vsfold5 Matthews Correlation Coefficient RDfolder: N/A Vsfold5: N/A Sensitivity RDfolder: N/A Vsfold5: N/A Positive Predictive Value RDfolder: N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.710 Vsfold5: 0.200 Sensitivity TurboFold(seed): 0.677 Vsfold5: 0.200 Positive Predictive Value TurboFold(seed): 0.746 Vsfold5: 0.203 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): N/A Vsfold5: N/A Sensitivity RNASampler(seed): N/A Vsfold5: N/A Positive Predictive Value RNASampler(seed): N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: N/A Alterna: N/A Sensitivity Vsfold5: N/A Alterna: N/A Positive Predictive Value Vsfold5: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.289 Carnac(seed): 0.000 Sensitivity Vsfold5: 0.276 Carnac(seed): 0.000 Positive Predictive Value Vsfold5: 0.306 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.369 Mastr(20): 0.000 Sensitivity Vsfold5: 0.342 Mastr(20): 0.000 Positive Predictive Value Vsfold5: 0.400 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.375 Mastr(seed): 0.000 Sensitivity Vsfold5: 0.347 Mastr(seed): 0.000 Positive Predictive Value Vsfold5: 0.407 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(seed)	15 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.708 CMfinder(seed): 0.350 Sensitivity ContextFold: 0.665 CMfinder(seed): 0.159 Positive Predictive Value ContextFold: 0.756 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	15 PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.413 CMfinder(seed): 0.350 Sensitivity PETfold_pre2.0(seed): 0.264 CMfinder(seed): 0.159 Positive Predictive Value PETfold_pre2.0(seed): 0.648 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.34821445183e-08	0 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	15 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.420 CMfinder(seed): 0.350 Sensitivity CentroidAlifold(seed): 0.246 CMfinder(seed): 0.159 Positive Predictive Value CentroidAlifold(seed): 0.717 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.22210847902e-08	15 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.667 CMfinder(seed): 0.350 Sensitivity CentroidHomfold‑LAST: 0.490 CMfinder(seed): 0.159 Positive Predictive Value CentroidHomfold‑LAST: 0.909 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.30549897711e-08	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	15 IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.632 CMfinder(seed): 0.350 Sensitivity IPknot: 0.573 CMfinder(seed): 0.159 Positive Predictive Value IPknot: 0.698 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	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	15 CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.592 CMfinder(seed): 0.350 Sensitivity CentroidFold: 0.519 CMfinder(seed): 0.159 Positive Predictive Value CentroidFold: 0.675 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	15 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.576 CMfinder(seed): 0.350 Sensitivity Contrafold: 0.556 CMfinder(seed): 0.159 Positive Predictive Value Contrafold: 0.597 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.32677072069e-08	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	15 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 MXScarna(seed): 0.283 Sensitivity CMfinder(seed): 0.159 MXScarna(seed): 0.165 Positive Predictive Value CMfinder(seed): 0.770 MXScarna(seed): 0.490 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.98760236454e-08	15 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.559 CMfinder(seed): 0.350 Sensitivity MaxExpect: 0.543 CMfinder(seed): 0.159 Positive Predictive Value MaxExpect: 0.576 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.87872347734e-08	15 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.554 CMfinder(seed): 0.350 Sensitivity ProbKnot: 0.550 CMfinder(seed): 0.159 Positive Predictive Value ProbKnot: 0.560 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.12160100812e-08	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	15 Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.601 CMfinder(seed): 0.350 Sensitivity Sfold: 0.529 CMfinder(seed): 0.159 Positive Predictive Value Sfold: 0.684 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.84041289224e-08	15 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.510 CMfinder(seed): 0.350 Sensitivity Fold: 0.516 CMfinder(seed): 0.159 Positive Predictive Value Fold: 0.505 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.48055519165e-08	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	15 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.487 CMfinder(seed): 0.350 Sensitivity UNAFold: 0.480 CMfinder(seed): 0.159 Positive Predictive Value UNAFold: 0.495 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.41358941668e-08	15 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.503 CMfinder(seed): 0.350 Sensitivity PknotsRG: 0.510 CMfinder(seed): 0.159 Positive Predictive Value PknotsRG: 0.496 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	15 RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.466 CMfinder(seed): 0.350 Sensitivity RNAfold: 0.468 CMfinder(seed): 0.159 Positive Predictive Value RNAfold: 0.465 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.94377603181e-08	13 Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.534 CMfinder(seed): 0.346 Sensitivity Afold: 0.528 CMfinder(seed): 0.160 Positive Predictive Value Afold: 0.543 CMfinder(seed): 0.753 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.5677163434e-08	15 RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.496 CMfinder(seed): 0.350 Sensitivity RNAsubopt: 0.505 CMfinder(seed): 0.159 Positive Predictive Value RNAsubopt: 0.488 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 3.42071836373e-08	15 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.472 CMfinder(seed): 0.350 Sensitivity McQFold: 0.456 CMfinder(seed): 0.159 Positive Predictive Value McQFold: 0.489 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.7402423548e-08	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	11 RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.450 CMfinder(seed): 0.356 Sensitivity RNASLOpt: 0.424 CMfinder(seed): 0.168 Positive Predictive Value RNASLOpt: 0.480 CMfinder(seed): 0.757 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.22797000563e-08	15 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.416 CMfinder(seed): 0.350 Sensitivity RNAalifold(seed): 0.219 CMfinder(seed): 0.159 Positive Predictive Value RNAalifold(seed): 0.791 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.89649746203e-08	13 RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.559 CMfinder(seed): 0.343 Sensitivity RNAshapes: 0.552 CMfinder(seed): 0.157 Positive Predictive Value RNAshapes: 0.568 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.39162260866e-08	15 CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.472 CMfinder(seed): 0.350 Sensitivity CRWrnafold: 0.482 CMfinder(seed): 0.159 Positive Predictive Value CRWrnafold: 0.465 CMfinder(seed): 0.770 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.78993384543e-08	13 Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: 0.392 CMfinder(seed): 0.343 Sensitivity Vsfold4: 0.361 CMfinder(seed): 0.157 Positive Predictive Value Vsfold4: 0.429 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.28439804626e-08	15 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.350 RNAwolf: 0.237 Sensitivity CMfinder(seed): 0.159 RNAwolf: 0.248 Positive Predictive Value CMfinder(seed): 0.770 RNAwolf: 0.229 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.24270395587e-08	13 Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: 0.346 CMfinder(seed): 0.343 Sensitivity Vsfold5: 0.322 CMfinder(seed): 0.157 Positive Predictive Value Vsfold5: 0.374 CMfinder(seed): 0.750 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0869137492703		? 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	? 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 NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.276 NanoFolder: 0.200 Sensitivity CMfinder(seed): 0.116 NanoFolder: 0.238 Positive Predictive Value CMfinder(seed): 0.659 NanoFolder: 0.170 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 RSpredict(seed): 0.000 Sensitivity CMfinder(seed): 0.159 RSpredict(seed): 0.000 Positive Predictive Value CMfinder(seed): 0.770 RSpredict(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	? CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 Carnac(seed): 0.000 Sensitivity CMfinder(seed): 0.159 Carnac(seed): 0.000 Positive Predictive Value CMfinder(seed): 0.770 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-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	+ CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 Mastr(seed): 0.000 Sensitivity CMfinder(seed): 0.159 Mastr(seed): 0.000 Positive Predictive Value CMfinder(seed): 0.770 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08
Carnac(20)	204 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.840 Carnac(20): 0.360 Sensitivity ContextFold: 0.791 Carnac(20): 0.151 Positive Predictive Value ContextFold: 0.892 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 Carnac(20): 0.360 Sensitivity PETfold_pre2.0(seed): 0.673 Carnac(20): 0.151 Positive Predictive Value PETfold_pre2.0(seed): 0.845 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.740 Carnac(20): 0.360 Sensitivity TurboFold(20): 0.685 Carnac(20): 0.151 Positive Predictive Value TurboFold(20): 0.801 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Carnac(20): 0.360 Sensitivity PETfold_pre2.0(20): 0.652 Carnac(20): 0.151 Positive Predictive Value PETfold_pre2.0(20): 0.829 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.734 Carnac(20): 0.365 Sensitivity PPfold(20): 0.635 Carnac(20): 0.156 Positive Predictive Value PPfold(20): 0.850 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Carnac(20): 0.360 Sensitivity CentroidAlifold(20): 0.561 Carnac(20): 0.151 Positive Predictive Value CentroidAlifold(20): 0.916 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 Carnac(20): 0.332 Sensitivity CentroidAlifold(seed): 0.548 Carnac(20): 0.126 Positive Predictive Value CentroidAlifold(seed): 0.951 Carnac(20): 0.880 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 Carnac(20): 0.360 Sensitivity CentroidHomfold‑LAST: 0.551 Carnac(20): 0.151 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Carnac(20): 0.360 Sensitivity RNAalifold(20): 0.532 Carnac(20): 0.151 Positive Predictive Value RNAalifold(20): 0.819 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.648 Carnac(20): 0.360 Sensitivity IPknot: 0.574 Carnac(20): 0.151 Positive Predictive Value IPknot: 0.733 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.649 Carnac(20): 0.346 Sensitivity Multilign(20): 0.590 Carnac(20): 0.140 Positive Predictive Value Multilign(20): 0.717 Carnac(20): 0.854 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.616 Carnac(20): 0.360 Sensitivity CentroidFold: 0.547 Carnac(20): 0.151 Positive Predictive Value CentroidFold: 0.695 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.601 Carnac(20): 0.360 Sensitivity Contrafold: 0.576 Carnac(20): 0.151 Positive Predictive Value Contrafold: 0.628 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.626 Carnac(20): 0.360 Sensitivity MXScarna(20): 0.551 Carnac(20): 0.151 Positive Predictive Value MXScarna(20): 0.712 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 Carnac(20): 0.331 Sensitivity MXScarna(seed): 0.542 Carnac(20): 0.125 Positive Predictive Value MXScarna(seed): 0.793 Carnac(20): 0.878 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.587 Carnac(20): 0.360 Sensitivity MaxExpect: 0.561 Carnac(20): 0.151 Positive Predictive Value MaxExpect: 0.615 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.586 Carnac(20): 0.360 Sensitivity ProbKnot: 0.564 Carnac(20): 0.151 Positive Predictive Value ProbKnot: 0.610 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.543 Carnac(20): 0.453 Sensitivity RNASampler(20): 0.425 Carnac(20): 0.249 Positive Predictive Value RNASampler(20): 0.695 Carnac(20): 0.827 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.568 Carnac(20): 0.360 Sensitivity Sfold: 0.503 Carnac(20): 0.151 Positive Predictive Value Sfold: 0.643 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.550 Carnac(20): 0.360 Sensitivity Fold: 0.541 Carnac(20): 0.151 Positive Predictive Value Fold: 0.560 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.548 Carnac(20): 0.387 Sensitivity Murlet(20): 0.415 Carnac(20): 0.175 Positive Predictive Value Murlet(20): 0.725 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.531 Carnac(20): 0.360 Sensitivity UNAFold: 0.519 Carnac(20): 0.151 Positive Predictive Value UNAFold: 0.545 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.512 Carnac(20): 0.360 Sensitivity PknotsRG: 0.503 Carnac(20): 0.151 Positive Predictive Value PknotsRG: 0.523 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAfold vs Carnac(20) Matthews Correlation Coefficient RNAfold: 0.527 Carnac(20): 0.360 Sensitivity RNAfold: 0.518 Carnac(20): 0.151 Positive Predictive Value RNAfold: 0.537 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 Afold vs Carnac(20) Matthews Correlation Coefficient Afold: 0.548 Carnac(20): 0.317 Sensitivity Afold: 0.533 Carnac(20): 0.114 Positive Predictive Value Afold: 0.564 Carnac(20): 0.879 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.519 Carnac(20): 0.360 Sensitivity RNAsubopt: 0.518 Carnac(20): 0.151 Positive Predictive Value RNAsubopt: 0.522 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.452 Carnac(20): 0.360 Sensitivity McQFold: 0.433 Carnac(20): 0.151 Positive Predictive Value McQFold: 0.474 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.479 Carnac(20): 0.360 Sensitivity CMfinder(20): 0.308 Carnac(20): 0.151 Positive Predictive Value CMfinder(20): 0.747 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.454 Carnac(20): 0.353 Sensitivity RNASLOpt: 0.419 Carnac(20): 0.146 Positive Predictive Value RNASLOpt: 0.494 Carnac(20): 0.854 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.446 Carnac(20): 0.332 Sensitivity RNAalifold(seed): 0.249 Carnac(20): 0.126 Positive Predictive Value RNAalifold(seed): 0.799 Carnac(20): 0.880 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.456 Carnac(20): 0.359 Sensitivity RNAshapes: 0.441 Carnac(20): 0.150 Positive Predictive Value RNAshapes: 0.473 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.454 Carnac(20): 0.360 Sensitivity CRWrnafold: 0.446 Carnac(20): 0.151 Positive Predictive Value CRWrnafold: 0.465 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 Vsfold4 vs Carnac(20) Matthews Correlation Coefficient Vsfold4: 0.390 Carnac(20): 0.358 Sensitivity Vsfold4: 0.352 Carnac(20): 0.150 Positive Predictive Value Vsfold4: 0.433 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAwolf vs Carnac(20) Matthews Correlation Coefficient RNAwolf: 0.367 Carnac(20): 0.360 Sensitivity RNAwolf: 0.377 Carnac(20): 0.151 Positive Predictive Value RNAwolf: 0.359 Carnac(20): 0.857 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 8.81311508309e-08	196 Vsfold5 vs Carnac(20) Matthews Correlation Coefficient Vsfold5: 0.369 Carnac(20): 0.359 Sensitivity Vsfold5: 0.342 Carnac(20): 0.150 Positive Predictive Value Vsfold5: 0.400 Carnac(20): 0.859 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 4.83792096436e-08	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		+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.360 RSpredict(20): 0.347 Sensitivity Carnac(20): 0.151 RSpredict(20): 0.220 Positive Predictive Value Carnac(20): 0.857 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.385 NanoFolder: 0.152 Sensitivity Carnac(20): 0.173 NanoFolder: 0.174 Positive Predictive Value Carnac(20): 0.859 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.331 RSpredict(seed): 0.054 Sensitivity Carnac(20): 0.125 RSpredict(seed): 0.014 Positive Predictive Value Carnac(20): 0.879 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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 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	? HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: N/A Carnac(20): N/A Sensitivity HotKnots: N/A Carnac(20): N/A Positive Predictive Value HotKnots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Carnac(20) Matthews Correlation Coefficient Pknots: N/A Carnac(20): N/A Sensitivity Pknots: N/A Carnac(20): N/A Positive Predictive Value Pknots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: N/A Carnac(20): N/A Sensitivity Cylofold: N/A Carnac(20): N/A Positive Predictive Value Cylofold: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): N/A MCFold: N/A Sensitivity Carnac(20): N/A MCFold: N/A Positive Predictive Value Carnac(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RDfolder vs Carnac(20) Matthews Correlation Coefficient RDfolder: N/A Carnac(20): N/A Sensitivity RDfolder: N/A Carnac(20): N/A Positive Predictive Value RDfolder: 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	? 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	? Alterna vs Carnac(20) Matthews Correlation Coefficient Alterna: N/A Carnac(20): N/A Sensitivity Alterna: N/A Carnac(20): N/A Positive Predictive Value Alterna: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.000 Carnac(seed): 0.000 Sensitivity Carnac(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Carnac(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.360 Mastr(20): 0.000 Sensitivity Carnac(20): 0.151 Mastr(20): 0.000 Positive Predictive Value Carnac(20): 0.857 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.334 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.127 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.880 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(20)	204 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.840 RSpredict(20): 0.347 Sensitivity ContextFold: 0.791 RSpredict(20): 0.220 Positive Predictive Value ContextFold: 0.892 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 RSpredict(20): 0.347 Sensitivity PETfold_pre2.0(seed): 0.673 RSpredict(20): 0.220 Positive Predictive Value PETfold_pre2.0(seed): 0.845 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.740 RSpredict(20): 0.347 Sensitivity TurboFold(20): 0.685 RSpredict(20): 0.220 Positive Predictive Value TurboFold(20): 0.801 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RSpredict(20): 0.347 Sensitivity PETfold_pre2.0(20): 0.652 RSpredict(20): 0.220 Positive Predictive Value PETfold_pre2.0(20): 0.829 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.734 RSpredict(20): 0.349 Sensitivity PPfold(20): 0.635 RSpredict(20): 0.222 Positive Predictive Value PPfold(20): 0.850 RSpredict(20): 0.551 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 RSpredict(20): 0.347 Sensitivity CentroidAlifold(20): 0.561 RSpredict(20): 0.220 Positive Predictive Value CentroidAlifold(20): 0.916 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 RSpredict(20): 0.306 Sensitivity CentroidAlifold(seed): 0.548 RSpredict(20): 0.174 Positive Predictive Value CentroidAlifold(seed): 0.951 RSpredict(20): 0.541 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 RSpredict(20): 0.347 Sensitivity CentroidHomfold‑LAST: 0.551 RSpredict(20): 0.220 Positive Predictive Value CentroidHomfold‑LAST: 0.896 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 RSpredict(20): 0.347 Sensitivity RNAalifold(20): 0.532 RSpredict(20): 0.220 Positive Predictive Value RNAalifold(20): 0.819 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.648 RSpredict(20): 0.347 Sensitivity IPknot: 0.574 RSpredict(20): 0.220 Positive Predictive Value IPknot: 0.733 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.649 RSpredict(20): 0.332 Sensitivity Multilign(20): 0.590 RSpredict(20): 0.207 Positive Predictive Value Multilign(20): 0.717 RSpredict(20): 0.533 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.616 RSpredict(20): 0.347 Sensitivity CentroidFold: 0.547 RSpredict(20): 0.220 Positive Predictive Value CentroidFold: 0.695 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.601 RSpredict(20): 0.347 Sensitivity Contrafold: 0.576 RSpredict(20): 0.220 Positive Predictive Value Contrafold: 0.628 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.626 RSpredict(20): 0.347 Sensitivity MXScarna(20): 0.551 RSpredict(20): 0.220 Positive Predictive Value MXScarna(20): 0.712 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 RSpredict(20): 0.304 Sensitivity MXScarna(seed): 0.542 RSpredict(20): 0.172 Positive Predictive Value MXScarna(seed): 0.793 RSpredict(20): 0.538 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.587 RSpredict(20): 0.347 Sensitivity MaxExpect: 0.561 RSpredict(20): 0.220 Positive Predictive Value MaxExpect: 0.615 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.586 RSpredict(20): 0.347 Sensitivity ProbKnot: 0.564 RSpredict(20): 0.220 Positive Predictive Value ProbKnot: 0.610 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.543 RSpredict(20): 0.477 Sensitivity RNASampler(20): 0.425 RSpredict(20): 0.406 Positive Predictive Value RNASampler(20): 0.695 RSpredict(20): 0.561 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.568 RSpredict(20): 0.347 Sensitivity Sfold: 0.503 RSpredict(20): 0.220 Positive Predictive Value Sfold: 0.643 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.550 RSpredict(20): 0.347 Sensitivity Fold: 0.541 RSpredict(20): 0.220 Positive Predictive Value Fold: 0.560 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.548 RSpredict(20): 0.378 Sensitivity Murlet(20): 0.415 RSpredict(20): 0.254 Positive Predictive Value Murlet(20): 0.725 RSpredict(20): 0.565 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.531 RSpredict(20): 0.347 Sensitivity UNAFold: 0.519 RSpredict(20): 0.220 Positive Predictive Value UNAFold: 0.545 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.512 RSpredict(20): 0.347 Sensitivity PknotsRG: 0.503 RSpredict(20): 0.220 Positive Predictive Value PknotsRG: 0.523 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.527 RSpredict(20): 0.347 Sensitivity RNAfold: 0.518 RSpredict(20): 0.220 Positive Predictive Value RNAfold: 0.537 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.548 RSpredict(20): 0.297 Sensitivity Afold: 0.533 RSpredict(20): 0.170 Positive Predictive Value Afold: 0.564 RSpredict(20): 0.523 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.519 RSpredict(20): 0.347 Sensitivity RNAsubopt: 0.518 RSpredict(20): 0.220 Positive Predictive Value RNAsubopt: 0.522 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.452 RSpredict(20): 0.347 Sensitivity McQFold: 0.433 RSpredict(20): 0.220 Positive Predictive Value McQFold: 0.474 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.479 RSpredict(20): 0.347 Sensitivity CMfinder(20): 0.308 RSpredict(20): 0.220 Positive Predictive Value CMfinder(20): 0.747 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.454 RSpredict(20): 0.352 Sensitivity RNASLOpt: 0.419 RSpredict(20): 0.224 Positive Predictive Value RNASLOpt: 0.494 RSpredict(20): 0.554 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.446 RSpredict(20): 0.306 Sensitivity RNAalifold(seed): 0.249 RSpredict(20): 0.174 Positive Predictive Value RNAalifold(seed): 0.799 RSpredict(20): 0.541 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.456 RSpredict(20): 0.352 Sensitivity RNAshapes: 0.441 RSpredict(20): 0.224 Positive Predictive Value RNAshapes: 0.473 RSpredict(20): 0.556 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.454 RSpredict(20): 0.347 Sensitivity CRWrnafold: 0.446 RSpredict(20): 0.220 Positive Predictive Value CRWrnafold: 0.465 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 Vsfold4 vs RSpredict(20) Matthews Correlation Coefficient Vsfold4: 0.390 RSpredict(20): 0.350 Sensitivity Vsfold4: 0.352 RSpredict(20): 0.223 Positive Predictive Value Vsfold4: 0.433 RSpredict(20): 0.553 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAwolf vs RSpredict(20) Matthews Correlation Coefficient RNAwolf: 0.367 RSpredict(20): 0.347 Sensitivity RNAwolf: 0.377 RSpredict(20): 0.220 Positive Predictive Value RNAwolf: 0.359 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 Vsfold5 vs RSpredict(20) Matthews Correlation Coefficient Vsfold5: 0.369 RSpredict(20): 0.351 Sensitivity Vsfold5: 0.342 RSpredict(20): 0.224 Positive Predictive Value Vsfold5: 0.400 RSpredict(20): 0.552 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	204 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.360 RSpredict(20): 0.347 Sensitivity Carnac(20): 0.151 RSpredict(20): 0.220 Positive Predictive Value Carnac(20): 0.857 RSpredict(20): 0.550 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.348 NanoFolder: 0.152 Sensitivity RSpredict(20): 0.218 NanoFolder: 0.174 Positive Predictive Value RSpredict(20): 0.558 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.305 RSpredict(seed): 0.054 Sensitivity RSpredict(20): 0.173 RSpredict(seed): 0.014 Positive Predictive Value RSpredict(20): 0.540 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	? 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	? 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	? RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): N/A HotKnots: N/A Sensitivity RSpredict(20): N/A HotKnots: N/A Positive Predictive Value RSpredict(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): N/A Pknots: N/A Sensitivity RSpredict(20): N/A Pknots: N/A Positive Predictive Value RSpredict(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): N/A Cylofold: N/A Sensitivity RSpredict(20): N/A Cylofold: N/A Positive Predictive Value RSpredict(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): N/A MCFold: N/A Sensitivity RSpredict(20): N/A MCFold: N/A Positive Predictive Value RSpredict(20): N/A MCFold: 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	? RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): N/A RDfolder: N/A Sensitivity RSpredict(20): N/A RDfolder: N/A Positive Predictive Value RSpredict(20): N/A RDfolder: 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	? 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	? RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): N/A Alterna: N/A Sensitivity RSpredict(20): N/A Alterna: N/A Positive Predictive Value RSpredict(20): N/A Alterna: 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): 0.469 Carnac(seed): 0.000 Sensitivity RSpredict(20): 0.323 Carnac(seed): 0.000 Positive Predictive Value RSpredict(20): 0.683 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.347 Mastr(20): 0.000 Sensitivity RSpredict(20): 0.220 Mastr(20): 0.000 Positive Predictive Value RSpredict(20): 0.550 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.303 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.171 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
NanoFolder	105 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.757 NanoFolder: 0.172 Sensitivity ContextFold: 0.714 NanoFolder: 0.204 Positive Predictive Value ContextFold: 0.804 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.691 NanoFolder: 0.176 Sensitivity PETfold_pre2.0(seed): 0.597 NanoFolder: 0.208 Positive Predictive Value PETfold_pre2.0(seed): 0.800 NanoFolder: 0.151 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.728 NanoFolder: 0.152 Sensitivity TurboFold(20): 0.674 NanoFolder: 0.174 Positive Predictive Value TurboFold(20): 0.787 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.733 NanoFolder: 0.152 Sensitivity PETfold_pre2.0(20): 0.649 NanoFolder: 0.174 Positive Predictive Value PETfold_pre2.0(20): 0.829 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.732 NanoFolder: 0.155 Sensitivity PPfold(20): 0.632 NanoFolder: 0.178 Positive Predictive Value PPfold(20): 0.849 NanoFolder: 0.138 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.711 NanoFolder: 0.152 Sensitivity CentroidAlifold(20): 0.560 NanoFolder: 0.174 Positive Predictive Value CentroidAlifold(20): 0.905 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 NanoFolder: 0.180 Sensitivity CentroidAlifold(seed): 0.512 NanoFolder: 0.206 Positive Predictive Value CentroidAlifold(seed): 0.912 NanoFolder: 0.161 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	103 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.647 NanoFolder: 0.174 Sensitivity CentroidHomfold‑LAST: 0.478 NanoFolder: 0.207 Positive Predictive Value CentroidHomfold‑LAST: 0.877 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.658 NanoFolder: 0.152 Sensitivity RNAalifold(20): 0.536 NanoFolder: 0.174 Positive Predictive Value RNAalifold(20): 0.810 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.627 NanoFolder: 0.172 Sensitivity IPknot: 0.564 NanoFolder: 0.204 Positive Predictive Value IPknot: 0.699 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.633 NanoFolder: 0.160 Sensitivity Multilign(20): 0.577 NanoFolder: 0.182 Positive Predictive Value Multilign(20): 0.696 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.585 NanoFolder: 0.172 Sensitivity CentroidFold: 0.527 NanoFolder: 0.204 Positive Predictive Value CentroidFold: 0.651 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.563 NanoFolder: 0.172 Sensitivity Contrafold: 0.549 NanoFolder: 0.204 Positive Predictive Value Contrafold: 0.580 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.629 NanoFolder: 0.152 Sensitivity MXScarna(20): 0.554 NanoFolder: 0.174 Positive Predictive Value MXScarna(20): 0.716 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.587 NanoFolder: 0.180 Sensitivity MXScarna(seed): 0.470 NanoFolder: 0.206 Positive Predictive Value MXScarna(seed): 0.734 NanoFolder: 0.161 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.549 NanoFolder: 0.172 Sensitivity MaxExpect: 0.532 NanoFolder: 0.204 Positive Predictive Value MaxExpect: 0.568 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.547 NanoFolder: 0.172 Sensitivity ProbKnot: 0.539 NanoFolder: 0.204 Positive Predictive Value ProbKnot: 0.557 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.618 NanoFolder: 0.097 Sensitivity RNASampler(20): 0.506 NanoFolder: 0.120 Positive Predictive Value RNASampler(20): 0.755 NanoFolder: 0.081 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	105 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.540 NanoFolder: 0.172 Sensitivity Sfold: 0.483 NanoFolder: 0.204 Positive Predictive Value Sfold: 0.605 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.511 NanoFolder: 0.172 Sensitivity Fold: 0.511 NanoFolder: 0.204 Positive Predictive Value Fold: 0.512 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.539 NanoFolder: 0.151 Sensitivity Murlet(20): 0.402 NanoFolder: 0.174 Positive Predictive Value Murlet(20): 0.723 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.498 NanoFolder: 0.172 Sensitivity UNAFold: 0.493 NanoFolder: 0.204 Positive Predictive Value UNAFold: 0.505 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.488 NanoFolder: 0.172 Sensitivity PknotsRG: 0.488 NanoFolder: 0.204 Positive Predictive Value PknotsRG: 0.490 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.493 NanoFolder: 0.172 Sensitivity RNAfold: 0.492 NanoFolder: 0.204 Positive Predictive Value RNAfold: 0.497 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.525 NanoFolder: 0.169 Sensitivity Afold: 0.516 NanoFolder: 0.195 Positive Predictive Value Afold: 0.535 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	103 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.505 NanoFolder: 0.174 Sensitivity RNAsubopt: 0.510 NanoFolder: 0.207 Positive Predictive Value RNAsubopt: 0.501 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.443 NanoFolder: 0.172 Sensitivity McQFold: 0.431 NanoFolder: 0.204 Positive Predictive Value McQFold: 0.457 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.482 NanoFolder: 0.152 Sensitivity CMfinder(20): 0.306 NanoFolder: 0.174 Positive Predictive Value CMfinder(20): 0.762 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.460 NanoFolder: 0.179 Sensitivity RNASLOpt: 0.428 NanoFolder: 0.210 Positive Predictive Value RNASLOpt: 0.496 NanoFolder: 0.155 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.454 NanoFolder: 0.180 Sensitivity RNAalifold(seed): 0.257 NanoFolder: 0.206 Positive Predictive Value RNAalifold(seed): 0.801 NanoFolder: 0.161 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	101 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.433 NanoFolder: 0.175 Sensitivity RNAshapes: 0.426 NanoFolder: 0.207 Positive Predictive Value RNAshapes: 0.443 NanoFolder: 0.151 Number of pairs reference - predicted secondary structure: 101 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.442 NanoFolder: 0.172 Sensitivity CRWrnafold: 0.443 NanoFolder: 0.204 Positive Predictive Value CRWrnafold: 0.443 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	102 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.360 NanoFolder: 0.175 Sensitivity Vsfold4: 0.328 NanoFolder: 0.208 Positive Predictive Value Vsfold4: 0.396 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.334 NanoFolder: 0.172 Sensitivity RNAwolf: 0.346 NanoFolder: 0.204 Positive Predictive Value RNAwolf: 0.324 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	100 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.340 NanoFolder: 0.176 Sensitivity Vsfold5: 0.319 NanoFolder: 0.208 Positive Predictive Value Vsfold5: 0.366 NanoFolder: 0.151 Number of pairs reference - predicted secondary structure: 100 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.276 NanoFolder: 0.200 Sensitivity CMfinder(seed): 0.116 NanoFolder: 0.238 Positive Predictive Value CMfinder(seed): 0.659 NanoFolder: 0.170 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	49 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.385 NanoFolder: 0.152 Sensitivity Carnac(20): 0.173 NanoFolder: 0.174 Positive Predictive Value Carnac(20): 0.859 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.348 NanoFolder: 0.152 Sensitivity RSpredict(20): 0.218 NanoFolder: 0.174 Positive Predictive Value RSpredict(20): 0.558 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.180 RSpredict(seed): 0.029 Sensitivity NanoFolder: 0.206 RSpredict(seed): 0.007 Positive Predictive Value NanoFolder: 0.161 RSpredict(seed): 0.122 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	? NanoFolder vs Murlet(seed) Matthews Correlation Coefficient NanoFolder: N/A Murlet(seed): N/A Sensitivity NanoFolder: N/A Murlet(seed): N/A Positive Predictive Value NanoFolder: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs Multilign(seed) Matthews Correlation Coefficient NanoFolder: N/A Multilign(seed): N/A Sensitivity NanoFolder: N/A Multilign(seed): N/A Positive Predictive Value NanoFolder: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs HotKnots Matthews Correlation Coefficient NanoFolder: N/A HotKnots: N/A Sensitivity NanoFolder: N/A HotKnots: N/A Positive Predictive Value NanoFolder: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs Pknots Matthews Correlation Coefficient NanoFolder: N/A Pknots: N/A Sensitivity NanoFolder: N/A Pknots: N/A Positive Predictive Value NanoFolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.378 NanoFolder: 0.076 Sensitivity Cylofold: 0.333 NanoFolder: 0.091 Positive Predictive Value Cylofold: 0.431 NanoFolder: 0.067 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: N/A MCFold: N/A Sensitivity NanoFolder: N/A MCFold: N/A Positive Predictive Value NanoFolder: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: N/A PPfold(seed): N/A Sensitivity NanoFolder: N/A PPfold(seed): N/A Positive Predictive Value NanoFolder: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: N/A RDfolder: N/A Sensitivity NanoFolder: N/A RDfolder: N/A Positive Predictive Value NanoFolder: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs TurboFold(seed) Matthews Correlation Coefficient NanoFolder: N/A TurboFold(seed): N/A Sensitivity NanoFolder: N/A TurboFold(seed): N/A Positive Predictive Value NanoFolder: N/A TurboFold(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: N/A RNASampler(seed): N/A Sensitivity NanoFolder: N/A RNASampler(seed): N/A Positive Predictive Value NanoFolder: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs Alterna Matthews Correlation Coefficient NanoFolder: N/A Alterna: N/A Sensitivity NanoFolder: N/A Alterna: N/A Positive Predictive Value NanoFolder: N/A Alterna: 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: 0.251 Carnac(seed): 0.000 Sensitivity NanoFolder: 0.296 Carnac(seed): 0.000 Positive Predictive Value NanoFolder: 0.215 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ NanoFolder vs Mastr(20) Matthews Correlation Coefficient NanoFolder: 0.152 Mastr(20): 0.000 Sensitivity NanoFolder: 0.174 Mastr(20): 0.000 Positive Predictive Value NanoFolder: 0.135 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.179 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.205 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.159 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(seed)	280 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.813 RSpredict(seed): 0.045 Sensitivity ContextFold: 0.765 RSpredict(seed): 0.011 Positive Predictive Value ContextFold: 0.864 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.721 RSpredict(seed): 0.045 Sensitivity PETfold_pre2.0(seed): 0.633 RSpredict(seed): 0.011 Positive Predictive Value PETfold_pre2.0(seed): 0.822 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 RSpredict(seed): 0.054 Sensitivity TurboFold(20): 0.703 RSpredict(seed): 0.014 Positive Predictive Value TurboFold(20): 0.823 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.755 RSpredict(seed): 0.054 Sensitivity PETfold_pre2.0(20): 0.671 RSpredict(seed): 0.014 Positive Predictive Value PETfold_pre2.0(20): 0.849 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	157 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.753 RSpredict(seed): 0.055 Sensitivity PPfold(20): 0.658 RSpredict(seed): 0.014 Positive Predictive Value PPfold(20): 0.862 RSpredict(seed): 0.219 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.724 RSpredict(seed): 0.054 Sensitivity CentroidAlifold(20): 0.563 RSpredict(seed): 0.014 Positive Predictive Value CentroidAlifold(20): 0.933 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	277 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.691 RSpredict(seed): 0.045 Sensitivity CentroidAlifold(seed): 0.521 RSpredict(seed): 0.011 Positive Predictive Value CentroidAlifold(seed): 0.919 RSpredict(seed): 0.186 Number of pairs reference - predicted secondary structure: 277 Wilcoxon single-rank test P-value: 3.56938820447e-08	276 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.675 RSpredict(seed): 0.046 Sensitivity CentroidHomfold‑LAST: 0.508 RSpredict(seed): 0.011 Positive Predictive Value CentroidHomfold‑LAST: 0.899 RSpredict(seed): 0.194 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.668 RSpredict(seed): 0.054 Sensitivity RNAalifold(20): 0.534 RSpredict(seed): 0.014 Positive Predictive Value RNAalifold(20): 0.838 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.640 RSpredict(seed): 0.045 Sensitivity IPknot: 0.567 RSpredict(seed): 0.011 Positive Predictive Value IPknot: 0.723 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.657 RSpredict(seed): 0.057 Sensitivity Multilign(20): 0.594 RSpredict(seed): 0.014 Positive Predictive Value Multilign(20): 0.728 RSpredict(seed): 0.228 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.621 RSpredict(seed): 0.045 Sensitivity CentroidFold: 0.553 RSpredict(seed): 0.011 Positive Predictive Value CentroidFold: 0.698 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.604 RSpredict(seed): 0.045 Sensitivity Contrafold: 0.579 RSpredict(seed): 0.011 Positive Predictive Value Contrafold: 0.631 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.651 RSpredict(seed): 0.054 Sensitivity MXScarna(20): 0.564 RSpredict(seed): 0.014 Positive Predictive Value MXScarna(20): 0.753 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	279 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.595 RSpredict(seed): 0.045 Sensitivity MXScarna(seed): 0.475 RSpredict(seed): 0.011 Positive Predictive Value MXScarna(seed): 0.746 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 279 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.589 RSpredict(seed): 0.045 Sensitivity MaxExpect: 0.564 RSpredict(seed): 0.011 Positive Predictive Value MaxExpect: 0.617 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.588 RSpredict(seed): 0.045 Sensitivity ProbKnot: 0.567 RSpredict(seed): 0.011 Positive Predictive Value ProbKnot: 0.611 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.480 RSpredict(seed): 0.006 Sensitivity RNASampler(20): 0.343 RSpredict(seed): 0.001 Positive Predictive Value RNASampler(20): 0.673 RSpredict(seed): 0.030 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	280 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.585 RSpredict(seed): 0.045 Sensitivity Sfold: 0.520 RSpredict(seed): 0.011 Positive Predictive Value Sfold: 0.660 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.552 RSpredict(seed): 0.045 Sensitivity Fold: 0.543 RSpredict(seed): 0.011 Positive Predictive Value Fold: 0.563 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.533 RSpredict(seed): 0.059 Sensitivity Murlet(20): 0.389 RSpredict(seed): 0.015 Positive Predictive Value Murlet(20): 0.732 RSpredict(seed): 0.233 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.544 RSpredict(seed): 0.045 Sensitivity UNAFold: 0.531 RSpredict(seed): 0.011 Positive Predictive Value UNAFold: 0.560 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.527 RSpredict(seed): 0.045 Sensitivity PknotsRG: 0.517 RSpredict(seed): 0.011 Positive Predictive Value PknotsRG: 0.539 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.535 RSpredict(seed): 0.045 Sensitivity RNAfold: 0.525 RSpredict(seed): 0.011 Positive Predictive Value RNAfold: 0.548 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.531 RSpredict(seed): 0.042 Sensitivity Afold: 0.518 RSpredict(seed): 0.010 Positive Predictive Value Afold: 0.545 RSpredict(seed): 0.179 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	276 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.534 RSpredict(seed): 0.046 Sensitivity RNAsubopt: 0.531 RSpredict(seed): 0.011 Positive Predictive Value RNAsubopt: 0.538 RSpredict(seed): 0.194 Number of pairs reference - predicted secondary structure: 276 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.479 RSpredict(seed): 0.045 Sensitivity McQFold: 0.458 RSpredict(seed): 0.011 Positive Predictive Value McQFold: 0.503 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.504 RSpredict(seed): 0.054 Sensitivity CMfinder(20): 0.331 RSpredict(seed): 0.014 Positive Predictive Value CMfinder(20): 0.769 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	231 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.475 RSpredict(seed): 0.036 Sensitivity RNASLOpt: 0.437 RSpredict(seed): 0.008 Positive Predictive Value RNASLOpt: 0.518 RSpredict(seed): 0.159 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08	278 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.469 RSpredict(seed): 0.045 Sensitivity RNAalifold(seed): 0.272 RSpredict(seed): 0.011 Positive Predictive Value RNAalifold(seed): 0.811 RSpredict(seed): 0.187 Number of pairs reference - predicted secondary structure: 278 Wilcoxon single-rank test P-value: 3.56938820447e-08	256 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.485 RSpredict(seed): 0.039 Sensitivity RNAshapes: 0.469 RSpredict(seed): 0.009 Positive Predictive Value RNAshapes: 0.504 RSpredict(seed): 0.166 Number of pairs reference - predicted secondary structure: 256 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.457 RSpredict(seed): 0.045 Sensitivity CRWrnafold: 0.449 RSpredict(seed): 0.011 Positive Predictive Value CRWrnafold: 0.467 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	262 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.406 RSpredict(seed): 0.044 Sensitivity Vsfold4: 0.366 RSpredict(seed): 0.011 Positive Predictive Value Vsfold4: 0.453 RSpredict(seed): 0.186 Number of pairs reference - predicted secondary structure: 262 Wilcoxon single-rank test P-value: 3.56938820447e-08	280 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.372 RSpredict(seed): 0.045 Sensitivity RNAwolf: 0.380 RSpredict(seed): 0.011 Positive Predictive Value RNAwolf: 0.365 RSpredict(seed): 0.189 Number of pairs reference - predicted secondary structure: 280 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.379 RSpredict(seed): 0.038 Sensitivity Vsfold5: 0.349 RSpredict(seed): 0.009 Positive Predictive Value Vsfold5: 0.414 RSpredict(seed): 0.164 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 RSpredict(seed): 0.000 Sensitivity CMfinder(seed): 0.159 RSpredict(seed): 0.000 Positive Predictive Value CMfinder(seed): 0.770 RSpredict(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.61939086268e-08	164 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.331 RSpredict(seed): 0.054 Sensitivity Carnac(20): 0.125 RSpredict(seed): 0.014 Positive Predictive Value Carnac(20): 0.879 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.305 RSpredict(seed): 0.054 Sensitivity RSpredict(20): 0.173 RSpredict(seed): 0.014 Positive Predictive Value RSpredict(20): 0.540 RSpredict(seed): 0.216 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.180 RSpredict(seed): 0.029 Sensitivity NanoFolder: 0.206 RSpredict(seed): 0.007 Positive Predictive Value NanoFolder: 0.161 RSpredict(seed): 0.122 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08		? RSpredict(seed) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(seed): N/A Murlet(seed): N/A Sensitivity RSpredict(seed): N/A Murlet(seed): N/A Positive Predictive Value RSpredict(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(seed): N/A Multilign(seed): N/A Sensitivity RSpredict(seed): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs HotKnots Matthews Correlation Coefficient RSpredict(seed): N/A HotKnots: N/A Sensitivity RSpredict(seed): N/A HotKnots: N/A Positive Predictive Value RSpredict(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs Pknots Matthews Correlation Coefficient RSpredict(seed): N/A Pknots: N/A Sensitivity RSpredict(seed): N/A Pknots: N/A Positive Predictive Value RSpredict(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs Cylofold Matthews Correlation Coefficient RSpredict(seed): N/A Cylofold: N/A Sensitivity RSpredict(seed): N/A Cylofold: N/A Positive Predictive Value RSpredict(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): N/A MCFold: N/A Sensitivity RSpredict(seed): N/A MCFold: N/A Positive Predictive Value RSpredict(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): N/A PPfold(seed): N/A Sensitivity RSpredict(seed): N/A PPfold(seed): N/A Positive Predictive Value RSpredict(seed): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): N/A RDfolder: N/A Sensitivity RSpredict(seed): N/A RDfolder: N/A Positive Predictive Value RSpredict(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 RSpredict(seed): 0.000 Sensitivity TurboFold(seed): 0.677 RSpredict(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.746 RSpredict(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): N/A RSpredict(seed): N/A Sensitivity RNASampler(seed): N/A RSpredict(seed): N/A Positive Predictive Value RNASampler(seed): N/A RSpredict(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): N/A Alterna: N/A Sensitivity RSpredict(seed): N/A Alterna: N/A Positive Predictive Value RSpredict(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.072 Carnac(seed): 0.000 Sensitivity RSpredict(seed): 0.016 Carnac(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.327 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(20) Matthews Correlation Coefficient RSpredict(seed): 0.054 Mastr(20): 0.000 Sensitivity RSpredict(seed): 0.014 Mastr(20): 0.000 Positive Predictive Value RSpredict(seed): 0.216 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.046 Mastr(seed): 0.000 Sensitivity RSpredict(seed): 0.011 Mastr(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.191 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 253 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(seed)	0 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: N/A Murlet(seed): N/A Sensitivity ContextFold: N/A Murlet(seed): N/A Positive Predictive Value ContextFold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Murlet(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity Murlet(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Murlet(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	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	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	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	0 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A Murlet(seed): N/A Sensitivity CentroidAlifold(seed): N/A Murlet(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Murlet(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity Murlet(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Murlet(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Murlet(seed) vs IPknot Matthews Correlation Coefficient Murlet(seed): N/A IPknot: N/A Sensitivity Murlet(seed): N/A IPknot: N/A Positive Predictive Value Murlet(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: N/A Murlet(seed): N/A Sensitivity CentroidFold: N/A Murlet(seed): N/A Positive Predictive Value CentroidFold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: N/A Murlet(seed): N/A Sensitivity Contrafold: N/A Murlet(seed): N/A Positive Predictive Value Contrafold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Murlet(seed) vs MXScarna(seed) Matthews Correlation Coefficient Murlet(seed): N/A MXScarna(seed): N/A Sensitivity Murlet(seed): N/A MXScarna(seed): N/A Positive Predictive Value Murlet(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: N/A Murlet(seed): N/A Sensitivity MaxExpect: N/A Murlet(seed): N/A Positive Predictive Value MaxExpect: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: N/A Murlet(seed): N/A Sensitivity ProbKnot: N/A Murlet(seed): N/A Positive Predictive Value ProbKnot: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Murlet(seed) vs Sfold Matthews Correlation Coefficient Murlet(seed): N/A Sfold: N/A Sensitivity Murlet(seed): N/A Sfold: N/A Positive Predictive Value Murlet(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: N/A Murlet(seed): N/A Sensitivity Fold: N/A Murlet(seed): N/A Positive Predictive Value Fold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: N/A Murlet(seed): N/A Sensitivity UNAFold: N/A Murlet(seed): N/A Positive Predictive Value UNAFold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: N/A Murlet(seed): N/A Sensitivity PknotsRG: N/A Murlet(seed): N/A Positive Predictive Value PknotsRG: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs RNAfold Matthews Correlation Coefficient Murlet(seed): N/A RNAfold: N/A Sensitivity Murlet(seed): N/A RNAfold: N/A Positive Predictive Value Murlet(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: N/A Murlet(seed): N/A Sensitivity Afold: N/A Murlet(seed): N/A Positive Predictive Value Afold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs RNAsubopt Matthews Correlation Coefficient Murlet(seed): N/A RNAsubopt: N/A Sensitivity Murlet(seed): N/A RNAsubopt: N/A Positive Predictive Value Murlet(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: N/A Murlet(seed): N/A Sensitivity McQFold: N/A Murlet(seed): N/A Positive Predictive Value McQFold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): N/A RNASLOpt: N/A Sensitivity Murlet(seed): N/A RNASLOpt: N/A Positive Predictive Value Murlet(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A Murlet(seed): N/A Sensitivity RNAalifold(seed): N/A Murlet(seed): N/A Positive Predictive Value RNAalifold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): N/A RNAshapes: N/A Sensitivity Murlet(seed): N/A RNAshapes: N/A Positive Predictive Value Murlet(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): N/A CRWrnafold: N/A Sensitivity Murlet(seed): N/A CRWrnafold: N/A Positive Predictive Value Murlet(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: N/A Murlet(seed): N/A Sensitivity Vsfold4: N/A Murlet(seed): N/A Positive Predictive Value Vsfold4: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): N/A RNAwolf: N/A Sensitivity Murlet(seed): N/A RNAwolf: N/A Positive Predictive Value Murlet(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs Murlet(seed) Matthews Correlation Coefficient Vsfold5: N/A Murlet(seed): N/A Sensitivity Vsfold5: N/A Murlet(seed): N/A Positive Predictive Value Vsfold5: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	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	0 NanoFolder vs Murlet(seed) Matthews Correlation Coefficient NanoFolder: N/A Murlet(seed): N/A Sensitivity NanoFolder: N/A Murlet(seed): N/A Positive Predictive Value NanoFolder: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(seed): N/A Murlet(seed): N/A Sensitivity RSpredict(seed): N/A Murlet(seed): N/A Positive Predictive Value RSpredict(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): N/A Murlet(seed): N/A Sensitivity Multilign(seed): N/A Murlet(seed): N/A Positive Predictive Value Multilign(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: N/A Murlet(seed): N/A Sensitivity HotKnots: N/A Murlet(seed): N/A Positive Predictive Value HotKnots: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: N/A Murlet(seed): N/A Sensitivity Pknots: N/A Murlet(seed): N/A Positive Predictive Value Pknots: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: N/A Murlet(seed): N/A Sensitivity Cylofold: N/A Murlet(seed): N/A Positive Predictive Value Cylofold: 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): N/A MCFold: N/A Sensitivity Murlet(seed): N/A MCFold: N/A Positive Predictive Value Murlet(seed): N/A MCFold: 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): N/A Murlet(seed): N/A Sensitivity PPfold(seed): N/A Murlet(seed): N/A Positive Predictive Value PPfold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: N/A Murlet(seed): N/A Sensitivity RDfolder: N/A Murlet(seed): N/A Positive Predictive Value RDfolder: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(seed): N/A Sensitivity TurboFold(seed): N/A Murlet(seed): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(seed): N/A Sensitivity RNASampler(seed): N/A Murlet(seed): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: N/A Murlet(seed): N/A Sensitivity Alterna: N/A Murlet(seed): N/A Positive Predictive Value Alterna: 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 Carnac(seed) Matthews Correlation Coefficient Murlet(seed): N/A Carnac(seed): N/A Sensitivity Murlet(seed): N/A Carnac(seed): N/A Positive Predictive Value Murlet(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? Mastr(seed) vs Murlet(seed) Matthews Correlation Coefficient Mastr(seed): N/A Murlet(seed): N/A Sensitivity Mastr(seed): N/A Murlet(seed): N/A Positive Predictive Value Mastr(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Multilign(seed)	0 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: N/A Multilign(seed): N/A Sensitivity ContextFold: N/A Multilign(seed): N/A Positive Predictive Value ContextFold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Multilign(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity Multilign(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Multilign(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	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	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	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	0 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A Multilign(seed): N/A Sensitivity CentroidAlifold(seed): N/A Multilign(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Multilign(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity Multilign(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Multilign(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Multilign(seed) vs IPknot Matthews Correlation Coefficient Multilign(seed): N/A IPknot: N/A Sensitivity Multilign(seed): N/A IPknot: N/A Positive Predictive Value Multilign(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): N/A CentroidFold: N/A Sensitivity Multilign(seed): N/A CentroidFold: N/A Positive Predictive Value Multilign(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs Contrafold Matthews Correlation Coefficient Multilign(seed): N/A Contrafold: N/A Sensitivity Multilign(seed): N/A Contrafold: N/A Positive Predictive Value Multilign(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(seed): N/A Sensitivity Multilign(seed): N/A MXScarna(seed): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: N/A Multilign(seed): N/A Sensitivity MaxExpect: N/A Multilign(seed): N/A Positive Predictive Value MaxExpect: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: N/A Multilign(seed): N/A Sensitivity ProbKnot: N/A Multilign(seed): N/A Positive Predictive Value ProbKnot: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): N/A Sfold: N/A Sensitivity Multilign(seed): N/A Sfold: N/A Positive Predictive Value Multilign(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs Multilign(seed) Matthews Correlation Coefficient Fold: N/A Multilign(seed): N/A Sensitivity Fold: N/A Multilign(seed): N/A Positive Predictive Value Fold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 UNAFold vs Multilign(seed) Matthews Correlation Coefficient UNAFold: N/A Multilign(seed): N/A Sensitivity UNAFold: N/A Multilign(seed): N/A Positive Predictive Value UNAFold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: N/A Multilign(seed): N/A Sensitivity PknotsRG: N/A Multilign(seed): N/A Positive Predictive Value PknotsRG: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): N/A RNAfold: N/A Sensitivity Multilign(seed): N/A RNAfold: N/A Positive Predictive Value Multilign(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): N/A Afold: N/A Sensitivity Multilign(seed): N/A Afold: N/A Positive Predictive Value Multilign(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): N/A RNAsubopt: N/A Sensitivity Multilign(seed): N/A RNAsubopt: N/A Positive Predictive Value Multilign(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: N/A Multilign(seed): N/A Sensitivity McQFold: N/A Multilign(seed): N/A Positive Predictive Value McQFold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): N/A RNASLOpt: N/A Sensitivity Multilign(seed): N/A RNASLOpt: N/A Positive Predictive Value Multilign(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A Multilign(seed): N/A Sensitivity RNAalifold(seed): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): N/A RNAshapes: N/A Sensitivity Multilign(seed): N/A RNAshapes: N/A Positive Predictive Value Multilign(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): N/A CRWrnafold: N/A Sensitivity Multilign(seed): N/A CRWrnafold: N/A Positive Predictive Value Multilign(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs Multilign(seed) Matthews Correlation Coefficient Vsfold4: N/A Multilign(seed): N/A Sensitivity Vsfold4: N/A Multilign(seed): N/A Positive Predictive Value Vsfold4: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): N/A RNAwolf: N/A Sensitivity Multilign(seed): N/A RNAwolf: N/A Positive Predictive Value Multilign(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs Multilign(seed) Matthews Correlation Coefficient Vsfold5: N/A Multilign(seed): N/A Sensitivity Vsfold5: N/A Multilign(seed): N/A Positive Predictive Value Vsfold5: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	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	0 NanoFolder vs Multilign(seed) Matthews Correlation Coefficient NanoFolder: N/A Multilign(seed): N/A Sensitivity NanoFolder: N/A Multilign(seed): N/A Positive Predictive Value NanoFolder: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(seed): N/A Multilign(seed): N/A Sensitivity RSpredict(seed): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): N/A Murlet(seed): N/A Sensitivity Multilign(seed): N/A Murlet(seed): N/A Positive Predictive Value Multilign(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: N/A Multilign(seed): N/A Sensitivity HotKnots: N/A Multilign(seed): N/A Positive Predictive Value HotKnots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: N/A Multilign(seed): N/A Sensitivity Pknots: N/A Multilign(seed): N/A Positive Predictive Value Pknots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: N/A Multilign(seed): N/A Sensitivity Cylofold: N/A Multilign(seed): N/A Positive Predictive Value Cylofold: 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): N/A MCFold: N/A Sensitivity Multilign(seed): N/A MCFold: N/A Positive Predictive Value Multilign(seed): N/A MCFold: 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): N/A Multilign(seed): N/A Sensitivity PPfold(seed): N/A Multilign(seed): N/A Positive Predictive Value PPfold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: N/A Multilign(seed): N/A Sensitivity RDfolder: N/A Multilign(seed): N/A Positive Predictive Value RDfolder: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): N/A Multilign(seed): N/A Sensitivity TurboFold(seed): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(seed): N/A Sensitivity RNASampler(seed): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(seed): 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 Alterna Matthews Correlation Coefficient Multilign(seed): N/A Alterna: N/A Sensitivity Multilign(seed): N/A Alterna: N/A Positive Predictive Value Multilign(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(seed): N/A Sensitivity Multilign(seed): N/A Carnac(seed): N/A Positive Predictive Value Multilign(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? Mastr(seed) vs Multilign(seed) Matthews Correlation Coefficient Mastr(seed): N/A Multilign(seed): N/A Sensitivity Mastr(seed): N/A Multilign(seed): N/A Positive Predictive Value Mastr(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
HotKnots	0 HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: N/A ContextFold: N/A Sensitivity HotKnots: N/A ContextFold: N/A Positive Predictive Value HotKnots: N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient HotKnots: N/A PETfold_pre2.0(seed): N/A Sensitivity HotKnots: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value HotKnots: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: N/A TurboFold(20): N/A Sensitivity HotKnots: N/A TurboFold(20): N/A Positive Predictive Value HotKnots: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs PETfold_pre2.0(20) Matthews Correlation Coefficient HotKnots: N/A PETfold_pre2.0(20): N/A Sensitivity HotKnots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value HotKnots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs PPfold(20) Matthews Correlation Coefficient HotKnots: N/A PPfold(20): N/A Sensitivity HotKnots: N/A PPfold(20): N/A Positive Predictive Value HotKnots: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CentroidAlifold(20) Matthews Correlation Coefficient HotKnots: N/A CentroidAlifold(20): N/A Sensitivity HotKnots: N/A CentroidAlifold(20): N/A Positive Predictive Value HotKnots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): N/A HotKnots: N/A Sensitivity CentroidAlifold(seed): N/A HotKnots: N/A Positive Predictive Value CentroidAlifold(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: N/A CentroidHomfold‑LAST: N/A Sensitivity HotKnots: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value HotKnots: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RNAalifold(20) Matthews Correlation Coefficient HotKnots: N/A RNAalifold(20): N/A Sensitivity HotKnots: N/A RNAalifold(20): N/A Positive Predictive Value HotKnots: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs IPknot Matthews Correlation Coefficient HotKnots: N/A IPknot: N/A Sensitivity HotKnots: N/A IPknot: N/A Positive Predictive Value HotKnots: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: N/A Multilign(20): N/A Sensitivity HotKnots: N/A Multilign(20): N/A Positive Predictive Value HotKnots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CentroidFold Matthews Correlation Coefficient HotKnots: N/A CentroidFold: N/A Sensitivity HotKnots: N/A CentroidFold: N/A Positive Predictive Value HotKnots: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: N/A Contrafold: N/A Sensitivity HotKnots: N/A Contrafold: N/A Positive Predictive Value HotKnots: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs MXScarna(20) Matthews Correlation Coefficient HotKnots: N/A MXScarna(20): N/A Sensitivity HotKnots: N/A MXScarna(20): N/A Positive Predictive Value HotKnots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: N/A MXScarna(seed): N/A Sensitivity HotKnots: N/A MXScarna(seed): N/A Positive Predictive Value HotKnots: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: N/A HotKnots: N/A Sensitivity MaxExpect: N/A HotKnots: N/A Positive Predictive Value MaxExpect: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: N/A ProbKnot: N/A Sensitivity HotKnots: N/A ProbKnot: N/A Positive Predictive Value HotKnots: N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): N/A HotKnots: N/A Sensitivity RNASampler(20): N/A HotKnots: N/A Positive Predictive Value RNASampler(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: N/A Sfold: N/A Sensitivity HotKnots: N/A Sfold: N/A Positive Predictive Value HotKnots: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs HotKnots Matthews Correlation Coefficient Fold: N/A HotKnots: N/A Sensitivity Fold: N/A HotKnots: N/A Positive Predictive Value Fold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Murlet(20) Matthews Correlation Coefficient HotKnots: N/A Murlet(20): N/A Sensitivity HotKnots: N/A Murlet(20): N/A Positive Predictive Value HotKnots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: N/A HotKnots: N/A Sensitivity UNAFold: N/A HotKnots: N/A Positive Predictive Value UNAFold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: N/A HotKnots: N/A Sensitivity PknotsRG: N/A HotKnots: N/A Positive Predictive Value PknotsRG: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: N/A RNAfold: N/A Sensitivity HotKnots: N/A RNAfold: N/A Positive Predictive Value HotKnots: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: N/A Afold: N/A Sensitivity HotKnots: N/A Afold: N/A Positive Predictive Value HotKnots: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: N/A RNAsubopt: N/A Sensitivity HotKnots: N/A RNAsubopt: N/A Positive Predictive Value HotKnots: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: N/A McQFold: N/A Sensitivity HotKnots: N/A McQFold: N/A Positive Predictive Value HotKnots: N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: N/A RNASLOpt: N/A Sensitivity HotKnots: N/A RNASLOpt: N/A Positive Predictive Value HotKnots: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: N/A RNAalifold(seed): N/A Sensitivity HotKnots: N/A RNAalifold(seed): N/A Positive Predictive Value HotKnots: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: N/A RNAshapes: N/A Sensitivity HotKnots: N/A RNAshapes: N/A Positive Predictive Value HotKnots: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: N/A CRWrnafold: N/A Sensitivity HotKnots: N/A CRWrnafold: N/A Positive Predictive Value HotKnots: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: N/A Vsfold4: N/A Sensitivity HotKnots: N/A Vsfold4: N/A Positive Predictive Value HotKnots: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: N/A RNAwolf: N/A Sensitivity HotKnots: N/A RNAwolf: N/A Positive Predictive Value HotKnots: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: N/A Vsfold5: N/A Sensitivity HotKnots: N/A Vsfold5: N/A Positive Predictive Value HotKnots: N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: N/A Carnac(20): N/A Sensitivity HotKnots: N/A Carnac(20): N/A Positive Predictive Value HotKnots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): N/A HotKnots: N/A Sensitivity RSpredict(20): N/A HotKnots: N/A Positive Predictive Value RSpredict(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs HotKnots Matthews Correlation Coefficient NanoFolder: N/A HotKnots: N/A Sensitivity NanoFolder: N/A HotKnots: N/A Positive Predictive Value NanoFolder: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs HotKnots Matthews Correlation Coefficient RSpredict(seed): N/A HotKnots: N/A Sensitivity RSpredict(seed): N/A HotKnots: N/A Positive Predictive Value RSpredict(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: N/A Murlet(seed): N/A Sensitivity HotKnots: N/A Murlet(seed): N/A Positive Predictive Value HotKnots: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: N/A Multilign(seed): N/A Sensitivity HotKnots: N/A Multilign(seed): N/A Positive Predictive Value HotKnots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: N/A Pknots: N/A Sensitivity HotKnots: N/A Pknots: N/A Positive Predictive Value HotKnots: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: N/A HotKnots: N/A Sensitivity Cylofold: N/A HotKnots: N/A Positive Predictive Value Cylofold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: N/A MCFold: N/A Sensitivity HotKnots: N/A MCFold: N/A Positive Predictive Value HotKnots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: N/A PPfold(seed): N/A Sensitivity HotKnots: N/A PPfold(seed): N/A Positive Predictive Value HotKnots: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: N/A RDfolder: N/A Sensitivity HotKnots: N/A RDfolder: N/A Positive Predictive Value HotKnots: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): N/A HotKnots: N/A Sensitivity TurboFold(seed): N/A HotKnots: N/A Positive Predictive Value TurboFold(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): N/A HotKnots: N/A Sensitivity RNASampler(seed): N/A HotKnots: N/A Positive Predictive Value RNASampler(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: N/A Alterna: N/A Sensitivity HotKnots: N/A Alterna: N/A Positive Predictive Value HotKnots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: N/A Carnac(seed): N/A Sensitivity HotKnots: N/A Carnac(seed): N/A Positive Predictive Value HotKnots: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): N/A HotKnots: N/A Sensitivity Mastr(20): N/A HotKnots: N/A Positive Predictive Value Mastr(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: N/A Mastr(seed): N/A Sensitivity HotKnots: N/A Mastr(seed): N/A Positive Predictive Value HotKnots: N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Pknots	0 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: N/A Pknots: N/A Sensitivity ContextFold: N/A Pknots: N/A Positive Predictive Value ContextFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(seed): N/A Sensitivity Pknots: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): N/A Pknots: N/A Sensitivity TurboFold(20): N/A Pknots: N/A Positive Predictive Value TurboFold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs PETfold_pre2.0(20) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(20): N/A Sensitivity Pknots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): N/A Pknots: N/A Sensitivity PPfold(20): N/A Pknots: N/A Positive Predictive Value PPfold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CentroidAlifold(20) Matthews Correlation Coefficient Pknots: N/A CentroidAlifold(20): N/A Sensitivity Pknots: N/A CentroidAlifold(20): N/A Positive Predictive Value Pknots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): N/A Pknots: N/A Sensitivity CentroidAlifold(seed): N/A Pknots: N/A Positive Predictive Value CentroidAlifold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: N/A CentroidHomfold‑LAST: N/A Sensitivity Pknots: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Pknots: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): N/A Pknots: N/A Sensitivity RNAalifold(20): N/A Pknots: N/A Positive Predictive Value RNAalifold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs IPknot Matthews Correlation Coefficient Pknots: N/A IPknot: N/A Sensitivity Pknots: N/A IPknot: N/A Positive Predictive Value Pknots: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Multilign(20) Matthews Correlation Coefficient Pknots: N/A Multilign(20): N/A Sensitivity Pknots: N/A Multilign(20): N/A Positive Predictive Value Pknots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: N/A CentroidFold: N/A Sensitivity Pknots: N/A CentroidFold: N/A Positive Predictive Value Pknots: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Contrafold Matthews Correlation Coefficient Pknots: N/A Contrafold: N/A Sensitivity Pknots: N/A Contrafold: N/A Positive Predictive Value Pknots: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs MXScarna(20) Matthews Correlation Coefficient Pknots: N/A MXScarna(20): N/A Sensitivity Pknots: N/A MXScarna(20): N/A Positive Predictive Value Pknots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: N/A MXScarna(seed): N/A Sensitivity Pknots: N/A MXScarna(seed): N/A Positive Predictive Value Pknots: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: N/A Pknots: N/A Sensitivity MaxExpect: N/A Pknots: N/A Positive Predictive Value MaxExpect: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: N/A Pknots: N/A Sensitivity ProbKnot: N/A Pknots: N/A Positive Predictive Value ProbKnot: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): N/A Pknots: N/A Sensitivity RNASampler(20): N/A Pknots: N/A Positive Predictive Value RNASampler(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Sfold Matthews Correlation Coefficient Pknots: N/A Sfold: N/A Sensitivity Pknots: N/A Sfold: N/A Positive Predictive Value Pknots: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs Pknots Matthews Correlation Coefficient Fold: N/A Pknots: N/A Sensitivity Fold: N/A Pknots: N/A Positive Predictive Value Fold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Murlet(20) Matthews Correlation Coefficient Pknots: N/A Murlet(20): N/A Sensitivity Pknots: N/A Murlet(20): N/A Positive Predictive Value Pknots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: N/A Pknots: N/A Sensitivity UNAFold: N/A Pknots: N/A Positive Predictive Value UNAFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: N/A Pknots: N/A Sensitivity PknotsRG: N/A Pknots: N/A Positive Predictive Value PknotsRG: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAfold Matthews Correlation Coefficient Pknots: N/A RNAfold: N/A Sensitivity Pknots: N/A RNAfold: N/A Positive Predictive Value Pknots: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Afold Matthews Correlation Coefficient Pknots: N/A Afold: N/A Sensitivity Pknots: N/A Afold: N/A Positive Predictive Value Pknots: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: N/A RNAsubopt: N/A Sensitivity Pknots: N/A RNAsubopt: N/A Positive Predictive Value Pknots: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs Pknots Matthews Correlation Coefficient McQFold: N/A Pknots: N/A Sensitivity McQFold: N/A Pknots: N/A Positive Predictive Value McQFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: N/A RNASLOpt: N/A Sensitivity Pknots: N/A RNASLOpt: N/A Positive Predictive Value Pknots: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: N/A RNAalifold(seed): N/A Sensitivity Pknots: N/A RNAalifold(seed): N/A Positive Predictive Value Pknots: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: N/A RNAshapes: N/A Sensitivity Pknots: N/A RNAshapes: N/A Positive Predictive Value Pknots: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: N/A CRWrnafold: N/A Sensitivity Pknots: N/A CRWrnafold: N/A Positive Predictive Value Pknots: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: N/A Vsfold4: N/A Sensitivity Pknots: N/A Vsfold4: N/A Positive Predictive Value Pknots: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: N/A RNAwolf: N/A Sensitivity Pknots: N/A RNAwolf: N/A Positive Predictive Value Pknots: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs Pknots Matthews Correlation Coefficient Vsfold5: N/A Pknots: N/A Sensitivity Vsfold5: N/A Pknots: N/A Positive Predictive Value Vsfold5: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Carnac(20) Matthews Correlation Coefficient Pknots: N/A Carnac(20): N/A Sensitivity Pknots: N/A Carnac(20): N/A Positive Predictive Value Pknots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): N/A Pknots: N/A Sensitivity RSpredict(20): N/A Pknots: N/A Positive Predictive Value RSpredict(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs Pknots Matthews Correlation Coefficient NanoFolder: N/A Pknots: N/A Sensitivity NanoFolder: N/A Pknots: N/A Positive Predictive Value NanoFolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs Pknots Matthews Correlation Coefficient RSpredict(seed): N/A Pknots: N/A Sensitivity RSpredict(seed): N/A Pknots: N/A Positive Predictive Value RSpredict(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: N/A Murlet(seed): N/A Sensitivity Pknots: N/A Murlet(seed): N/A Positive Predictive Value Pknots: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: N/A Multilign(seed): N/A Sensitivity Pknots: N/A Multilign(seed): N/A Positive Predictive Value Pknots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: N/A Pknots: N/A Sensitivity HotKnots: N/A Pknots: N/A Positive Predictive Value HotKnots: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: N/A Pknots: N/A Sensitivity Cylofold: N/A Pknots: N/A Positive Predictive Value Cylofold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs MCFold Matthews Correlation Coefficient Pknots: N/A MCFold: N/A Sensitivity Pknots: N/A MCFold: N/A Positive Predictive Value Pknots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Pknots Matthews Correlation Coefficient PPfold(seed): N/A Pknots: N/A Sensitivity PPfold(seed): N/A Pknots: N/A Positive Predictive Value PPfold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Pknots Matthews Correlation Coefficient RDfolder: N/A Pknots: N/A Sensitivity RDfolder: N/A Pknots: N/A Positive Predictive Value RDfolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): N/A Pknots: N/A Sensitivity TurboFold(seed): N/A Pknots: N/A Positive Predictive Value TurboFold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): N/A Pknots: N/A Sensitivity RNASampler(seed): N/A Pknots: N/A Positive Predictive Value RNASampler(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Alterna Matthews Correlation Coefficient Pknots: N/A Alterna: N/A Sensitivity Pknots: N/A Alterna: N/A Positive Predictive Value Pknots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: N/A Carnac(seed): N/A Sensitivity Pknots: N/A Carnac(seed): N/A Positive Predictive Value Pknots: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): N/A Pknots: N/A Sensitivity Mastr(20): N/A Pknots: N/A Positive Predictive Value Mastr(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs Pknots Matthews Correlation Coefficient Mastr(seed): N/A Pknots: N/A Sensitivity Mastr(seed): N/A Pknots: N/A Positive Predictive Value Mastr(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Cylofold	2 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.944 Cylofold: 0.271 Sensitivity ContextFold: 0.905 Cylofold: 0.241 Positive Predictive Value ContextFold: 0.984 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: N/A TurboFold(20): N/A Sensitivity Cylofold: N/A TurboFold(20): N/A Positive Predictive Value Cylofold: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs PETfold_pre2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(20): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs PPfold(20) Matthews Correlation Coefficient Cylofold: N/A PPfold(20): N/A Sensitivity Cylofold: N/A PPfold(20): N/A Positive Predictive Value Cylofold: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CentroidAlifold(20) Matthews Correlation Coefficient Cylofold: N/A CentroidAlifold(20): N/A Sensitivity Cylofold: N/A CentroidAlifold(20): N/A Positive Predictive Value Cylofold: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): N/A Cylofold: N/A Sensitivity CentroidAlifold(seed): N/A Cylofold: N/A Positive Predictive Value CentroidAlifold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Cylofold: 0.271 Sensitivity CentroidHomfold‑LAST: 0.613 Cylofold: 0.241 Positive Predictive Value CentroidHomfold‑LAST: 0.808 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs RNAalifold(20) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(20): N/A Sensitivity Cylofold: N/A RNAalifold(20): N/A Positive Predictive Value Cylofold: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.648 Cylofold: 0.271 Sensitivity IPknot: 0.584 Cylofold: 0.241 Positive Predictive Value IPknot: 0.721 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: N/A Multilign(20): N/A Sensitivity Cylofold: N/A Multilign(20): N/A Positive Predictive Value Cylofold: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.626 Cylofold: 0.271 Sensitivity CentroidFold: 0.584 Cylofold: 0.241 Positive Predictive Value CentroidFold: 0.672 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.616 Cylofold: 0.271 Sensitivity Contrafold: 0.591 Cylofold: 0.241 Positive Predictive Value Contrafold: 0.643 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs MXScarna(20) Matthews Correlation Coefficient Cylofold: N/A MXScarna(20): N/A Sensitivity Cylofold: N/A MXScarna(20): N/A Positive Predictive Value Cylofold: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: N/A MXScarna(seed): N/A Sensitivity Cylofold: N/A MXScarna(seed): N/A Positive Predictive Value Cylofold: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.631 Cylofold: 0.271 Sensitivity MaxExpect: 0.620 Cylofold: 0.241 Positive Predictive Value MaxExpect: 0.644 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.634 Cylofold: 0.271 Sensitivity ProbKnot: 0.620 Cylofold: 0.241 Positive Predictive Value ProbKnot: 0.649 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): N/A Cylofold: N/A Sensitivity RNASampler(20): N/A Cylofold: N/A Positive Predictive Value RNASampler(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.657 Cylofold: 0.271 Sensitivity Sfold: 0.562 Cylofold: 0.241 Positive Predictive Value Sfold: 0.770 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.597 Cylofold: 0.271 Sensitivity Fold: 0.591 Cylofold: 0.241 Positive Predictive Value Fold: 0.604 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: N/A Murlet(20): N/A Sensitivity Cylofold: N/A Murlet(20): N/A Positive Predictive Value Cylofold: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.443 Cylofold: 0.271 Sensitivity UNAFold: 0.431 Cylofold: 0.241 Positive Predictive Value UNAFold: 0.457 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.437 Cylofold: 0.271 Sensitivity PknotsRG: 0.438 Cylofold: 0.241 Positive Predictive Value PknotsRG: 0.438 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.446 Cylofold: 0.271 Sensitivity RNAfold: 0.431 Cylofold: 0.241 Positive Predictive Value RNAfold: 0.465 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.460 Cylofold: 0.271 Sensitivity Afold: 0.460 Cylofold: 0.241 Positive Predictive Value Afold: 0.463 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.437 Cylofold: 0.271 Sensitivity RNAsubopt: 0.431 Cylofold: 0.241 Positive Predictive Value RNAsubopt: 0.447 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.526 Cylofold: 0.271 Sensitivity McQFold: 0.489 Cylofold: 0.241 Positive Predictive Value McQFold: 0.568 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.382 Cylofold: 0.271 Sensitivity RNASLOpt: 0.358 Cylofold: 0.241 Positive Predictive Value RNASLOpt: 0.412 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(seed): N/A Sensitivity Cylofold: N/A RNAalifold(seed): N/A Positive Predictive Value Cylofold: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.455 Cylofold: 0.271 Sensitivity RNAshapes: 0.453 Cylofold: 0.241 Positive Predictive Value RNAshapes: 0.459 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.470 Cylofold: 0.271 Sensitivity CRWrnafold: 0.474 Cylofold: 0.241 Positive Predictive Value CRWrnafold: 0.468 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.271 Vsfold4: 0.267 Sensitivity Cylofold: 0.241 Vsfold4: 0.241 Positive Predictive Value Cylofold: 0.308 Vsfold4: 0.300 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNAwolf vs Cylofold Matthews Correlation Coefficient RNAwolf: 0.339 Cylofold: 0.271 Sensitivity RNAwolf: 0.350 Cylofold: 0.241 Positive Predictive Value RNAwolf: 0.331 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 Vsfold5 vs Cylofold Matthews Correlation Coefficient Vsfold5: 0.357 Cylofold: 0.271 Sensitivity Vsfold5: 0.336 Cylofold: 0.241 Positive Predictive Value Vsfold5: 0.383 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: N/A Carnac(20): N/A Sensitivity Cylofold: N/A Carnac(20): N/A Positive Predictive Value Cylofold: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): N/A Cylofold: N/A Sensitivity RSpredict(20): N/A Cylofold: N/A Positive Predictive Value RSpredict(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.378 NanoFolder: 0.076 Sensitivity Cylofold: 0.333 NanoFolder: 0.091 Positive Predictive Value Cylofold: 0.431 NanoFolder: 0.067 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(seed) vs Cylofold Matthews Correlation Coefficient RSpredict(seed): N/A Cylofold: N/A Sensitivity RSpredict(seed): N/A Cylofold: N/A Positive Predictive Value RSpredict(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: N/A Murlet(seed): N/A Sensitivity Cylofold: N/A Murlet(seed): N/A Positive Predictive Value Cylofold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: N/A Multilign(seed): N/A Sensitivity Cylofold: N/A Multilign(seed): N/A Positive Predictive Value Cylofold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: N/A HotKnots: N/A Sensitivity Cylofold: N/A HotKnots: N/A Positive Predictive Value Cylofold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: N/A Pknots: N/A Sensitivity Cylofold: N/A Pknots: N/A Positive Predictive Value Cylofold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: N/A MCFold: N/A Sensitivity Cylofold: N/A MCFold: N/A Positive Predictive Value Cylofold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: N/A PPfold(seed): N/A Sensitivity Cylofold: N/A PPfold(seed): N/A Positive Predictive Value Cylofold: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: N/A RDfolder: N/A Sensitivity Cylofold: N/A RDfolder: N/A Positive Predictive Value Cylofold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): N/A Cylofold: N/A Sensitivity TurboFold(seed): N/A Cylofold: N/A Positive Predictive Value TurboFold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): N/A Cylofold: N/A Sensitivity RNASampler(seed): N/A Cylofold: N/A Positive Predictive Value RNASampler(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: N/A Alterna: N/A Sensitivity Cylofold: N/A Alterna: N/A Positive Predictive Value Cylofold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: N/A Carnac(seed): N/A Sensitivity Cylofold: N/A Carnac(seed): N/A Positive Predictive Value Cylofold: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): N/A Cylofold: N/A Sensitivity Mastr(20): N/A Cylofold: N/A Positive Predictive Value Mastr(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: N/A Mastr(seed): N/A Sensitivity Cylofold: N/A Mastr(seed): N/A Positive Predictive Value Cylofold: N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MCFold	0 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: N/A MCFold: N/A Sensitivity ContextFold: N/A MCFold: N/A Positive Predictive Value ContextFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A MCFold: N/A Sensitivity PETfold_pre2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): N/A MCFold: N/A Sensitivity TurboFold(20): N/A MCFold: N/A Positive Predictive Value TurboFold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): N/A MCFold: N/A Sensitivity PETfold_pre2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): N/A MCFold: N/A Sensitivity PPfold(20): N/A MCFold: N/A Positive Predictive Value PPfold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): N/A MCFold: N/A Sensitivity CentroidAlifold(20): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): N/A MCFold: N/A Sensitivity CentroidAlifold(seed): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A MCFold: N/A Sensitivity CentroidHomfold‑LAST: N/A MCFold: N/A Positive Predictive Value CentroidHomfold‑LAST: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): N/A MCFold: N/A Sensitivity RNAalifold(20): N/A MCFold: N/A Positive Predictive Value RNAalifold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs IPknot Matthews Correlation Coefficient MCFold: N/A IPknot: N/A Sensitivity MCFold: N/A IPknot: N/A Positive Predictive Value MCFold: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): N/A MCFold: N/A Sensitivity Multilign(20): N/A MCFold: N/A Positive Predictive Value Multilign(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: N/A MCFold: N/A Sensitivity CentroidFold: N/A MCFold: N/A Positive Predictive Value CentroidFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: N/A MCFold: N/A Sensitivity Contrafold: N/A MCFold: N/A Positive Predictive Value Contrafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): N/A MCFold: N/A Sensitivity MXScarna(20): N/A MCFold: N/A Positive Predictive Value MXScarna(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): N/A MCFold: N/A Sensitivity MXScarna(seed): N/A MCFold: N/A Positive Predictive Value MXScarna(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: N/A MCFold: N/A Sensitivity MaxExpect: N/A MCFold: N/A Positive Predictive Value MaxExpect: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: N/A MCFold: N/A Sensitivity ProbKnot: N/A MCFold: N/A Positive Predictive Value ProbKnot: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): N/A MCFold: N/A Sensitivity RNASampler(20): N/A MCFold: N/A Positive Predictive Value RNASampler(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs MCFold Matthews Correlation Coefficient Sfold: N/A MCFold: N/A Sensitivity Sfold: N/A MCFold: N/A Positive Predictive Value Sfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs MCFold Matthews Correlation Coefficient Fold: N/A MCFold: N/A Sensitivity Fold: N/A MCFold: N/A Positive Predictive Value Fold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): N/A MCFold: N/A Sensitivity Murlet(20): N/A MCFold: N/A Positive Predictive Value Murlet(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: N/A MCFold: N/A Sensitivity UNAFold: N/A MCFold: N/A Positive Predictive Value UNAFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: N/A MCFold: N/A Sensitivity PknotsRG: N/A MCFold: N/A Positive Predictive Value PknotsRG: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: N/A MCFold: N/A Sensitivity RNAfold: N/A MCFold: N/A Positive Predictive Value RNAfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs MCFold Matthews Correlation Coefficient Afold: N/A MCFold: N/A Sensitivity Afold: N/A MCFold: N/A Positive Predictive Value Afold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: N/A MCFold: N/A Sensitivity RNAsubopt: N/A MCFold: N/A Positive Predictive Value RNAsubopt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs MCFold Matthews Correlation Coefficient McQFold: N/A MCFold: N/A Sensitivity McQFold: N/A MCFold: N/A Positive Predictive Value McQFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: N/A MCFold: N/A Sensitivity RNASLOpt: N/A MCFold: N/A Positive Predictive Value RNASLOpt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): N/A MCFold: N/A Sensitivity RNAalifold(seed): N/A MCFold: N/A Positive Predictive Value RNAalifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: N/A MCFold: N/A Sensitivity RNAshapes: N/A MCFold: N/A Positive Predictive Value RNAshapes: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: N/A MCFold: N/A Sensitivity CRWrnafold: N/A MCFold: N/A Positive Predictive Value CRWrnafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: N/A MCFold: N/A Sensitivity Vsfold4: N/A MCFold: N/A Positive Predictive Value Vsfold4: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: N/A MCFold: N/A Sensitivity RNAwolf: N/A MCFold: N/A Positive Predictive Value RNAwolf: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: N/A MCFold: N/A Sensitivity Vsfold5: N/A MCFold: N/A Positive Predictive Value Vsfold5: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): N/A MCFold: N/A Sensitivity Carnac(20): N/A MCFold: N/A Positive Predictive Value Carnac(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): N/A MCFold: N/A Sensitivity RSpredict(20): N/A MCFold: N/A Positive Predictive Value RSpredict(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: N/A MCFold: N/A Sensitivity NanoFolder: N/A MCFold: N/A Positive Predictive Value NanoFolder: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): N/A MCFold: N/A Sensitivity RSpredict(seed): N/A MCFold: N/A Positive Predictive Value RSpredict(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): N/A MCFold: N/A Sensitivity Murlet(seed): N/A MCFold: N/A Positive Predictive Value Murlet(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): N/A MCFold: N/A Sensitivity Multilign(seed): N/A MCFold: N/A Positive Predictive Value Multilign(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: N/A MCFold: N/A Sensitivity HotKnots: N/A MCFold: N/A Positive Predictive Value HotKnots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs MCFold Matthews Correlation Coefficient Pknots: N/A MCFold: N/A Sensitivity Pknots: N/A MCFold: N/A Positive Predictive Value Pknots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: N/A MCFold: N/A Sensitivity Cylofold: N/A MCFold: N/A Positive Predictive Value Cylofold: N/A MCFold: 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): N/A MCFold: N/A Sensitivity PPfold(seed): N/A MCFold: N/A Positive Predictive Value PPfold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: N/A MCFold: N/A Sensitivity RDfolder: N/A MCFold: N/A Positive Predictive Value RDfolder: N/A MCFold: 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): N/A MCFold: N/A Sensitivity TurboFold(seed): N/A MCFold: N/A Positive Predictive Value TurboFold(seed): N/A MCFold: 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): N/A MCFold: N/A Sensitivity RNASampler(seed): N/A MCFold: N/A Positive Predictive Value RNASampler(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs MCFold Matthews Correlation Coefficient Alterna: N/A MCFold: N/A Sensitivity Alterna: N/A MCFold: N/A Positive Predictive Value Alterna: N/A MCFold: 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): N/A MCFold: N/A Sensitivity Carnac(seed): N/A MCFold: N/A Positive Predictive Value Carnac(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): N/A MCFold: N/A Sensitivity Mastr(20): N/A MCFold: N/A Positive Predictive Value Mastr(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): N/A MCFold: N/A Sensitivity Mastr(seed): N/A MCFold: N/A Positive Predictive Value Mastr(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PPfold(seed)	0 PPfold(seed) vs ContextFold Matthews Correlation Coefficient PPfold(seed): N/A ContextFold: N/A Sensitivity PPfold(seed): N/A ContextFold: N/A Positive Predictive Value PPfold(seed): N/A ContextFold: 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(seed) Matthews Correlation Coefficient PPfold(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity PPfold(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value PPfold(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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	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 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 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A PPfold(seed): N/A Sensitivity CentroidAlifold(seed): N/A PPfold(seed): N/A Positive Predictive Value CentroidAlifold(seed): 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 CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity PPfold(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value PPfold(seed): N/A CentroidHomfold‑LAST: 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 PPfold(seed) vs IPknot Matthews Correlation Coefficient PPfold(seed): N/A IPknot: N/A Sensitivity PPfold(seed): N/A IPknot: N/A Positive Predictive Value PPfold(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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 PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): N/A CentroidFold: N/A Sensitivity PPfold(seed): N/A CentroidFold: N/A Positive Predictive Value PPfold(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): N/A Contrafold: N/A Sensitivity PPfold(seed): N/A Contrafold: N/A Positive Predictive Value PPfold(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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 PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): N/A MXScarna(seed): N/A Sensitivity PPfold(seed): N/A MXScarna(seed): N/A Positive Predictive Value PPfold(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: N/A PPfold(seed): N/A Sensitivity MaxExpect: N/A PPfold(seed): N/A Positive Predictive Value MaxExpect: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: N/A PPfold(seed): N/A Sensitivity ProbKnot: N/A PPfold(seed): N/A Positive Predictive Value ProbKnot: 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 Sfold Matthews Correlation Coefficient PPfold(seed): N/A Sfold: N/A Sensitivity PPfold(seed): N/A Sfold: N/A Positive Predictive Value PPfold(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: N/A PPfold(seed): N/A Sensitivity Fold: N/A PPfold(seed): N/A Positive Predictive Value Fold: 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 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 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: N/A PPfold(seed): N/A Sensitivity UNAFold: N/A PPfold(seed): N/A Positive Predictive Value UNAFold: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: N/A PPfold(seed): N/A Sensitivity PknotsRG: N/A PPfold(seed): N/A Positive Predictive Value PknotsRG: 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 RNAfold Matthews Correlation Coefficient PPfold(seed): N/A RNAfold: N/A Sensitivity PPfold(seed): N/A RNAfold: N/A Positive Predictive Value PPfold(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): N/A Afold: N/A Sensitivity PPfold(seed): N/A Afold: N/A Positive Predictive Value PPfold(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): N/A RNAsubopt: N/A Sensitivity PPfold(seed): N/A RNAsubopt: N/A Positive Predictive Value PPfold(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs McQFold Matthews Correlation Coefficient PPfold(seed): N/A McQFold: N/A Sensitivity PPfold(seed): N/A McQFold: N/A Positive Predictive Value PPfold(seed): N/A McQFold: 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 RNASLOpt Matthews Correlation Coefficient PPfold(seed): N/A RNASLOpt: N/A Sensitivity PPfold(seed): N/A RNASLOpt: N/A Positive Predictive Value PPfold(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): N/A RNAalifold(seed): N/A Sensitivity PPfold(seed): N/A RNAalifold(seed): N/A Positive Predictive Value PPfold(seed): N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): N/A RNAshapes: N/A Sensitivity PPfold(seed): N/A RNAshapes: N/A Positive Predictive Value PPfold(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): N/A CRWrnafold: N/A Sensitivity PPfold(seed): N/A CRWrnafold: N/A Positive Predictive Value PPfold(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): N/A Vsfold4: N/A Sensitivity PPfold(seed): N/A Vsfold4: N/A Positive Predictive Value PPfold(seed): N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): N/A RNAwolf: N/A Sensitivity PPfold(seed): N/A RNAwolf: N/A Positive Predictive Value PPfold(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: N/A PPfold(seed): N/A Sensitivity Vsfold5: N/A PPfold(seed): N/A Positive Predictive Value Vsfold5: 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(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	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 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: N/A PPfold(seed): N/A Sensitivity NanoFolder: N/A PPfold(seed): N/A Positive Predictive Value NanoFolder: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): N/A PPfold(seed): N/A Sensitivity RSpredict(seed): N/A PPfold(seed): N/A Positive Predictive Value RSpredict(seed): 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 Murlet(seed) Matthews Correlation Coefficient PPfold(seed): N/A Murlet(seed): N/A Sensitivity PPfold(seed): N/A Murlet(seed): N/A Positive Predictive Value PPfold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): N/A Multilign(seed): N/A Sensitivity PPfold(seed): N/A Multilign(seed): N/A Positive Predictive Value PPfold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: N/A PPfold(seed): N/A Sensitivity HotKnots: N/A PPfold(seed): N/A Positive Predictive Value HotKnots: 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 Pknots Matthews Correlation Coefficient PPfold(seed): N/A Pknots: N/A Sensitivity PPfold(seed): N/A Pknots: N/A Positive Predictive Value PPfold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: N/A PPfold(seed): N/A Sensitivity Cylofold: N/A PPfold(seed): N/A Positive Predictive Value Cylofold: 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 MCFold Matthews Correlation Coefficient PPfold(seed): N/A MCFold: N/A Sensitivity PPfold(seed): N/A MCFold: N/A Positive Predictive Value PPfold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: N/A PPfold(seed): N/A Sensitivity RDfolder: N/A PPfold(seed): N/A Positive Predictive Value RDfolder: 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 PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): N/A PPfold(seed): N/A Sensitivity TurboFold(seed): N/A PPfold(seed): N/A Positive Predictive Value TurboFold(seed): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(seed): N/A Sensitivity RNASampler(seed): N/A PPfold(seed): N/A Positive Predictive Value RNASampler(seed): 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 Alterna Matthews Correlation Coefficient PPfold(seed): N/A Alterna: N/A Sensitivity PPfold(seed): N/A Alterna: N/A Positive Predictive Value PPfold(seed): N/A Alterna: 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): N/A Carnac(seed): N/A Sensitivity PPfold(seed): N/A Carnac(seed): N/A Positive Predictive Value PPfold(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? Mastr(seed) vs PPfold(seed) Matthews Correlation Coefficient Mastr(seed): N/A PPfold(seed): N/A Sensitivity Mastr(seed): N/A PPfold(seed): N/A Positive Predictive Value Mastr(seed): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RDfolder	0 RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: N/A ContextFold: N/A Sensitivity RDfolder: N/A ContextFold: N/A Positive Predictive Value RDfolder: N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs TurboFold(20) Matthews Correlation Coefficient RDfolder: N/A TurboFold(20): N/A Sensitivity RDfolder: N/A TurboFold(20): N/A Positive Predictive Value RDfolder: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PETfold_pre2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(20): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): N/A RDfolder: N/A Sensitivity PPfold(20): N/A RDfolder: N/A Positive Predictive Value PPfold(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CentroidAlifold(20) Matthews Correlation Coefficient RDfolder: N/A CentroidAlifold(20): N/A Sensitivity RDfolder: N/A CentroidAlifold(20): N/A Positive Predictive Value RDfolder: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): N/A RDfolder: N/A Sensitivity CentroidAlifold(seed): N/A RDfolder: N/A Positive Predictive Value CentroidAlifold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CentroidHomfold‑LAST Matthews Correlation Coefficient RDfolder: N/A CentroidHomfold‑LAST: N/A Sensitivity RDfolder: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value RDfolder: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAalifold(20) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(20): N/A Sensitivity RDfolder: N/A RNAalifold(20): N/A Positive Predictive Value RDfolder: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs IPknot Matthews Correlation Coefficient RDfolder: N/A IPknot: N/A Sensitivity RDfolder: N/A IPknot: N/A Positive Predictive Value RDfolder: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Multilign(20) Matthews Correlation Coefficient RDfolder: N/A Multilign(20): N/A Sensitivity RDfolder: N/A Multilign(20): N/A Positive Predictive Value RDfolder: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CentroidFold Matthews Correlation Coefficient RDfolder: N/A CentroidFold: N/A Sensitivity RDfolder: N/A CentroidFold: N/A Positive Predictive Value RDfolder: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Contrafold Matthews Correlation Coefficient RDfolder: N/A Contrafold: N/A Sensitivity RDfolder: N/A Contrafold: N/A Positive Predictive Value RDfolder: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs MXScarna(20) Matthews Correlation Coefficient RDfolder: N/A MXScarna(20): N/A Sensitivity RDfolder: N/A MXScarna(20): N/A Positive Predictive Value RDfolder: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: N/A MXScarna(seed): N/A Sensitivity RDfolder: N/A MXScarna(seed): N/A Positive Predictive Value RDfolder: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: N/A RDfolder: N/A Sensitivity MaxExpect: N/A RDfolder: N/A Positive Predictive Value MaxExpect: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs ProbKnot Matthews Correlation Coefficient RDfolder: N/A ProbKnot: N/A Sensitivity RDfolder: N/A ProbKnot: N/A Positive Predictive Value RDfolder: N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): N/A RDfolder: N/A Sensitivity RNASampler(20): N/A RDfolder: N/A Positive Predictive Value RNASampler(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: N/A Sfold: N/A Sensitivity RDfolder: N/A Sfold: N/A Positive Predictive Value RDfolder: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs RDfolder Matthews Correlation Coefficient Fold: N/A RDfolder: N/A Sensitivity Fold: N/A RDfolder: N/A Positive Predictive Value Fold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Murlet(20) Matthews Correlation Coefficient RDfolder: N/A Murlet(20): N/A Sensitivity RDfolder: N/A Murlet(20): N/A Positive Predictive Value RDfolder: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: N/A RDfolder: N/A Sensitivity UNAFold: N/A RDfolder: N/A Positive Predictive Value UNAFold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: N/A RDfolder: N/A Sensitivity PknotsRG: N/A RDfolder: N/A Positive Predictive Value PknotsRG: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: N/A RNAfold: N/A Sensitivity RDfolder: N/A RNAfold: N/A Positive Predictive Value RDfolder: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Afold Matthews Correlation Coefficient RDfolder: N/A Afold: N/A Sensitivity RDfolder: N/A Afold: N/A Positive Predictive Value RDfolder: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: N/A RNAsubopt: N/A Sensitivity RDfolder: N/A RNAsubopt: N/A Positive Predictive Value RDfolder: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs McQFold Matthews Correlation Coefficient RDfolder: N/A McQFold: N/A Sensitivity RDfolder: N/A McQFold: N/A Positive Predictive Value RDfolder: N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNASLOpt Matthews Correlation Coefficient RDfolder: N/A RNASLOpt: N/A Sensitivity RDfolder: N/A RNASLOpt: N/A Positive Predictive Value RDfolder: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAalifold(seed) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(seed): N/A Sensitivity RDfolder: N/A RNAalifold(seed): N/A Positive Predictive Value RDfolder: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: N/A RNAshapes: N/A Sensitivity RDfolder: N/A RNAshapes: N/A Positive Predictive Value RDfolder: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: N/A CRWrnafold: N/A Sensitivity RDfolder: N/A CRWrnafold: N/A Positive Predictive Value RDfolder: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: N/A Vsfold4: N/A Sensitivity RDfolder: N/A Vsfold4: N/A Positive Predictive Value RDfolder: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: N/A RNAwolf: N/A Sensitivity RDfolder: N/A RNAwolf: N/A Positive Predictive Value RDfolder: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Vsfold5 Matthews Correlation Coefficient RDfolder: N/A Vsfold5: N/A Sensitivity RDfolder: N/A Vsfold5: N/A Positive Predictive Value RDfolder: N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Carnac(20) Matthews Correlation Coefficient RDfolder: N/A Carnac(20): N/A Sensitivity RDfolder: N/A Carnac(20): N/A Positive Predictive Value RDfolder: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): N/A RDfolder: N/A Sensitivity RSpredict(20): N/A RDfolder: N/A Positive Predictive Value RSpredict(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: N/A RDfolder: N/A Sensitivity NanoFolder: N/A RDfolder: N/A Positive Predictive Value NanoFolder: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): N/A RDfolder: N/A Sensitivity RSpredict(seed): N/A RDfolder: N/A Positive Predictive Value RSpredict(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: N/A Murlet(seed): N/A Sensitivity RDfolder: N/A Murlet(seed): N/A Positive Predictive Value RDfolder: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: N/A Multilign(seed): N/A Sensitivity RDfolder: N/A Multilign(seed): N/A Positive Predictive Value RDfolder: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: N/A RDfolder: N/A Sensitivity HotKnots: N/A RDfolder: N/A Positive Predictive Value HotKnots: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Pknots Matthews Correlation Coefficient RDfolder: N/A Pknots: N/A Sensitivity RDfolder: N/A Pknots: N/A Positive Predictive Value RDfolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: N/A RDfolder: N/A Sensitivity Cylofold: N/A RDfolder: N/A Positive Predictive Value Cylofold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: N/A MCFold: N/A Sensitivity RDfolder: N/A MCFold: N/A Positive Predictive Value RDfolder: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: N/A PPfold(seed): N/A Sensitivity RDfolder: N/A PPfold(seed): N/A Positive Predictive Value RDfolder: 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 RDfolder Matthews Correlation Coefficient TurboFold(seed): N/A RDfolder: N/A Sensitivity TurboFold(seed): N/A RDfolder: N/A Positive Predictive Value TurboFold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): N/A RDfolder: N/A Sensitivity RNASampler(seed): N/A RDfolder: N/A Positive Predictive Value RNASampler(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: N/A Alterna: N/A Sensitivity RDfolder: N/A Alterna: N/A Positive Predictive Value RDfolder: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: N/A Carnac(seed): N/A Sensitivity RDfolder: N/A Carnac(seed): N/A Positive Predictive Value RDfolder: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): N/A RDfolder: N/A Sensitivity Mastr(20): N/A RDfolder: N/A Positive Predictive Value Mastr(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs RDfolder Matthews Correlation Coefficient Mastr(seed): N/A RDfolder: N/A Sensitivity Mastr(seed): N/A RDfolder: N/A Positive Predictive Value Mastr(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
TurboFold(seed)	1 TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.710 ContextFold: 0.703 Sensitivity TurboFold(seed): 0.677 ContextFold: 0.692 Positive Predictive Value TurboFold(seed): 0.746 ContextFold: 0.714 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 PETfold_pre2.0(seed): 0.677 Sensitivity TurboFold(seed): 0.677 PETfold_pre2.0(seed): 0.646 Positive Predictive Value TurboFold(seed): 0.746 PETfold_pre2.0(seed): 0.712 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	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 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	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	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	1 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.744 TurboFold(seed): 0.710 Sensitivity CentroidAlifold(seed): 0.646 TurboFold(seed): 0.677 Positive Predictive Value CentroidAlifold(seed): 0.857 TurboFold(seed): 0.746 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.789 TurboFold(seed): 0.710 Sensitivity CentroidHomfold‑LAST: 0.692 TurboFold(seed): 0.677 Positive Predictive Value CentroidHomfold‑LAST: 0.900 TurboFold(seed): 0.746 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	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	1 TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.710 IPknot: 0.579 Sensitivity TurboFold(seed): 0.677 IPknot: 0.585 Positive Predictive Value TurboFold(seed): 0.746 IPknot: 0.576 Number of pairs reference - predicted secondary structure: 1 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	1 TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.710 CentroidFold: 0.645 Sensitivity TurboFold(seed): 0.677 CentroidFold: 0.646 Positive Predictive Value TurboFold(seed): 0.746 CentroidFold: 0.646 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.710 Contrafold: 0.581 Sensitivity TurboFold(seed): 0.677 Contrafold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 Contrafold: 0.565 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	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	1 TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 MXScarna(seed): 0.695 Sensitivity TurboFold(seed): 0.677 MXScarna(seed): 0.538 Positive Predictive Value TurboFold(seed): 0.746 MXScarna(seed): 0.897 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.710 MaxExpect: 0.651 Sensitivity TurboFold(seed): 0.677 MaxExpect: 0.662 Positive Predictive Value TurboFold(seed): 0.746 MaxExpect: 0.642 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.710 ProbKnot: 0.641 Sensitivity TurboFold(seed): 0.677 ProbKnot: 0.662 Positive Predictive Value TurboFold(seed): 0.746 ProbKnot: 0.623 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	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	1 TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.710 Sfold: 0.594 Sensitivity TurboFold(seed): 0.677 Sfold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 Sfold: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.710 Fold: 0.651 Sensitivity TurboFold(seed): 0.677 Fold: 0.662 Positive Predictive Value TurboFold(seed): 0.746 Fold: 0.642 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	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	1 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.710 UNAFold: 0.594 Sensitivity TurboFold(seed): 0.677 UNAFold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 UNAFold: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs PknotsRG Matthews Correlation Coefficient TurboFold(seed): 0.710 PknotsRG: 0.594 Sensitivity TurboFold(seed): 0.677 PknotsRG: 0.600 Positive Predictive Value TurboFold(seed): 0.746 PknotsRG: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAfold: 0.594 Sensitivity TurboFold(seed): 0.677 RNAfold: 0.600 Positive Predictive Value TurboFold(seed): 0.746 RNAfold: 0.591 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.710 Afold: 0.605 Sensitivity TurboFold(seed): 0.677 Afold: 0.615 Positive Predictive Value TurboFold(seed): 0.746 Afold: 0.597 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAsubopt: 0.472 Sensitivity TurboFold(seed): 0.677 RNAsubopt: 0.477 Positive Predictive Value TurboFold(seed): 0.746 RNAsubopt: 0.470 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.710 McQFold: 0.566 Sensitivity TurboFold(seed): 0.677 McQFold: 0.554 Positive Predictive Value TurboFold(seed): 0.746 McQFold: 0.581 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.710 RNASLOpt: 0.357 Sensitivity TurboFold(seed): 0.677 RNASLOpt: 0.338 Positive Predictive Value TurboFold(seed): 0.746 RNASLOpt: 0.379 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAalifold(seed): 0.680 Sensitivity TurboFold(seed): 0.677 RNAalifold(seed): 0.554 Positive Predictive Value TurboFold(seed): 0.746 RNAalifold(seed): 0.837 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAshapes: 0.553 Sensitivity TurboFold(seed): 0.677 RNAshapes: 0.554 Positive Predictive Value TurboFold(seed): 0.746 RNAshapes: 0.554 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.710 CRWrnafold: 0.483 Sensitivity TurboFold(seed): 0.677 CRWrnafold: 0.477 Positive Predictive Value TurboFold(seed): 0.746 CRWrnafold: 0.492 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.710 Vsfold4: 0.099 Sensitivity TurboFold(seed): 0.677 Vsfold4: 0.092 Positive Predictive Value TurboFold(seed): 0.746 Vsfold4: 0.111 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.710 RNAwolf: 0.620 Sensitivity TurboFold(seed): 0.677 RNAwolf: 0.631 Positive Predictive Value TurboFold(seed): 0.746 RNAwolf: 0.612 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.710 Vsfold5: 0.200 Sensitivity TurboFold(seed): 0.677 Vsfold5: 0.200 Positive Predictive Value TurboFold(seed): 0.746 Vsfold5: 0.203 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	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	0 NanoFolder vs TurboFold(seed) Matthews Correlation Coefficient NanoFolder: N/A TurboFold(seed): N/A Sensitivity NanoFolder: N/A TurboFold(seed): N/A Positive Predictive Value NanoFolder: N/A TurboFold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 RSpredict(seed): 0.000 Sensitivity TurboFold(seed): 0.677 RSpredict(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.746 RSpredict(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(seed): N/A Sensitivity TurboFold(seed): N/A Murlet(seed): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): N/A Multilign(seed): N/A Sensitivity TurboFold(seed): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): N/A HotKnots: N/A Sensitivity TurboFold(seed): N/A HotKnots: N/A Positive Predictive Value TurboFold(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): N/A Pknots: N/A Sensitivity TurboFold(seed): N/A Pknots: N/A Positive Predictive Value TurboFold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): N/A Cylofold: N/A Sensitivity TurboFold(seed): N/A Cylofold: N/A Positive Predictive Value TurboFold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): N/A MCFold: N/A Sensitivity TurboFold(seed): N/A MCFold: N/A Positive Predictive Value TurboFold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): N/A PPfold(seed): N/A Sensitivity TurboFold(seed): N/A PPfold(seed): N/A Positive Predictive Value TurboFold(seed): 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 RDfolder Matthews Correlation Coefficient TurboFold(seed): N/A RDfolder: N/A Sensitivity TurboFold(seed): N/A RDfolder: N/A Positive Predictive Value TurboFold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): N/A RNASampler(seed): N/A Sensitivity TurboFold(seed): N/A RNASampler(seed): N/A Positive Predictive Value TurboFold(seed): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): N/A Alterna: N/A Sensitivity TurboFold(seed): N/A Alterna: N/A Positive Predictive Value TurboFold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 Carnac(seed): 0.000 Sensitivity TurboFold(seed): 0.677 Carnac(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.746 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 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	? TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.677 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.746 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0
RNASampler(seed)	0 RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): N/A ContextFold: N/A Sensitivity RNASampler(seed): N/A ContextFold: N/A Positive Predictive Value RNASampler(seed): N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	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	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	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	0 RNASampler(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(seed): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(seed): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient RNASampler(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity RNASampler(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value RNASampler(seed): N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): N/A IPknot: N/A Sensitivity RNASampler(seed): N/A IPknot: N/A Positive Predictive Value RNASampler(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): N/A CentroidFold: N/A Sensitivity RNASampler(seed): N/A CentroidFold: N/A Positive Predictive Value RNASampler(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): N/A Contrafold: N/A Sensitivity RNASampler(seed): N/A Contrafold: N/A Positive Predictive Value RNASampler(seed): N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(seed): N/A Sensitivity RNASampler(seed): N/A MXScarna(seed): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: N/A RNASampler(seed): N/A Sensitivity MaxExpect: N/A RNASampler(seed): N/A Positive Predictive Value MaxExpect: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): N/A ProbKnot: N/A Sensitivity RNASampler(seed): N/A ProbKnot: N/A Positive Predictive Value RNASampler(seed): N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): N/A Sfold: N/A Sensitivity RNASampler(seed): N/A Sfold: N/A Positive Predictive Value RNASampler(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs RNASampler(seed) Matthews Correlation Coefficient Fold: N/A RNASampler(seed): N/A Sensitivity Fold: N/A RNASampler(seed): N/A Positive Predictive Value Fold: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: N/A RNASampler(seed): N/A Sensitivity UNAFold: N/A RNASampler(seed): N/A Positive Predictive Value UNAFold: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: N/A RNASampler(seed): N/A Sensitivity PknotsRG: N/A RNASampler(seed): N/A Positive Predictive Value PknotsRG: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): N/A RNAfold: N/A Sensitivity RNASampler(seed): N/A RNAfold: N/A Positive Predictive Value RNASampler(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): N/A Afold: N/A Sensitivity RNASampler(seed): N/A Afold: N/A Positive Predictive Value RNASampler(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): N/A RNAsubopt: N/A Sensitivity RNASampler(seed): N/A RNAsubopt: N/A Positive Predictive Value RNASampler(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): N/A McQFold: N/A Sensitivity RNASampler(seed): N/A McQFold: N/A Positive Predictive Value RNASampler(seed): N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): N/A RNASLOpt: N/A Sensitivity RNASampler(seed): N/A RNASLOpt: N/A Positive Predictive Value RNASampler(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(seed): N/A Sensitivity RNASampler(seed): N/A RNAalifold(seed): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): N/A RNAshapes: N/A Sensitivity RNASampler(seed): N/A RNAshapes: N/A Positive Predictive Value RNASampler(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): N/A CRWrnafold: N/A Sensitivity RNASampler(seed): N/A CRWrnafold: N/A Positive Predictive Value RNASampler(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): N/A Vsfold4: N/A Sensitivity RNASampler(seed): N/A Vsfold4: N/A Positive Predictive Value RNASampler(seed): N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): N/A RNAwolf: N/A Sensitivity RNASampler(seed): N/A RNAwolf: N/A Positive Predictive Value RNASampler(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): N/A Vsfold5: N/A Sensitivity RNASampler(seed): N/A Vsfold5: N/A Positive Predictive Value RNASampler(seed): N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(seed): N/A Sensitivity RNASampler(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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	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	0 NanoFolder vs RNASampler(seed) Matthews Correlation Coefficient NanoFolder: N/A RNASampler(seed): N/A Sensitivity NanoFolder: N/A RNASampler(seed): N/A Positive Predictive Value NanoFolder: N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): N/A RSpredict(seed): N/A Sensitivity RNASampler(seed): N/A RSpredict(seed): N/A Positive Predictive Value RNASampler(seed): N/A RSpredict(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(seed): N/A Sensitivity RNASampler(seed): N/A Murlet(seed): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(seed): N/A Sensitivity RNASampler(seed): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): N/A HotKnots: N/A Sensitivity RNASampler(seed): N/A HotKnots: N/A Positive Predictive Value RNASampler(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): N/A Pknots: N/A Sensitivity RNASampler(seed): N/A Pknots: N/A Positive Predictive Value RNASampler(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): N/A Cylofold: N/A Sensitivity RNASampler(seed): N/A Cylofold: N/A Positive Predictive Value RNASampler(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): N/A MCFold: N/A Sensitivity RNASampler(seed): N/A MCFold: N/A Positive Predictive Value RNASampler(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(seed): N/A Sensitivity RNASampler(seed): N/A PPfold(seed): N/A Positive Predictive Value RNASampler(seed): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): N/A RDfolder: N/A Sensitivity RNASampler(seed): N/A RDfolder: N/A Positive Predictive Value RNASampler(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): N/A RNASampler(seed): N/A Sensitivity TurboFold(seed): N/A RNASampler(seed): N/A Positive Predictive Value TurboFold(seed): 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 Alterna Matthews Correlation Coefficient RNASampler(seed): N/A Alterna: N/A Sensitivity RNASampler(seed): N/A Alterna: N/A Positive Predictive Value RNASampler(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(seed): N/A Sensitivity RNASampler(seed): N/A Carnac(seed): N/A Positive Predictive Value RNASampler(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Mastr(seed): N/A Sensitivity RNASampler(seed): N/A Mastr(seed): N/A Positive Predictive Value RNASampler(seed): N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Alterna	0 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: N/A Alterna: N/A Sensitivity ContextFold: N/A Alterna: N/A Positive Predictive Value ContextFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_pre2.0(seed): N/A Sensitivity Alterna: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): N/A Alterna: N/A Sensitivity TurboFold(20): N/A Alterna: N/A Positive Predictive Value TurboFold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): N/A Alterna: N/A Sensitivity PPfold(20): N/A Alterna: N/A Positive Predictive Value PPfold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CentroidAlifold(20) Matthews Correlation Coefficient Alterna: N/A CentroidAlifold(20): N/A Sensitivity Alterna: N/A CentroidAlifold(20): N/A Positive Predictive Value Alterna: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): N/A Alterna: N/A Sensitivity CentroidAlifold(seed): N/A Alterna: N/A Positive Predictive Value CentroidAlifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CentroidHomfold‑LAST Matthews Correlation Coefficient Alterna: N/A CentroidHomfold‑LAST: N/A Sensitivity Alterna: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Alterna: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): N/A Alterna: N/A Sensitivity RNAalifold(20): N/A Alterna: N/A Positive Predictive Value RNAalifold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs IPknot Matthews Correlation Coefficient Alterna: N/A IPknot: N/A Sensitivity Alterna: N/A IPknot: N/A Positive Predictive Value Alterna: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Multilign(20) Matthews Correlation Coefficient Alterna: N/A Multilign(20): N/A Sensitivity Alterna: N/A Multilign(20): N/A Positive Predictive Value Alterna: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CentroidFold Matthews Correlation Coefficient Alterna: N/A CentroidFold: N/A Sensitivity Alterna: N/A CentroidFold: N/A Positive Predictive Value Alterna: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: N/A Alterna: N/A Sensitivity Contrafold: N/A Alterna: N/A Positive Predictive Value Contrafold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs MXScarna(20) Matthews Correlation Coefficient Alterna: N/A MXScarna(20): N/A Sensitivity Alterna: N/A MXScarna(20): N/A Positive Predictive Value Alterna: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs MXScarna(seed) Matthews Correlation Coefficient Alterna: N/A MXScarna(seed): N/A Sensitivity Alterna: N/A MXScarna(seed): N/A Positive Predictive Value Alterna: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: N/A Alterna: N/A Sensitivity MaxExpect: N/A Alterna: N/A Positive Predictive Value MaxExpect: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: N/A Alterna: N/A Sensitivity ProbKnot: N/A Alterna: N/A Positive Predictive Value ProbKnot: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): N/A Alterna: N/A Sensitivity RNASampler(20): N/A Alterna: N/A Positive Predictive Value RNASampler(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Sfold Matthews Correlation Coefficient Alterna: N/A Sfold: N/A Sensitivity Alterna: N/A Sfold: N/A Positive Predictive Value Alterna: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs Alterna Matthews Correlation Coefficient Fold: N/A Alterna: N/A Sensitivity Fold: N/A Alterna: N/A Positive Predictive Value Fold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): N/A Alterna: N/A Sensitivity Murlet(20): N/A Alterna: N/A Positive Predictive Value Murlet(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: N/A Alterna: N/A Sensitivity UNAFold: N/A Alterna: N/A Positive Predictive Value UNAFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: N/A Alterna: N/A Sensitivity PknotsRG: N/A Alterna: N/A Positive Predictive Value PknotsRG: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAfold Matthews Correlation Coefficient Alterna: N/A RNAfold: N/A Sensitivity Alterna: N/A RNAfold: N/A Positive Predictive Value Alterna: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Afold Matthews Correlation Coefficient Alterna: N/A Afold: N/A Sensitivity Alterna: N/A Afold: N/A Positive Predictive Value Alterna: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAsubopt Matthews Correlation Coefficient Alterna: N/A RNAsubopt: N/A Sensitivity Alterna: N/A RNAsubopt: N/A Positive Predictive Value Alterna: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs Alterna Matthews Correlation Coefficient McQFold: N/A Alterna: N/A Sensitivity McQFold: N/A Alterna: N/A Positive Predictive Value McQFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: N/A RNASLOpt: N/A Sensitivity Alterna: N/A RNASLOpt: N/A Positive Predictive Value Alterna: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): N/A Alterna: N/A Sensitivity RNAalifold(seed): N/A Alterna: N/A Positive Predictive Value RNAalifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAshapes Matthews Correlation Coefficient Alterna: N/A RNAshapes: N/A Sensitivity Alterna: N/A RNAshapes: N/A Positive Predictive Value Alterna: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CRWrnafold Matthews Correlation Coefficient Alterna: N/A CRWrnafold: N/A Sensitivity Alterna: N/A CRWrnafold: N/A Positive Predictive Value Alterna: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: N/A Alterna: N/A Sensitivity Vsfold4: N/A Alterna: N/A Positive Predictive Value Vsfold4: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: N/A RNAwolf: N/A Sensitivity Alterna: N/A RNAwolf: N/A Positive Predictive Value Alterna: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: N/A Alterna: N/A Sensitivity Vsfold5: N/A Alterna: N/A Positive Predictive Value Vsfold5: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Carnac(20) Matthews Correlation Coefficient Alterna: N/A Carnac(20): N/A Sensitivity Alterna: N/A Carnac(20): N/A Positive Predictive Value Alterna: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): N/A Alterna: N/A Sensitivity RSpredict(20): N/A Alterna: N/A Positive Predictive Value RSpredict(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs Alterna Matthews Correlation Coefficient NanoFolder: N/A Alterna: N/A Sensitivity NanoFolder: N/A Alterna: N/A Positive Predictive Value NanoFolder: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): N/A Alterna: N/A Sensitivity RSpredict(seed): N/A Alterna: N/A Positive Predictive Value RSpredict(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: N/A Murlet(seed): N/A Sensitivity Alterna: N/A Murlet(seed): N/A Positive Predictive Value Alterna: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): N/A Alterna: N/A Sensitivity Multilign(seed): N/A Alterna: N/A Positive Predictive Value Multilign(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: N/A Alterna: N/A Sensitivity HotKnots: N/A Alterna: N/A Positive Predictive Value HotKnots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Alterna Matthews Correlation Coefficient Pknots: N/A Alterna: N/A Sensitivity Pknots: N/A Alterna: N/A Positive Predictive Value Pknots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: N/A Alterna: N/A Sensitivity Cylofold: N/A Alterna: N/A Positive Predictive Value Cylofold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs MCFold Matthews Correlation Coefficient Alterna: N/A MCFold: N/A Sensitivity Alterna: N/A MCFold: N/A Positive Predictive Value Alterna: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Alterna Matthews Correlation Coefficient PPfold(seed): N/A Alterna: N/A Sensitivity PPfold(seed): N/A Alterna: N/A Positive Predictive Value PPfold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: N/A Alterna: N/A Sensitivity RDfolder: N/A Alterna: N/A Positive Predictive Value RDfolder: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): N/A Alterna: N/A Sensitivity TurboFold(seed): N/A Alterna: N/A Positive Predictive Value TurboFold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): N/A Alterna: N/A Sensitivity RNASampler(seed): N/A Alterna: N/A Positive Predictive Value RNASampler(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: N/A Carnac(seed): N/A Sensitivity Alterna: N/A Carnac(seed): N/A Positive Predictive Value Alterna: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): N/A Alterna: N/A Sensitivity Mastr(20): N/A Alterna: N/A Positive Predictive Value Mastr(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs Alterna Matthews Correlation Coefficient Mastr(seed): N/A Alterna: N/A Sensitivity Mastr(seed): N/A Alterna: N/A Positive Predictive Value Mastr(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Carnac(seed)	48 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.659 Carnac(seed): 0.000 Sensitivity ContextFold: 0.623 Carnac(seed): 0.000 Positive Predictive Value ContextFold: 0.697 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.625 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.497 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.788 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.781 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.777 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.786 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.818 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.760 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.881 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	2 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.818 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.738 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.907 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	3 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.885 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.842 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.932 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	48 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.650 Carnac(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.475 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.891 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.636 Carnac(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.463 Carnac(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.874 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.716 Carnac(seed): 0.000 Sensitivity RNAalifold(20): 0.616 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.833 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	48 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.563 Carnac(seed): 0.000 Sensitivity IPknot: 0.516 Carnac(seed): 0.000 Positive Predictive Value IPknot: 0.615 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	2 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.644 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.627 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.662 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	48 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.565 Carnac(seed): 0.000 Sensitivity CentroidFold: 0.517 Carnac(seed): 0.000 Positive Predictive Value CentroidFold: 0.618 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.546 Carnac(seed): 0.000 Sensitivity Contrafold: 0.537 Carnac(seed): 0.000 Positive Predictive Value Contrafold: 0.556 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.695 Carnac(seed): 0.000 Sensitivity MXScarna(20): 0.680 Carnac(seed): 0.000 Positive Predictive Value MXScarna(20): 0.712 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	48 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.504 Carnac(seed): 0.000 Sensitivity MXScarna(seed): 0.364 Carnac(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.700 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.516 Carnac(seed): 0.000 Sensitivity MaxExpect: 0.509 Carnac(seed): 0.000 Positive Predictive Value MaxExpect: 0.525 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.513 Carnac(seed): 0.000 Sensitivity ProbKnot: 0.509 Carnac(seed): 0.000 Positive Predictive Value ProbKnot: 0.519 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	48 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.544 Carnac(seed): 0.000 Sensitivity Sfold: 0.487 Carnac(seed): 0.000 Positive Predictive Value Sfold: 0.609 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.488 Carnac(seed): 0.000 Sensitivity Fold: 0.493 Carnac(seed): 0.000 Positive Predictive Value Fold: 0.484 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.333 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.243 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.456 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	48 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.486 Carnac(seed): 0.000 Sensitivity UNAFold: 0.486 Carnac(seed): 0.000 Positive Predictive Value UNAFold: 0.488 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.487 Carnac(seed): 0.000 Sensitivity PknotsRG: 0.493 Carnac(seed): 0.000 Positive Predictive Value PknotsRG: 0.483 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.475 Carnac(seed): 0.000 Sensitivity RNAfold: 0.479 Carnac(seed): 0.000 Positive Predictive Value RNAfold: 0.472 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.472 Carnac(seed): 0.000 Sensitivity Afold: 0.474 Carnac(seed): 0.000 Positive Predictive Value Afold: 0.472 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.488 Carnac(seed): 0.000 Sensitivity RNAsubopt: 0.498 Carnac(seed): 0.000 Positive Predictive Value RNAsubopt: 0.481 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.448 Carnac(seed): 0.000 Sensitivity McQFold: 0.441 Carnac(seed): 0.000 Positive Predictive Value McQFold: 0.457 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	3 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.140 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.085 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.232 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	31 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.449 Carnac(seed): 0.000 Sensitivity RNASLOpt: 0.414 Carnac(seed): 0.000 Positive Predictive Value RNASLOpt: 0.488 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.619 Carnac(seed): 0.000 Sensitivity RNAalifold(seed): 0.427 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.899 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	34 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.469 Carnac(seed): 0.000 Sensitivity RNAshapes: 0.460 Carnac(seed): 0.000 Positive Predictive Value RNAshapes: 0.479 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 34 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.436 Carnac(seed): 0.000 Sensitivity CRWrnafold: 0.444 Carnac(seed): 0.000 Positive Predictive Value CRWrnafold: 0.430 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.310 Carnac(seed): 0.000 Sensitivity Vsfold4: 0.286 Carnac(seed): 0.000 Positive Predictive Value Vsfold4: 0.340 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.290 Carnac(seed): 0.000 Sensitivity RNAwolf: 0.306 Carnac(seed): 0.000 Positive Predictive Value RNAwolf: 0.277 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.289 Carnac(seed): 0.000 Sensitivity Vsfold5: 0.276 Carnac(seed): 0.000 Positive Predictive Value Vsfold5: 0.306 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	15 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 Carnac(seed): 0.000 Sensitivity CMfinder(seed): 0.159 Carnac(seed): 0.000 Positive Predictive Value CMfinder(seed): 0.770 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.36983135185e-08	3 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.000 Carnac(seed): 0.000 Sensitivity Carnac(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Carnac(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.469 Carnac(seed): 0.000 Sensitivity RSpredict(20): 0.323 Carnac(seed): 0.000 Positive Predictive Value RSpredict(20): 0.683 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	6 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.251 Carnac(seed): 0.000 Sensitivity NanoFolder: 0.296 Carnac(seed): 0.000 Positive Predictive Value NanoFolder: 0.215 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	48 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.072 Carnac(seed): 0.000 Sensitivity RSpredict(seed): 0.016 Carnac(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.327 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): N/A Carnac(seed): N/A Sensitivity Murlet(seed): N/A Carnac(seed): N/A Positive Predictive Value Murlet(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(seed): N/A Sensitivity Multilign(seed): N/A Carnac(seed): N/A Positive Predictive Value Multilign(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: N/A Carnac(seed): N/A Sensitivity HotKnots: N/A Carnac(seed): N/A Positive Predictive Value HotKnots: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: N/A Carnac(seed): N/A Sensitivity Pknots: N/A Carnac(seed): N/A Positive Predictive Value Pknots: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: N/A Carnac(seed): N/A Sensitivity Cylofold: N/A Carnac(seed): N/A Positive Predictive Value Cylofold: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(seed) vs MCFold Matthews Correlation Coefficient Carnac(seed): N/A MCFold: N/A Sensitivity Carnac(seed): N/A MCFold: N/A Positive Predictive Value Carnac(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): N/A Carnac(seed): N/A Sensitivity PPfold(seed): N/A Carnac(seed): N/A Positive Predictive Value PPfold(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: N/A Carnac(seed): N/A Sensitivity RDfolder: N/A Carnac(seed): N/A Positive Predictive Value RDfolder: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 Carnac(seed): 0.000 Sensitivity TurboFold(seed): 0.677 Carnac(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.746 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(seed): N/A Sensitivity RNASampler(seed): N/A Carnac(seed): N/A Positive Predictive Value RNASampler(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: N/A Carnac(seed): N/A Sensitivity Alterna: N/A Carnac(seed): N/A Positive Predictive Value Alterna: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	= Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(seed): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(seed): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 0.0
Mastr(20)	204 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.840 Mastr(20): 0.000 Sensitivity ContextFold: 0.791 Mastr(20): 0.000 Positive Predictive Value ContextFold: 0.892 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.754 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(seed): 0.673 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.845 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.740 Mastr(20): 0.000 Sensitivity TurboFold(20): 0.685 Mastr(20): 0.000 Positive Predictive Value TurboFold(20): 0.801 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(20): 0.652 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.829 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.734 Mastr(20): 0.000 Sensitivity PPfold(20): 0.635 Mastr(20): 0.000 Positive Predictive Value PPfold(20): 0.850 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.717 Mastr(20): 0.000 Sensitivity CentroidAlifold(20): 0.561 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(20): 0.916 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.722 Mastr(20): 0.000 Sensitivity CentroidAlifold(seed): 0.548 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.951 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.702 Mastr(20): 0.000 Sensitivity CentroidHomfold‑LAST: 0.551 Mastr(20): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.660 Mastr(20): 0.000 Sensitivity RNAalifold(20): 0.532 Mastr(20): 0.000 Positive Predictive Value RNAalifold(20): 0.819 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.648 Mastr(20): 0.000 Sensitivity IPknot: 0.574 Mastr(20): 0.000 Positive Predictive Value IPknot: 0.733 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	191 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.649 Mastr(20): 0.000 Sensitivity Multilign(20): 0.590 Mastr(20): 0.000 Positive Predictive Value Multilign(20): 0.717 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 191 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.616 Mastr(20): 0.000 Sensitivity CentroidFold: 0.547 Mastr(20): 0.000 Positive Predictive Value CentroidFold: 0.695 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.601 Mastr(20): 0.000 Sensitivity Contrafold: 0.576 Mastr(20): 0.000 Positive Predictive Value Contrafold: 0.628 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.626 Mastr(20): 0.000 Sensitivity MXScarna(20): 0.551 Mastr(20): 0.000 Positive Predictive Value MXScarna(20): 0.712 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.655 Mastr(20): 0.000 Sensitivity MXScarna(seed): 0.542 Mastr(20): 0.000 Positive Predictive Value MXScarna(seed): 0.793 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.587 Mastr(20): 0.000 Sensitivity MaxExpect: 0.561 Mastr(20): 0.000 Positive Predictive Value MaxExpect: 0.615 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.586 Mastr(20): 0.000 Sensitivity ProbKnot: 0.564 Mastr(20): 0.000 Positive Predictive Value ProbKnot: 0.610 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.543 Mastr(20): 0.000 Sensitivity RNASampler(20): 0.425 Mastr(20): 0.000 Positive Predictive Value RNASampler(20): 0.695 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.568 Mastr(20): 0.000 Sensitivity Sfold: 0.503 Mastr(20): 0.000 Positive Predictive Value Sfold: 0.643 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.550 Mastr(20): 0.000 Sensitivity Fold: 0.541 Mastr(20): 0.000 Positive Predictive Value Fold: 0.560 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.548 Mastr(20): 0.000 Sensitivity Murlet(20): 0.415 Mastr(20): 0.000 Positive Predictive Value Murlet(20): 0.725 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.531 Mastr(20): 0.000 Sensitivity UNAFold: 0.519 Mastr(20): 0.000 Positive Predictive Value UNAFold: 0.545 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.512 Mastr(20): 0.000 Sensitivity PknotsRG: 0.503 Mastr(20): 0.000 Positive Predictive Value PknotsRG: 0.523 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.527 Mastr(20): 0.000 Sensitivity RNAfold: 0.518 Mastr(20): 0.000 Positive Predictive Value RNAfold: 0.537 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	152 Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.548 Mastr(20): 0.000 Sensitivity Afold: 0.533 Mastr(20): 0.000 Positive Predictive Value Afold: 0.564 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.519 Mastr(20): 0.000 Sensitivity RNAsubopt: 0.518 Mastr(20): 0.000 Positive Predictive Value RNAsubopt: 0.522 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.452 Mastr(20): 0.000 Sensitivity McQFold: 0.433 Mastr(20): 0.000 Positive Predictive Value McQFold: 0.474 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.479 Mastr(20): 0.000 Sensitivity CMfinder(20): 0.308 Mastr(20): 0.000 Positive Predictive Value CMfinder(20): 0.747 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.454 Mastr(20): 0.000 Sensitivity RNASLOpt: 0.419 Mastr(20): 0.000 Positive Predictive Value RNASLOpt: 0.494 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.446 Mastr(20): 0.000 Sensitivity RNAalifold(seed): 0.249 Mastr(20): 0.000 Positive Predictive Value RNAalifold(seed): 0.799 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	194 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.456 Mastr(20): 0.000 Sensitivity RNAshapes: 0.441 Mastr(20): 0.000 Positive Predictive Value RNAshapes: 0.473 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 194 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.454 Mastr(20): 0.000 Sensitivity CRWrnafold: 0.446 Mastr(20): 0.000 Positive Predictive Value CRWrnafold: 0.465 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.390 Mastr(20): 0.000 Sensitivity Vsfold4: 0.352 Mastr(20): 0.000 Positive Predictive Value Vsfold4: 0.433 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.367 Mastr(20): 0.000 Sensitivity RNAwolf: 0.377 Mastr(20): 0.000 Positive Predictive Value RNAwolf: 0.359 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.369 Mastr(20): 0.000 Sensitivity Vsfold5: 0.342 Mastr(20): 0.000 Positive Predictive Value Vsfold5: 0.400 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	204 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.360 Mastr(20): 0.000 Sensitivity Carnac(20): 0.151 Mastr(20): 0.000 Positive Predictive Value Carnac(20): 0.857 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	204 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.347 Mastr(20): 0.000 Sensitivity RSpredict(20): 0.220 Mastr(20): 0.000 Positive Predictive Value RSpredict(20): 0.550 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 204 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 NanoFolder vs Mastr(20) Matthews Correlation Coefficient NanoFolder: 0.152 Mastr(20): 0.000 Sensitivity NanoFolder: 0.174 Mastr(20): 0.000 Positive Predictive Value NanoFolder: 0.135 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	164 RSpredict(seed) vs Mastr(20) Matthews Correlation Coefficient RSpredict(seed): 0.054 Mastr(20): 0.000 Sensitivity RSpredict(seed): 0.014 Mastr(20): 0.000 Positive Predictive Value RSpredict(seed): 0.216 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 164 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	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	0 Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): N/A HotKnots: N/A Sensitivity Mastr(20): N/A HotKnots: N/A Positive Predictive Value Mastr(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): N/A Pknots: N/A Sensitivity Mastr(20): N/A Pknots: N/A Positive Predictive Value Mastr(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): N/A Cylofold: N/A Sensitivity Mastr(20): N/A Cylofold: N/A Positive Predictive Value Mastr(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): N/A MCFold: N/A Sensitivity Mastr(20): N/A MCFold: N/A Positive Predictive Value Mastr(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	0 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): N/A RDfolder: N/A Sensitivity Mastr(20): N/A RDfolder: N/A Positive Predictive Value Mastr(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	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	0 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): N/A Alterna: N/A Sensitivity Mastr(20): N/A Alterna: N/A Positive Predictive Value Mastr(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	3 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0		= Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.000 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 0.0
Mastr(seed)	258 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.804 Mastr(seed): 0.000 Sensitivity ContextFold: 0.757 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.854 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.720 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.632 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.820 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.760 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.703 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.822 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.675 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.849 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	142 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.755 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.660 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.863 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 142 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.728 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.567 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.934 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	250 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.692 Mastr(seed): 0.000 Sensitivity CentroidAlifold(seed): 0.523 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.918 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 250 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.511 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.896 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.669 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.536 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.836 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.637 Mastr(seed): 0.000 Sensitivity IPknot: 0.566 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.717 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	138 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.660 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.598 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.729 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 138 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.619 Mastr(seed): 0.000 Sensitivity CentroidFold: 0.553 Mastr(seed): 0.000 Positive Predictive Value CentroidFold: 0.694 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.602 Mastr(seed): 0.000 Sensitivity Contrafold: 0.578 Mastr(seed): 0.000 Positive Predictive Value Contrafold: 0.627 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.659 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.573 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.759 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	255 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.596 Mastr(seed): 0.000 Sensitivity MXScarna(seed): 0.476 Mastr(seed): 0.000 Positive Predictive Value MXScarna(seed): 0.747 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 255 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.585 Mastr(seed): 0.000 Sensitivity MaxExpect: 0.561 Mastr(seed): 0.000 Positive Predictive Value MaxExpect: 0.612 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.585 Mastr(seed): 0.000 Sensitivity ProbKnot: 0.566 Mastr(seed): 0.000 Positive Predictive Value ProbKnot: 0.606 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.480 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.343 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.673 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	258 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.581 Mastr(seed): 0.000 Sensitivity Sfold: 0.518 Mastr(seed): 0.000 Positive Predictive Value Sfold: 0.653 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.550 Mastr(seed): 0.000 Sensitivity Fold: 0.542 Mastr(seed): 0.000 Positive Predictive Value Fold: 0.559 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.537 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.394 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.734 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.540 Mastr(seed): 0.000 Sensitivity UNAFold: 0.528 Mastr(seed): 0.000 Positive Predictive Value UNAFold: 0.554 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.523 Mastr(seed): 0.000 Sensitivity PknotsRG: 0.515 Mastr(seed): 0.000 Positive Predictive Value PknotsRG: 0.533 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.532 Mastr(seed): 0.000 Sensitivity RNAfold: 0.523 Mastr(seed): 0.000 Positive Predictive Value RNAfold: 0.543 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.527 Mastr(seed): 0.000 Sensitivity Afold: 0.516 Mastr(seed): 0.000 Positive Predictive Value Afold: 0.539 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.534 Mastr(seed): 0.000 Sensitivity RNAsubopt: 0.533 Mastr(seed): 0.000 Positive Predictive Value RNAsubopt: 0.537 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.483 Mastr(seed): 0.000 Sensitivity McQFold: 0.463 Mastr(seed): 0.000 Positive Predictive Value McQFold: 0.505 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.503 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.332 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.764 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.473 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.436 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.515 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.475 Mastr(seed): 0.000 Sensitivity RNAalifold(seed): 0.278 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(seed): 0.814 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	236 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.482 Mastr(seed): 0.000 Sensitivity RNAshapes: 0.466 Mastr(seed): 0.000 Positive Predictive Value RNAshapes: 0.499 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 236 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.455 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.449 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.464 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.400 Mastr(seed): 0.000 Sensitivity Vsfold4: 0.361 Mastr(seed): 0.000 Positive Predictive Value Vsfold4: 0.445 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.368 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.377 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.361 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.375 Mastr(seed): 0.000 Sensitivity Vsfold5: 0.347 Mastr(seed): 0.000 Positive Predictive Value Vsfold5: 0.407 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.350 Mastr(seed): 0.000 Sensitivity CMfinder(seed): 0.159 Mastr(seed): 0.000 Positive Predictive Value CMfinder(seed): 0.770 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.96907987703e-08	148 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.334 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.127 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.880 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.303 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.171 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.179 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.205 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.159 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	253 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.046 Mastr(seed): 0.000 Sensitivity RSpredict(seed): 0.011 Mastr(seed): 0.000 Positive Predictive Value RSpredict(seed): 0.191 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 253 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Mastr(seed) vs Murlet(seed) Matthews Correlation Coefficient Mastr(seed): N/A Murlet(seed): N/A Sensitivity Mastr(seed): N/A Murlet(seed): N/A Positive Predictive Value Mastr(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs Multilign(seed) Matthews Correlation Coefficient Mastr(seed): N/A Multilign(seed): N/A Sensitivity Mastr(seed): N/A Multilign(seed): N/A Positive Predictive Value Mastr(seed): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: N/A Mastr(seed): N/A Sensitivity HotKnots: N/A Mastr(seed): N/A Positive Predictive Value HotKnots: N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs Pknots Matthews Correlation Coefficient Mastr(seed): N/A Pknots: N/A Sensitivity Mastr(seed): N/A Pknots: N/A Positive Predictive Value Mastr(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: N/A Mastr(seed): N/A Sensitivity Cylofold: N/A Mastr(seed): N/A Positive Predictive Value Cylofold: N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): N/A MCFold: N/A Sensitivity Mastr(seed): N/A MCFold: N/A Positive Predictive Value Mastr(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs PPfold(seed) Matthews Correlation Coefficient Mastr(seed): N/A PPfold(seed): N/A Sensitivity Mastr(seed): N/A PPfold(seed): N/A Positive Predictive Value Mastr(seed): N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs RDfolder Matthews Correlation Coefficient Mastr(seed): N/A RDfolder: N/A Sensitivity Mastr(seed): N/A RDfolder: N/A Positive Predictive Value Mastr(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.710 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.677 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.746 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): N/A Mastr(seed): N/A Sensitivity RNASampler(seed): N/A Mastr(seed): N/A Positive Predictive Value RNASampler(seed): N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs Alterna Matthews Correlation Coefficient Mastr(seed): N/A Alterna: N/A Sensitivity Mastr(seed): N/A Alterna: N/A Positive Predictive Value Mastr(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	48 Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(seed): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(seed): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 0.0	148 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.000 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 148 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).