CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

All RNAs from the PDB dataset
standard base pair definition

	All RNAs from the PDB dataset were used to benchmark RNA secondary structure prediction methods. Standard base pair definition is used - it corresponds to the Leontis and Westhof classification i.e. the canonical A-U, G-C and Wobble G-U pairs that belong to the cis Watson-Crick/Watson-Crick geometry are considered as the secondary structure.
Updated: Oct. 2, 2012
Base pair definition: standard
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 30000
Number of RNA sequences: 121
Robustness test: no

Important! This ranking will be updated in future, when predictions for new RNAs are generated by the methods being tested. This ranking shows the performance of methods as of Oct. 2, 2012.

In the summary below ranks have been assigned only to methods, for which at least 40% of comparisons with other methods is valid (i.e. at least 40% (in case of this ranking: 21) of the comparisons were based on at least 10 predictions for common targets).

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

Summary of pairwise comparisons

54 methods predicting RNA secondary structure were compared with each other (thus each method has 53 comparisons with other methods (sum of values from columns "Wins", "Losses", "=" and "?" in each row)).

Legend:

=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)
N/A	a method for which more than 32 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Tested since	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	MXScarna(seed)	no	2009-06-15	38	3	0	12	44	44
2	CentroidAlifold(20)	yes	2009-07-01	36	0	0	17	26	26
3	CentroidFold	yes	2009-08-01	36	8	1	8	106	106
4	RNAalifold(20)	no	2009-02-18	34	2	0	17	28	28
5	Sfold	no	2009-02-18	33	11	1	8	121	121
5	Fold	no	2010-03-15	33	11	1	8	82	82
7	RNASampler(20)	no	2009-02-18	32	3	1	17	28	28
7	MXScarna(20)	no	2009-02-18	32	3	1	17	28	28
9	CentroidHomfold‑LAST	yes	2011-05-11	30	1	1	21	45	44
10	UNAFold	no	2009-02-18	30	13	2	8	121	121
10	HotKnots	no	2009-02-18	30	13	2	8	121	118
12	Contrafold	yes	2009-02-18	29	11	5	8	121	121
13	IPknot	yes	2011-07-01	28	2	2	21	38	38
14	ContextFold	yes	2011-11-15	27	0	0	26	30	30
15	RNAshapes	no	2009-02-18	27	14	4	8	121	118
16	MaxExpect	yes	2009-10-15	27	15	3	8	100	99
17	PknotsRG	no	2009-02-18	25	19	1	8	121	121
18	RNAfold	no	2009-02-18	24	18	3	8	121	121
19	ProbKnot	yes	2010-08-10	23	19	2	9	74	74
20	Murlet(20)	yes	2009-02-18	22	12	2	17	28	28
21	CentroidAlifold(seed)	yes	2009-07-01	20	13	8	12	43	43
22	Afold	no	2009-02-18	20	22	1	10	121	95
23	RNAsubopt	no	2009-02-18	18	26	1	8	121	118
24	Carnac(20)	no	2009-02-18	17	16	3	17	28	28
25	Cylofold	no	2010-06-08	15	25	2	11	76	63
26	McQFold	yes	2009-02-18	15	29	1	8	121	120
27	CRWrnafold	yes	2011-08-23	14	11	2	26	36	32
28	RNAalifold(seed)	no	2009-02-18	14	19	3	17	45	29
29	Pknots	no	2009-02-18	14	29	2	8	121	116
30	RNASampler(seed)	no	2009-02-18	13	12	1	27	45	17
31	Mastr(20)	yes	2009-02-18	12	23	1	17	28	28
32	RSpredict(20)	no	2009-06-03	12	24	0	17	27	27
33	Alterna	no	2009-02-18	12	29	1	11	121	89
34	RNASLOpt	no	2011-11-01	9	17	1	26	30	30
35	Multilign(20)	no	2011-03-01	8	18	2	25	10	10
36	Vsfold4	no	2009-02-18	8	35	2	8	121	118
37	MCFold	yes	2009-02-18	7	34	2	10	121	109
38	RNAwolf	yes	2011-07-01	6	25	1	21	38	38
39	Murlet(seed)	yes	2009-02-18	6	28	2	17	45	26
40	Vsfold5	no	2009-02-18	5	39	1	8	121	117
41	RSpredict(seed)	no	2009-06-03	3	38	0	12	44	44
42	RDfolder	no	2009-02-18	3	37	2	11	121	92
43	PPfold(seed)	yes	2011-04-18	1	22	0	30	12	11
44	Mastr(seed)	yes	2009-02-18	1	40	0	12	45	45
45	NanoFolder	yes	2011-11-17	0	24	1	28	20	17
46	Carnac(seed)	no	2009-02-18	0	36	0	17	45	30
N/A	Multilign(seed)	no	2011-03-01	0	0	0	53	13	5
N/A	TurboFold(seed)	no	2011-04-20	0	0	0	53	12	9
N/A	TurboFold(20)	no	2011-04-20	0	0	0	53	9	9
N/A	PPfold(20)	yes	2011-04-18	0	0	0	53	9	9
N/A	PETfold_pre2.0(seed)	no	2011-11-03	0	0	0	53	8	8
N/A	PETfold_pre2.0(20)	no	2011-11-03	0	0	0	53	5	5
N/A	CMfinder(seed)	yes	2012-09-01	0	0	0	53	0	0
N/A	CMfinder(20)	yes	2012-09-01	0	0	0	53	0	0

Detailed results of pairwise comparisons between methods

Legend:

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

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


MXScarna(seed)		- CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 MXScarna(seed): 0.780 Sensitivity CentroidAlifold(20): 0.716 MXScarna(seed): 0.739 Positive Predictive Value CentroidAlifold(20): 0.921 MXScarna(seed): 0.827 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.774 CentroidFold: 0.724 Sensitivity MXScarna(seed): 0.733 CentroidFold: 0.727 Positive Predictive Value MXScarna(seed): 0.822 CentroidFold: 0.726 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 RNAalifold(20): 0.775 Sensitivity MXScarna(seed): 0.743 RNAalifold(20): 0.682 Positive Predictive Value MXScarna(seed): 0.829 RNAalifold(20): 0.884 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 8.09943589199e-07	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.776 Sfold: 0.709 Sensitivity MXScarna(seed): 0.736 Sfold: 0.701 Positive Predictive Value MXScarna(seed): 0.824 Sfold: 0.722 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.753 Fold: 0.722 Sensitivity MXScarna(seed): 0.713 Fold: 0.750 Positive Predictive Value MXScarna(seed): 0.799 Fold: 0.700 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 RNASampler(20): 0.766 Sensitivity MXScarna(seed): 0.743 RNASampler(20): 0.676 Positive Predictive Value MXScarna(seed): 0.829 RNASampler(20): 0.872 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.64876692942e-07	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 MXScarna(20): 0.760 Sensitivity MXScarna(seed): 0.743 MXScarna(20): 0.726 Positive Predictive Value MXScarna(seed): 0.829 MXScarna(20): 0.800 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	- CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 MXScarna(seed): 0.716 Sensitivity CentroidHomfold‑LAST: 0.690 MXScarna(seed): 0.667 Positive Predictive Value CentroidHomfold‑LAST: 0.829 MXScarna(seed): 0.777 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.776 HotKnots: 0.701 Sensitivity MXScarna(seed): 0.736 HotKnots: 0.732 Positive Predictive Value MXScarna(seed): 0.824 HotKnots: 0.676 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.776 UNAFold: 0.700 Sensitivity MXScarna(seed): 0.736 UNAFold: 0.721 Positive Predictive Value MXScarna(seed): 0.824 UNAFold: 0.685 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.776 Contrafold: 0.698 Sensitivity MXScarna(seed): 0.736 Contrafold: 0.726 Positive Predictive Value MXScarna(seed): 0.824 Contrafold: 0.677 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.728 IPknot: 0.701 Sensitivity MXScarna(seed): 0.675 IPknot: 0.658 Positive Predictive Value MXScarna(seed): 0.792 IPknot: 0.755 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.52299983238e-08	? ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.732 MXScarna(seed): 0.679 Sensitivity ContextFold: 0.673 MXScarna(seed): 0.620 Positive Predictive Value ContextFold: 0.804 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.776 RNAshapes: 0.699 Sensitivity MXScarna(seed): 0.736 RNAshapes: 0.720 Positive Predictive Value MXScarna(seed): 0.824 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.768 MaxExpect: 0.703 Sensitivity MXScarna(seed): 0.729 MaxExpect: 0.725 Positive Predictive Value MXScarna(seed): 0.813 MaxExpect: 0.687 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.776 PknotsRG: 0.703 Sensitivity MXScarna(seed): 0.736 PknotsRG: 0.732 Positive Predictive Value MXScarna(seed): 0.824 PknotsRG: 0.681 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.776 RNAfold: 0.704 Sensitivity MXScarna(seed): 0.736 RNAfold: 0.730 Positive Predictive Value MXScarna(seed): 0.824 RNAfold: 0.685 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.740 ProbKnot: 0.657 Sensitivity MXScarna(seed): 0.699 ProbKnot: 0.701 Positive Predictive Value MXScarna(seed): 0.788 ProbKnot: 0.622 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 Murlet(20): 0.698 Sensitivity MXScarna(seed): 0.743 Murlet(20): 0.590 Positive Predictive Value MXScarna(seed): 0.829 Murlet(20): 0.832 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.774 CentroidAlifold(seed): 0.690 Sensitivity MXScarna(seed): 0.733 CentroidAlifold(seed): 0.552 Positive Predictive Value MXScarna(seed): 0.822 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.758 Afold: 0.657 Sensitivity MXScarna(seed): 0.709 Afold: 0.693 Positive Predictive Value MXScarna(seed): 0.815 Afold: 0.629 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.776 RNAsubopt: 0.664 Sensitivity MXScarna(seed): 0.736 RNAsubopt: 0.693 Positive Predictive Value MXScarna(seed): 0.824 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 Carnac(20): 0.695 Sensitivity MXScarna(seed): 0.743 Carnac(20): 0.518 Positive Predictive Value MXScarna(seed): 0.829 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.774 Cylofold: 0.732 Sensitivity MXScarna(seed): 0.730 Cylofold: 0.726 Positive Predictive Value MXScarna(seed): 0.827 Cylofold: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 2.87980998248e-07	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.776 McQFold: 0.655 Sensitivity MXScarna(seed): 0.736 McQFold: 0.671 Positive Predictive Value MXScarna(seed): 0.824 McQFold: 0.646 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.705 CRWrnafold: 0.647 Sensitivity MXScarna(seed): 0.660 CRWrnafold: 0.655 Positive Predictive Value MXScarna(seed): 0.761 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.722 RNAalifold(seed): 0.676 Sensitivity MXScarna(seed): 0.677 RNAalifold(seed): 0.525 Positive Predictive Value MXScarna(seed): 0.776 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.802 Pknots: 0.720 Sensitivity MXScarna(seed): 0.760 Pknots: 0.751 Positive Predictive Value MXScarna(seed): 0.852 Pknots: 0.698 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 MXScarna(seed): 0.759 Sensitivity RNASampler(seed): 0.687 MXScarna(seed): 0.719 Positive Predictive Value RNASampler(seed): 0.859 MXScarna(seed): 0.808 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.38571919282e-05	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 Mastr(20): 0.635 Sensitivity MXScarna(seed): 0.743 Mastr(20): 0.478 Positive Predictive Value MXScarna(seed): 0.829 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 RSpredict(20): 0.663 Sensitivity MXScarna(seed): 0.743 RSpredict(20): 0.593 Positive Predictive Value MXScarna(seed): 0.829 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.828 Alterna: 0.757 Sensitivity MXScarna(seed): 0.776 Alterna: 0.765 Positive Predictive Value MXScarna(seed): 0.892 Alterna: 0.760 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	? MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.679 RNASLOpt: 0.560 Sensitivity MXScarna(seed): 0.620 RNASLOpt: 0.526 Positive Predictive Value MXScarna(seed): 0.752 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.732 Multilign(20): 0.612 Sensitivity MXScarna(seed): 0.689 Multilign(20): 0.581 Positive Predictive Value MXScarna(seed): 0.787 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.16841705202e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.776 Vsfold4: 0.595 Sensitivity MXScarna(seed): 0.736 Vsfold4: 0.595 Positive Predictive Value MXScarna(seed): 0.824 Vsfold4: 0.603 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.806 MCFold: 0.602 Sensitivity MXScarna(seed): 0.767 MCFold: 0.650 Positive Predictive Value MXScarna(seed): 0.854 MCFold: 0.568 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.728 RNAwolf: 0.499 Sensitivity MXScarna(seed): 0.675 RNAwolf: 0.490 Positive Predictive Value MXScarna(seed): 0.792 RNAwolf: 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.761 Murlet(seed): 0.620 Sensitivity MXScarna(seed): 0.719 Murlet(seed): 0.442 Positive Predictive Value MXScarna(seed): 0.812 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.776 Vsfold5: 0.570 Sensitivity MXScarna(seed): 0.736 Vsfold5: 0.575 Positive Predictive Value MXScarna(seed): 0.824 Vsfold5: 0.573 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.776 RSpredict(seed): 0.372 Sensitivity MXScarna(seed): 0.736 RSpredict(seed): 0.222 Positive Predictive Value MXScarna(seed): 0.824 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.809 RDfolder: 0.637 Sensitivity MXScarna(seed): 0.754 RDfolder: 0.604 Positive Predictive Value MXScarna(seed): 0.876 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.728 PPfold(seed): 0.122 Sensitivity MXScarna(seed): 0.675 PPfold(seed): 0.029 Positive Predictive Value MXScarna(seed): 0.792 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.36849473644e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.776 Mastr(seed): 0.310 Sensitivity MXScarna(seed): 0.736 Mastr(seed): 0.108 Positive Predictive Value MXScarna(seed): 0.824 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 MXScarna(seed): 0.630 Sensitivity Multilign(seed): 0.636 MXScarna(seed): 0.593 Positive Predictive Value Multilign(seed): 0.750 MXScarna(seed): 0.686 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 MXScarna(seed): 0.679 Sensitivity PETfold_pre2.0(seed): 0.772 MXScarna(seed): 0.620 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 MXScarna(seed): 0.732 Sensitivity TurboFold(20): 0.694 MXScarna(seed): 0.689 Positive Predictive Value TurboFold(20): 0.781 MXScarna(seed): 0.785 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): N/A CMfinder(20): N/A Sensitivity MXScarna(seed): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 MXScarna(seed): 0.691 Sensitivity PETfold_pre2.0(20): 0.707 MXScarna(seed): 0.638 Positive Predictive Value PETfold_pre2.0(20): 0.796 MXScarna(seed): 0.755 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.653 TurboFold(seed): 0.650 Sensitivity MXScarna(seed): 0.605 TurboFold(seed): 0.624 Positive Predictive Value MXScarna(seed): 0.717 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.780 MXScarna(seed): 0.732 Sensitivity PPfold(20): 0.714 MXScarna(seed): 0.689 Positive Predictive Value PPfold(20): 0.860 MXScarna(seed): 0.785 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.691 NanoFolder: 0.412 Sensitivity MXScarna(seed): 0.641 NanoFolder: 0.506 Positive Predictive Value MXScarna(seed): 0.752 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.781 Carnac(seed): 0.299 Sensitivity MXScarna(seed): 0.746 Carnac(seed): 0.090 Positive Predictive Value MXScarna(seed): 0.825 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(20)	26 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 MXScarna(seed): 0.780 Sensitivity CentroidAlifold(20): 0.716 MXScarna(seed): 0.739 Positive Predictive Value CentroidAlifold(20): 0.921 MXScarna(seed): 0.827 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08		+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 CentroidFold: 0.708 Sensitivity CentroidAlifold(20): 0.716 CentroidFold: 0.697 Positive Predictive Value CentroidAlifold(20): 0.921 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAalifold(20): 0.777 Sensitivity CentroidAlifold(20): 0.716 RNAalifold(20): 0.686 Positive Predictive Value CentroidAlifold(20): 0.921 RNAalifold(20): 0.884 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Sfold: 0.705 Sensitivity CentroidAlifold(20): 0.716 Sfold: 0.681 Positive Predictive Value CentroidAlifold(20): 0.921 Sfold: 0.735 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.787 Fold: 0.720 Sensitivity CentroidAlifold(20): 0.674 Fold: 0.735 Positive Predictive Value CentroidAlifold(20): 0.922 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.48104284388e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNASampler(20): 0.762 Sensitivity CentroidAlifold(20): 0.716 RNASampler(20): 0.671 Positive Predictive Value CentroidAlifold(20): 0.921 RNASampler(20): 0.870 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 MXScarna(20): 0.756 Sensitivity CentroidAlifold(20): 0.716 MXScarna(20): 0.722 Positive Predictive Value CentroidAlifold(20): 0.921 MXScarna(20): 0.797 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.805 CentroidHomfold‑LAST: 0.782 Sensitivity CentroidAlifold(20): 0.714 CentroidHomfold‑LAST: 0.723 Positive Predictive Value CentroidAlifold(20): 0.913 CentroidHomfold‑LAST: 0.851 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.810 HotKnots: 0.690 Sensitivity CentroidAlifold(20): 0.716 HotKnots: 0.712 Positive Predictive Value CentroidAlifold(20): 0.921 HotKnots: 0.674 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 UNAFold: 0.704 Sensitivity CentroidAlifold(20): 0.716 UNAFold: 0.710 Positive Predictive Value CentroidAlifold(20): 0.921 UNAFold: 0.704 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Contrafold: 0.659 Sensitivity CentroidAlifold(20): 0.716 Contrafold: 0.677 Positive Predictive Value CentroidAlifold(20): 0.921 Contrafold: 0.647 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.825 IPknot: 0.684 Sensitivity CentroidAlifold(20): 0.729 IPknot: 0.654 Positive Predictive Value CentroidAlifold(20): 0.938 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.779 ContextFold: 0.698 Sensitivity CentroidAlifold(20): 0.672 ContextFold: 0.638 Positive Predictive Value CentroidAlifold(20): 0.907 ContextFold: 0.771 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAshapes: 0.699 Sensitivity CentroidAlifold(20): 0.716 RNAshapes: 0.704 Positive Predictive Value CentroidAlifold(20): 0.921 RNAshapes: 0.698 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.810 MaxExpect: 0.700 Sensitivity CentroidAlifold(20): 0.716 MaxExpect: 0.710 Positive Predictive Value CentroidAlifold(20): 0.921 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.810 PknotsRG: 0.690 Sensitivity CentroidAlifold(20): 0.716 PknotsRG: 0.710 Positive Predictive Value CentroidAlifold(20): 0.921 PknotsRG: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAfold: 0.679 Sensitivity CentroidAlifold(20): 0.716 RNAfold: 0.694 Positive Predictive Value CentroidAlifold(20): 0.921 RNAfold: 0.669 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.787 ProbKnot: 0.686 Sensitivity CentroidAlifold(20): 0.674 ProbKnot: 0.713 Positive Predictive Value CentroidAlifold(20): 0.922 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Murlet(20): 0.698 Sensitivity CentroidAlifold(20): 0.716 Murlet(20): 0.591 Positive Predictive Value CentroidAlifold(20): 0.921 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 CentroidAlifold(seed): 0.728 Sensitivity CentroidAlifold(20): 0.716 CentroidAlifold(seed): 0.580 Positive Predictive Value CentroidAlifold(20): 0.921 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.764 Afold: 0.614 Sensitivity CentroidAlifold(20): 0.657 Afold: 0.640 Positive Predictive Value CentroidAlifold(20): 0.891 Afold: 0.596 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAsubopt: 0.669 Sensitivity CentroidAlifold(20): 0.716 RNAsubopt: 0.690 Positive Predictive Value CentroidAlifold(20): 0.921 RNAsubopt: 0.654 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Carnac(20): 0.694 Sensitivity CentroidAlifold(20): 0.716 Carnac(20): 0.516 Positive Predictive Value CentroidAlifold(20): 0.921 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.823 Cylofold: 0.703 Sensitivity CentroidAlifold(20): 0.718 Cylofold: 0.703 Positive Predictive Value CentroidAlifold(20): 0.948 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 McQFold: 0.629 Sensitivity CentroidAlifold(20): 0.716 McQFold: 0.641 Positive Predictive Value CentroidAlifold(20): 0.921 McQFold: 0.624 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.819 CRWrnafold: 0.668 Sensitivity CentroidAlifold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value CentroidAlifold(20): 0.930 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.748 RNAalifold(seed): 0.675 Sensitivity CentroidAlifold(20): 0.625 RNAalifold(seed): 0.496 Positive Predictive Value CentroidAlifold(20): 0.900 RNAalifold(seed): 0.924 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.830 Pknots: 0.647 Sensitivity CentroidAlifold(20): 0.748 Pknots: 0.688 Positive Predictive Value CentroidAlifold(20): 0.926 Pknots: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.714 RNASampler(seed): 0.694 Sensitivity CentroidAlifold(20): 0.628 RNASampler(seed): 0.635 Positive Predictive Value CentroidAlifold(20): 0.816 RNASampler(seed): 0.764 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Mastr(20): 0.628 Sensitivity CentroidAlifold(20): 0.716 Mastr(20): 0.471 Positive Predictive Value CentroidAlifold(20): 0.921 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RSpredict(20): 0.660 Sensitivity CentroidAlifold(20): 0.716 RSpredict(20): 0.590 Positive Predictive Value CentroidAlifold(20): 0.921 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.886 Alterna: 0.658 Sensitivity CentroidAlifold(20): 0.823 Alterna: 0.667 Positive Predictive Value CentroidAlifold(20): 0.958 Alterna: 0.661 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.39551335374e-08	? CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.779 RNASLOpt: 0.560 Sensitivity CentroidAlifold(20): 0.672 RNASLOpt: 0.543 Positive Predictive Value CentroidAlifold(20): 0.907 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.762 Multilign(20): 0.612 Sensitivity CentroidAlifold(20): 0.639 Multilign(20): 0.581 Positive Predictive Value CentroidAlifold(20): 0.917 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Vsfold4: 0.530 Sensitivity CentroidAlifold(20): 0.716 Vsfold4: 0.524 Positive Predictive Value CentroidAlifold(20): 0.921 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.831 MCFold: 0.512 Sensitivity CentroidAlifold(20): 0.752 MCFold: 0.571 Positive Predictive Value CentroidAlifold(20): 0.922 MCFold: 0.471 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.825 RNAwolf: 0.453 Sensitivity CentroidAlifold(20): 0.729 RNAwolf: 0.447 Positive Predictive Value CentroidAlifold(20): 0.938 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.765 Murlet(seed): 0.588 Sensitivity CentroidAlifold(20): 0.651 Murlet(seed): 0.379 Positive Predictive Value CentroidAlifold(20): 0.905 Murlet(seed): 0.920 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Vsfold5: 0.494 Sensitivity CentroidAlifold(20): 0.716 Vsfold5: 0.495 Positive Predictive Value CentroidAlifold(20): 0.921 Vsfold5: 0.502 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RSpredict(seed): 0.284 Sensitivity CentroidAlifold(20): 0.716 RSpredict(seed): 0.146 Positive Predictive Value CentroidAlifold(20): 0.921 RSpredict(seed): 0.564 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.872 RDfolder: 0.611 Sensitivity CentroidAlifold(20): 0.792 RDfolder: 0.578 Positive Predictive Value CentroidAlifold(20): 0.964 RDfolder: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	? CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.825 PPfold(seed): 0.031 Sensitivity CentroidAlifold(20): 0.729 PPfold(seed): 0.005 Positive Predictive Value CentroidAlifold(20): 0.938 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.716 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.921 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-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 Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.818 Multilign(seed): 0.795 Sensitivity CentroidAlifold(20): 0.730 Multilign(seed): 0.750 Positive Predictive Value CentroidAlifold(20): 0.924 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 CentroidAlifold(20): 0.779 Sensitivity PETfold_pre2.0(seed): 0.784 CentroidAlifold(20): 0.672 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidAlifold(20): 0.907 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 TurboFold(20): 0.733 Sensitivity CentroidAlifold(20): 0.714 TurboFold(20): 0.694 Positive Predictive Value CentroidAlifold(20): 0.913 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(20): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.779 PETfold_pre2.0(20): 0.747 Sensitivity CentroidAlifold(20): 0.672 PETfold_pre2.0(20): 0.707 Positive Predictive Value CentroidAlifold(20): 0.907 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.783 TurboFold(seed): 0.712 Sensitivity CentroidAlifold(20): 0.684 TurboFold(seed): 0.684 Positive Predictive Value CentroidAlifold(20): 0.901 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 PPfold(20): 0.780 Sensitivity CentroidAlifold(20): 0.714 PPfold(20): 0.714 Positive Predictive Value CentroidAlifold(20): 0.913 PPfold(20): 0.860 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.780 NanoFolder: 0.389 Sensitivity CentroidAlifold(20): 0.683 NanoFolder: 0.475 Positive Predictive Value CentroidAlifold(20): 0.896 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.801 Carnac(seed): 0.187 Sensitivity CentroidAlifold(20): 0.708 Carnac(seed): 0.035 Positive Predictive Value CentroidAlifold(20): 0.910 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08
CentroidFold	43 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.774 CentroidFold: 0.724 Sensitivity MXScarna(seed): 0.733 CentroidFold: 0.727 Positive Predictive Value MXScarna(seed): 0.822 CentroidFold: 0.726 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 CentroidFold: 0.708 Sensitivity CentroidAlifold(20): 0.716 CentroidFold: 0.697 Positive Predictive Value CentroidAlifold(20): 0.921 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08		- RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.777 CentroidFold: 0.708 Sensitivity RNAalifold(20): 0.686 CentroidFold: 0.697 Positive Predictive Value RNAalifold(20): 0.884 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.711 Sfold: 0.657 Sensitivity CentroidFold: 0.707 Sfold: 0.655 Positive Predictive Value CentroidFold: 0.715 Sfold: 0.659 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.786 Fold: 0.777 Sensitivity CentroidFold: 0.781 Fold: 0.796 Positive Predictive Value CentroidFold: 0.797 Fold: 0.764 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 1.06521910535e-06	- RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.762 CentroidFold: 0.708 Sensitivity RNASampler(20): 0.671 CentroidFold: 0.697 Positive Predictive Value RNASampler(20): 0.870 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	- MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.756 CentroidFold: 0.708 Sensitivity MXScarna(20): 0.722 CentroidFold: 0.697 Positive Predictive Value MXScarna(20): 0.797 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.98172311752e-08	- CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 CentroidFold: 0.774 Sensitivity CentroidHomfold‑LAST: 0.691 CentroidFold: 0.752 Positive Predictive Value CentroidHomfold‑LAST: 0.893 CentroidFold: 0.804 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.08902352868e-05	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.780 HotKnots: 0.767 Sensitivity CentroidFold: 0.775 HotKnots: 0.790 Positive Predictive Value CentroidFold: 0.791 HotKnots: 0.750 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 7.5939721025e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.711 UNAFold: 0.630 Sensitivity CentroidFold: 0.707 UNAFold: 0.666 Positive Predictive Value CentroidFold: 0.715 UNAFold: 0.596 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.711 Contrafold: 0.695 Sensitivity CentroidFold: 0.707 Contrafold: 0.722 Positive Predictive Value CentroidFold: 0.715 Contrafold: 0.669 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 0.00208354999408	- IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.782 CentroidFold: 0.766 Sensitivity IPknot: 0.752 CentroidFold: 0.743 Positive Predictive Value IPknot: 0.820 CentroidFold: 0.798 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.816 CentroidFold: 0.747 Sensitivity ContextFold: 0.780 CentroidFold: 0.721 Positive Predictive Value ContextFold: 0.861 CentroidFold: 0.783 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.780 RNAshapes: 0.756 Sensitivity CentroidFold: 0.775 RNAshapes: 0.768 Positive Predictive Value CentroidFold: 0.791 RNAshapes: 0.750 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.762 MaxExpect: 0.729 Sensitivity CentroidFold: 0.747 MaxExpect: 0.740 Positive Predictive Value CentroidFold: 0.779 MaxExpect: 0.719 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.711 PknotsRG: 0.609 Sensitivity CentroidFold: 0.707 PknotsRG: 0.652 Positive Predictive Value CentroidFold: 0.715 PknotsRG: 0.570 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.711 RNAfold: 0.620 Sensitivity CentroidFold: 0.707 RNAfold: 0.663 Positive Predictive Value CentroidFold: 0.715 RNAfold: 0.582 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.768 ProbKnot: 0.741 Sensitivity CentroidFold: 0.763 ProbKnot: 0.774 Positive Predictive Value CentroidFold: 0.777 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.708 Murlet(20): 0.698 Sensitivity CentroidFold: 0.697 Murlet(20): 0.591 Positive Predictive Value CentroidFold: 0.724 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.000493106477465	+ CentroidFold vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidFold: 0.724 CentroidAlifold(seed): 0.690 Sensitivity CentroidFold: 0.727 CentroidAlifold(seed): 0.552 Positive Predictive Value CentroidFold: 0.726 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.700 Afold: 0.600 Sensitivity CentroidFold: 0.699 Afold: 0.648 Positive Predictive Value CentroidFold: 0.702 Afold: 0.556 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.780 RNAsubopt: 0.737 Sensitivity CentroidFold: 0.775 RNAsubopt: 0.758 Positive Predictive Value CentroidFold: 0.791 RNAsubopt: 0.724 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.708 Carnac(20): 0.694 Sensitivity CentroidFold: 0.697 Carnac(20): 0.516 Positive Predictive Value CentroidFold: 0.724 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 1.43482349379e-06	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.815 Cylofold: 0.741 Sensitivity CentroidFold: 0.796 Cylofold: 0.724 Positive Predictive Value CentroidFold: 0.841 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.709 McQFold: 0.570 Sensitivity CentroidFold: 0.706 McQFold: 0.525 Positive Predictive Value CentroidFold: 0.714 McQFold: 0.620 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.737 CRWrnafold: 0.683 Sensitivity CentroidFold: 0.717 CRWrnafold: 0.690 Positive Predictive Value CentroidFold: 0.767 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.712 RNAalifold(seed): 0.677 Sensitivity CentroidFold: 0.713 RNAalifold(seed): 0.528 Positive Predictive Value CentroidFold: 0.716 RNAalifold(seed): 0.873 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.810 Pknots: 0.739 Sensitivity CentroidFold: 0.797 Pknots: 0.761 Positive Predictive Value CentroidFold: 0.831 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.811 RNASampler(seed): 0.757 Sensitivity CentroidFold: 0.809 RNASampler(seed): 0.678 Positive Predictive Value CentroidFold: 0.819 RNASampler(seed): 0.853 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.708 Mastr(20): 0.628 Sensitivity CentroidFold: 0.697 Mastr(20): 0.471 Positive Predictive Value CentroidFold: 0.724 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.708 RSpredict(20): 0.660 Sensitivity CentroidFold: 0.697 RSpredict(20): 0.590 Positive Predictive Value CentroidFold: 0.724 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.848 Alterna: 0.750 Sensitivity CentroidFold: 0.827 Alterna: 0.762 Positive Predictive Value CentroidFold: 0.877 Alterna: 0.750 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.747 RNASLOpt: 0.679 Sensitivity CentroidFold: 0.721 RNASLOpt: 0.649 Positive Predictive Value CentroidFold: 0.783 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.633 Multilign(20): 0.612 Sensitivity CentroidFold: 0.606 Multilign(20): 0.581 Positive Predictive Value CentroidFold: 0.673 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.60185372136e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.780 Vsfold4: 0.648 Sensitivity CentroidFold: 0.775 Vsfold4: 0.638 Positive Predictive Value CentroidFold: 0.791 Vsfold4: 0.667 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.814 MCFold: 0.664 Sensitivity CentroidFold: 0.803 MCFold: 0.704 Positive Predictive Value CentroidFold: 0.833 MCFold: 0.637 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.766 RNAwolf: 0.594 Sensitivity CentroidFold: 0.743 RNAwolf: 0.584 Positive Predictive Value CentroidFold: 0.798 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.778 Murlet(seed): 0.621 Sensitivity CentroidFold: 0.757 Murlet(seed): 0.445 Positive Predictive Value CentroidFold: 0.806 Murlet(seed): 0.878 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.779 Vsfold5: 0.607 Sensitivity CentroidFold: 0.774 Vsfold5: 0.606 Positive Predictive Value CentroidFold: 0.790 Vsfold5: 0.617 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.724 RSpredict(seed): 0.365 Sensitivity CentroidFold: 0.727 RSpredict(seed): 0.216 Positive Predictive Value CentroidFold: 0.726 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.840 RDfolder: 0.664 Sensitivity CentroidFold: 0.817 RDfolder: 0.625 Positive Predictive Value CentroidFold: 0.871 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.682 PPfold(seed): 0.122 Sensitivity CentroidFold: 0.650 PPfold(seed): 0.029 Positive Predictive Value CentroidFold: 0.725 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.724 Mastr(seed): 0.311 Sensitivity CentroidFold: 0.727 Mastr(seed): 0.109 Positive Predictive Value CentroidFold: 0.726 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidFold Matthews Correlation Coefficient CMfinder(seed): N/A CentroidFold: N/A Sensitivity CMfinder(seed): N/A CentroidFold: N/A Positive Predictive Value CMfinder(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.704 Multilign(seed): 0.683 Sensitivity CentroidFold: 0.661 Multilign(seed): 0.636 Positive Predictive Value CentroidFold: 0.765 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 CentroidFold: 0.634 Sensitivity PETfold_pre2.0(seed): 0.772 CentroidFold: 0.602 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidFold: 0.678 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.733 CentroidFold: 0.708 Sensitivity TurboFold(20): 0.694 CentroidFold: 0.689 Positive Predictive Value TurboFold(20): 0.781 CentroidFold: 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: N/A CMfinder(20): N/A Sensitivity CentroidFold: N/A CMfinder(20): N/A Positive Predictive Value CentroidFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CentroidFold: 0.618 Sensitivity PETfold_pre2.0(20): 0.707 CentroidFold: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 CentroidFold: 0.642 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.683 TurboFold(seed): 0.650 Sensitivity CentroidFold: 0.654 TurboFold(seed): 0.624 Positive Predictive Value CentroidFold: 0.724 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.780 CentroidFold: 0.708 Sensitivity PPfold(20): 0.714 CentroidFold: 0.689 Positive Predictive Value PPfold(20): 0.860 CentroidFold: 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.768 NanoFolder: 0.562 Sensitivity CentroidFold: 0.746 NanoFolder: 0.656 Positive Predictive Value CentroidFold: 0.798 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.779 Carnac(seed): 0.276 Sensitivity CentroidFold: 0.768 Carnac(seed): 0.077 Positive Predictive Value CentroidFold: 0.796 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08
RNAalifold(20)	27 MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 RNAalifold(20): 0.775 Sensitivity MXScarna(seed): 0.743 RNAalifold(20): 0.682 Positive Predictive Value MXScarna(seed): 0.829 RNAalifold(20): 0.884 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 8.09943589199e-07	26 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAalifold(20): 0.777 Sensitivity CentroidAlifold(20): 0.716 RNAalifold(20): 0.686 Positive Predictive Value CentroidAlifold(20): 0.921 RNAalifold(20): 0.884 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.777 CentroidFold: 0.708 Sensitivity RNAalifold(20): 0.686 CentroidFold: 0.697 Positive Predictive Value RNAalifold(20): 0.884 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08		+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.782 Sfold: 0.712 Sensitivity RNAalifold(20): 0.690 Sfold: 0.689 Positive Predictive Value RNAalifold(20): 0.889 Sfold: 0.742 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.741 Fold: 0.720 Sensitivity RNAalifold(20): 0.639 Fold: 0.735 Positive Predictive Value RNAalifold(20): 0.863 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 RNASampler(20): 0.765 Sensitivity RNAalifold(20): 0.690 RNASampler(20): 0.671 Positive Predictive Value RNAalifold(20): 0.889 RNASampler(20): 0.875 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 MXScarna(20): 0.761 Sensitivity RNAalifold(20): 0.690 MXScarna(20): 0.727 Positive Predictive Value RNAalifold(20): 0.889 MXScarna(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAalifold(20): 0.724 Sensitivity CentroidHomfold‑LAST: 0.723 RNAalifold(20): 0.665 Positive Predictive Value CentroidHomfold‑LAST: 0.851 RNAalifold(20): 0.797 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.782 HotKnots: 0.697 Sensitivity RNAalifold(20): 0.690 HotKnots: 0.718 Positive Predictive Value RNAalifold(20): 0.889 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.782 UNAFold: 0.711 Sensitivity RNAalifold(20): 0.690 UNAFold: 0.716 Positive Predictive Value RNAalifold(20): 0.889 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.782 Contrafold: 0.656 Sensitivity RNAalifold(20): 0.690 Contrafold: 0.675 Positive Predictive Value RNAalifold(20): 0.889 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	? RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.744 IPknot: 0.684 Sensitivity RNAalifold(20): 0.681 IPknot: 0.654 Positive Predictive Value RNAalifold(20): 0.821 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.698 RNAalifold(20): 0.656 Sensitivity ContextFold: 0.638 RNAalifold(20): 0.578 Positive Predictive Value ContextFold: 0.771 RNAalifold(20): 0.753 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.782 RNAshapes: 0.699 Sensitivity RNAalifold(20): 0.690 RNAshapes: 0.704 Positive Predictive Value RNAalifold(20): 0.889 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.777 MaxExpect: 0.700 Sensitivity RNAalifold(20): 0.686 MaxExpect: 0.710 Positive Predictive Value RNAalifold(20): 0.884 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.782 PknotsRG: 0.699 Sensitivity RNAalifold(20): 0.690 PknotsRG: 0.719 Positive Predictive Value RNAalifold(20): 0.889 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.782 RNAfold: 0.687 Sensitivity RNAalifold(20): 0.690 RNAfold: 0.701 Positive Predictive Value RNAalifold(20): 0.889 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.741 ProbKnot: 0.686 Sensitivity RNAalifold(20): 0.639 ProbKnot: 0.713 Positive Predictive Value RNAalifold(20): 0.863 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 Murlet(20): 0.704 Sensitivity RNAalifold(20): 0.690 Murlet(20): 0.596 Positive Predictive Value RNAalifold(20): 0.889 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.777 CentroidAlifold(seed): 0.728 Sensitivity RNAalifold(20): 0.686 CentroidAlifold(seed): 0.580 Positive Predictive Value RNAalifold(20): 0.884 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.731 Afold: 0.627 Sensitivity RNAalifold(20): 0.632 Afold: 0.650 Positive Predictive Value RNAalifold(20): 0.850 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.782 RNAsubopt: 0.663 Sensitivity RNAalifold(20): 0.690 RNAsubopt: 0.686 Positive Predictive Value RNAalifold(20): 0.889 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 Carnac(20): 0.696 Sensitivity RNAalifold(20): 0.690 Carnac(20): 0.518 Positive Predictive Value RNAalifold(20): 0.889 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.787 Cylofold: 0.703 Sensitivity RNAalifold(20): 0.689 Cylofold: 0.703 Positive Predictive Value RNAalifold(20): 0.904 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.782 McQFold: 0.625 Sensitivity RNAalifold(20): 0.690 McQFold: 0.638 Positive Predictive Value RNAalifold(20): 0.889 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.735 CRWrnafold: 0.668 Sensitivity RNAalifold(20): 0.677 CRWrnafold: 0.683 Positive Predictive Value RNAalifold(20): 0.804 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.699 RNAalifold(seed): 0.673 Sensitivity RNAalifold(20): 0.586 RNAalifold(seed): 0.492 Positive Predictive Value RNAalifold(20): 0.839 RNAalifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78038963586e-08	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.800 Pknots: 0.639 Sensitivity RNAalifold(20): 0.721 Pknots: 0.683 Positive Predictive Value RNAalifold(20): 0.891 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 RNAalifold(20): 0.636 Sensitivity RNASampler(seed): 0.658 RNAalifold(20): 0.608 Positive Predictive Value RNASampler(seed): 0.782 RNAalifold(20): 0.671 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 Mastr(20): 0.636 Sensitivity RNAalifold(20): 0.690 Mastr(20): 0.483 Positive Predictive Value RNAalifold(20): 0.889 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.775 RSpredict(20): 0.663 Sensitivity RNAalifold(20): 0.682 RSpredict(20): 0.593 Positive Predictive Value RNAalifold(20): 0.884 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.865 Alterna: 0.671 Sensitivity RNAalifold(20): 0.803 Alterna: 0.680 Positive Predictive Value RNAalifold(20): 0.937 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	? RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.656 RNASLOpt: 0.560 Sensitivity RNAalifold(20): 0.578 RNASLOpt: 0.543 Positive Predictive Value RNAalifold(20): 0.753 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.689 Multilign(20): 0.612 Sensitivity RNAalifold(20): 0.598 Multilign(20): 0.581 Positive Predictive Value RNAalifold(20): 0.804 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.88760648134e-09	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.782 Vsfold4: 0.531 Sensitivity RNAalifold(20): 0.690 Vsfold4: 0.528 Positive Predictive Value RNAalifold(20): 0.889 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.793 MCFold: 0.520 Sensitivity RNAalifold(20): 0.722 MCFold: 0.579 Positive Predictive Value RNAalifold(20): 0.876 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.744 RNAwolf: 0.453 Sensitivity RNAalifold(20): 0.681 RNAwolf: 0.447 Positive Predictive Value RNAalifold(20): 0.821 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.711 Murlet(seed): 0.587 Sensitivity RNAalifold(20): 0.610 Murlet(seed): 0.377 Positive Predictive Value RNAalifold(20): 0.834 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.782 Vsfold5: 0.484 Sensitivity RNAalifold(20): 0.690 Vsfold5: 0.488 Positive Predictive Value RNAalifold(20): 0.889 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.775 RSpredict(seed): 0.298 Sensitivity RNAalifold(20): 0.682 RSpredict(seed): 0.156 Positive Predictive Value RNAalifold(20): 0.884 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.840 RDfolder: 0.624 Sensitivity RNAalifold(20): 0.752 RDfolder: 0.591 Positive Predictive Value RNAalifold(20): 0.945 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.02344513449e-08	? RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.744 PPfold(seed): 0.031 Sensitivity RNAalifold(20): 0.681 PPfold(seed): 0.005 Positive Predictive Value RNAalifold(20): 0.821 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.782 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.690 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.889 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-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	? Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.795 RNAalifold(20): 0.776 Sensitivity Multilign(seed): 0.750 RNAalifold(20): 0.720 Positive Predictive Value Multilign(seed): 0.852 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RNAalifold(20): 0.656 Sensitivity PETfold_pre2.0(seed): 0.784 RNAalifold(20): 0.578 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAalifold(20): 0.753 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.733 RNAalifold(20): 0.724 Sensitivity TurboFold(20): 0.694 RNAalifold(20): 0.665 Positive Predictive Value TurboFold(20): 0.781 RNAalifold(20): 0.797 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(20): N/A Sensitivity RNAalifold(20): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAalifold(20): 0.656 Sensitivity PETfold_pre2.0(20): 0.707 RNAalifold(20): 0.578 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAalifold(20): 0.753 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 RNAalifold(20): 0.694 Sensitivity TurboFold(seed): 0.684 RNAalifold(20): 0.631 Positive Predictive Value TurboFold(seed): 0.749 RNAalifold(20): 0.771 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.780 RNAalifold(20): 0.724 Sensitivity PPfold(20): 0.714 RNAalifold(20): 0.665 Positive Predictive Value PPfold(20): 0.860 RNAalifold(20): 0.797 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.677 NanoFolder: 0.389 Sensitivity RNAalifold(20): 0.624 NanoFolder: 0.475 Positive Predictive Value RNAalifold(20): 0.741 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.756 Carnac(seed): 0.231 Sensitivity RNAalifold(20): 0.668 Carnac(seed): 0.054 Positive Predictive Value RNAalifold(20): 0.861 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08
Sfold	44 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.776 Sfold: 0.709 Sensitivity MXScarna(seed): 0.736 Sfold: 0.701 Positive Predictive Value MXScarna(seed): 0.824 Sfold: 0.722 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Sfold: 0.705 Sensitivity CentroidAlifold(20): 0.716 Sfold: 0.681 Positive Predictive Value CentroidAlifold(20): 0.921 Sfold: 0.735 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	106 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.711 Sfold: 0.657 Sensitivity CentroidFold: 0.707 Sfold: 0.655 Positive Predictive Value CentroidFold: 0.715 Sfold: 0.659 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.782 Sfold: 0.712 Sensitivity RNAalifold(20): 0.690 Sfold: 0.689 Positive Predictive Value RNAalifold(20): 0.889 Sfold: 0.742 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08		= Fold vs Sfold Matthews Correlation Coefficient Fold: 0.777 Sfold: 0.775 Sensitivity Fold: 0.796 Sfold: 0.768 Positive Predictive Value Fold: 0.764 Sfold: 0.786 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.0481694229406	- RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.765 Sfold: 0.712 Sensitivity RNASampler(20): 0.671 Sfold: 0.689 Positive Predictive Value RNASampler(20): 0.875 Sfold: 0.742 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	- MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.761 Sfold: 0.712 Sensitivity MXScarna(20): 0.727 Sfold: 0.689 Positive Predictive Value MXScarna(20): 0.800 Sfold: 0.742 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	- CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Sfold: 0.750 Sensitivity CentroidHomfold‑LAST: 0.691 Sfold: 0.730 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Sfold: 0.780 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.778 HotKnots: 0.772 Sensitivity Sfold: 0.768 HotKnots: 0.793 Positive Predictive Value Sfold: 0.793 HotKnots: 0.757 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 9.49173053431e-08	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.633 UNAFold: 0.610 Sensitivity Sfold: 0.631 UNAFold: 0.641 Positive Predictive Value Sfold: 0.636 UNAFold: 0.581 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.699 Sfold: 0.633 Sensitivity Contrafold: 0.722 Sfold: 0.631 Positive Predictive Value Contrafold: 0.677 Sfold: 0.636 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	- IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.782 Sfold: 0.736 Sensitivity IPknot: 0.752 Sfold: 0.713 Positive Predictive Value IPknot: 0.820 Sfold: 0.769 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.816 Sfold: 0.722 Sensitivity ContextFold: 0.780 Sfold: 0.697 Positive Predictive Value ContextFold: 0.861 Sfold: 0.758 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.778 RNAshapes: 0.759 Sensitivity Sfold: 0.768 RNAshapes: 0.770 Positive Predictive Value Sfold: 0.793 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.729 Sfold: 0.701 Sensitivity MaxExpect: 0.740 Sfold: 0.686 Positive Predictive Value MaxExpect: 0.719 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 1.70738736246e-07	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.633 PknotsRG: 0.592 Sensitivity Sfold: 0.631 PknotsRG: 0.630 Positive Predictive Value Sfold: 0.636 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.633 RNAfold: 0.604 Sensitivity Sfold: 0.631 RNAfold: 0.641 Positive Predictive Value Sfold: 0.636 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.761 ProbKnot: 0.741 Sensitivity Sfold: 0.756 ProbKnot: 0.774 Positive Predictive Value Sfold: 0.772 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.712 Murlet(20): 0.704 Sensitivity Sfold: 0.689 Murlet(20): 0.596 Positive Predictive Value Sfold: 0.742 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000332141622515	+ Sfold vs CentroidAlifold(seed) Matthews Correlation Coefficient Sfold: 0.706 CentroidAlifold(seed): 0.690 Sensitivity Sfold: 0.698 CentroidAlifold(seed): 0.552 Positive Predictive Value Sfold: 0.719 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.75828119249e-07	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.618 Afold: 0.590 Sensitivity Sfold: 0.618 Afold: 0.630 Positive Predictive Value Sfold: 0.618 Afold: 0.553 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.778 RNAsubopt: 0.738 Sensitivity Sfold: 0.768 RNAsubopt: 0.757 Positive Predictive Value Sfold: 0.793 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.712 Carnac(20): 0.696 Sensitivity Sfold: 0.689 Carnac(20): 0.518 Positive Predictive Value Sfold: 0.742 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.83595875043e-07	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.800 Cylofold: 0.741 Sensitivity Sfold: 0.781 Cylofold: 0.724 Positive Predictive Value Sfold: 0.826 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.632 McQFold: 0.534 Sensitivity Sfold: 0.630 McQFold: 0.503 Positive Predictive Value Sfold: 0.635 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.711 CRWrnafold: 0.683 Sensitivity Sfold: 0.692 CRWrnafold: 0.690 Positive Predictive Value Sfold: 0.741 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.6410608252e-08	+ Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.716 RNAalifold(seed): 0.676 Sensitivity Sfold: 0.710 RNAalifold(seed): 0.525 Positive Predictive Value Sfold: 0.727 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.807 Pknots: 0.740 Sensitivity Sfold: 0.790 Pknots: 0.763 Positive Predictive Value Sfold: 0.831 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.827 RNASampler(seed): 0.765 Sensitivity Sfold: 0.820 RNASampler(seed): 0.687 Positive Predictive Value Sfold: 0.840 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.78774507289e-09	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.712 Mastr(20): 0.636 Sensitivity Sfold: 0.689 Mastr(20): 0.483 Positive Predictive Value Sfold: 0.742 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.710 RSpredict(20): 0.663 Sensitivity Sfold: 0.686 RSpredict(20): 0.593 Positive Predictive Value Sfold: 0.739 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.827 Alterna: 0.767 Sensitivity Sfold: 0.809 Alterna: 0.777 Positive Predictive Value Sfold: 0.854 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.722 RNASLOpt: 0.679 Sensitivity Sfold: 0.697 RNASLOpt: 0.649 Positive Predictive Value Sfold: 0.758 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.672 Multilign(20): 0.612 Sensitivity Sfold: 0.639 Multilign(20): 0.581 Positive Predictive Value Sfold: 0.716 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.778 Vsfold4: 0.650 Sensitivity Sfold: 0.768 Vsfold4: 0.640 Positive Predictive Value Sfold: 0.793 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.818 MCFold: 0.678 Sensitivity Sfold: 0.805 MCFold: 0.717 Positive Predictive Value Sfold: 0.839 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.736 RNAwolf: 0.594 Sensitivity Sfold: 0.713 RNAwolf: 0.584 Positive Predictive Value Sfold: 0.769 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.787 Murlet(seed): 0.620 Sensitivity Sfold: 0.759 Murlet(seed): 0.442 Positive Predictive Value Sfold: 0.822 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.777 Vsfold5: 0.612 Sensitivity Sfold: 0.767 Vsfold5: 0.613 Positive Predictive Value Sfold: 0.793 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.709 RSpredict(seed): 0.372 Sensitivity Sfold: 0.701 RSpredict(seed): 0.222 Positive Predictive Value Sfold: 0.722 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.824 RDfolder: 0.682 Sensitivity Sfold: 0.803 RDfolder: 0.643 Positive Predictive Value Sfold: 0.853 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.641 PPfold(seed): 0.122 Sensitivity Sfold: 0.601 PPfold(seed): 0.029 Positive Predictive Value Sfold: 0.695 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.710 Mastr(seed): 0.306 Sensitivity Sfold: 0.703 Mastr(seed): 0.105 Positive Predictive Value Sfold: 0.724 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.751 Multilign(seed): 0.683 Sensitivity Sfold: 0.703 Multilign(seed): 0.636 Positive Predictive Value Sfold: 0.814 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Sfold: 0.562 Sensitivity PETfold_pre2.0(seed): 0.772 Sfold: 0.526 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Sfold: 0.612 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.733 Sfold: 0.721 Sensitivity TurboFold(20): 0.694 Sfold: 0.689 Positive Predictive Value TurboFold(20): 0.781 Sfold: 0.763 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: N/A CMfinder(20): N/A Sensitivity Sfold: N/A CMfinder(20): N/A Positive Predictive Value Sfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Sfold: 0.612 Sensitivity PETfold_pre2.0(20): 0.707 Sfold: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.796 Sfold: 0.648 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.693 TurboFold(seed): 0.650 Sensitivity Sfold: 0.654 TurboFold(seed): 0.624 Positive Predictive Value Sfold: 0.744 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.780 Sfold: 0.721 Sensitivity PPfold(20): 0.714 Sfold: 0.689 Positive Predictive Value PPfold(20): 0.860 Sfold: 0.763 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.707 NanoFolder: 0.562 Sensitivity Sfold: 0.687 NanoFolder: 0.656 Positive Predictive Value Sfold: 0.738 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.798 Carnac(seed): 0.299 Sensitivity Sfold: 0.777 Carnac(seed): 0.090 Positive Predictive Value Sfold: 0.826 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	31 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.753 Fold: 0.722 Sensitivity MXScarna(seed): 0.713 Fold: 0.750 Positive Predictive Value MXScarna(seed): 0.799 Fold: 0.700 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.787 Fold: 0.720 Sensitivity CentroidAlifold(20): 0.674 Fold: 0.735 Positive Predictive Value CentroidAlifold(20): 0.922 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.48104284388e-08	82 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.786 Fold: 0.777 Sensitivity CentroidFold: 0.781 Fold: 0.796 Positive Predictive Value CentroidFold: 0.797 Fold: 0.764 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 1.06521910535e-06	18 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.741 Fold: 0.720 Sensitivity RNAalifold(20): 0.639 Fold: 0.735 Positive Predictive Value RNAalifold(20): 0.863 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.08252958266e-08	82 Fold vs Sfold Matthews Correlation Coefficient Fold: 0.777 Sfold: 0.775 Sensitivity Fold: 0.796 Sfold: 0.768 Positive Predictive Value Fold: 0.764 Sfold: 0.786 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.0481694229406		- RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.730 Fold: 0.720 Sensitivity RNASampler(20): 0.624 Fold: 0.735 Positive Predictive Value RNASampler(20): 0.858 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.63637731641e-07	- MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.738 Fold: 0.720 Sensitivity MXScarna(20): 0.700 Fold: 0.735 Positive Predictive Value MXScarna(20): 0.784 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.1413769576e-08	- CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Fold: 0.709 Sensitivity CentroidHomfold‑LAST: 0.691 Fold: 0.720 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Fold: 0.710 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.777 HotKnots: 0.772 Sensitivity Fold: 0.796 HotKnots: 0.798 Positive Predictive Value Fold: 0.764 HotKnots: 0.752 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 5.90626908729e-06	+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.777 UNAFold: 0.765 Sensitivity Fold: 0.796 UNAFold: 0.782 Positive Predictive Value Fold: 0.764 UNAFold: 0.755 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 5.3419901105e-07	+ Fold vs Contrafold Matthews Correlation Coefficient Fold: 0.777 Contrafold: 0.773 Sensitivity Fold: 0.796 Contrafold: 0.790 Positive Predictive Value Fold: 0.764 Contrafold: 0.763 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.000284355681826	- IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.782 Fold: 0.703 Sensitivity IPknot: 0.752 Fold: 0.712 Positive Predictive Value IPknot: 0.820 Fold: 0.707 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.816 Fold: 0.696 Sensitivity ContextFold: 0.780 Fold: 0.699 Positive Predictive Value ContextFold: 0.861 Fold: 0.704 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.777 RNAshapes: 0.766 Sensitivity Fold: 0.796 RNAshapes: 0.781 Positive Predictive Value Fold: 0.764 RNAshapes: 0.757 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs MaxExpect Matthews Correlation Coefficient Fold: 0.777 MaxExpect: 0.758 Sensitivity Fold: 0.796 MaxExpect: 0.773 Positive Predictive Value Fold: 0.764 MaxExpect: 0.749 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.777 PknotsRG: 0.751 Sensitivity Fold: 0.796 PknotsRG: 0.777 Positive Predictive Value Fold: 0.764 PknotsRG: 0.732 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.777 RNAfold: 0.754 Sensitivity Fold: 0.796 RNAfold: 0.776 Positive Predictive Value Fold: 0.764 RNAfold: 0.740 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs ProbKnot Matthews Correlation Coefficient Fold: 0.758 ProbKnot: 0.741 Sensitivity Fold: 0.779 ProbKnot: 0.774 Positive Predictive Value Fold: 0.743 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.720 Murlet(20): 0.675 Sensitivity Fold: 0.735 Murlet(20): 0.562 Positive Predictive Value Fold: 0.710 Murlet(20): 0.816 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ Fold vs CentroidAlifold(seed) Matthews Correlation Coefficient Fold: 0.722 CentroidAlifold(seed): 0.684 Sensitivity Fold: 0.750 CentroidAlifold(seed): 0.548 Positive Predictive Value Fold: 0.700 CentroidAlifold(seed): 0.859 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.779 Afold: 0.751 Sensitivity Fold: 0.805 Afold: 0.784 Positive Predictive Value Fold: 0.758 Afold: 0.726 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.777 RNAsubopt: 0.756 Sensitivity Fold: 0.796 RNAsubopt: 0.776 Positive Predictive Value Fold: 0.764 RNAsubopt: 0.742 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.720 Carnac(20): 0.647 Sensitivity Fold: 0.735 Carnac(20): 0.457 Positive Predictive Value Fold: 0.710 Carnac(20): 0.922 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.806 Cylofold: 0.741 Sensitivity Fold: 0.813 Cylofold: 0.724 Positive Predictive Value Fold: 0.806 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.775 McQFold: 0.733 Sensitivity Fold: 0.794 McQFold: 0.732 Positive Predictive Value Fold: 0.762 McQFold: 0.741 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.683 Fold: 0.662 Sensitivity CRWrnafold: 0.690 Fold: 0.674 Positive Predictive Value CRWrnafold: 0.689 Fold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.667 RNAalifold(seed): 0.643 Sensitivity Fold: 0.701 RNAalifold(seed): 0.487 Positive Predictive Value Fold: 0.640 RNAalifold(seed): 0.855 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.27071136365e-07	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.818 Pknots: 0.754 Sensitivity Fold: 0.826 Pknots: 0.770 Positive Predictive Value Fold: 0.817 Pknots: 0.747 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.734 Fold: 0.724 Sensitivity RNASampler(seed): 0.651 Fold: 0.758 Positive Predictive Value RNASampler(seed): 0.837 Fold: 0.700 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.000537170415527	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.720 Mastr(20): 0.582 Sensitivity Fold: 0.735 Mastr(20): 0.407 Positive Predictive Value Fold: 0.710 Mastr(20): 0.840 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.720 RSpredict(20): 0.619 Sensitivity Fold: 0.735 RSpredict(20): 0.547 Positive Predictive Value Fold: 0.710 RSpredict(20): 0.707 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.51155234096e-08	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.845 Alterna: 0.788 Sensitivity Fold: 0.853 Alterna: 0.801 Positive Predictive Value Fold: 0.846 Alterna: 0.785 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.696 RNASLOpt: 0.679 Sensitivity Fold: 0.699 RNASLOpt: 0.649 Positive Predictive Value Fold: 0.704 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.27481660653e-07	+ Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.702 Multilign(20): 0.612 Sensitivity Fold: 0.710 Multilign(20): 0.581 Positive Predictive Value Fold: 0.704 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.5161825748e-09	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.777 Vsfold4: 0.648 Sensitivity Fold: 0.796 Vsfold4: 0.641 Positive Predictive Value Fold: 0.764 Vsfold4: 0.665 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.819 MCFold: 0.698 Sensitivity Fold: 0.830 MCFold: 0.729 Positive Predictive Value Fold: 0.815 MCFold: 0.679 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.703 RNAwolf: 0.594 Sensitivity Fold: 0.712 RNAwolf: 0.584 Positive Predictive Value Fold: 0.707 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.740 Murlet(seed): 0.614 Sensitivity Fold: 0.752 Murlet(seed): 0.435 Positive Predictive Value Fold: 0.736 Murlet(seed): 0.877 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.776 Vsfold5: 0.612 Sensitivity Fold: 0.795 Vsfold5: 0.613 Positive Predictive Value Fold: 0.763 Vsfold5: 0.620 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.722 RSpredict(seed): 0.336 Sensitivity Fold: 0.750 RSpredict(seed): 0.196 Positive Predictive Value Fold: 0.700 RSpredict(seed): 0.585 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.821 RDfolder: 0.695 Sensitivity Fold: 0.825 RDfolder: 0.657 Positive Predictive Value Fold: 0.827 RDfolder: 0.752 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.613 PPfold(seed): 0.122 Sensitivity Fold: 0.617 PPfold(seed): 0.029 Positive Predictive Value Fold: 0.620 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.722 Mastr(seed): 0.326 Sensitivity Fold: 0.750 Mastr(seed): 0.121 Positive Predictive Value Fold: 0.700 Mastr(seed): 0.885 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.683 Fold: 0.653 Sensitivity Multilign(seed): 0.636 Fold: 0.636 Positive Predictive Value Multilign(seed): 0.750 Fold: 0.688 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Fold: 0.550 Sensitivity PETfold_pre2.0(seed): 0.772 Fold: 0.556 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Fold: 0.556 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.733 Fold: 0.652 Sensitivity TurboFold(20): 0.694 Fold: 0.660 Positive Predictive Value TurboFold(20): 0.781 Fold: 0.654 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: N/A CMfinder(20): N/A Sensitivity Fold: N/A CMfinder(20): N/A Positive Predictive Value Fold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Fold: 0.531 Sensitivity PETfold_pre2.0(20): 0.707 Fold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 Fold: 0.529 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.650 Fold: 0.590 Sensitivity TurboFold(seed): 0.624 Fold: 0.590 Positive Predictive Value TurboFold(seed): 0.688 Fold: 0.602 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.780 Fold: 0.652 Sensitivity PPfold(20): 0.714 Fold: 0.660 Positive Predictive Value PPfold(20): 0.860 Fold: 0.654 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.722 NanoFolder: 0.562 Sensitivity Fold: 0.732 NanoFolder: 0.656 Positive Predictive Value Fold: 0.722 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.763 Carnac(seed): 0.312 Sensitivity Fold: 0.773 Carnac(seed): 0.099 Positive Predictive Value Fold: 0.759 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08
RNASampler(20)	27 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 RNASampler(20): 0.766 Sensitivity MXScarna(seed): 0.743 RNASampler(20): 0.676 Positive Predictive Value MXScarna(seed): 0.829 RNASampler(20): 0.872 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.64876692942e-07	26 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNASampler(20): 0.762 Sensitivity CentroidAlifold(20): 0.716 RNASampler(20): 0.671 Positive Predictive Value CentroidAlifold(20): 0.921 RNASampler(20): 0.870 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.762 CentroidFold: 0.708 Sensitivity RNASampler(20): 0.671 CentroidFold: 0.697 Positive Predictive Value RNASampler(20): 0.870 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 RNASampler(20): 0.765 Sensitivity RNAalifold(20): 0.690 RNASampler(20): 0.671 Positive Predictive Value RNAalifold(20): 0.889 RNASampler(20): 0.875 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.59469103578e-08	28 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.765 Sfold: 0.712 Sensitivity RNASampler(20): 0.671 Sfold: 0.689 Positive Predictive Value RNASampler(20): 0.875 Sfold: 0.742 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	18 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.730 Fold: 0.720 Sensitivity RNASampler(20): 0.624 Fold: 0.735 Positive Predictive Value RNASampler(20): 0.858 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.63637731641e-07		= RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.765 MXScarna(20): 0.761 Sensitivity RNASampler(20): 0.671 MXScarna(20): 0.727 Positive Predictive Value RNASampler(20): 0.875 MXScarna(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0347955950157	? CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNASampler(20): 0.779 Sensitivity CentroidHomfold‑LAST: 0.723 RNASampler(20): 0.704 Positive Predictive Value CentroidHomfold‑LAST: 0.851 RNASampler(20): 0.868 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.765 HotKnots: 0.697 Sensitivity RNASampler(20): 0.671 HotKnots: 0.718 Positive Predictive Value RNASampler(20): 0.875 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.765 UNAFold: 0.711 Sensitivity RNASampler(20): 0.671 UNAFold: 0.716 Positive Predictive Value RNASampler(20): 0.875 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.765 Contrafold: 0.656 Sensitivity RNASampler(20): 0.671 Contrafold: 0.675 Positive Predictive Value RNASampler(20): 0.875 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	? RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.762 IPknot: 0.684 Sensitivity RNASampler(20): 0.681 IPknot: 0.654 Positive Predictive Value RNASampler(20): 0.859 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.698 RNASampler(20): 0.686 Sensitivity ContextFold: 0.638 RNASampler(20): 0.603 Positive Predictive Value ContextFold: 0.771 RNASampler(20): 0.787 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.765 RNAshapes: 0.699 Sensitivity RNASampler(20): 0.671 RNAshapes: 0.704 Positive Predictive Value RNASampler(20): 0.875 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.762 MaxExpect: 0.700 Sensitivity RNASampler(20): 0.671 MaxExpect: 0.710 Positive Predictive Value RNASampler(20): 0.870 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.765 PknotsRG: 0.699 Sensitivity RNASampler(20): 0.671 PknotsRG: 0.719 Positive Predictive Value RNASampler(20): 0.875 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.765 RNAfold: 0.687 Sensitivity RNASampler(20): 0.671 RNAfold: 0.701 Positive Predictive Value RNASampler(20): 0.875 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.730 ProbKnot: 0.686 Sensitivity RNASampler(20): 0.624 ProbKnot: 0.713 Positive Predictive Value RNASampler(20): 0.858 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.765 Murlet(20): 0.704 Sensitivity RNASampler(20): 0.671 Murlet(20): 0.596 Positive Predictive Value RNASampler(20): 0.875 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.762 CentroidAlifold(seed): 0.728 Sensitivity RNASampler(20): 0.671 CentroidAlifold(seed): 0.580 Positive Predictive Value RNASampler(20): 0.870 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.724 Afold: 0.627 Sensitivity RNASampler(20): 0.632 Afold: 0.650 Positive Predictive Value RNASampler(20): 0.834 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.765 RNAsubopt: 0.663 Sensitivity RNASampler(20): 0.671 RNAsubopt: 0.686 Positive Predictive Value RNASampler(20): 0.875 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.765 Carnac(20): 0.696 Sensitivity RNASampler(20): 0.671 Carnac(20): 0.518 Positive Predictive Value RNASampler(20): 0.875 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.797 Cylofold: 0.703 Sensitivity RNASampler(20): 0.689 Cylofold: 0.703 Positive Predictive Value RNASampler(20): 0.928 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.06761512825e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.765 McQFold: 0.625 Sensitivity RNASampler(20): 0.671 McQFold: 0.638 Positive Predictive Value RNASampler(20): 0.875 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.740 CRWrnafold: 0.668 Sensitivity RNASampler(20): 0.659 CRWrnafold: 0.683 Positive Predictive Value RNASampler(20): 0.837 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.693 RNAalifold(seed): 0.673 Sensitivity RNASampler(20): 0.592 RNAalifold(seed): 0.492 Positive Predictive Value RNASampler(20): 0.815 RNAalifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.77512146924e-08	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.798 Pknots: 0.639 Sensitivity RNASampler(20): 0.710 Pknots: 0.683 Positive Predictive Value RNASampler(20): 0.902 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): 0.720 RNASampler(seed): 0.715 Sensitivity RNASampler(20): 0.709 RNASampler(seed): 0.658 Positive Predictive Value RNASampler(20): 0.737 RNASampler(seed): 0.782 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.765 Mastr(20): 0.636 Sensitivity RNASampler(20): 0.671 Mastr(20): 0.483 Positive Predictive Value RNASampler(20): 0.875 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.766 RSpredict(20): 0.663 Sensitivity RNASampler(20): 0.676 RSpredict(20): 0.593 Positive Predictive Value RNASampler(20): 0.872 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.912 Alterna: 0.671 Sensitivity RNASampler(20): 0.846 Alterna: 0.680 Positive Predictive Value RNASampler(20): 0.986 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	? RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.686 RNASLOpt: 0.560 Sensitivity RNASampler(20): 0.603 RNASLOpt: 0.543 Positive Predictive Value RNASampler(20): 0.787 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.731 Multilign(20): 0.612 Sensitivity RNASampler(20): 0.618 Multilign(20): 0.581 Positive Predictive Value RNASampler(20): 0.871 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.79651608537e-09	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold4: 0.531 Sensitivity RNASampler(20): 0.671 Vsfold4: 0.528 Positive Predictive Value RNASampler(20): 0.875 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.810 MCFold: 0.520 Sensitivity RNASampler(20): 0.734 MCFold: 0.579 Positive Predictive Value RNASampler(20): 0.897 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.762 RNAwolf: 0.453 Sensitivity RNASampler(20): 0.681 RNAwolf: 0.447 Positive Predictive Value RNASampler(20): 0.859 RNAwolf: 0.475 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): 0.731 Murlet(seed): 0.587 Sensitivity RNASampler(20): 0.635 Murlet(seed): 0.377 Positive Predictive Value RNASampler(20): 0.848 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold5: 0.484 Sensitivity RNASampler(20): 0.671 Vsfold5: 0.488 Positive Predictive Value RNASampler(20): 0.875 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.766 RSpredict(seed): 0.298 Sensitivity RNASampler(20): 0.676 RSpredict(seed): 0.156 Positive Predictive Value RNASampler(20): 0.872 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.881 RDfolder: 0.624 Sensitivity RNASampler(20): 0.799 RDfolder: 0.591 Positive Predictive Value RNASampler(20): 0.977 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	? RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.762 PPfold(seed): 0.031 Sensitivity RNASampler(20): 0.681 PPfold(seed): 0.005 Positive Predictive Value RNASampler(20): 0.859 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.765 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.671 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.875 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-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 Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.829 Multilign(seed): 0.795 Sensitivity RNASampler(20): 0.740 Multilign(seed): 0.750 Positive Predictive Value RNASampler(20): 0.937 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RNASampler(20): 0.686 Sensitivity PETfold_pre2.0(seed): 0.784 RNASampler(20): 0.603 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNASampler(20): 0.787 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.779 TurboFold(20): 0.733 Sensitivity RNASampler(20): 0.704 TurboFold(20): 0.694 Positive Predictive Value RNASampler(20): 0.868 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(20): N/A Sensitivity RNASampler(20): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNASampler(20): 0.686 Sensitivity PETfold_pre2.0(20): 0.707 RNASampler(20): 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNASampler(20): 0.787 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.760 TurboFold(seed): 0.712 Sensitivity RNASampler(20): 0.679 TurboFold(seed): 0.684 Positive Predictive Value RNASampler(20): 0.858 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.780 RNASampler(20): 0.779 Sensitivity PPfold(20): 0.714 RNASampler(20): 0.704 Positive Predictive Value PPfold(20): 0.860 RNASampler(20): 0.868 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.689 NanoFolder: 0.389 Sensitivity RNASampler(20): 0.624 NanoFolder: 0.475 Positive Predictive Value RNASampler(20): 0.768 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.769 Carnac(seed): 0.231 Sensitivity RNASampler(20): 0.676 Carnac(seed): 0.054 Positive Predictive Value RNASampler(20): 0.880 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08
MXScarna(20)	27 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 MXScarna(20): 0.760 Sensitivity MXScarna(seed): 0.743 MXScarna(20): 0.726 Positive Predictive Value MXScarna(seed): 0.829 MXScarna(20): 0.800 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 MXScarna(20): 0.756 Sensitivity CentroidAlifold(20): 0.716 MXScarna(20): 0.722 Positive Predictive Value CentroidAlifold(20): 0.921 MXScarna(20): 0.797 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.756 CentroidFold: 0.708 Sensitivity MXScarna(20): 0.722 CentroidFold: 0.697 Positive Predictive Value MXScarna(20): 0.797 CentroidFold: 0.724 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.98172311752e-08	28 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 MXScarna(20): 0.761 Sensitivity RNAalifold(20): 0.690 MXScarna(20): 0.727 Positive Predictive Value RNAalifold(20): 0.889 MXScarna(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.761 Sfold: 0.712 Sensitivity MXScarna(20): 0.727 Sfold: 0.689 Positive Predictive Value MXScarna(20): 0.800 Sfold: 0.742 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.738 Fold: 0.720 Sensitivity MXScarna(20): 0.700 Fold: 0.735 Positive Predictive Value MXScarna(20): 0.784 Fold: 0.710 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.1413769576e-08	28 RNASampler(20) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(20): 0.765 MXScarna(20): 0.761 Sensitivity RNASampler(20): 0.671 MXScarna(20): 0.727 Positive Predictive Value RNASampler(20): 0.875 MXScarna(20): 0.800 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0347955950157		? CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 MXScarna(20): 0.693 Sensitivity CentroidHomfold‑LAST: 0.723 MXScarna(20): 0.655 Positive Predictive Value CentroidHomfold‑LAST: 0.851 MXScarna(20): 0.742 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.761 HotKnots: 0.697 Sensitivity MXScarna(20): 0.727 HotKnots: 0.718 Positive Predictive Value MXScarna(20): 0.800 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.761 UNAFold: 0.711 Sensitivity MXScarna(20): 0.727 UNAFold: 0.716 Positive Predictive Value MXScarna(20): 0.800 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.761 Contrafold: 0.656 Sensitivity MXScarna(20): 0.727 Contrafold: 0.675 Positive Predictive Value MXScarna(20): 0.800 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	? MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.689 IPknot: 0.684 Sensitivity MXScarna(20): 0.649 IPknot: 0.654 Positive Predictive Value MXScarna(20): 0.739 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.698 MXScarna(20): 0.586 Sensitivity ContextFold: 0.638 MXScarna(20): 0.543 Positive Predictive Value ContextFold: 0.771 MXScarna(20): 0.643 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.761 RNAshapes: 0.699 Sensitivity MXScarna(20): 0.727 RNAshapes: 0.704 Positive Predictive Value MXScarna(20): 0.800 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.756 MaxExpect: 0.700 Sensitivity MXScarna(20): 0.722 MaxExpect: 0.710 Positive Predictive Value MXScarna(20): 0.797 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.761 PknotsRG: 0.699 Sensitivity MXScarna(20): 0.727 PknotsRG: 0.719 Positive Predictive Value MXScarna(20): 0.800 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.761 RNAfold: 0.687 Sensitivity MXScarna(20): 0.727 RNAfold: 0.701 Positive Predictive Value MXScarna(20): 0.800 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.738 ProbKnot: 0.686 Sensitivity MXScarna(20): 0.700 ProbKnot: 0.713 Positive Predictive Value MXScarna(20): 0.784 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.761 Murlet(20): 0.704 Sensitivity MXScarna(20): 0.727 Murlet(20): 0.596 Positive Predictive Value MXScarna(20): 0.800 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.756 CentroidAlifold(seed): 0.728 Sensitivity MXScarna(20): 0.722 CentroidAlifold(seed): 0.580 Positive Predictive Value MXScarna(20): 0.797 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.738 Afold: 0.627 Sensitivity MXScarna(20): 0.706 Afold: 0.650 Positive Predictive Value MXScarna(20): 0.776 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.761 RNAsubopt: 0.663 Sensitivity MXScarna(20): 0.727 RNAsubopt: 0.686 Positive Predictive Value MXScarna(20): 0.800 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.761 Carnac(20): 0.696 Sensitivity MXScarna(20): 0.727 Carnac(20): 0.518 Positive Predictive Value MXScarna(20): 0.800 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.804 Cylofold: 0.703 Sensitivity MXScarna(20): 0.757 Cylofold: 0.703 Positive Predictive Value MXScarna(20): 0.859 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.761 McQFold: 0.625 Sensitivity MXScarna(20): 0.727 McQFold: 0.638 Positive Predictive Value MXScarna(20): 0.800 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CRWrnafold vs MXScarna(20) Matthews Correlation Coefficient CRWrnafold: 0.668 MXScarna(20): 0.666 Sensitivity CRWrnafold: 0.683 MXScarna(20): 0.634 Positive Predictive Value CRWrnafold: 0.663 MXScarna(20): 0.707 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.709 RNAalifold(seed): 0.673 Sensitivity MXScarna(20): 0.667 RNAalifold(seed): 0.492 Positive Predictive Value MXScarna(20): 0.758 RNAalifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.787 Pknots: 0.639 Sensitivity MXScarna(20): 0.755 Pknots: 0.683 Positive Predictive Value MXScarna(20): 0.824 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 MXScarna(20): 0.687 Sensitivity RNASampler(seed): 0.658 MXScarna(20): 0.684 Positive Predictive Value RNASampler(seed): 0.782 MXScarna(20): 0.697 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.761 Mastr(20): 0.636 Sensitivity MXScarna(20): 0.727 Mastr(20): 0.483 Positive Predictive Value MXScarna(20): 0.800 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.760 RSpredict(20): 0.663 Sensitivity MXScarna(20): 0.726 RSpredict(20): 0.593 Positive Predictive Value MXScarna(20): 0.800 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.846 Alterna: 0.671 Sensitivity MXScarna(20): 0.803 Alterna: 0.680 Positive Predictive Value MXScarna(20): 0.897 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.34821445183e-08	? MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.586 RNASLOpt: 0.560 Sensitivity MXScarna(20): 0.543 RNASLOpt: 0.543 Positive Predictive Value MXScarna(20): 0.643 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.721 Multilign(20): 0.612 Sensitivity MXScarna(20): 0.685 Multilign(20): 0.581 Positive Predictive Value MXScarna(20): 0.767 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.53487163866e-09	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.761 Vsfold4: 0.531 Sensitivity MXScarna(20): 0.727 Vsfold4: 0.528 Positive Predictive Value MXScarna(20): 0.800 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.794 MCFold: 0.520 Sensitivity MXScarna(20): 0.760 MCFold: 0.579 Positive Predictive Value MXScarna(20): 0.833 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	? MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.689 RNAwolf: 0.453 Sensitivity MXScarna(20): 0.649 RNAwolf: 0.447 Positive Predictive Value MXScarna(20): 0.739 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.738 Murlet(seed): 0.587 Sensitivity MXScarna(20): 0.697 Murlet(seed): 0.377 Positive Predictive Value MXScarna(20): 0.787 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.761 Vsfold5: 0.484 Sensitivity MXScarna(20): 0.727 Vsfold5: 0.488 Positive Predictive Value MXScarna(20): 0.800 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.760 RSpredict(seed): 0.298 Sensitivity MXScarna(20): 0.726 RSpredict(seed): 0.156 Positive Predictive Value MXScarna(20): 0.800 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.804 RDfolder: 0.624 Sensitivity MXScarna(20): 0.745 RDfolder: 0.591 Positive Predictive Value MXScarna(20): 0.875 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.20167918023e-08	? MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 PPfold(seed): 0.031 Sensitivity MXScarna(20): 0.649 PPfold(seed): 0.005 Positive Predictive Value MXScarna(20): 0.739 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.761 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.727 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.800 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-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	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.795 MXScarna(20): 0.747 Sensitivity Multilign(seed): 0.750 MXScarna(20): 0.730 Positive Predictive Value Multilign(seed): 0.852 MXScarna(20): 0.777 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 MXScarna(20): 0.586 Sensitivity PETfold_pre2.0(seed): 0.784 MXScarna(20): 0.543 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MXScarna(20): 0.643 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.733 MXScarna(20): 0.693 Sensitivity TurboFold(20): 0.694 MXScarna(20): 0.655 Positive Predictive Value TurboFold(20): 0.781 MXScarna(20): 0.742 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): N/A CMfinder(20): N/A Sensitivity MXScarna(20): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 MXScarna(20): 0.586 Sensitivity PETfold_pre2.0(20): 0.707 MXScarna(20): 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 MXScarna(20): 0.643 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 MXScarna(20): 0.660 Sensitivity TurboFold(seed): 0.684 MXScarna(20): 0.620 Positive Predictive Value TurboFold(seed): 0.749 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.780 MXScarna(20): 0.693 Sensitivity PPfold(20): 0.714 MXScarna(20): 0.655 Positive Predictive Value PPfold(20): 0.860 MXScarna(20): 0.742 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.619 NanoFolder: 0.389 Sensitivity MXScarna(20): 0.604 NanoFolder: 0.475 Positive Predictive Value MXScarna(20): 0.642 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.763 Carnac(seed): 0.231 Sensitivity MXScarna(20): 0.729 Carnac(seed): 0.054 Positive Predictive Value MXScarna(20): 0.803 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08
CentroidHomfold‑LAST	12 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 MXScarna(seed): 0.716 Sensitivity CentroidHomfold‑LAST: 0.690 MXScarna(seed): 0.667 Positive Predictive Value CentroidHomfold‑LAST: 0.829 MXScarna(seed): 0.777 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.50834591464e-08	9 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.805 CentroidHomfold‑LAST: 0.782 Sensitivity CentroidAlifold(20): 0.714 CentroidHomfold‑LAST: 0.723 Positive Predictive Value CentroidAlifold(20): 0.913 CentroidHomfold‑LAST: 0.851 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	44 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 CentroidFold: 0.774 Sensitivity CentroidHomfold‑LAST: 0.691 CentroidFold: 0.752 Positive Predictive Value CentroidHomfold‑LAST: 0.893 CentroidFold: 0.804 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.08902352868e-05	9 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAalifold(20): 0.724 Sensitivity CentroidHomfold‑LAST: 0.723 RNAalifold(20): 0.665 Positive Predictive Value CentroidHomfold‑LAST: 0.851 RNAalifold(20): 0.797 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	44 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Sfold: 0.750 Sensitivity CentroidHomfold‑LAST: 0.691 Sfold: 0.730 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Sfold: 0.780 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.85233844192e-08	44 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Fold: 0.709 Sensitivity CentroidHomfold‑LAST: 0.691 Fold: 0.720 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Fold: 0.710 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNASampler(20): 0.779 Sensitivity CentroidHomfold‑LAST: 0.723 RNASampler(20): 0.704 Positive Predictive Value CentroidHomfold‑LAST: 0.851 RNASampler(20): 0.868 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 MXScarna(20): 0.693 Sensitivity CentroidHomfold‑LAST: 0.723 MXScarna(20): 0.655 Positive Predictive Value CentroidHomfold‑LAST: 0.851 MXScarna(20): 0.742 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0		+ CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 HotKnots: 0.755 Sensitivity CentroidHomfold‑LAST: 0.691 HotKnots: 0.772 Positive Predictive Value CentroidHomfold‑LAST: 0.893 HotKnots: 0.748 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 UNAFold: 0.719 Sensitivity CentroidHomfold‑LAST: 0.691 UNAFold: 0.725 Positive Predictive Value CentroidHomfold‑LAST: 0.893 UNAFold: 0.725 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Contrafold: 0.769 Sensitivity CentroidHomfold‑LAST: 0.691 Contrafold: 0.767 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Contrafold: 0.781 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 1.03971108356e-05	= CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.783 IPknot: 0.776 Sensitivity CentroidHomfold‑LAST: 0.697 IPknot: 0.746 Positive Predictive Value CentroidHomfold‑LAST: 0.887 IPknot: 0.815 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.0348339286697	- ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.810 CentroidHomfold‑LAST: 0.752 Sensitivity ContextFold: 0.773 CentroidHomfold‑LAST: 0.664 Positive Predictive Value ContextFold: 0.856 CentroidHomfold‑LAST: 0.861 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAshapes: 0.734 Sensitivity CentroidHomfold‑LAST: 0.691 RNAshapes: 0.739 Positive Predictive Value CentroidHomfold‑LAST: 0.893 RNAshapes: 0.739 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 MaxExpect: 0.710 Sensitivity CentroidHomfold‑LAST: 0.691 MaxExpect: 0.715 Positive Predictive Value CentroidHomfold‑LAST: 0.893 MaxExpect: 0.716 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 PknotsRG: 0.750 Sensitivity CentroidHomfold‑LAST: 0.691 PknotsRG: 0.765 Positive Predictive Value CentroidHomfold‑LAST: 0.893 PknotsRG: 0.744 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAfold: 0.741 Sensitivity CentroidHomfold‑LAST: 0.691 RNAfold: 0.746 Positive Predictive Value CentroidHomfold‑LAST: 0.893 RNAfold: 0.746 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 ProbKnot: 0.708 Sensitivity CentroidHomfold‑LAST: 0.691 ProbKnot: 0.733 Positive Predictive Value CentroidHomfold‑LAST: 0.893 ProbKnot: 0.696 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Murlet(20): 0.677 Sensitivity CentroidHomfold‑LAST: 0.723 Murlet(20): 0.602 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 CentroidAlifold(seed): 0.676 Sensitivity CentroidHomfold‑LAST: 0.690 CentroidAlifold(seed): 0.494 Positive Predictive Value CentroidHomfold‑LAST: 0.829 CentroidAlifold(seed): 0.935 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.02533530638e-08	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.776 Afold: 0.754 Sensitivity CentroidHomfold‑LAST: 0.703 Afold: 0.779 Positive Predictive Value CentroidHomfold‑LAST: 0.864 Afold: 0.740 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.12827206146e-07	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAsubopt: 0.709 Sensitivity CentroidHomfold‑LAST: 0.691 RNAsubopt: 0.720 Positive Predictive Value CentroidHomfold‑LAST: 0.893 RNAsubopt: 0.709 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Carnac(20): 0.632 Sensitivity CentroidHomfold‑LAST: 0.723 Carnac(20): 0.471 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.777 Cylofold: 0.685 Sensitivity CentroidHomfold‑LAST: 0.663 Cylofold: 0.673 Positive Predictive Value CentroidHomfold‑LAST: 0.919 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 McQFold: 0.714 Sensitivity CentroidHomfold‑LAST: 0.691 McQFold: 0.706 Positive Predictive Value CentroidHomfold‑LAST: 0.893 McQFold: 0.733 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.758 CRWrnafold: 0.674 Sensitivity CentroidHomfold‑LAST: 0.670 CRWrnafold: 0.681 Positive Predictive Value CentroidHomfold‑LAST: 0.866 CRWrnafold: 0.679 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.680 RNAalifold(seed): 0.606 Sensitivity CentroidHomfold‑LAST: 0.607 RNAalifold(seed): 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.773 RNAalifold(seed): 0.804 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Pknots: 0.676 Sensitivity CentroidHomfold‑LAST: 0.691 Pknots: 0.693 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Pknots: 0.672 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.594 RNASampler(seed): 0.581 Sensitivity CentroidHomfold‑LAST: 0.541 RNASampler(seed): 0.495 Positive Predictive Value CentroidHomfold‑LAST: 0.663 RNASampler(seed): 0.692 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Mastr(20): 0.694 Sensitivity CentroidHomfold‑LAST: 0.723 Mastr(20): 0.573 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RSpredict(20): 0.582 Sensitivity CentroidHomfold‑LAST: 0.723 RSpredict(20): 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.851 RSpredict(20): 0.665 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.810 Alterna: 0.711 Sensitivity CentroidHomfold‑LAST: 0.719 Alterna: 0.734 Positive Predictive Value CentroidHomfold‑LAST: 0.922 Alterna: 0.704 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.752 RNASLOpt: 0.668 Sensitivity CentroidHomfold‑LAST: 0.664 RNASLOpt: 0.638 Positive Predictive Value CentroidHomfold‑LAST: 0.861 RNASLOpt: 0.711 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Multilign(20): 0.683 Sensitivity CentroidHomfold‑LAST: 0.723 Multilign(20): 0.680 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Multilign(20): 0.697 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Vsfold4: 0.636 Sensitivity CentroidHomfold‑LAST: 0.691 Vsfold4: 0.620 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Vsfold4: 0.667 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.786 MCFold: 0.669 Sensitivity CentroidHomfold‑LAST: 0.705 MCFold: 0.701 Positive Predictive Value CentroidHomfold‑LAST: 0.885 MCFold: 0.652 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.783 RNAwolf: 0.585 Sensitivity CentroidHomfold‑LAST: 0.697 RNAwolf: 0.575 Positive Predictive Value CentroidHomfold‑LAST: 0.887 RNAwolf: 0.611 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.680 Murlet(seed): 0.535 Sensitivity CentroidHomfold‑LAST: 0.607 Murlet(seed): 0.375 Positive Predictive Value CentroidHomfold‑LAST: 0.773 Murlet(seed): 0.778 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.779 Vsfold5: 0.570 Sensitivity CentroidHomfold‑LAST: 0.687 Vsfold5: 0.575 Positive Predictive Value CentroidHomfold‑LAST: 0.891 Vsfold5: 0.580 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 RSpredict(seed): 0.264 Sensitivity CentroidHomfold‑LAST: 0.690 RSpredict(seed): 0.149 Positive Predictive Value CentroidHomfold‑LAST: 0.829 RSpredict(seed): 0.488 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.13392142882e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.815 RDfolder: 0.621 Sensitivity CentroidHomfold‑LAST: 0.721 RDfolder: 0.567 Positive Predictive Value CentroidHomfold‑LAST: 0.932 RDfolder: 0.700 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.738 PPfold(seed): 0.122 Sensitivity CentroidHomfold‑LAST: 0.671 PPfold(seed): 0.029 Positive Predictive Value CentroidHomfold‑LAST: 0.819 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.14531876181e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.690 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.829 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	? CMfinder(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value CMfinder(seed): 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 Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Multilign(seed): 0.683 Sensitivity CentroidHomfold‑LAST: 0.636 Multilign(seed): 0.636 Positive Predictive Value CentroidHomfold‑LAST: 0.843 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 CentroidHomfold‑LAST: 0.692 Sensitivity PETfold_pre2.0(seed): 0.772 CentroidHomfold‑LAST: 0.632 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidHomfold‑LAST: 0.766 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 TurboFold(20): 0.733 Sensitivity CentroidHomfold‑LAST: 0.723 TurboFold(20): 0.694 Positive Predictive Value CentroidHomfold‑LAST: 0.851 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(20): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CentroidHomfold‑LAST: 0.715 Sensitivity PETfold_pre2.0(20): 0.707 CentroidHomfold‑LAST: 0.664 Positive Predictive Value PETfold_pre2.0(20): 0.796 CentroidHomfold‑LAST: 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.704 TurboFold(seed): 0.650 Sensitivity CentroidHomfold‑LAST: 0.639 TurboFold(seed): 0.624 Positive Predictive Value CentroidHomfold‑LAST: 0.784 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 PPfold(20): 0.780 Sensitivity CentroidHomfold‑LAST: 0.723 PPfold(20): 0.714 Positive Predictive Value CentroidHomfold‑LAST: 0.851 PPfold(20): 0.860 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 NanoFolder: 0.543 Sensitivity CentroidHomfold‑LAST: 0.650 NanoFolder: 0.639 Positive Predictive Value CentroidHomfold‑LAST: 0.818 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.18141491686e-08	? CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.704 Carnac(seed): 0.325 Sensitivity CentroidHomfold‑LAST: 0.639 Carnac(seed): 0.107 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
HotKnots	44 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.776 HotKnots: 0.701 Sensitivity MXScarna(seed): 0.736 HotKnots: 0.732 Positive Predictive Value MXScarna(seed): 0.824 HotKnots: 0.676 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.810 HotKnots: 0.690 Sensitivity CentroidAlifold(20): 0.716 HotKnots: 0.712 Positive Predictive Value CentroidAlifold(20): 0.921 HotKnots: 0.674 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 4.94031556815e-08	104 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.780 HotKnots: 0.767 Sensitivity CentroidFold: 0.775 HotKnots: 0.790 Positive Predictive Value CentroidFold: 0.791 HotKnots: 0.750 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 7.5939721025e-08	28 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.782 HotKnots: 0.697 Sensitivity RNAalifold(20): 0.690 HotKnots: 0.718 Positive Predictive Value RNAalifold(20): 0.889 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	118 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.778 HotKnots: 0.772 Sensitivity Sfold: 0.768 HotKnots: 0.793 Positive Predictive Value Sfold: 0.793 HotKnots: 0.757 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 9.49173053431e-08	82 Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.777 HotKnots: 0.772 Sensitivity Fold: 0.796 HotKnots: 0.798 Positive Predictive Value Fold: 0.764 HotKnots: 0.752 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 5.90626908729e-06	28 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.765 HotKnots: 0.697 Sensitivity RNASampler(20): 0.671 HotKnots: 0.718 Positive Predictive Value RNASampler(20): 0.875 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.761 HotKnots: 0.697 Sensitivity MXScarna(20): 0.727 HotKnots: 0.718 Positive Predictive Value MXScarna(20): 0.800 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	44 CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 HotKnots: 0.755 Sensitivity CentroidHomfold‑LAST: 0.691 HotKnots: 0.772 Positive Predictive Value CentroidHomfold‑LAST: 0.893 HotKnots: 0.748 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 5.21776328505e-08		- UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.775 HotKnots: 0.772 Sensitivity UNAFold: 0.786 HotKnots: 0.793 Positive Predictive Value UNAFold: 0.769 HotKnots: 0.757 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 1.82713256396e-06	= HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.772 Contrafold: 0.769 Sensitivity HotKnots: 0.793 Contrafold: 0.784 Positive Predictive Value HotKnots: 0.757 Contrafold: 0.761 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.0215355173778	- IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.782 HotKnots: 0.742 Sensitivity IPknot: 0.752 HotKnots: 0.759 Positive Predictive Value IPknot: 0.820 HotKnots: 0.735 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	- ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.816 HotKnots: 0.734 Sensitivity ContextFold: 0.780 HotKnots: 0.753 Positive Predictive Value ContextFold: 0.861 HotKnots: 0.725 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.772 RNAshapes: 0.759 Sensitivity HotKnots: 0.793 RNAshapes: 0.770 Positive Predictive Value HotKnots: 0.757 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.764 MaxExpect: 0.754 Sensitivity HotKnots: 0.789 MaxExpect: 0.769 Positive Predictive Value HotKnots: 0.747 MaxExpect: 0.746 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.772 PknotsRG: 0.752 Sensitivity HotKnots: 0.793 PknotsRG: 0.774 Positive Predictive Value HotKnots: 0.757 PknotsRG: 0.737 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.772 RNAfold: 0.758 Sensitivity HotKnots: 0.793 RNAfold: 0.776 Positive Predictive Value HotKnots: 0.757 RNAfold: 0.748 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.752 ProbKnot: 0.741 Sensitivity HotKnots: 0.781 ProbKnot: 0.774 Positive Predictive Value HotKnots: 0.729 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 4.48494289621e-08	- Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.704 HotKnots: 0.697 Sensitivity Murlet(20): 0.596 HotKnots: 0.718 Positive Predictive Value Murlet(20): 0.837 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000287947293659	+ HotKnots vs CentroidAlifold(seed) Matthews Correlation Coefficient HotKnots: 0.698 CentroidAlifold(seed): 0.690 Sensitivity HotKnots: 0.729 CentroidAlifold(seed): 0.552 Positive Predictive Value HotKnots: 0.674 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.000741474702242	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.773 Afold: 0.747 Sensitivity HotKnots: 0.799 Afold: 0.774 Positive Predictive Value HotKnots: 0.754 Afold: 0.729 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.772 RNAsubopt: 0.738 Sensitivity HotKnots: 0.793 RNAsubopt: 0.757 Positive Predictive Value HotKnots: 0.757 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	= HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: 0.697 Carnac(20): 0.696 Sensitivity HotKnots: 0.718 Carnac(20): 0.518 Positive Predictive Value HotKnots: 0.682 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.51155202041	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.800 Cylofold: 0.741 Sensitivity HotKnots: 0.814 Cylofold: 0.724 Positive Predictive Value HotKnots: 0.794 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.770 McQFold: 0.718 Sensitivity HotKnots: 0.791 McQFold: 0.719 Positive Predictive Value HotKnots: 0.755 McQFold: 0.725 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.725 CRWrnafold: 0.683 Sensitivity HotKnots: 0.747 CRWrnafold: 0.690 Positive Predictive Value HotKnots: 0.712 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.704 RNAalifold(seed): 0.676 Sensitivity HotKnots: 0.743 RNAalifold(seed): 0.525 Positive Predictive Value HotKnots: 0.673 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.804 Pknots: 0.740 Sensitivity HotKnots: 0.815 Pknots: 0.763 Positive Predictive Value HotKnots: 0.801 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASampler(seed) Matthews Correlation Coefficient HotKnots: 0.803 RNASampler(seed): 0.765 Sensitivity HotKnots: 0.841 RNASampler(seed): 0.687 Positive Predictive Value HotKnots: 0.773 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.697 Mastr(20): 0.636 Sensitivity HotKnots: 0.718 Mastr(20): 0.483 Positive Predictive Value HotKnots: 0.682 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.694 RSpredict(20): 0.663 Sensitivity HotKnots: 0.716 RSpredict(20): 0.593 Positive Predictive Value HotKnots: 0.678 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.830 Alterna: 0.767 Sensitivity HotKnots: 0.835 Alterna: 0.777 Positive Predictive Value HotKnots: 0.833 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.734 RNASLOpt: 0.679 Sensitivity HotKnots: 0.753 RNASLOpt: 0.649 Positive Predictive Value HotKnots: 0.725 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.702 Multilign(20): 0.612 Sensitivity HotKnots: 0.710 Multilign(20): 0.581 Positive Predictive Value HotKnots: 0.704 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.84390417318e-09	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.772 Vsfold4: 0.650 Sensitivity HotKnots: 0.793 Vsfold4: 0.640 Positive Predictive Value HotKnots: 0.757 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.812 MCFold: 0.678 Sensitivity HotKnots: 0.826 MCFold: 0.717 Positive Predictive Value HotKnots: 0.806 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.742 RNAwolf: 0.594 Sensitivity HotKnots: 0.759 RNAwolf: 0.584 Positive Predictive Value HotKnots: 0.735 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.781 Murlet(seed): 0.620 Sensitivity HotKnots: 0.795 Murlet(seed): 0.442 Positive Predictive Value HotKnots: 0.774 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.771 Vsfold5: 0.612 Sensitivity HotKnots: 0.792 Vsfold5: 0.613 Positive Predictive Value HotKnots: 0.756 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.701 RSpredict(seed): 0.372 Sensitivity HotKnots: 0.732 RSpredict(seed): 0.222 Positive Predictive Value HotKnots: 0.676 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.833 RDfolder: 0.682 Sensitivity HotKnots: 0.838 RDfolder: 0.643 Positive Predictive Value HotKnots: 0.837 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.675 PPfold(seed): 0.122 Sensitivity HotKnots: 0.687 PPfold(seed): 0.029 Positive Predictive Value HotKnots: 0.673 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.91686328089e-09	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.702 Mastr(seed): 0.306 Sensitivity HotKnots: 0.733 Mastr(seed): 0.105 Positive Predictive Value HotKnots: 0.679 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: N/A CMfinder(seed): N/A Sensitivity HotKnots: N/A CMfinder(seed): N/A Positive Predictive Value HotKnots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.770 Multilign(seed): 0.683 Sensitivity HotKnots: 0.746 Multilign(seed): 0.636 Positive Predictive Value HotKnots: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 HotKnots: 0.618 Sensitivity PETfold_pre2.0(seed): 0.772 HotKnots: 0.643 Positive Predictive Value PETfold_pre2.0(seed): 0.892 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.759 TurboFold(20): 0.733 Sensitivity HotKnots: 0.772 TurboFold(20): 0.694 Positive Predictive Value HotKnots: 0.754 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 HotKnots: 0.688 Sensitivity PETfold_pre2.0(20): 0.707 HotKnots: 0.724 Positive Predictive Value PETfold_pre2.0(20): 0.796 HotKnots: 0.661 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.745 TurboFold(seed): 0.650 Sensitivity HotKnots: 0.756 TurboFold(seed): 0.624 Positive Predictive Value HotKnots: 0.742 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.780 HotKnots: 0.759 Sensitivity PPfold(20): 0.714 HotKnots: 0.772 Positive Predictive Value PPfold(20): 0.860 HotKnots: 0.754 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.728 NanoFolder: 0.562 Sensitivity HotKnots: 0.749 NanoFolder: 0.656 Positive Predictive Value HotKnots: 0.717 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.795 Carnac(seed): 0.299 Sensitivity HotKnots: 0.808 Carnac(seed): 0.090 Positive Predictive Value HotKnots: 0.788 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
UNAFold	44 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.776 UNAFold: 0.700 Sensitivity MXScarna(seed): 0.736 UNAFold: 0.721 Positive Predictive Value MXScarna(seed): 0.824 UNAFold: 0.685 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 UNAFold: 0.704 Sensitivity CentroidAlifold(20): 0.716 UNAFold: 0.710 Positive Predictive Value CentroidAlifold(20): 0.921 UNAFold: 0.704 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	106 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.711 UNAFold: 0.630 Sensitivity CentroidFold: 0.707 UNAFold: 0.666 Positive Predictive Value CentroidFold: 0.715 UNAFold: 0.596 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.782 UNAFold: 0.711 Sensitivity RNAalifold(20): 0.690 UNAFold: 0.716 Positive Predictive Value RNAalifold(20): 0.889 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.633 UNAFold: 0.610 Sensitivity Sfold: 0.631 UNAFold: 0.641 Positive Predictive Value Sfold: 0.636 UNAFold: 0.581 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.777 UNAFold: 0.765 Sensitivity Fold: 0.796 UNAFold: 0.782 Positive Predictive Value Fold: 0.764 UNAFold: 0.755 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 5.3419901105e-07	28 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.765 UNAFold: 0.711 Sensitivity RNASampler(20): 0.671 UNAFold: 0.716 Positive Predictive Value RNASampler(20): 0.875 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.761 UNAFold: 0.711 Sensitivity MXScarna(20): 0.727 UNAFold: 0.716 Positive Predictive Value MXScarna(20): 0.800 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	44 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 UNAFold: 0.719 Sensitivity CentroidHomfold‑LAST: 0.691 UNAFold: 0.725 Positive Predictive Value CentroidHomfold‑LAST: 0.893 UNAFold: 0.725 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.775 HotKnots: 0.772 Sensitivity UNAFold: 0.786 HotKnots: 0.793 Positive Predictive Value UNAFold: 0.769 HotKnots: 0.757 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 1.82713256396e-06		- Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.699 UNAFold: 0.610 Sensitivity Contrafold: 0.722 UNAFold: 0.641 Positive Predictive Value Contrafold: 0.677 UNAFold: 0.581 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	- IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.782 UNAFold: 0.706 Sensitivity IPknot: 0.752 UNAFold: 0.713 Positive Predictive Value IPknot: 0.820 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	- ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.816 UNAFold: 0.690 Sensitivity ContextFold: 0.780 UNAFold: 0.697 Positive Predictive Value ContextFold: 0.861 UNAFold: 0.695 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.775 RNAshapes: 0.759 Sensitivity UNAFold: 0.786 RNAshapes: 0.770 Positive Predictive Value UNAFold: 0.769 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	- MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.729 UNAFold: 0.686 Sensitivity MaxExpect: 0.740 UNAFold: 0.701 Positive Predictive Value MaxExpect: 0.719 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 7.5939721025e-08	+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.610 PknotsRG: 0.592 Sensitivity UNAFold: 0.641 PknotsRG: 0.630 Positive Predictive Value UNAFold: 0.581 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.610 RNAfold: 0.604 Sensitivity UNAFold: 0.641 RNAfold: 0.641 Positive Predictive Value UNAFold: 0.581 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.745 ProbKnot: 0.741 Sensitivity UNAFold: 0.763 ProbKnot: 0.774 Positive Predictive Value UNAFold: 0.732 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.83595875043e-07	+ UNAFold vs Murlet(20) Matthews Correlation Coefficient UNAFold: 0.711 Murlet(20): 0.704 Sensitivity UNAFold: 0.716 Murlet(20): 0.596 Positive Predictive Value UNAFold: 0.711 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.4733335145e-06	= UNAFold vs CentroidAlifold(seed) Matthews Correlation Coefficient UNAFold: 0.697 CentroidAlifold(seed): 0.690 Sensitivity UNAFold: 0.718 CentroidAlifold(seed): 0.552 Positive Predictive Value UNAFold: 0.682 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.128796078713	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.594 Afold: 0.590 Sensitivity UNAFold: 0.628 Afold: 0.630 Positive Predictive Value UNAFold: 0.562 Afold: 0.553 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.26115971074e-07	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.775 RNAsubopt: 0.738 Sensitivity UNAFold: 0.786 RNAsubopt: 0.757 Positive Predictive Value UNAFold: 0.769 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.711 Carnac(20): 0.696 Sensitivity UNAFold: 0.716 Carnac(20): 0.518 Positive Predictive Value UNAFold: 0.711 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 7.66564282849e-07	+ UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.789 Cylofold: 0.741 Sensitivity UNAFold: 0.791 Cylofold: 0.724 Positive Predictive Value UNAFold: 0.794 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.609 McQFold: 0.534 Sensitivity UNAFold: 0.640 McQFold: 0.503 Positive Predictive Value UNAFold: 0.580 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.683 UNAFold: 0.683 Sensitivity CRWrnafold: 0.690 UNAFold: 0.694 Positive Predictive Value CRWrnafold: 0.689 UNAFold: 0.684 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.536377815296	+ UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.696 RNAalifold(seed): 0.676 Sensitivity UNAFold: 0.721 RNAalifold(seed): 0.525 Positive Predictive Value UNAFold: 0.677 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.95107997107e-08	+ UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.806 Pknots: 0.740 Sensitivity UNAFold: 0.808 Pknots: 0.763 Positive Predictive Value UNAFold: 0.812 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.794 RNASampler(seed): 0.765 Sensitivity UNAFold: 0.817 RNASampler(seed): 0.687 Positive Predictive Value UNAFold: 0.777 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.26346675981e-08	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.711 Mastr(20): 0.636 Sensitivity UNAFold: 0.716 Mastr(20): 0.483 Positive Predictive Value UNAFold: 0.711 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.709 RSpredict(20): 0.663 Sensitivity UNAFold: 0.714 RSpredict(20): 0.593 Positive Predictive Value UNAFold: 0.708 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.831 Alterna: 0.767 Sensitivity UNAFold: 0.829 Alterna: 0.777 Positive Predictive Value UNAFold: 0.842 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.690 RNASLOpt: 0.679 Sensitivity UNAFold: 0.697 RNASLOpt: 0.649 Positive Predictive Value UNAFold: 0.695 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.90626908729e-06	+ UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.656 Multilign(20): 0.612 Sensitivity UNAFold: 0.651 Multilign(20): 0.581 Positive Predictive Value UNAFold: 0.671 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.47941000302e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.775 Vsfold4: 0.650 Sensitivity UNAFold: 0.786 Vsfold4: 0.640 Positive Predictive Value UNAFold: 0.769 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.815 MCFold: 0.678 Sensitivity UNAFold: 0.819 MCFold: 0.717 Positive Predictive Value UNAFold: 0.818 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.706 RNAwolf: 0.594 Sensitivity UNAFold: 0.713 RNAwolf: 0.584 Positive Predictive Value UNAFold: 0.711 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.767 Murlet(seed): 0.620 Sensitivity UNAFold: 0.766 Murlet(seed): 0.442 Positive Predictive Value UNAFold: 0.774 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.774 Vsfold5: 0.612 Sensitivity UNAFold: 0.786 Vsfold5: 0.613 Positive Predictive Value UNAFold: 0.768 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.700 RSpredict(seed): 0.372 Sensitivity UNAFold: 0.721 RSpredict(seed): 0.222 Positive Predictive Value UNAFold: 0.685 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.827 RDfolder: 0.682 Sensitivity UNAFold: 0.822 RDfolder: 0.643 Positive Predictive Value UNAFold: 0.841 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.584 PPfold(seed): 0.122 Sensitivity UNAFold: 0.584 PPfold(seed): 0.029 Positive Predictive Value UNAFold: 0.597 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.27752322258e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.701 Mastr(seed): 0.306 Sensitivity UNAFold: 0.722 Mastr(seed): 0.105 Positive Predictive Value UNAFold: 0.687 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: N/A CMfinder(seed): N/A Sensitivity UNAFold: N/A CMfinder(seed): N/A Positive Predictive Value UNAFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.683 UNAFold: 0.674 Sensitivity Multilign(seed): 0.636 UNAFold: 0.653 Positive Predictive Value Multilign(seed): 0.750 UNAFold: 0.713 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 UNAFold: 0.489 Sensitivity PETfold_pre2.0(seed): 0.772 UNAFold: 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.892 UNAFold: 0.494 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.733 UNAFold: 0.706 Sensitivity TurboFold(20): 0.694 UNAFold: 0.704 Positive Predictive Value TurboFold(20): 0.781 UNAFold: 0.718 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: N/A CMfinder(20): N/A Sensitivity UNAFold: N/A CMfinder(20): N/A Positive Predictive Value UNAFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 UNAFold: 0.593 Sensitivity PETfold_pre2.0(20): 0.707 UNAFold: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 UNAFold: 0.593 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.650 UNAFold: 0.638 Sensitivity TurboFold(seed): 0.624 UNAFold: 0.634 Positive Predictive Value TurboFold(seed): 0.688 UNAFold: 0.653 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.780 UNAFold: 0.706 Sensitivity PPfold(20): 0.714 UNAFold: 0.704 Positive Predictive Value PPfold(20): 0.860 UNAFold: 0.718 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.663 NanoFolder: 0.562 Sensitivity UNAFold: 0.677 NanoFolder: 0.656 Positive Predictive Value UNAFold: 0.661 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.33194562506e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.783 Carnac(seed): 0.299 Sensitivity UNAFold: 0.784 Carnac(seed): 0.090 Positive Predictive Value UNAFold: 0.788 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
Contrafold	44 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.776 Contrafold: 0.698 Sensitivity MXScarna(seed): 0.736 Contrafold: 0.726 Positive Predictive Value MXScarna(seed): 0.824 Contrafold: 0.677 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Contrafold: 0.659 Sensitivity CentroidAlifold(20): 0.716 Contrafold: 0.677 Positive Predictive Value CentroidAlifold(20): 0.921 Contrafold: 0.647 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	106 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.711 Contrafold: 0.695 Sensitivity CentroidFold: 0.707 Contrafold: 0.722 Positive Predictive Value CentroidFold: 0.715 Contrafold: 0.669 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 0.00208354999408	28 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.782 Contrafold: 0.656 Sensitivity RNAalifold(20): 0.690 Contrafold: 0.675 Positive Predictive Value RNAalifold(20): 0.889 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.98172311752e-08	121 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.699 Sfold: 0.633 Sensitivity Contrafold: 0.722 Sfold: 0.631 Positive Predictive Value Contrafold: 0.677 Sfold: 0.636 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs Contrafold Matthews Correlation Coefficient Fold: 0.777 Contrafold: 0.773 Sensitivity Fold: 0.796 Contrafold: 0.790 Positive Predictive Value Fold: 0.764 Contrafold: 0.763 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 0.000284355681826	28 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.765 Contrafold: 0.656 Sensitivity RNASampler(20): 0.671 Contrafold: 0.675 Positive Predictive Value RNASampler(20): 0.875 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.761 Contrafold: 0.656 Sensitivity MXScarna(20): 0.727 Contrafold: 0.675 Positive Predictive Value MXScarna(20): 0.800 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	44 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Contrafold: 0.769 Sensitivity CentroidHomfold‑LAST: 0.691 Contrafold: 0.767 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Contrafold: 0.781 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 1.03971108356e-05	118 HotKnots vs Contrafold Matthews Correlation Coefficient HotKnots: 0.772 Contrafold: 0.769 Sensitivity HotKnots: 0.793 Contrafold: 0.784 Positive Predictive Value HotKnots: 0.757 Contrafold: 0.761 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.0215355173778	121 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.699 UNAFold: 0.610 Sensitivity Contrafold: 0.722 UNAFold: 0.641 Positive Predictive Value Contrafold: 0.677 UNAFold: 0.581 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08		- IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.782 Contrafold: 0.759 Sensitivity IPknot: 0.752 Contrafold: 0.756 Positive Predictive Value IPknot: 0.820 Contrafold: 0.772 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.85233844192e-08	- ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.816 Contrafold: 0.745 Sensitivity ContextFold: 0.780 Contrafold: 0.737 Positive Predictive Value ContextFold: 0.861 Contrafold: 0.763 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.769 RNAshapes: 0.759 Sensitivity Contrafold: 0.784 RNAshapes: 0.770 Positive Predictive Value Contrafold: 0.761 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.744 MaxExpect: 0.729 Sensitivity Contrafold: 0.756 MaxExpect: 0.740 Positive Predictive Value Contrafold: 0.732 MaxExpect: 0.719 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.699 PknotsRG: 0.592 Sensitivity Contrafold: 0.722 PknotsRG: 0.630 Positive Predictive Value Contrafold: 0.677 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.699 RNAfold: 0.604 Sensitivity Contrafold: 0.722 RNAfold: 0.641 Positive Predictive Value Contrafold: 0.677 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.753 ProbKnot: 0.741 Sensitivity Contrafold: 0.771 ProbKnot: 0.774 Positive Predictive Value Contrafold: 0.741 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.85233844192e-08	- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.704 Contrafold: 0.656 Sensitivity Murlet(20): 0.596 Contrafold: 0.675 Positive Predictive Value Murlet(20): 0.837 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	= Contrafold vs CentroidAlifold(seed) Matthews Correlation Coefficient Contrafold: 0.696 CentroidAlifold(seed): 0.690 Sensitivity Contrafold: 0.724 CentroidAlifold(seed): 0.552 Positive Predictive Value Contrafold: 0.674 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.726733689455	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.690 Afold: 0.590 Sensitivity Contrafold: 0.715 Afold: 0.630 Positive Predictive Value Contrafold: 0.666 Afold: 0.553 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.769 RNAsubopt: 0.738 Sensitivity Contrafold: 0.784 RNAsubopt: 0.757 Positive Predictive Value Contrafold: 0.761 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.696 Contrafold: 0.656 Sensitivity Carnac(20): 0.518 Contrafold: 0.675 Positive Predictive Value Carnac(20): 0.941 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.800 Cylofold: 0.741 Sensitivity Contrafold: 0.804 Cylofold: 0.724 Positive Predictive Value Contrafold: 0.803 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.698 McQFold: 0.534 Sensitivity Contrafold: 0.721 McQFold: 0.503 Positive Predictive Value Contrafold: 0.676 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.733 CRWrnafold: 0.683 Sensitivity Contrafold: 0.731 CRWrnafold: 0.690 Positive Predictive Value Contrafold: 0.745 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.693 RNAalifold(seed): 0.676 Sensitivity Contrafold: 0.718 RNAalifold(seed): 0.525 Positive Predictive Value Contrafold: 0.674 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 1.16758253407e-07	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.798 Pknots: 0.740 Sensitivity Contrafold: 0.805 Pknots: 0.763 Positive Predictive Value Contrafold: 0.799 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.794 RNASampler(seed): 0.765 Sensitivity Contrafold: 0.812 RNASampler(seed): 0.687 Positive Predictive Value Contrafold: 0.782 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	= Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.656 Mastr(20): 0.636 Sensitivity Contrafold: 0.675 Mastr(20): 0.483 Positive Predictive Value Contrafold: 0.643 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0019918072826	+ Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.664 RSpredict(20): 0.663 Sensitivity Contrafold: 0.682 RSpredict(20): 0.593 Positive Predictive Value Contrafold: 0.652 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000632812409388	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.845 Alterna: 0.767 Sensitivity Contrafold: 0.840 Alterna: 0.777 Positive Predictive Value Contrafold: 0.857 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.745 RNASLOpt: 0.679 Sensitivity Contrafold: 0.737 RNASLOpt: 0.649 Positive Predictive Value Contrafold: 0.763 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.615 Multilign(20): 0.612 Sensitivity Contrafold: 0.614 Multilign(20): 0.581 Positive Predictive Value Contrafold: 0.627 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.323670796354	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.769 Vsfold4: 0.650 Sensitivity Contrafold: 0.784 Vsfold4: 0.640 Positive Predictive Value Contrafold: 0.761 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.801 MCFold: 0.678 Sensitivity Contrafold: 0.809 MCFold: 0.717 Positive Predictive Value Contrafold: 0.801 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.759 RNAwolf: 0.594 Sensitivity Contrafold: 0.756 RNAwolf: 0.584 Positive Predictive Value Contrafold: 0.772 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.757 Murlet(seed): 0.620 Sensitivity Contrafold: 0.761 Murlet(seed): 0.442 Positive Predictive Value Contrafold: 0.761 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.768 Vsfold5: 0.612 Sensitivity Contrafold: 0.783 Vsfold5: 0.613 Positive Predictive Value Contrafold: 0.760 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.698 RSpredict(seed): 0.372 Sensitivity Contrafold: 0.726 RSpredict(seed): 0.222 Positive Predictive Value Contrafold: 0.677 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.838 RDfolder: 0.682 Sensitivity Contrafold: 0.831 RDfolder: 0.643 Positive Predictive Value Contrafold: 0.853 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.666 PPfold(seed): 0.122 Sensitivity Contrafold: 0.658 PPfold(seed): 0.029 Positive Predictive Value Contrafold: 0.684 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.692 Mastr(seed): 0.306 Sensitivity Contrafold: 0.721 Mastr(seed): 0.105 Positive Predictive Value Contrafold: 0.670 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.693 Multilign(seed): 0.683 Sensitivity Contrafold: 0.669 Multilign(seed): 0.636 Positive Predictive Value Contrafold: 0.731 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Contrafold: 0.626 Sensitivity PETfold_pre2.0(seed): 0.772 Contrafold: 0.614 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Contrafold: 0.648 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.733 Contrafold: 0.700 Sensitivity TurboFold(20): 0.694 Contrafold: 0.699 Positive Predictive Value TurboFold(20): 0.781 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: N/A CMfinder(20): N/A Sensitivity Contrafold: N/A CMfinder(20): N/A Positive Predictive Value Contrafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Contrafold: 0.624 Sensitivity PETfold_pre2.0(20): 0.707 Contrafold: 0.621 Positive Predictive Value PETfold_pre2.0(20): 0.796 Contrafold: 0.637 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.677 TurboFold(seed): 0.650 Sensitivity Contrafold: 0.663 TurboFold(seed): 0.624 Positive Predictive Value Contrafold: 0.701 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.780 Contrafold: 0.700 Sensitivity PPfold(20): 0.714 Contrafold: 0.699 Positive Predictive Value PPfold(20): 0.860 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.761 NanoFolder: 0.562 Sensitivity Contrafold: 0.756 NanoFolder: 0.656 Positive Predictive Value Contrafold: 0.775 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.760 Carnac(seed): 0.299 Sensitivity Contrafold: 0.773 Carnac(seed): 0.090 Positive Predictive Value Contrafold: 0.754 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
IPknot	11 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.728 IPknot: 0.701 Sensitivity MXScarna(seed): 0.675 IPknot: 0.658 Positive Predictive Value MXScarna(seed): 0.792 IPknot: 0.755 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.52299983238e-08	8 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.825 IPknot: 0.684 Sensitivity CentroidAlifold(20): 0.729 IPknot: 0.654 Positive Predictive Value CentroidAlifold(20): 0.938 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.782 CentroidFold: 0.766 Sensitivity IPknot: 0.752 CentroidFold: 0.743 Positive Predictive Value IPknot: 0.820 CentroidFold: 0.798 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.744 IPknot: 0.684 Sensitivity RNAalifold(20): 0.681 IPknot: 0.654 Positive Predictive Value RNAalifold(20): 0.821 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.782 Sfold: 0.736 Sensitivity IPknot: 0.752 Sfold: 0.713 Positive Predictive Value IPknot: 0.820 Sfold: 0.769 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.782 Fold: 0.703 Sensitivity IPknot: 0.752 Fold: 0.712 Positive Predictive Value IPknot: 0.820 Fold: 0.707 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASampler(20) vs IPknot Matthews Correlation Coefficient RNASampler(20): 0.762 IPknot: 0.684 Sensitivity RNASampler(20): 0.681 IPknot: 0.654 Positive Predictive Value RNASampler(20): 0.859 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.689 IPknot: 0.684 Sensitivity MXScarna(20): 0.649 IPknot: 0.654 Positive Predictive Value MXScarna(20): 0.739 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	37 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.783 IPknot: 0.776 Sensitivity CentroidHomfold‑LAST: 0.697 IPknot: 0.746 Positive Predictive Value CentroidHomfold‑LAST: 0.887 IPknot: 0.815 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 0.0348339286697	38 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.782 HotKnots: 0.742 Sensitivity IPknot: 0.752 HotKnots: 0.759 Positive Predictive Value IPknot: 0.820 HotKnots: 0.735 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.782 UNAFold: 0.706 Sensitivity IPknot: 0.752 UNAFold: 0.713 Positive Predictive Value IPknot: 0.820 UNAFold: 0.711 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.782 Contrafold: 0.759 Sensitivity IPknot: 0.752 Contrafold: 0.756 Positive Predictive Value IPknot: 0.820 Contrafold: 0.772 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.85233844192e-08		- ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.816 IPknot: 0.765 Sensitivity ContextFold: 0.780 IPknot: 0.735 Positive Predictive Value ContextFold: 0.861 IPknot: 0.805 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.782 RNAshapes: 0.722 Sensitivity IPknot: 0.752 RNAshapes: 0.727 Positive Predictive Value IPknot: 0.820 RNAshapes: 0.726 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.782 MaxExpect: 0.704 Sensitivity IPknot: 0.752 MaxExpect: 0.706 Positive Predictive Value IPknot: 0.820 MaxExpect: 0.713 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.782 PknotsRG: 0.738 Sensitivity IPknot: 0.752 PknotsRG: 0.756 Positive Predictive Value IPknot: 0.820 PknotsRG: 0.731 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.782 RNAfold: 0.726 Sensitivity IPknot: 0.752 RNAfold: 0.731 Positive Predictive Value IPknot: 0.820 RNAfold: 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.782 ProbKnot: 0.701 Sensitivity IPknot: 0.752 ProbKnot: 0.724 Positive Predictive Value IPknot: 0.820 ProbKnot: 0.691 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.693 IPknot: 0.684 Sensitivity Murlet(20): 0.612 IPknot: 0.654 Positive Predictive Value Murlet(20): 0.793 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	= IPknot vs CentroidAlifold(seed) Matthews Correlation Coefficient IPknot: 0.701 CentroidAlifold(seed): 0.694 Sensitivity IPknot: 0.658 CentroidAlifold(seed): 0.494 Positive Predictive Value IPknot: 0.755 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.811904790494	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.829 Afold: 0.764 Sensitivity IPknot: 0.801 Afold: 0.783 Positive Predictive Value IPknot: 0.865 Afold: 0.754 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.782 RNAsubopt: 0.691 Sensitivity IPknot: 0.752 RNAsubopt: 0.703 Positive Predictive Value IPknot: 0.820 RNAsubopt: 0.692 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.684 Carnac(20): 0.662 Sensitivity IPknot: 0.654 Carnac(20): 0.516 Positive Predictive Value IPknot: 0.724 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.777 Cylofold: 0.676 Sensitivity IPknot: 0.738 Cylofold: 0.663 Positive Predictive Value IPknot: 0.826 Cylofold: 0.702 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.776 McQFold: 0.696 Sensitivity IPknot: 0.746 McQFold: 0.690 Positive Predictive Value IPknot: 0.815 McQFold: 0.713 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.757 CRWrnafold: 0.683 Sensitivity IPknot: 0.731 CRWrnafold: 0.690 Positive Predictive Value IPknot: 0.793 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.610 IPknot: 0.601 Sensitivity RNAalifold(seed): 0.473 IPknot: 0.560 Positive Predictive Value RNAalifold(seed): 0.798 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.782 Pknots: 0.663 Sensitivity IPknot: 0.752 Pknots: 0.683 Positive Predictive Value IPknot: 0.820 Pknots: 0.656 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.597 RNASampler(seed): 0.559 Sensitivity IPknot: 0.560 RNASampler(seed): 0.484 Positive Predictive Value IPknot: 0.646 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.684 Mastr(20): 0.674 Sensitivity IPknot: 0.654 Mastr(20): 0.548 Positive Predictive Value IPknot: 0.724 Mastr(20): 0.837 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.684 RSpredict(20): 0.586 Sensitivity IPknot: 0.654 RSpredict(20): 0.521 Positive Predictive Value IPknot: 0.724 RSpredict(20): 0.671 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.791 Alterna: 0.684 Sensitivity IPknot: 0.754 Alterna: 0.705 Positive Predictive Value IPknot: 0.840 Alterna: 0.679 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.765 RNASLOpt: 0.679 Sensitivity IPknot: 0.735 RNASLOpt: 0.649 Positive Predictive Value IPknot: 0.805 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	? IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.684 Multilign(20): 0.653 Sensitivity IPknot: 0.654 Multilign(20): 0.649 Positive Predictive Value IPknot: 0.724 Multilign(20): 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.782 Vsfold4: 0.620 Sensitivity IPknot: 0.752 Vsfold4: 0.609 Positive Predictive Value IPknot: 0.820 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.792 MCFold: 0.668 Sensitivity IPknot: 0.763 MCFold: 0.698 Positive Predictive Value IPknot: 0.831 MCFold: 0.652 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.782 RNAwolf: 0.594 Sensitivity IPknot: 0.752 RNAwolf: 0.584 Positive Predictive Value IPknot: 0.820 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.601 Murlet(seed): 0.531 Sensitivity IPknot: 0.560 Murlet(seed): 0.373 Positive Predictive Value IPknot: 0.656 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.778 Vsfold5: 0.558 Sensitivity IPknot: 0.749 Vsfold5: 0.566 Positive Predictive Value IPknot: 0.818 Vsfold5: 0.568 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.701 RSpredict(seed): 0.231 Sensitivity IPknot: 0.658 RSpredict(seed): 0.123 Positive Predictive Value IPknot: 0.755 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.756 RDfolder: 0.567 Sensitivity IPknot: 0.718 RDfolder: 0.513 Positive Predictive Value IPknot: 0.808 RDfolder: 0.651 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.701 PPfold(seed): 0.122 Sensitivity IPknot: 0.658 PPfold(seed): 0.029 Positive Predictive Value IPknot: 0.755 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.77162746897e-09	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.701 Mastr(seed): 0.000 Sensitivity IPknot: 0.658 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.755 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	? CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.656 Multilign(seed): 0.629 Sensitivity IPknot: 0.600 Multilign(seed): 0.580 Positive Predictive Value IPknot: 0.732 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 IPknot: 0.653 Sensitivity PETfold_pre2.0(seed): 0.772 IPknot: 0.614 Positive Predictive Value PETfold_pre2.0(seed): 0.892 IPknot: 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.712 IPknot: 0.684 Sensitivity TurboFold(20): 0.670 IPknot: 0.654 Positive Predictive Value TurboFold(20): 0.764 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: N/A CMfinder(20): N/A Sensitivity IPknot: N/A CMfinder(20): N/A Positive Predictive Value IPknot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 IPknot: 0.606 Sensitivity PETfold_pre2.0(20): 0.707 IPknot: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.796 IPknot: 0.636 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.648 TurboFold(seed): 0.621 Sensitivity IPknot: 0.610 TurboFold(seed): 0.594 Positive Predictive Value IPknot: 0.699 TurboFold(seed): 0.661 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.790 IPknot: 0.684 Sensitivity PPfold(20): 0.734 IPknot: 0.654 Positive Predictive Value PPfold(20): 0.857 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.785 NanoFolder: 0.562 Sensitivity IPknot: 0.759 NanoFolder: 0.656 Positive Predictive Value IPknot: 0.819 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-08	? IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.648 Carnac(seed): 0.145 Sensitivity IPknot: 0.610 Carnac(seed): 0.021 Positive Predictive Value IPknot: 0.699 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
ContextFold	8 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.732 MXScarna(seed): 0.679 Sensitivity ContextFold: 0.673 MXScarna(seed): 0.620 Positive Predictive Value ContextFold: 0.804 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs ContextFold Matthews Correlation Coefficient CentroidAlifold(20): 0.779 ContextFold: 0.698 Sensitivity CentroidAlifold(20): 0.672 ContextFold: 0.638 Positive Predictive Value CentroidAlifold(20): 0.907 ContextFold: 0.771 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.816 CentroidFold: 0.747 Sensitivity ContextFold: 0.780 CentroidFold: 0.721 Positive Predictive Value ContextFold: 0.861 CentroidFold: 0.783 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.698 RNAalifold(20): 0.656 Sensitivity ContextFold: 0.638 RNAalifold(20): 0.578 Positive Predictive Value ContextFold: 0.771 RNAalifold(20): 0.753 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.816 Sfold: 0.722 Sensitivity ContextFold: 0.780 Sfold: 0.697 Positive Predictive Value ContextFold: 0.861 Sfold: 0.758 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.816 Fold: 0.696 Sensitivity ContextFold: 0.780 Fold: 0.699 Positive Predictive Value ContextFold: 0.861 Fold: 0.704 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.698 RNASampler(20): 0.686 Sensitivity ContextFold: 0.638 RNASampler(20): 0.603 Positive Predictive Value ContextFold: 0.771 RNASampler(20): 0.787 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.698 MXScarna(20): 0.586 Sensitivity ContextFold: 0.638 MXScarna(20): 0.543 Positive Predictive Value ContextFold: 0.771 MXScarna(20): 0.643 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	29 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.810 CentroidHomfold‑LAST: 0.752 Sensitivity ContextFold: 0.773 CentroidHomfold‑LAST: 0.664 Positive Predictive Value ContextFold: 0.856 CentroidHomfold‑LAST: 0.861 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	30 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.816 HotKnots: 0.734 Sensitivity ContextFold: 0.780 HotKnots: 0.753 Positive Predictive Value ContextFold: 0.861 HotKnots: 0.725 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.816 UNAFold: 0.690 Sensitivity ContextFold: 0.780 UNAFold: 0.697 Positive Predictive Value ContextFold: 0.861 UNAFold: 0.695 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.816 Contrafold: 0.745 Sensitivity ContextFold: 0.780 Contrafold: 0.737 Positive Predictive Value ContextFold: 0.861 Contrafold: 0.763 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.816 IPknot: 0.765 Sensitivity ContextFold: 0.780 IPknot: 0.735 Positive Predictive Value ContextFold: 0.861 IPknot: 0.805 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.816 RNAshapes: 0.713 Sensitivity ContextFold: 0.780 RNAshapes: 0.715 Positive Predictive Value ContextFold: 0.861 RNAshapes: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.816 MaxExpect: 0.693 Sensitivity ContextFold: 0.780 MaxExpect: 0.690 Positive Predictive Value ContextFold: 0.861 MaxExpect: 0.707 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.816 PknotsRG: 0.735 Sensitivity ContextFold: 0.780 PknotsRG: 0.751 Positive Predictive Value ContextFold: 0.861 PknotsRG: 0.729 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.816 RNAfold: 0.719 Sensitivity ContextFold: 0.780 RNAfold: 0.719 Positive Predictive Value ContextFold: 0.861 RNAfold: 0.729 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.816 ProbKnot: 0.696 Sensitivity ContextFold: 0.780 ProbKnot: 0.717 Positive Predictive Value ContextFold: 0.861 ProbKnot: 0.686 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.698 Murlet(20): 0.594 Sensitivity ContextFold: 0.638 Murlet(20): 0.500 Positive Predictive Value ContextFold: 0.771 Murlet(20): 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.732 CentroidAlifold(seed): 0.646 Sensitivity ContextFold: 0.673 CentroidAlifold(seed): 0.427 Positive Predictive Value ContextFold: 0.804 CentroidAlifold(seed): 0.986 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.801 Afold: 0.764 Sensitivity ContextFold: 0.774 Afold: 0.781 Positive Predictive Value ContextFold: 0.837 Afold: 0.755 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 5.86050763602e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.816 RNAsubopt: 0.664 Sensitivity ContextFold: 0.780 RNAsubopt: 0.676 Positive Predictive Value ContextFold: 0.861 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.698 Carnac(20): 0.562 Sensitivity ContextFold: 0.638 Carnac(20): 0.397 Positive Predictive Value ContextFold: 0.771 Carnac(20): 0.807 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.811 Cylofold: 0.666 Sensitivity ContextFold: 0.771 Cylofold: 0.646 Positive Predictive Value ContextFold: 0.861 Cylofold: 0.699 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.810 McQFold: 0.662 Sensitivity ContextFold: 0.773 McQFold: 0.661 Positive Predictive Value ContextFold: 0.856 McQFold: 0.675 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.799 CRWrnafold: 0.688 Sensitivity ContextFold: 0.762 CRWrnafold: 0.684 Positive Predictive Value ContextFold: 0.844 CRWrnafold: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	? ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.570 RNAalifold(seed): 0.542 Sensitivity ContextFold: 0.515 RNAalifold(seed): 0.392 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.760 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.816 Pknots: 0.628 Sensitivity ContextFold: 0.780 Pknots: 0.649 Positive Predictive Value ContextFold: 0.861 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.413 RNASampler(seed): 0.232 Sensitivity ContextFold: 0.395 RNASampler(seed): 0.211 Positive Predictive Value ContextFold: 0.441 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.698 Mastr(20): 0.581 Sensitivity ContextFold: 0.638 Mastr(20): 0.431 Positive Predictive Value ContextFold: 0.771 Mastr(20): 0.794 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.698 RSpredict(20): 0.428 Sensitivity ContextFold: 0.638 RSpredict(20): 0.362 Positive Predictive Value ContextFold: 0.771 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.782 Alterna: 0.691 Sensitivity ContextFold: 0.757 Alterna: 0.701 Positive Predictive Value ContextFold: 0.820 Alterna: 0.697 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.816 RNASLOpt: 0.679 Sensitivity ContextFold: 0.780 RNASLOpt: 0.649 Positive Predictive Value ContextFold: 0.861 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.698 Multilign(20): 0.583 Sensitivity ContextFold: 0.638 Multilign(20): 0.578 Positive Predictive Value ContextFold: 0.771 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.816 Vsfold4: 0.618 Sensitivity ContextFold: 0.780 Vsfold4: 0.602 Positive Predictive Value ContextFold: 0.861 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.825 MCFold: 0.683 Sensitivity ContextFold: 0.790 MCFold: 0.710 Positive Predictive Value ContextFold: 0.868 MCFold: 0.668 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.816 RNAwolf: 0.555 Sensitivity ContextFold: 0.780 RNAwolf: 0.544 Positive Predictive Value ContextFold: 0.861 RNAwolf: 0.583 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.570 Murlet(seed): 0.495 Sensitivity ContextFold: 0.515 Murlet(seed): 0.340 Positive Predictive Value ContextFold: 0.641 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.813 Vsfold5: 0.543 Sensitivity ContextFold: 0.776 Vsfold5: 0.547 Positive Predictive Value ContextFold: 0.858 Vsfold5: 0.556 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	? ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.732 RSpredict(seed): 0.131 Sensitivity ContextFold: 0.673 RSpredict(seed): 0.070 Positive Predictive Value ContextFold: 0.804 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.750 RDfolder: 0.537 Sensitivity ContextFold: 0.709 RDfolder: 0.485 Positive Predictive Value ContextFold: 0.808 RDfolder: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	? ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.732 PPfold(seed): 0.146 Sensitivity ContextFold: 0.673 PPfold(seed): 0.041 Positive Predictive Value ContextFold: 0.804 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.732 Mastr(seed): 0.000 Sensitivity ContextFold: 0.673 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.804 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.606 Multilign(seed): 0.458 Sensitivity ContextFold: 0.574 Multilign(seed): 0.404 Positive Predictive Value ContextFold: 0.659 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 ContextFold: 0.732 Sensitivity PETfold_pre2.0(seed): 0.772 ContextFold: 0.673 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ContextFold: 0.804 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.698 TurboFold(20): 0.655 Sensitivity ContextFold: 0.638 TurboFold(20): 0.612 Positive Predictive Value ContextFold: 0.771 TurboFold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: N/A CMfinder(20): N/A Sensitivity ContextFold: N/A CMfinder(20): N/A Positive Predictive Value ContextFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 ContextFold: 0.698 Sensitivity PETfold_pre2.0(20): 0.707 ContextFold: 0.638 Positive Predictive Value PETfold_pre2.0(20): 0.796 ContextFold: 0.771 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.682 TurboFold(seed): 0.552 Sensitivity ContextFold: 0.627 TurboFold(seed): 0.530 Positive Predictive Value ContextFold: 0.750 TurboFold(seed): 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.732 ContextFold: 0.698 Sensitivity PPfold(20): 0.672 ContextFold: 0.638 Positive Predictive Value PPfold(20): 0.804 ContextFold: 0.771 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.823 NanoFolder: 0.562 Sensitivity ContextFold: 0.784 NanoFolder: 0.656 Positive Predictive Value ContextFold: 0.870 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-08	? ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.682 Carnac(seed): 0.172 Sensitivity ContextFold: 0.627 Carnac(seed): 0.030 Positive Predictive Value ContextFold: 0.750 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
RNAshapes	44 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.776 RNAshapes: 0.699 Sensitivity MXScarna(seed): 0.736 RNAshapes: 0.720 Positive Predictive Value MXScarna(seed): 0.824 RNAshapes: 0.685 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAshapes: 0.699 Sensitivity CentroidAlifold(20): 0.716 RNAshapes: 0.704 Positive Predictive Value CentroidAlifold(20): 0.921 RNAshapes: 0.698 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	104 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.780 RNAshapes: 0.756 Sensitivity CentroidFold: 0.775 RNAshapes: 0.768 Positive Predictive Value CentroidFold: 0.791 RNAshapes: 0.750 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.782 RNAshapes: 0.699 Sensitivity RNAalifold(20): 0.690 RNAshapes: 0.704 Positive Predictive Value RNAalifold(20): 0.889 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.778 RNAshapes: 0.759 Sensitivity Sfold: 0.768 RNAshapes: 0.770 Positive Predictive Value Sfold: 0.793 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.777 RNAshapes: 0.766 Sensitivity Fold: 0.796 RNAshapes: 0.781 Positive Predictive Value Fold: 0.764 RNAshapes: 0.757 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.765 RNAshapes: 0.699 Sensitivity RNASampler(20): 0.671 RNAshapes: 0.704 Positive Predictive Value RNASampler(20): 0.875 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.761 RNAshapes: 0.699 Sensitivity MXScarna(20): 0.727 RNAshapes: 0.704 Positive Predictive Value MXScarna(20): 0.800 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	44 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAshapes: 0.734 Sensitivity CentroidHomfold‑LAST: 0.691 RNAshapes: 0.739 Positive Predictive Value CentroidHomfold‑LAST: 0.893 RNAshapes: 0.739 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.772 RNAshapes: 0.759 Sensitivity HotKnots: 0.793 RNAshapes: 0.770 Positive Predictive Value HotKnots: 0.757 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 4.48494289621e-08	118 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.775 RNAshapes: 0.759 Sensitivity UNAFold: 0.786 RNAshapes: 0.770 Positive Predictive Value UNAFold: 0.769 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.769 RNAshapes: 0.759 Sensitivity Contrafold: 0.784 RNAshapes: 0.770 Positive Predictive Value Contrafold: 0.761 RNAshapes: 0.755 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.85233844192e-08	38 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.782 RNAshapes: 0.722 Sensitivity IPknot: 0.752 RNAshapes: 0.727 Positive Predictive Value IPknot: 0.820 RNAshapes: 0.726 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.816 RNAshapes: 0.713 Sensitivity ContextFold: 0.780 RNAshapes: 0.715 Positive Predictive Value ContextFold: 0.861 RNAshapes: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAshapes vs MaxExpect Matthews Correlation Coefficient RNAshapes: 0.759 MaxExpect: 0.754 Sensitivity RNAshapes: 0.771 MaxExpect: 0.769 Positive Predictive Value RNAshapes: 0.752 MaxExpect: 0.746 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 0.000349712763079	+ RNAshapes vs PknotsRG Matthews Correlation Coefficient RNAshapes: 0.759 PknotsRG: 0.752 Sensitivity RNAshapes: 0.770 PknotsRG: 0.774 Positive Predictive Value RNAshapes: 0.755 PknotsRG: 0.737 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 6.53888633552e-08	= RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.759 RNAfold: 0.758 Sensitivity RNAshapes: 0.770 RNAfold: 0.776 Positive Predictive Value RNAshapes: 0.755 RNAfold: 0.748 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.618957769369	+ RNAshapes vs ProbKnot Matthews Correlation Coefficient RNAshapes: 0.748 ProbKnot: 0.741 Sensitivity RNAshapes: 0.765 ProbKnot: 0.774 Positive Predictive Value RNAshapes: 0.738 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 2.54546175831e-06	= Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.704 RNAshapes: 0.699 Sensitivity Murlet(20): 0.596 RNAshapes: 0.704 Positive Predictive Value Murlet(20): 0.837 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0017098773264	= RNAshapes vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAshapes: 0.697 CentroidAlifold(seed): 0.690 Sensitivity RNAshapes: 0.717 CentroidAlifold(seed): 0.552 Positive Predictive Value RNAshapes: 0.682 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.122165152257	+ RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.763 Afold: 0.747 Sensitivity RNAshapes: 0.778 Afold: 0.774 Positive Predictive Value RNAshapes: 0.753 Afold: 0.729 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.759 RNAsubopt: 0.738 Sensitivity RNAshapes: 0.770 RNAsubopt: 0.757 Positive Predictive Value RNAshapes: 0.755 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.699 Carnac(20): 0.696 Sensitivity RNAshapes: 0.704 Carnac(20): 0.518 Positive Predictive Value RNAshapes: 0.699 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.233182913621	+ RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.794 Cylofold: 0.741 Sensitivity RNAshapes: 0.796 Cylofold: 0.724 Positive Predictive Value RNAshapes: 0.800 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.758 McQFold: 0.718 Sensitivity RNAshapes: 0.768 McQFold: 0.719 Positive Predictive Value RNAshapes: 0.754 McQFold: 0.725 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.704 CRWrnafold: 0.683 Sensitivity RNAshapes: 0.710 CRWrnafold: 0.690 Positive Predictive Value RNAshapes: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 8.67590017402e-07	+ RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.717 RNAalifold(seed): 0.676 Sensitivity RNAshapes: 0.742 RNAalifold(seed): 0.525 Positive Predictive Value RNAshapes: 0.698 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.792 Pknots: 0.740 Sensitivity RNAshapes: 0.793 Pknots: 0.763 Positive Predictive Value RNAshapes: 0.799 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.805 RNASampler(seed): 0.765 Sensitivity RNAshapes: 0.826 RNASampler(seed): 0.687 Positive Predictive Value RNAshapes: 0.789 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.699 Mastr(20): 0.636 Sensitivity RNAshapes: 0.704 Mastr(20): 0.483 Positive Predictive Value RNAshapes: 0.699 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.703 RSpredict(20): 0.663 Sensitivity RNAshapes: 0.709 RSpredict(20): 0.593 Positive Predictive Value RNAshapes: 0.703 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.54865340847e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.806 Alterna: 0.767 Sensitivity RNAshapes: 0.803 Alterna: 0.777 Positive Predictive Value RNAshapes: 0.819 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.713 RNASLOpt: 0.679 Sensitivity RNAshapes: 0.715 RNASLOpt: 0.649 Positive Predictive Value RNAshapes: 0.721 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.748 Multilign(20): 0.612 Sensitivity RNAshapes: 0.743 Multilign(20): 0.581 Positive Predictive Value RNAshapes: 0.762 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.02007144414e-09	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.759 Vsfold4: 0.650 Sensitivity RNAshapes: 0.770 Vsfold4: 0.640 Positive Predictive Value RNAshapes: 0.755 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.808 MCFold: 0.678 Sensitivity RNAshapes: 0.810 MCFold: 0.717 Positive Predictive Value RNAshapes: 0.814 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.722 RNAwolf: 0.594 Sensitivity RNAshapes: 0.727 RNAwolf: 0.584 Positive Predictive Value RNAshapes: 0.726 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.803 Murlet(seed): 0.620 Sensitivity RNAshapes: 0.803 Murlet(seed): 0.442 Positive Predictive Value RNAshapes: 0.809 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.758 Vsfold5: 0.612 Sensitivity RNAshapes: 0.769 Vsfold5: 0.613 Positive Predictive Value RNAshapes: 0.754 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.699 RSpredict(seed): 0.372 Sensitivity RNAshapes: 0.720 RSpredict(seed): 0.222 Positive Predictive Value RNAshapes: 0.685 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.805 RDfolder: 0.682 Sensitivity RNAshapes: 0.797 RDfolder: 0.643 Positive Predictive Value RNAshapes: 0.822 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.648 PPfold(seed): 0.122 Sensitivity RNAshapes: 0.646 PPfold(seed): 0.029 Positive Predictive Value RNAshapes: 0.660 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.697 Mastr(seed): 0.306 Sensitivity RNAshapes: 0.716 Mastr(seed): 0.105 Positive Predictive Value RNAshapes: 0.683 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAshapes vs Multilign(seed) Matthews Correlation Coefficient RNAshapes: 0.770 Multilign(seed): 0.683 Sensitivity RNAshapes: 0.746 Multilign(seed): 0.636 Positive Predictive Value RNAshapes: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAshapes: 0.577 Sensitivity PETfold_pre2.0(seed): 0.772 RNAshapes: 0.585 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAshapes: 0.581 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.733 RNAshapes: 0.705 Sensitivity TurboFold(20): 0.694 RNAshapes: 0.699 Positive Predictive Value TurboFold(20): 0.781 RNAshapes: 0.720 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: N/A CMfinder(20): N/A Sensitivity RNAshapes: N/A CMfinder(20): N/A Positive Predictive Value RNAshapes: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAshapes: 0.590 Sensitivity PETfold_pre2.0(20): 0.707 RNAshapes: 0.595 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.690 TurboFold(seed): 0.650 Sensitivity RNAshapes: 0.683 TurboFold(seed): 0.624 Positive Predictive Value RNAshapes: 0.707 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.780 RNAshapes: 0.705 Sensitivity PPfold(20): 0.714 RNAshapes: 0.699 Positive Predictive Value PPfold(20): 0.860 RNAshapes: 0.720 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.715 NanoFolder: 0.562 Sensitivity RNAshapes: 0.729 NanoFolder: 0.656 Positive Predictive Value RNAshapes: 0.711 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.800 Carnac(seed): 0.299 Sensitivity RNAshapes: 0.801 Carnac(seed): 0.090 Positive Predictive Value RNAshapes: 0.804 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
MaxExpect	40 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.768 MaxExpect: 0.703 Sensitivity MXScarna(seed): 0.729 MaxExpect: 0.725 Positive Predictive Value MXScarna(seed): 0.813 MaxExpect: 0.687 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.810 MaxExpect: 0.700 Sensitivity CentroidAlifold(20): 0.716 MaxExpect: 0.710 Positive Predictive Value CentroidAlifold(20): 0.921 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	99 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.762 MaxExpect: 0.729 Sensitivity CentroidFold: 0.747 MaxExpect: 0.740 Positive Predictive Value CentroidFold: 0.779 MaxExpect: 0.719 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.777 MaxExpect: 0.700 Sensitivity RNAalifold(20): 0.686 MaxExpect: 0.710 Positive Predictive Value RNAalifold(20): 0.884 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	99 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.729 Sfold: 0.701 Sensitivity MaxExpect: 0.740 Sfold: 0.686 Positive Predictive Value MaxExpect: 0.719 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 1.70738736246e-07	82 Fold vs MaxExpect Matthews Correlation Coefficient Fold: 0.777 MaxExpect: 0.758 Sensitivity Fold: 0.796 MaxExpect: 0.773 Positive Predictive Value Fold: 0.764 MaxExpect: 0.749 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 4.48494289621e-08	26 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.762 MaxExpect: 0.700 Sensitivity RNASampler(20): 0.671 MaxExpect: 0.710 Positive Predictive Value RNASampler(20): 0.870 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.756 MaxExpect: 0.700 Sensitivity MXScarna(20): 0.722 MaxExpect: 0.710 Positive Predictive Value MXScarna(20): 0.797 MaxExpect: 0.696 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	44 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 MaxExpect: 0.710 Sensitivity CentroidHomfold‑LAST: 0.691 MaxExpect: 0.715 Positive Predictive Value CentroidHomfold‑LAST: 0.893 MaxExpect: 0.716 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.764 MaxExpect: 0.754 Sensitivity HotKnots: 0.789 MaxExpect: 0.769 Positive Predictive Value HotKnots: 0.747 MaxExpect: 0.746 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	99 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.729 UNAFold: 0.686 Sensitivity MaxExpect: 0.740 UNAFold: 0.701 Positive Predictive Value MaxExpect: 0.719 UNAFold: 0.672 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 7.5939721025e-08	99 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.744 MaxExpect: 0.729 Sensitivity Contrafold: 0.756 MaxExpect: 0.740 Positive Predictive Value Contrafold: 0.732 MaxExpect: 0.719 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 4.48494289621e-08	38 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.782 MaxExpect: 0.704 Sensitivity IPknot: 0.752 MaxExpect: 0.706 Positive Predictive Value IPknot: 0.820 MaxExpect: 0.713 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.816 MaxExpect: 0.693 Sensitivity ContextFold: 0.780 MaxExpect: 0.690 Positive Predictive Value ContextFold: 0.861 MaxExpect: 0.707 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 RNAshapes vs MaxExpect Matthews Correlation Coefficient RNAshapes: 0.759 MaxExpect: 0.754 Sensitivity RNAshapes: 0.771 MaxExpect: 0.769 Positive Predictive Value RNAshapes: 0.752 MaxExpect: 0.746 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 0.000349712763079		+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.729 PknotsRG: 0.659 Sensitivity MaxExpect: 0.740 PknotsRG: 0.683 Positive Predictive Value MaxExpect: 0.719 PknotsRG: 0.637 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.729 RNAfold: 0.674 Sensitivity MaxExpect: 0.740 RNAfold: 0.695 Positive Predictive Value MaxExpect: 0.719 RNAfold: 0.655 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.747 ProbKnot: 0.741 Sensitivity MaxExpect: 0.765 ProbKnot: 0.774 Positive Predictive Value MaxExpect: 0.735 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.700 Murlet(20): 0.698 Sensitivity MaxExpect: 0.710 Murlet(20): 0.591 Positive Predictive Value MaxExpect: 0.696 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.605451749002	+ MaxExpect vs CentroidAlifold(seed) Matthews Correlation Coefficient MaxExpect: 0.703 CentroidAlifold(seed): 0.690 Sensitivity MaxExpect: 0.725 CentroidAlifold(seed): 0.556 Positive Predictive Value MaxExpect: 0.687 CentroidAlifold(seed): 0.863 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 0.000108348164592	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.721 Afold: 0.664 Sensitivity MaxExpect: 0.737 Afold: 0.690 Positive Predictive Value MaxExpect: 0.707 Afold: 0.640 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.754 RNAsubopt: 0.739 Sensitivity MaxExpect: 0.769 RNAsubopt: 0.759 Positive Predictive Value MaxExpect: 0.746 RNAsubopt: 0.725 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.700 Carnac(20): 0.694 Sensitivity MaxExpect: 0.710 Carnac(20): 0.516 Positive Predictive Value MaxExpect: 0.696 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.000349666881076	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.791 Cylofold: 0.741 Sensitivity MaxExpect: 0.796 Cylofold: 0.724 Positive Predictive Value MaxExpect: 0.794 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.728 McQFold: 0.612 Sensitivity MaxExpect: 0.739 McQFold: 0.613 Positive Predictive Value MaxExpect: 0.718 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.683 MaxExpect: 0.662 Sensitivity CRWrnafold: 0.690 MaxExpect: 0.667 Positive Predictive Value CRWrnafold: 0.689 MaxExpect: 0.669 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.48494289621e-08	= RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.672 MaxExpect: 0.668 Sensitivity RNAalifold(seed): 0.524 MaxExpect: 0.697 Positive Predictive Value RNAalifold(seed): 0.867 MaxExpect: 0.647 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.657358697881	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.785 Pknots: 0.737 Sensitivity MaxExpect: 0.791 Pknots: 0.760 Positive Predictive Value MaxExpect: 0.787 Pknots: 0.723 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.757 MaxExpect: 0.742 Sensitivity RNASampler(seed): 0.685 MaxExpect: 0.777 Positive Predictive Value RNASampler(seed): 0.843 MaxExpect: 0.716 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.56588588961e-07	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.700 Mastr(20): 0.628 Sensitivity MaxExpect: 0.710 Mastr(20): 0.471 Positive Predictive Value MaxExpect: 0.696 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.700 RSpredict(20): 0.660 Sensitivity MaxExpect: 0.710 RSpredict(20): 0.590 Positive Predictive Value MaxExpect: 0.696 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.59469103578e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.815 Alterna: 0.750 Sensitivity MaxExpect: 0.815 Alterna: 0.764 Positive Predictive Value MaxExpect: 0.823 Alterna: 0.749 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.693 RNASLOpt: 0.679 Sensitivity MaxExpect: 0.690 RNASLOpt: 0.649 Positive Predictive Value MaxExpect: 0.707 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.06521910535e-06	= MaxExpect vs Multilign(20) Matthews Correlation Coefficient MaxExpect: 0.617 Multilign(20): 0.612 Sensitivity MaxExpect: 0.622 Multilign(20): 0.581 Positive Predictive Value MaxExpect: 0.622 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.376887793106	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.754 Vsfold4: 0.643 Sensitivity MaxExpect: 0.769 Vsfold4: 0.634 Positive Predictive Value MaxExpect: 0.746 Vsfold4: 0.662 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.783 MCFold: 0.654 Sensitivity MaxExpect: 0.792 MCFold: 0.695 Positive Predictive Value MaxExpect: 0.782 MCFold: 0.627 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.704 RNAwolf: 0.594 Sensitivity MaxExpect: 0.706 RNAwolf: 0.584 Positive Predictive Value MaxExpect: 0.713 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.726 Murlet(seed): 0.621 Sensitivity MaxExpect: 0.736 Murlet(seed): 0.447 Positive Predictive Value MaxExpect: 0.725 Murlet(seed): 0.872 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.753 Vsfold5: 0.599 Sensitivity MaxExpect: 0.767 Vsfold5: 0.598 Positive Predictive Value MaxExpect: 0.745 Vsfold5: 0.610 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.703 RSpredict(seed): 0.362 Sensitivity MaxExpect: 0.725 RSpredict(seed): 0.216 Positive Predictive Value MaxExpect: 0.687 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.803 RDfolder: 0.674 Sensitivity MaxExpect: 0.801 RDfolder: 0.631 Positive Predictive Value MaxExpect: 0.815 RDfolder: 0.736 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.603 PPfold(seed): 0.122 Sensitivity MaxExpect: 0.601 PPfold(seed): 0.029 Positive Predictive Value MaxExpect: 0.616 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.52299983238e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.703 Mastr(seed): 0.322 Sensitivity MaxExpect: 0.725 Mastr(seed): 0.116 Positive Predictive Value MaxExpect: 0.687 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(seed): N/A Sensitivity MaxExpect: N/A CMfinder(seed): N/A Positive Predictive Value MaxExpect: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.683 MaxExpect: 0.656 Sensitivity Multilign(seed): 0.636 MaxExpect: 0.636 Positive Predictive Value Multilign(seed): 0.750 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 MaxExpect: 0.532 Sensitivity PETfold_pre2.0(seed): 0.772 MaxExpect: 0.532 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MaxExpect: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.733 MaxExpect: 0.681 Sensitivity TurboFold(20): 0.694 MaxExpect: 0.684 Positive Predictive Value TurboFold(20): 0.781 MaxExpect: 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(20): N/A Sensitivity MaxExpect: N/A CMfinder(20): N/A Positive Predictive Value MaxExpect: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 MaxExpect: 0.579 Sensitivity PETfold_pre2.0(20): 0.707 MaxExpect: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.796 MaxExpect: 0.581 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.650 MaxExpect: 0.620 Sensitivity TurboFold(seed): 0.624 MaxExpect: 0.615 Positive Predictive Value TurboFold(seed): 0.688 MaxExpect: 0.636 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.780 MaxExpect: 0.681 Sensitivity PPfold(20): 0.714 MaxExpect: 0.684 Positive Predictive Value PPfold(20): 0.860 MaxExpect: 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.687 NanoFolder: 0.562 Sensitivity MaxExpect: 0.691 NanoFolder: 0.656 Positive Predictive Value MaxExpect: 0.693 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.750 Carnac(seed): 0.283 Sensitivity MaxExpect: 0.760 Carnac(seed): 0.081 Positive Predictive Value MaxExpect: 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08
PknotsRG	44 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.776 PknotsRG: 0.703 Sensitivity MXScarna(seed): 0.736 PknotsRG: 0.732 Positive Predictive Value MXScarna(seed): 0.824 PknotsRG: 0.681 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.810 PknotsRG: 0.690 Sensitivity CentroidAlifold(20): 0.716 PknotsRG: 0.710 Positive Predictive Value CentroidAlifold(20): 0.921 PknotsRG: 0.675 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	106 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.711 PknotsRG: 0.609 Sensitivity CentroidFold: 0.707 PknotsRG: 0.652 Positive Predictive Value CentroidFold: 0.715 PknotsRG: 0.570 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.782 PknotsRG: 0.699 Sensitivity RNAalifold(20): 0.690 PknotsRG: 0.719 Positive Predictive Value RNAalifold(20): 0.889 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	121 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.633 PknotsRG: 0.592 Sensitivity Sfold: 0.631 PknotsRG: 0.630 Positive Predictive Value Sfold: 0.636 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.777 PknotsRG: 0.751 Sensitivity Fold: 0.796 PknotsRG: 0.777 Positive Predictive Value Fold: 0.764 PknotsRG: 0.732 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.765 PknotsRG: 0.699 Sensitivity RNASampler(20): 0.671 PknotsRG: 0.719 Positive Predictive Value RNASampler(20): 0.875 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.761 PknotsRG: 0.699 Sensitivity MXScarna(20): 0.727 PknotsRG: 0.719 Positive Predictive Value MXScarna(20): 0.800 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	44 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 PknotsRG: 0.750 Sensitivity CentroidHomfold‑LAST: 0.691 PknotsRG: 0.765 Positive Predictive Value CentroidHomfold‑LAST: 0.893 PknotsRG: 0.744 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.772 PknotsRG: 0.752 Sensitivity HotKnots: 0.793 PknotsRG: 0.774 Positive Predictive Value HotKnots: 0.757 PknotsRG: 0.737 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.610 PknotsRG: 0.592 Sensitivity UNAFold: 0.641 PknotsRG: 0.630 Positive Predictive Value UNAFold: 0.581 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.699 PknotsRG: 0.592 Sensitivity Contrafold: 0.722 PknotsRG: 0.630 Positive Predictive Value Contrafold: 0.677 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.782 PknotsRG: 0.738 Sensitivity IPknot: 0.752 PknotsRG: 0.756 Positive Predictive Value IPknot: 0.820 PknotsRG: 0.731 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.816 PknotsRG: 0.735 Sensitivity ContextFold: 0.780 PknotsRG: 0.751 Positive Predictive Value ContextFold: 0.861 PknotsRG: 0.729 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs PknotsRG Matthews Correlation Coefficient RNAshapes: 0.759 PknotsRG: 0.752 Sensitivity RNAshapes: 0.770 PknotsRG: 0.774 Positive Predictive Value RNAshapes: 0.755 PknotsRG: 0.737 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 6.53888633552e-08	99 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.729 PknotsRG: 0.659 Sensitivity MaxExpect: 0.740 PknotsRG: 0.683 Positive Predictive Value MaxExpect: 0.719 PknotsRG: 0.637 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.604 PknotsRG: 0.592 Sensitivity RNAfold: 0.641 PknotsRG: 0.630 Positive Predictive Value RNAfold: 0.570 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.746 ProbKnot: 0.741 Sensitivity PknotsRG: 0.775 ProbKnot: 0.774 Positive Predictive Value PknotsRG: 0.724 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.37177523642e-07	- Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.704 PknotsRG: 0.699 Sensitivity Murlet(20): 0.596 PknotsRG: 0.719 Positive Predictive Value Murlet(20): 0.837 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000195172284771	+ PknotsRG vs CentroidAlifold(seed) Matthews Correlation Coefficient PknotsRG: 0.700 CentroidAlifold(seed): 0.690 Sensitivity PknotsRG: 0.729 CentroidAlifold(seed): 0.552 Positive Predictive Value PknotsRG: 0.678 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 1.49438993542e-06	- Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.590 PknotsRG: 0.571 Sensitivity Afold: 0.630 PknotsRG: 0.612 Positive Predictive Value Afold: 0.553 PknotsRG: 0.533 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.752 RNAsubopt: 0.738 Sensitivity PknotsRG: 0.774 RNAsubopt: 0.757 Positive Predictive Value PknotsRG: 0.737 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	= PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.699 Carnac(20): 0.696 Sensitivity PknotsRG: 0.719 Carnac(20): 0.518 Positive Predictive Value PknotsRG: 0.684 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00416853265544	+ PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.778 Cylofold: 0.741 Sensitivity PknotsRG: 0.790 Cylofold: 0.724 Positive Predictive Value PknotsRG: 0.774 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.591 McQFold: 0.534 Sensitivity PknotsRG: 0.629 McQFold: 0.503 Positive Predictive Value PknotsRG: 0.556 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.720 CRWrnafold: 0.683 Sensitivity PknotsRG: 0.743 CRWrnafold: 0.690 Positive Predictive Value PknotsRG: 0.708 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.707 RNAalifold(seed): 0.676 Sensitivity PknotsRG: 0.745 RNAalifold(seed): 0.525 Positive Predictive Value PknotsRG: 0.677 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.782 Pknots: 0.740 Sensitivity PknotsRG: 0.794 Pknots: 0.763 Positive Predictive Value PknotsRG: 0.779 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.792 RNASampler(seed): 0.765 Sensitivity PknotsRG: 0.820 RNASampler(seed): 0.687 Positive Predictive Value PknotsRG: 0.771 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.77586369438e-08	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.699 Mastr(20): 0.636 Sensitivity PknotsRG: 0.719 Mastr(20): 0.483 Positive Predictive Value PknotsRG: 0.684 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.694 RSpredict(20): 0.663 Sensitivity PknotsRG: 0.714 RSpredict(20): 0.593 Positive Predictive Value PknotsRG: 0.680 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 9.34100095224e-08	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.803 Alterna: 0.767 Sensitivity PknotsRG: 0.808 Alterna: 0.777 Positive Predictive Value PknotsRG: 0.808 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.735 RNASLOpt: 0.679 Sensitivity PknotsRG: 0.751 RNASLOpt: 0.649 Positive Predictive Value PknotsRG: 0.729 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.689 Multilign(20): 0.612 Sensitivity PknotsRG: 0.701 Multilign(20): 0.581 Positive Predictive Value PknotsRG: 0.687 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.752 Vsfold4: 0.650 Sensitivity PknotsRG: 0.774 Vsfold4: 0.640 Positive Predictive Value PknotsRG: 0.737 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.796 MCFold: 0.678 Sensitivity PknotsRG: 0.810 MCFold: 0.717 Positive Predictive Value PknotsRG: 0.791 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.738 RNAwolf: 0.594 Sensitivity PknotsRG: 0.756 RNAwolf: 0.584 Positive Predictive Value PknotsRG: 0.731 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.786 Murlet(seed): 0.620 Sensitivity PknotsRG: 0.797 Murlet(seed): 0.442 Positive Predictive Value PknotsRG: 0.782 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.751 Vsfold5: 0.612 Sensitivity PknotsRG: 0.773 Vsfold5: 0.613 Positive Predictive Value PknotsRG: 0.736 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.703 RSpredict(seed): 0.372 Sensitivity PknotsRG: 0.732 RSpredict(seed): 0.222 Positive Predictive Value PknotsRG: 0.681 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.808 RDfolder: 0.682 Sensitivity PknotsRG: 0.812 RDfolder: 0.643 Positive Predictive Value PknotsRG: 0.813 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.714 PPfold(seed): 0.122 Sensitivity PknotsRG: 0.720 PPfold(seed): 0.029 Positive Predictive Value PknotsRG: 0.717 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.20383511129e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.706 Mastr(seed): 0.306 Sensitivity PknotsRG: 0.735 Mastr(seed): 0.105 Positive Predictive Value PknotsRG: 0.684 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(seed): N/A Sensitivity PknotsRG: N/A CMfinder(seed): N/A Positive Predictive Value PknotsRG: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.765 Multilign(seed): 0.683 Sensitivity PknotsRG: 0.737 Multilign(seed): 0.636 Positive Predictive Value PknotsRG: 0.806 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 PknotsRG: 0.678 Sensitivity PETfold_pre2.0(seed): 0.772 PknotsRG: 0.696 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PknotsRG: 0.669 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.744 TurboFold(20): 0.733 Sensitivity PknotsRG: 0.762 TurboFold(20): 0.694 Positive Predictive Value PknotsRG: 0.734 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(20): N/A Sensitivity PknotsRG: N/A CMfinder(20): N/A Positive Predictive Value PknotsRG: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 PknotsRG: 0.672 Sensitivity PETfold_pre2.0(20): 0.707 PknotsRG: 0.716 Positive Predictive Value PETfold_pre2.0(20): 0.796 PknotsRG: 0.638 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.731 TurboFold(seed): 0.650 Sensitivity PknotsRG: 0.746 TurboFold(seed): 0.624 Positive Predictive Value PknotsRG: 0.725 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.780 PknotsRG: 0.744 Sensitivity PPfold(20): 0.714 PknotsRG: 0.762 Positive Predictive Value PPfold(20): 0.860 PknotsRG: 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.745 NanoFolder: 0.562 Sensitivity PknotsRG: 0.766 NanoFolder: 0.656 Positive Predictive Value PknotsRG: 0.734 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.784 Carnac(seed): 0.299 Sensitivity PknotsRG: 0.795 Carnac(seed): 0.090 Positive Predictive Value PknotsRG: 0.779 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	44 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.776 RNAfold: 0.704 Sensitivity MXScarna(seed): 0.736 RNAfold: 0.730 Positive Predictive Value MXScarna(seed): 0.824 RNAfold: 0.685 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAfold: 0.679 Sensitivity CentroidAlifold(20): 0.716 RNAfold: 0.694 Positive Predictive Value CentroidAlifold(20): 0.921 RNAfold: 0.669 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	106 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.711 RNAfold: 0.620 Sensitivity CentroidFold: 0.707 RNAfold: 0.663 Positive Predictive Value CentroidFold: 0.715 RNAfold: 0.582 Number of pairs reference - predicted secondary structure: 106 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.782 RNAfold: 0.687 Sensitivity RNAalifold(20): 0.690 RNAfold: 0.701 Positive Predictive Value RNAalifold(20): 0.889 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	121 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.633 RNAfold: 0.604 Sensitivity Sfold: 0.631 RNAfold: 0.641 Positive Predictive Value Sfold: 0.636 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.777 RNAfold: 0.754 Sensitivity Fold: 0.796 RNAfold: 0.776 Positive Predictive Value Fold: 0.764 RNAfold: 0.740 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.765 RNAfold: 0.687 Sensitivity RNASampler(20): 0.671 RNAfold: 0.701 Positive Predictive Value RNASampler(20): 0.875 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.761 RNAfold: 0.687 Sensitivity MXScarna(20): 0.727 RNAfold: 0.701 Positive Predictive Value MXScarna(20): 0.800 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	44 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAfold: 0.741 Sensitivity CentroidHomfold‑LAST: 0.691 RNAfold: 0.746 Positive Predictive Value CentroidHomfold‑LAST: 0.893 RNAfold: 0.746 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.772 RNAfold: 0.758 Sensitivity HotKnots: 0.793 RNAfold: 0.776 Positive Predictive Value HotKnots: 0.757 RNAfold: 0.748 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.610 RNAfold: 0.604 Sensitivity UNAFold: 0.641 RNAfold: 0.641 Positive Predictive Value UNAFold: 0.581 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.699 RNAfold: 0.604 Sensitivity Contrafold: 0.722 RNAfold: 0.641 Positive Predictive Value Contrafold: 0.677 RNAfold: 0.570 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.782 RNAfold: 0.726 Sensitivity IPknot: 0.752 RNAfold: 0.731 Positive Predictive Value IPknot: 0.820 RNAfold: 0.732 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.816 RNAfold: 0.719 Sensitivity ContextFold: 0.780 RNAfold: 0.719 Positive Predictive Value ContextFold: 0.861 RNAfold: 0.729 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.759 RNAfold: 0.758 Sensitivity RNAshapes: 0.770 RNAfold: 0.776 Positive Predictive Value RNAshapes: 0.755 RNAfold: 0.748 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 0.618957769369	99 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.729 RNAfold: 0.674 Sensitivity MaxExpect: 0.740 RNAfold: 0.695 Positive Predictive Value MaxExpect: 0.719 RNAfold: 0.655 Number of pairs reference - predicted secondary structure: 99 Wilcoxon single-rank test P-value: 5.62644058675e-08	121 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.604 PknotsRG: 0.592 Sensitivity RNAfold: 0.641 PknotsRG: 0.630 Positive Predictive Value RNAfold: 0.570 PknotsRG: 0.557 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08		= RNAfold vs ProbKnot Matthews Correlation Coefficient RNAfold: 0.744 ProbKnot: 0.741 Sensitivity RNAfold: 0.767 ProbKnot: 0.774 Positive Predictive Value RNAfold: 0.727 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.0466667757771	- Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.704 RNAfold: 0.687 Sensitivity Murlet(20): 0.596 RNAfold: 0.701 Positive Predictive Value Murlet(20): 0.837 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.51337059456e-07	= RNAfold vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAfold: 0.702 CentroidAlifold(seed): 0.690 Sensitivity RNAfold: 0.727 CentroidAlifold(seed): 0.552 Positive Predictive Value RNAfold: 0.683 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.00284536525437	- Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.590 RNAfold: 0.585 Sensitivity Afold: 0.630 RNAfold: 0.626 Positive Predictive Value Afold: 0.553 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.758 RNAsubopt: 0.738 Sensitivity RNAfold: 0.776 RNAsubopt: 0.757 Positive Predictive Value RNAfold: 0.748 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.696 RNAfold: 0.687 Sensitivity Carnac(20): 0.518 RNAfold: 0.701 Positive Predictive Value Carnac(20): 0.941 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.66698692294e-05	+ RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.774 Cylofold: 0.741 Sensitivity RNAfold: 0.779 Cylofold: 0.724 Positive Predictive Value RNAfold: 0.777 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.603 McQFold: 0.534 Sensitivity RNAfold: 0.639 McQFold: 0.503 Positive Predictive Value RNAfold: 0.569 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.706 CRWrnafold: 0.683 Sensitivity RNAfold: 0.715 CRWrnafold: 0.690 Positive Predictive Value RNAfold: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.5875416339e-07	+ RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.707 RNAalifold(seed): 0.676 Sensitivity RNAfold: 0.739 RNAalifold(seed): 0.525 Positive Predictive Value RNAfold: 0.681 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.790 Pknots: 0.740 Sensitivity RNAfold: 0.796 Pknots: 0.763 Positive Predictive Value RNAfold: 0.792 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.822 RNASampler(seed): 0.765 Sensitivity RNAfold: 0.849 RNASampler(seed): 0.687 Positive Predictive Value RNAfold: 0.801 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.687 Mastr(20): 0.636 Sensitivity RNAfold: 0.701 Mastr(20): 0.483 Positive Predictive Value RNAfold: 0.678 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.683 RSpredict(20): 0.663 Sensitivity RNAfold: 0.699 RSpredict(20): 0.593 Positive Predictive Value RNAfold: 0.674 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.43482349379e-06	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.817 Alterna: 0.767 Sensitivity RNAfold: 0.820 Alterna: 0.777 Positive Predictive Value RNAfold: 0.824 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.719 RNASLOpt: 0.679 Sensitivity RNAfold: 0.719 RNASLOpt: 0.649 Positive Predictive Value RNAfold: 0.729 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.654 Multilign(20): 0.612 Sensitivity RNAfold: 0.651 Multilign(20): 0.581 Positive Predictive Value RNAfold: 0.668 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.09606974296e-09	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.758 Vsfold4: 0.650 Sensitivity RNAfold: 0.776 Vsfold4: 0.640 Positive Predictive Value RNAfold: 0.748 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.805 MCFold: 0.678 Sensitivity RNAfold: 0.814 MCFold: 0.717 Positive Predictive Value RNAfold: 0.805 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.726 RNAwolf: 0.594 Sensitivity RNAfold: 0.731 RNAwolf: 0.584 Positive Predictive Value RNAfold: 0.732 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.786 Murlet(seed): 0.620 Sensitivity RNAfold: 0.790 Murlet(seed): 0.442 Positive Predictive Value RNAfold: 0.788 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.757 Vsfold5: 0.612 Sensitivity RNAfold: 0.775 Vsfold5: 0.613 Positive Predictive Value RNAfold: 0.747 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.704 RSpredict(seed): 0.372 Sensitivity RNAfold: 0.730 RSpredict(seed): 0.222 Positive Predictive Value RNAfold: 0.685 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.813 RDfolder: 0.682 Sensitivity RNAfold: 0.813 RDfolder: 0.643 Positive Predictive Value RNAfold: 0.823 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.679 PPfold(seed): 0.122 Sensitivity RNAfold: 0.671 PPfold(seed): 0.029 Positive Predictive Value RNAfold: 0.697 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.706 Mastr(seed): 0.306 Sensitivity RNAfold: 0.731 Mastr(seed): 0.105 Positive Predictive Value RNAfold: 0.688 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAfold vs Multilign(seed) Matthews Correlation Coefficient RNAfold: 0.770 Multilign(seed): 0.683 Sensitivity RNAfold: 0.746 Multilign(seed): 0.636 Positive Predictive Value RNAfold: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAfold: 0.620 Sensitivity PETfold_pre2.0(seed): 0.772 RNAfold: 0.620 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAfold: 0.631 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.733 RNAfold: 0.705 Sensitivity TurboFold(20): 0.694 RNAfold: 0.704 Positive Predictive Value TurboFold(20): 0.781 RNAfold: 0.714 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: N/A CMfinder(20): N/A Sensitivity RNAfold: N/A CMfinder(20): N/A Positive Predictive Value RNAfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAfold: 0.591 Sensitivity PETfold_pre2.0(20): 0.707 RNAfold: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.690 TurboFold(seed): 0.650 Sensitivity RNAfold: 0.688 TurboFold(seed): 0.624 Positive Predictive Value RNAfold: 0.701 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.780 RNAfold: 0.705 Sensitivity PPfold(20): 0.714 RNAfold: 0.704 Positive Predictive Value PPfold(20): 0.860 RNAfold: 0.714 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.741 NanoFolder: 0.562 Sensitivity RNAfold: 0.749 NanoFolder: 0.656 Positive Predictive Value RNAfold: 0.741 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.785 Carnac(seed): 0.299 Sensitivity RNAfold: 0.791 Carnac(seed): 0.090 Positive Predictive Value RNAfold: 0.785 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	26 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.740 ProbKnot: 0.657 Sensitivity MXScarna(seed): 0.699 ProbKnot: 0.701 Positive Predictive Value MXScarna(seed): 0.788 ProbKnot: 0.622 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.787 ProbKnot: 0.686 Sensitivity CentroidAlifold(20): 0.674 ProbKnot: 0.713 Positive Predictive Value CentroidAlifold(20): 0.922 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	74 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.768 ProbKnot: 0.741 Sensitivity CentroidFold: 0.763 ProbKnot: 0.774 Positive Predictive Value CentroidFold: 0.777 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.741 ProbKnot: 0.686 Sensitivity RNAalifold(20): 0.639 ProbKnot: 0.713 Positive Predictive Value RNAalifold(20): 0.863 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	74 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.761 ProbKnot: 0.741 Sensitivity Sfold: 0.756 ProbKnot: 0.774 Positive Predictive Value Sfold: 0.772 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 Fold vs ProbKnot Matthews Correlation Coefficient Fold: 0.758 ProbKnot: 0.741 Sensitivity Fold: 0.779 ProbKnot: 0.774 Positive Predictive Value Fold: 0.743 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 4.48494289621e-08	18 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.730 ProbKnot: 0.686 Sensitivity RNASampler(20): 0.624 ProbKnot: 0.713 Positive Predictive Value RNASampler(20): 0.858 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.87872347734e-08	18 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.738 ProbKnot: 0.686 Sensitivity MXScarna(20): 0.700 ProbKnot: 0.713 Positive Predictive Value MXScarna(20): 0.784 ProbKnot: 0.665 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	44 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 ProbKnot: 0.708 Sensitivity CentroidHomfold‑LAST: 0.691 ProbKnot: 0.733 Positive Predictive Value CentroidHomfold‑LAST: 0.893 ProbKnot: 0.696 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.752 ProbKnot: 0.741 Sensitivity HotKnots: 0.781 ProbKnot: 0.774 Positive Predictive Value HotKnots: 0.729 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 4.48494289621e-08	74 UNAFold vs ProbKnot Matthews Correlation Coefficient UNAFold: 0.745 ProbKnot: 0.741 Sensitivity UNAFold: 0.763 ProbKnot: 0.774 Positive Predictive Value UNAFold: 0.732 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.83595875043e-07	74 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.753 ProbKnot: 0.741 Sensitivity Contrafold: 0.771 ProbKnot: 0.774 Positive Predictive Value Contrafold: 0.741 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.85233844192e-08	38 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.782 ProbKnot: 0.701 Sensitivity IPknot: 0.752 ProbKnot: 0.724 Positive Predictive Value IPknot: 0.820 ProbKnot: 0.691 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.816 ProbKnot: 0.696 Sensitivity ContextFold: 0.780 ProbKnot: 0.717 Positive Predictive Value ContextFold: 0.861 ProbKnot: 0.686 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 RNAshapes vs ProbKnot Matthews Correlation Coefficient RNAshapes: 0.748 ProbKnot: 0.741 Sensitivity RNAshapes: 0.765 ProbKnot: 0.774 Positive Predictive Value RNAshapes: 0.738 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 2.54546175831e-06	74 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.747 ProbKnot: 0.741 Sensitivity MaxExpect: 0.765 ProbKnot: 0.774 Positive Predictive Value MaxExpect: 0.735 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 PknotsRG vs ProbKnot Matthews Correlation Coefficient PknotsRG: 0.746 ProbKnot: 0.741 Sensitivity PknotsRG: 0.775 ProbKnot: 0.774 Positive Predictive Value PknotsRG: 0.724 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.37177523642e-07	74 RNAfold vs ProbKnot Matthews Correlation Coefficient RNAfold: 0.744 ProbKnot: 0.741 Sensitivity RNAfold: 0.767 ProbKnot: 0.774 Positive Predictive Value RNAfold: 0.727 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 0.0466667757771		+ ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.686 Murlet(20): 0.675 Sensitivity ProbKnot: 0.713 Murlet(20): 0.562 Positive Predictive Value ProbKnot: 0.665 Murlet(20): 0.816 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.60582114976e-08	- CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 ProbKnot: 0.657 Sensitivity CentroidAlifold(seed): 0.546 ProbKnot: 0.701 Positive Predictive Value CentroidAlifold(seed): 0.885 ProbKnot: 0.622 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.36778461742e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.737 Afold: 0.725 Sensitivity ProbKnot: 0.774 Afold: 0.761 Positive Predictive Value ProbKnot: 0.708 Afold: 0.697 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 2.28033735003e-07	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.741 RNAsubopt: 0.736 Sensitivity ProbKnot: 0.774 RNAsubopt: 0.759 Positive Predictive Value ProbKnot: 0.715 RNAsubopt: 0.721 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.14023792096e-06	+ ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.686 Carnac(20): 0.647 Sensitivity ProbKnot: 0.713 Carnac(20): 0.457 Positive Predictive Value ProbKnot: 0.665 Carnac(20): 0.922 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.781 Cylofold: 0.738 Sensitivity ProbKnot: 0.804 Cylofold: 0.722 Positive Predictive Value ProbKnot: 0.767 Cylofold: 0.764 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.738 McQFold: 0.720 Sensitivity ProbKnot: 0.772 McQFold: 0.728 Positive Predictive Value ProbKnot: 0.712 McQFold: 0.719 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 1.02208072244e-07	- CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.683 ProbKnot: 0.667 Sensitivity CRWrnafold: 0.690 ProbKnot: 0.692 Positive Predictive Value CRWrnafold: 0.689 ProbKnot: 0.654 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.97386617324e-07	= ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.591 RNAalifold(seed): 0.586 Sensitivity ProbKnot: 0.635 RNAalifold(seed): 0.421 Positive Predictive Value ProbKnot: 0.556 RNAalifold(seed): 0.821 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.0153885189249	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.781 Pknots: 0.745 Sensitivity ProbKnot: 0.805 Pknots: 0.764 Positive Predictive Value ProbKnot: 0.765 Pknots: 0.737 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.640 ProbKnot: 0.621 Sensitivity RNASampler(seed): 0.551 ProbKnot: 0.680 Positive Predictive Value RNASampler(seed): 0.754 ProbKnot: 0.576 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.686 Mastr(20): 0.582 Sensitivity ProbKnot: 0.713 Mastr(20): 0.407 Positive Predictive Value ProbKnot: 0.665 Mastr(20): 0.840 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.686 RSpredict(20): 0.619 Sensitivity ProbKnot: 0.713 RSpredict(20): 0.547 Positive Predictive Value ProbKnot: 0.665 RSpredict(20): 0.707 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.819 Alterna: 0.781 Sensitivity ProbKnot: 0.847 Alterna: 0.798 Positive Predictive Value ProbKnot: 0.801 Alterna: 0.776 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.696 RNASLOpt: 0.679 Sensitivity ProbKnot: 0.717 RNASLOpt: 0.649 Positive Predictive Value ProbKnot: 0.686 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.02208072244e-07	+ ProbKnot vs Multilign(20) Matthews Correlation Coefficient ProbKnot: 0.621 Multilign(20): 0.612 Sensitivity ProbKnot: 0.643 Multilign(20): 0.581 Positive Predictive Value ProbKnot: 0.610 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.61569565073e-07	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.741 Vsfold4: 0.623 Sensitivity ProbKnot: 0.774 Vsfold4: 0.617 Positive Predictive Value ProbKnot: 0.715 Vsfold4: 0.638 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.782 MCFold: 0.681 Sensitivity ProbKnot: 0.809 MCFold: 0.714 Positive Predictive Value ProbKnot: 0.764 MCFold: 0.661 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.701 RNAwolf: 0.594 Sensitivity ProbKnot: 0.724 RNAwolf: 0.584 Positive Predictive Value ProbKnot: 0.691 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.639 Murlet(seed): 0.573 Sensitivity ProbKnot: 0.668 Murlet(seed): 0.384 Positive Predictive Value ProbKnot: 0.622 Murlet(seed): 0.866 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.739 Vsfold5: 0.589 Sensitivity ProbKnot: 0.773 Vsfold5: 0.592 Positive Predictive Value ProbKnot: 0.713 Vsfold5: 0.595 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.657 RSpredict(seed): 0.267 Sensitivity ProbKnot: 0.701 RSpredict(seed): 0.145 Positive Predictive Value ProbKnot: 0.622 RSpredict(seed): 0.502 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.804 RDfolder: 0.684 Sensitivity ProbKnot: 0.826 RDfolder: 0.650 Positive Predictive Value ProbKnot: 0.793 RDfolder: 0.738 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.604 PPfold(seed): 0.122 Sensitivity ProbKnot: 0.634 PPfold(seed): 0.029 Positive Predictive Value ProbKnot: 0.588 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.24019667966e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.657 Mastr(seed): 0.252 Sensitivity ProbKnot: 0.701 Mastr(seed): 0.064 Positive Predictive Value ProbKnot: 0.622 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	? ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.683 ProbKnot: 0.641 Sensitivity Multilign(seed): 0.636 ProbKnot: 0.636 Positive Predictive Value Multilign(seed): 0.750 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 ProbKnot: 0.544 Sensitivity PETfold_pre2.0(seed): 0.772 ProbKnot: 0.579 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ProbKnot: 0.524 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.733 ProbKnot: 0.681 Sensitivity TurboFold(20): 0.694 ProbKnot: 0.709 Positive Predictive Value TurboFold(20): 0.781 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(20): N/A Sensitivity ProbKnot: N/A CMfinder(20): N/A Positive Predictive Value ProbKnot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 ProbKnot: 0.592 Sensitivity PETfold_pre2.0(20): 0.707 ProbKnot: 0.629 Positive Predictive Value PETfold_pre2.0(20): 0.796 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.650 ProbKnot: 0.618 Sensitivity TurboFold(seed): 0.624 ProbKnot: 0.639 Positive Predictive Value TurboFold(seed): 0.688 ProbKnot: 0.609 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.780 ProbKnot: 0.681 Sensitivity PPfold(20): 0.714 ProbKnot: 0.709 Positive Predictive Value PPfold(20): 0.860 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.694 NanoFolder: 0.562 Sensitivity ProbKnot: 0.722 NanoFolder: 0.656 Positive Predictive Value ProbKnot: 0.677 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.694 Carnac(seed): 0.214 Sensitivity ProbKnot: 0.719 Carnac(seed): 0.047 Positive Predictive Value ProbKnot: 0.677 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08
Murlet(20)	27 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 Murlet(20): 0.698 Sensitivity MXScarna(seed): 0.743 Murlet(20): 0.590 Positive Predictive Value MXScarna(seed): 0.829 Murlet(20): 0.832 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Murlet(20): 0.698 Sensitivity CentroidAlifold(20): 0.716 Murlet(20): 0.591 Positive Predictive Value CentroidAlifold(20): 0.921 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.708 Murlet(20): 0.698 Sensitivity CentroidFold: 0.697 Murlet(20): 0.591 Positive Predictive Value CentroidFold: 0.724 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.000493106477465	28 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 Murlet(20): 0.704 Sensitivity RNAalifold(20): 0.690 Murlet(20): 0.596 Positive Predictive Value RNAalifold(20): 0.889 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 Sfold vs Murlet(20) Matthews Correlation Coefficient Sfold: 0.712 Murlet(20): 0.704 Sensitivity Sfold: 0.689 Murlet(20): 0.596 Positive Predictive Value Sfold: 0.742 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000332141622515	18 Fold vs Murlet(20) Matthews Correlation Coefficient Fold: 0.720 Murlet(20): 0.675 Sensitivity Fold: 0.735 Murlet(20): 0.562 Positive Predictive Value Fold: 0.710 Murlet(20): 0.816 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.1413769576e-08	28 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.765 Murlet(20): 0.704 Sensitivity RNASampler(20): 0.671 Murlet(20): 0.596 Positive Predictive Value RNASampler(20): 0.875 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.761 Murlet(20): 0.704 Sensitivity MXScarna(20): 0.727 Murlet(20): 0.596 Positive Predictive Value MXScarna(20): 0.800 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Murlet(20): 0.677 Sensitivity CentroidHomfold‑LAST: 0.723 Murlet(20): 0.602 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	28 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.704 HotKnots: 0.697 Sensitivity Murlet(20): 0.596 HotKnots: 0.718 Positive Predictive Value Murlet(20): 0.837 HotKnots: 0.682 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000287947293659	28 UNAFold vs Murlet(20) Matthews Correlation Coefficient UNAFold: 0.711 Murlet(20): 0.704 Sensitivity UNAFold: 0.716 Murlet(20): 0.596 Positive Predictive Value UNAFold: 0.711 Murlet(20): 0.837 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.4733335145e-06	28 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.704 Contrafold: 0.656 Sensitivity Murlet(20): 0.596 Contrafold: 0.675 Positive Predictive Value Murlet(20): 0.837 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 Murlet(20) vs IPknot Matthews Correlation Coefficient Murlet(20): 0.693 IPknot: 0.684 Sensitivity Murlet(20): 0.612 IPknot: 0.654 Positive Predictive Value Murlet(20): 0.793 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.698 Murlet(20): 0.594 Sensitivity ContextFold: 0.638 Murlet(20): 0.500 Positive Predictive Value ContextFold: 0.771 Murlet(20): 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	28 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.704 RNAshapes: 0.699 Sensitivity Murlet(20): 0.596 RNAshapes: 0.704 Positive Predictive Value Murlet(20): 0.837 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0017098773264	26 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.700 Murlet(20): 0.698 Sensitivity MaxExpect: 0.710 Murlet(20): 0.591 Positive Predictive Value MaxExpect: 0.696 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.605451749002	28 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.704 PknotsRG: 0.699 Sensitivity Murlet(20): 0.596 PknotsRG: 0.719 Positive Predictive Value Murlet(20): 0.837 PknotsRG: 0.684 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000195172284771	28 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.704 RNAfold: 0.687 Sensitivity Murlet(20): 0.596 RNAfold: 0.701 Positive Predictive Value Murlet(20): 0.837 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.51337059456e-07	18 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.686 Murlet(20): 0.675 Sensitivity ProbKnot: 0.713 Murlet(20): 0.562 Positive Predictive Value ProbKnot: 0.665 Murlet(20): 0.816 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 6.60582114976e-08		- CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Murlet(20): 0.698 Sensitivity CentroidAlifold(seed): 0.580 Murlet(20): 0.591 Positive Predictive Value CentroidAlifold(seed): 0.918 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.660 Afold: 0.627 Sensitivity Murlet(20): 0.551 Afold: 0.650 Positive Predictive Value Murlet(20): 0.795 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.58591186215e-08	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.704 RNAsubopt: 0.663 Sensitivity Murlet(20): 0.596 RNAsubopt: 0.686 Positive Predictive Value Murlet(20): 0.837 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.704 Carnac(20): 0.696 Sensitivity Murlet(20): 0.596 Carnac(20): 0.518 Positive Predictive Value Murlet(20): 0.837 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.14354614608e-05	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.757 Cylofold: 0.703 Sensitivity Murlet(20): 0.653 Cylofold: 0.703 Positive Predictive Value Murlet(20): 0.885 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.704 McQFold: 0.625 Sensitivity Murlet(20): 0.596 McQFold: 0.638 Positive Predictive Value Murlet(20): 0.837 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.677 CRWrnafold: 0.668 Sensitivity Murlet(20): 0.604 CRWrnafold: 0.683 Positive Predictive Value Murlet(20): 0.767 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	- RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 Murlet(20): 0.627 Sensitivity RNAalifold(seed): 0.492 Murlet(20): 0.498 Positive Predictive Value RNAalifold(seed): 0.925 Murlet(20): 0.795 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.735 Pknots: 0.639 Sensitivity Murlet(20): 0.636 Pknots: 0.683 Positive Predictive Value Murlet(20): 0.855 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 Murlet(20): 0.613 Sensitivity RNASampler(seed): 0.658 Murlet(20): 0.570 Positive Predictive Value RNASampler(seed): 0.782 Murlet(20): 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.704 Mastr(20): 0.636 Sensitivity Murlet(20): 0.596 Mastr(20): 0.483 Positive Predictive Value Murlet(20): 0.837 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.698 RSpredict(20): 0.663 Sensitivity Murlet(20): 0.590 RSpredict(20): 0.593 Positive Predictive Value Murlet(20): 0.832 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.780 Alterna: 0.671 Sensitivity Murlet(20): 0.695 Alterna: 0.680 Positive Predictive Value Murlet(20): 0.882 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	? Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.594 RNASLOpt: 0.560 Sensitivity Murlet(20): 0.500 RNASLOpt: 0.543 Positive Predictive Value Murlet(20): 0.716 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.647 Multilign(20): 0.612 Sensitivity Murlet(20): 0.544 Multilign(20): 0.581 Positive Predictive Value Murlet(20): 0.780 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.37002943053e-07	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.704 Vsfold4: 0.531 Sensitivity Murlet(20): 0.596 Vsfold4: 0.528 Positive Predictive Value Murlet(20): 0.837 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.727 MCFold: 0.520 Sensitivity Murlet(20): 0.637 MCFold: 0.579 Positive Predictive Value Murlet(20): 0.837 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.693 RNAwolf: 0.453 Sensitivity Murlet(20): 0.612 RNAwolf: 0.447 Positive Predictive Value Murlet(20): 0.793 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.661 Murlet(seed): 0.587 Sensitivity Murlet(20): 0.538 Murlet(seed): 0.377 Positive Predictive Value Murlet(20): 0.819 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.704 Vsfold5: 0.484 Sensitivity Murlet(20): 0.596 Vsfold5: 0.488 Positive Predictive Value Murlet(20): 0.837 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.698 RSpredict(seed): 0.298 Sensitivity Murlet(20): 0.590 RSpredict(seed): 0.156 Positive Predictive Value Murlet(20): 0.832 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.768 RDfolder: 0.624 Sensitivity Murlet(20): 0.664 RDfolder: 0.591 Positive Predictive Value Murlet(20): 0.898 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	? Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.693 PPfold(seed): 0.031 Sensitivity Murlet(20): 0.612 PPfold(seed): 0.005 Positive Predictive Value Murlet(20): 0.793 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.704 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.596 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.837 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-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	? Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Murlet(20): 0.775 Sensitivity Multilign(seed): 0.750 Murlet(20): 0.710 Positive Predictive Value Multilign(seed): 0.852 Murlet(20): 0.855 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Murlet(20): 0.594 Sensitivity PETfold_pre2.0(seed): 0.784 Murlet(20): 0.500 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Murlet(20): 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Murlet(20): 0.677 Sensitivity TurboFold(20): 0.694 Murlet(20): 0.602 Positive Predictive Value TurboFold(20): 0.781 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(20): N/A Sensitivity Murlet(20): N/A CMfinder(20): N/A Positive Predictive Value Murlet(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Murlet(20): 0.594 Sensitivity PETfold_pre2.0(20): 0.707 Murlet(20): 0.500 Positive Predictive Value PETfold_pre2.0(20): 0.796 Murlet(20): 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Murlet(20): 0.652 Sensitivity TurboFold(seed): 0.684 Murlet(20): 0.572 Positive Predictive Value TurboFold(seed): 0.749 Murlet(20): 0.754 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.780 Murlet(20): 0.677 Sensitivity PPfold(20): 0.714 Murlet(20): 0.602 Positive Predictive Value PPfold(20): 0.860 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.609 NanoFolder: 0.389 Sensitivity Murlet(20): 0.535 NanoFolder: 0.475 Positive Predictive Value Murlet(20): 0.701 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.707 Carnac(seed): 0.231 Sensitivity Murlet(20): 0.595 Carnac(seed): 0.054 Positive Predictive Value Murlet(20): 0.847 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08
CentroidAlifold(seed)	43 MXScarna(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.774 CentroidAlifold(seed): 0.690 Sensitivity MXScarna(seed): 0.733 CentroidAlifold(seed): 0.552 Positive Predictive Value MXScarna(seed): 0.822 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 CentroidAlifold(seed): 0.728 Sensitivity CentroidAlifold(20): 0.716 CentroidAlifold(seed): 0.580 Positive Predictive Value CentroidAlifold(20): 0.921 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	43 CentroidFold vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidFold: 0.724 CentroidAlifold(seed): 0.690 Sensitivity CentroidFold: 0.727 CentroidAlifold(seed): 0.552 Positive Predictive Value CentroidFold: 0.726 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 RNAalifold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.777 CentroidAlifold(seed): 0.728 Sensitivity RNAalifold(20): 0.686 CentroidAlifold(seed): 0.580 Positive Predictive Value RNAalifold(20): 0.884 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	43 Sfold vs CentroidAlifold(seed) Matthews Correlation Coefficient Sfold: 0.706 CentroidAlifold(seed): 0.690 Sensitivity Sfold: 0.698 CentroidAlifold(seed): 0.552 Positive Predictive Value Sfold: 0.719 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.75828119249e-07	31 Fold vs CentroidAlifold(seed) Matthews Correlation Coefficient Fold: 0.722 CentroidAlifold(seed): 0.684 Sensitivity Fold: 0.750 CentroidAlifold(seed): 0.548 Positive Predictive Value Fold: 0.700 CentroidAlifold(seed): 0.859 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 RNASampler(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.762 CentroidAlifold(seed): 0.728 Sensitivity RNASampler(20): 0.671 CentroidAlifold(seed): 0.580 Positive Predictive Value RNASampler(20): 0.870 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 MXScarna(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.756 CentroidAlifold(seed): 0.728 Sensitivity MXScarna(20): 0.722 CentroidAlifold(seed): 0.580 Positive Predictive Value MXScarna(20): 0.797 CentroidAlifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 CentroidAlifold(seed): 0.676 Sensitivity CentroidHomfold‑LAST: 0.690 CentroidAlifold(seed): 0.494 Positive Predictive Value CentroidHomfold‑LAST: 0.829 CentroidAlifold(seed): 0.935 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.02533530638e-08	43 HotKnots vs CentroidAlifold(seed) Matthews Correlation Coefficient HotKnots: 0.698 CentroidAlifold(seed): 0.690 Sensitivity HotKnots: 0.729 CentroidAlifold(seed): 0.552 Positive Predictive Value HotKnots: 0.674 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.000741474702242	43 UNAFold vs CentroidAlifold(seed) Matthews Correlation Coefficient UNAFold: 0.697 CentroidAlifold(seed): 0.690 Sensitivity UNAFold: 0.718 CentroidAlifold(seed): 0.552 Positive Predictive Value UNAFold: 0.682 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.128796078713	43 Contrafold vs CentroidAlifold(seed) Matthews Correlation Coefficient Contrafold: 0.696 CentroidAlifold(seed): 0.690 Sensitivity Contrafold: 0.724 CentroidAlifold(seed): 0.552 Positive Predictive Value Contrafold: 0.674 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.726733689455	11 IPknot vs CentroidAlifold(seed) Matthews Correlation Coefficient IPknot: 0.701 CentroidAlifold(seed): 0.694 Sensitivity IPknot: 0.658 CentroidAlifold(seed): 0.494 Positive Predictive Value IPknot: 0.755 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 0.811904790494	8 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.732 CentroidAlifold(seed): 0.646 Sensitivity ContextFold: 0.673 CentroidAlifold(seed): 0.427 Positive Predictive Value ContextFold: 0.804 CentroidAlifold(seed): 0.986 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	43 RNAshapes vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAshapes: 0.697 CentroidAlifold(seed): 0.690 Sensitivity RNAshapes: 0.717 CentroidAlifold(seed): 0.552 Positive Predictive Value RNAshapes: 0.682 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.122165152257	40 MaxExpect vs CentroidAlifold(seed) Matthews Correlation Coefficient MaxExpect: 0.703 CentroidAlifold(seed): 0.690 Sensitivity MaxExpect: 0.725 CentroidAlifold(seed): 0.556 Positive Predictive Value MaxExpect: 0.687 CentroidAlifold(seed): 0.863 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 0.000108348164592	43 PknotsRG vs CentroidAlifold(seed) Matthews Correlation Coefficient PknotsRG: 0.700 CentroidAlifold(seed): 0.690 Sensitivity PknotsRG: 0.729 CentroidAlifold(seed): 0.552 Positive Predictive Value PknotsRG: 0.678 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 1.49438993542e-06	43 RNAfold vs CentroidAlifold(seed) Matthews Correlation Coefficient RNAfold: 0.702 CentroidAlifold(seed): 0.690 Sensitivity RNAfold: 0.727 CentroidAlifold(seed): 0.552 Positive Predictive Value RNAfold: 0.683 CentroidAlifold(seed): 0.870 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 0.00284536525437	26 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 ProbKnot: 0.657 Sensitivity CentroidAlifold(seed): 0.546 ProbKnot: 0.701 Positive Predictive Value CentroidAlifold(seed): 0.885 ProbKnot: 0.622 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.36778461742e-08	26 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Murlet(20): 0.698 Sensitivity CentroidAlifold(seed): 0.580 Murlet(20): 0.591 Positive Predictive Value CentroidAlifold(seed): 0.918 Murlet(20): 0.831 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08		+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.671 Afold: 0.653 Sensitivity CentroidAlifold(seed): 0.541 Afold: 0.689 Positive Predictive Value CentroidAlifold(seed): 0.837 Afold: 0.624 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 1.69864039739e-05	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 RNAsubopt: 0.661 Sensitivity CentroidAlifold(seed): 0.552 RNAsubopt: 0.690 Positive Predictive Value CentroidAlifold(seed): 0.870 RNAsubopt: 0.640 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Carnac(20): 0.694 Sensitivity CentroidAlifold(seed): 0.580 Carnac(20): 0.516 Positive Predictive Value CentroidAlifold(seed): 0.918 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.54865340847e-08	= CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.734 Cylofold: 0.732 Sensitivity CentroidAlifold(seed): 0.575 Cylofold: 0.726 Positive Predictive Value CentroidAlifold(seed): 0.943 Cylofold: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.011312336181	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 McQFold: 0.652 Sensitivity CentroidAlifold(seed): 0.552 McQFold: 0.668 Positive Predictive Value CentroidAlifold(seed): 0.870 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.678 CRWrnafold: 0.647 Sensitivity CentroidAlifold(seed): 0.473 CRWrnafold: 0.655 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.740 RNAalifold(seed): 0.677 Sensitivity CentroidAlifold(seed): 0.648 RNAalifold(seed): 0.528 Positive Predictive Value CentroidAlifold(seed): 0.848 RNAalifold(seed): 0.873 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	= Pknots vs CentroidAlifold(seed) Matthews Correlation Coefficient Pknots: 0.717 CentroidAlifold(seed): 0.711 Sensitivity Pknots: 0.748 CentroidAlifold(seed): 0.564 Positive Predictive Value Pknots: 0.695 CentroidAlifold(seed): 0.904 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.103865234064	= RNASampler(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.757 CentroidAlifold(seed): 0.752 Sensitivity RNASampler(seed): 0.678 CentroidAlifold(seed): 0.678 Positive Predictive Value RNASampler(seed): 0.853 CentroidAlifold(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.0214507655873	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Mastr(20): 0.628 Sensitivity CentroidAlifold(seed): 0.580 Mastr(20): 0.471 Positive Predictive Value CentroidAlifold(seed): 0.918 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 RSpredict(20): 0.660 Sensitivity CentroidAlifold(seed): 0.580 RSpredict(20): 0.590 Positive Predictive Value CentroidAlifold(seed): 0.918 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	- Alterna vs CentroidAlifold(seed) Matthews Correlation Coefficient Alterna: 0.753 CentroidAlifold(seed): 0.673 Sensitivity Alterna: 0.761 CentroidAlifold(seed): 0.531 Positive Predictive Value Alterna: 0.756 CentroidAlifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.646 RNASLOpt: 0.560 Sensitivity CentroidAlifold(seed): 0.427 RNASLOpt: 0.526 Positive Predictive Value CentroidAlifold(seed): 0.986 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.745 Multilign(20): 0.612 Sensitivity CentroidAlifold(seed): 0.602 Multilign(20): 0.581 Positive Predictive Value CentroidAlifold(seed): 0.929 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Vsfold4: 0.592 Sensitivity CentroidAlifold(seed): 0.552 Vsfold4: 0.591 Positive Predictive Value CentroidAlifold(seed): 0.870 Vsfold4: 0.600 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.711 MCFold: 0.597 Sensitivity CentroidAlifold(seed): 0.569 MCFold: 0.646 Positive Predictive Value CentroidAlifold(seed): 0.896 MCFold: 0.564 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 RNAwolf: 0.499 Sensitivity CentroidAlifold(seed): 0.494 RNAwolf: 0.490 Positive Predictive Value CentroidAlifold(seed): 0.984 RNAwolf: 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.47941000302e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.791 Murlet(seed): 0.621 Sensitivity CentroidAlifold(seed): 0.710 Murlet(seed): 0.445 Positive Predictive Value CentroidAlifold(seed): 0.886 Murlet(seed): 0.878 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Vsfold5: 0.567 Sensitivity CentroidAlifold(seed): 0.552 Vsfold5: 0.572 Positive Predictive Value CentroidAlifold(seed): 0.870 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 RSpredict(seed): 0.365 Sensitivity CentroidAlifold(seed): 0.552 RSpredict(seed): 0.216 Positive Predictive Value CentroidAlifold(seed): 0.870 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 RDfolder: 0.630 Sensitivity CentroidAlifold(seed): 0.551 RDfolder: 0.597 Positive Predictive Value CentroidAlifold(seed): 0.877 RDfolder: 0.681 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 PPfold(seed): 0.122 Sensitivity CentroidAlifold(seed): 0.494 PPfold(seed): 0.029 Positive Predictive Value CentroidAlifold(seed): 0.984 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Mastr(seed): 0.311 Sensitivity CentroidAlifold(seed): 0.552 Mastr(seed): 0.109 Positive Predictive Value CentroidAlifold(seed): 0.870 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(seed): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.747 Multilign(seed): 0.683 Sensitivity CentroidAlifold(seed): 0.627 Multilign(seed): 0.636 Positive Predictive Value CentroidAlifold(seed): 0.902 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 CentroidAlifold(seed): 0.646 Sensitivity PETfold_pre2.0(seed): 0.772 CentroidAlifold(seed): 0.427 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidAlifold(seed): 0.986 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 CentroidAlifold(seed): 0.730 Sensitivity TurboFold(20): 0.694 CentroidAlifold(seed): 0.578 Positive Predictive Value TurboFold(20): 0.781 CentroidAlifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CentroidAlifold(seed): 0.729 Sensitivity PETfold_pre2.0(20): 0.707 CentroidAlifold(seed): 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.715 TurboFold(seed): 0.650 Sensitivity CentroidAlifold(seed): 0.556 TurboFold(seed): 0.624 Positive Predictive Value CentroidAlifold(seed): 0.927 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.780 CentroidAlifold(seed): 0.730 Sensitivity PPfold(20): 0.714 CentroidAlifold(seed): 0.578 Positive Predictive Value PPfold(20): 0.860 CentroidAlifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.638 NanoFolder: 0.412 Sensitivity CentroidAlifold(seed): 0.417 NanoFolder: 0.506 Positive Predictive Value CentroidAlifold(seed): 0.985 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.772 Carnac(seed): 0.276 Sensitivity CentroidAlifold(seed): 0.670 Carnac(seed): 0.077 Positive Predictive Value CentroidAlifold(seed): 0.895 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08
Afold	32 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.758 Afold: 0.657 Sensitivity MXScarna(seed): 0.709 Afold: 0.693 Positive Predictive Value MXScarna(seed): 0.815 Afold: 0.629 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.764 Afold: 0.614 Sensitivity CentroidAlifold(20): 0.657 Afold: 0.640 Positive Predictive Value CentroidAlifold(20): 0.891 Afold: 0.596 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	80 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.700 Afold: 0.600 Sensitivity CentroidFold: 0.699 Afold: 0.648 Positive Predictive Value CentroidFold: 0.702 Afold: 0.556 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.731 Afold: 0.627 Sensitivity RNAalifold(20): 0.632 Afold: 0.650 Positive Predictive Value RNAalifold(20): 0.850 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.10499527239e-08	95 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.618 Afold: 0.590 Sensitivity Sfold: 0.618 Afold: 0.630 Positive Predictive Value Sfold: 0.618 Afold: 0.553 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 Fold vs Afold Matthews Correlation Coefficient Fold: 0.779 Afold: 0.751 Sensitivity Fold: 0.805 Afold: 0.784 Positive Predictive Value Fold: 0.758 Afold: 0.726 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.724 Afold: 0.627 Sensitivity RNASampler(20): 0.632 Afold: 0.650 Positive Predictive Value RNASampler(20): 0.834 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	19 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.738 Afold: 0.627 Sensitivity MXScarna(20): 0.706 Afold: 0.650 Positive Predictive Value MXScarna(20): 0.776 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.36130997681e-08	25 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.776 Afold: 0.754 Sensitivity CentroidHomfold‑LAST: 0.703 Afold: 0.779 Positive Predictive Value CentroidHomfold‑LAST: 0.864 Afold: 0.740 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.12827206146e-07	92 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.773 Afold: 0.747 Sensitivity HotKnots: 0.799 Afold: 0.774 Positive Predictive Value HotKnots: 0.754 Afold: 0.729 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	95 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.594 Afold: 0.590 Sensitivity UNAFold: 0.628 Afold: 0.630 Positive Predictive Value UNAFold: 0.562 Afold: 0.553 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.26115971074e-07	95 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.690 Afold: 0.590 Sensitivity Contrafold: 0.715 Afold: 0.630 Positive Predictive Value Contrafold: 0.666 Afold: 0.553 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.829 Afold: 0.764 Sensitivity IPknot: 0.801 Afold: 0.783 Positive Predictive Value IPknot: 0.865 Afold: 0.754 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.801 Afold: 0.764 Sensitivity ContextFold: 0.774 Afold: 0.781 Positive Predictive Value ContextFold: 0.837 Afold: 0.755 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 5.86050763602e-08	92 RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.763 Afold: 0.747 Sensitivity RNAshapes: 0.778 Afold: 0.774 Positive Predictive Value RNAshapes: 0.753 Afold: 0.729 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.85233844192e-08	73 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.721 Afold: 0.664 Sensitivity MaxExpect: 0.737 Afold: 0.690 Positive Predictive Value MaxExpect: 0.707 Afold: 0.640 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.85233844192e-08	95 Afold vs PknotsRG Matthews Correlation Coefficient Afold: 0.590 PknotsRG: 0.571 Sensitivity Afold: 0.630 PknotsRG: 0.612 Positive Predictive Value Afold: 0.553 PknotsRG: 0.533 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 3.56938820447e-08	95 Afold vs RNAfold Matthews Correlation Coefficient Afold: 0.590 RNAfold: 0.585 Sensitivity Afold: 0.630 RNAfold: 0.626 Positive Predictive Value Afold: 0.553 RNAfold: 0.547 Number of pairs reference - predicted secondary structure: 95 Wilcoxon single-rank test P-value: 5.21776328505e-08	50 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.737 Afold: 0.725 Sensitivity ProbKnot: 0.774 Afold: 0.761 Positive Predictive Value ProbKnot: 0.708 Afold: 0.697 Number of pairs reference - predicted secondary structure: 50 Wilcoxon single-rank test P-value: 2.28033735003e-07	19 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.660 Afold: 0.627 Sensitivity Murlet(20): 0.551 Afold: 0.650 Positive Predictive Value Murlet(20): 0.795 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.58591186215e-08	31 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.671 Afold: 0.653 Sensitivity CentroidAlifold(seed): 0.541 Afold: 0.689 Positive Predictive Value CentroidAlifold(seed): 0.837 Afold: 0.624 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 1.69864039739e-05		= Afold vs RNAsubopt Matthews Correlation Coefficient Afold: 0.747 RNAsubopt: 0.745 Sensitivity Afold: 0.774 RNAsubopt: 0.768 Positive Predictive Value Afold: 0.729 RNAsubopt: 0.729 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 0.0231119356319	- Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.694 Afold: 0.627 Sensitivity Carnac(20): 0.502 Afold: 0.650 Positive Predictive Value Carnac(20): 0.965 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.805 Cylofold: 0.752 Sensitivity Afold: 0.818 Cylofold: 0.731 Positive Predictive Value Afold: 0.800 Cylofold: 0.783 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.589 McQFold: 0.517 Sensitivity Afold: 0.629 McQFold: 0.484 Positive Predictive Value Afold: 0.552 McQFold: 0.553 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.728 CRWrnafold: 0.652 Sensitivity Afold: 0.756 CRWrnafold: 0.669 Positive Predictive Value Afold: 0.710 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.681 RNAalifold(seed): 0.640 Sensitivity Afold: 0.724 RNAalifold(seed): 0.490 Positive Predictive Value Afold: 0.646 RNAalifold(seed): 0.843 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Afold vs Pknots Matthews Correlation Coefficient Afold: 0.790 Pknots: 0.774 Sensitivity Afold: 0.802 Pknots: 0.800 Positive Predictive Value Afold: 0.786 Pknots: 0.757 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.822 RNASampler(seed): 0.770 Sensitivity Afold: 0.851 RNASampler(seed): 0.699 Positive Predictive Value Afold: 0.798 RNASampler(seed): 0.853 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.86595104665e-08	- Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.642 Afold: 0.627 Sensitivity Mastr(20): 0.478 Afold: 0.650 Positive Predictive Value Mastr(20): 0.868 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.61352083003e-05	- RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.672 Afold: 0.622 Sensitivity RSpredict(20): 0.626 Afold: 0.647 Positive Predictive Value RSpredict(20): 0.727 Afold: 0.604 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ Afold vs Alterna Matthews Correlation Coefficient Afold: 0.810 Alterna: 0.778 Sensitivity Afold: 0.820 Alterna: 0.785 Positive Predictive Value Afold: 0.810 Alterna: 0.782 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.764 RNASLOpt: 0.727 Sensitivity Afold: 0.781 RNASLOpt: 0.721 Positive Predictive Value Afold: 0.755 RNASLOpt: 0.743 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.69132796717e-08	? Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.576 Multilign(20): 0.474 Sensitivity Afold: 0.589 Multilign(20): 0.438 Positive Predictive Value Afold: 0.574 Multilign(20): 0.527 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.747 Vsfold4: 0.656 Sensitivity Afold: 0.774 Vsfold4: 0.647 Positive Predictive Value Afold: 0.729 Vsfold4: 0.674 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.795 MCFold: 0.716 Sensitivity Afold: 0.811 MCFold: 0.756 Positive Predictive Value Afold: 0.787 MCFold: 0.690 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.764 RNAwolf: 0.687 Sensitivity Afold: 0.783 RNAwolf: 0.668 Positive Predictive Value Afold: 0.754 RNAwolf: 0.719 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.788 Murlet(seed): 0.624 Sensitivity Afold: 0.794 Murlet(seed): 0.463 Positive Predictive Value Afold: 0.789 Murlet(seed): 0.853 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.746 Vsfold5: 0.624 Sensitivity Afold: 0.772 Vsfold5: 0.622 Positive Predictive Value Afold: 0.727 Vsfold5: 0.635 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.657 RSpredict(seed): 0.440 Sensitivity Afold: 0.693 RSpredict(seed): 0.281 Positive Predictive Value Afold: 0.629 RSpredict(seed): 0.697 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.811 RDfolder: 0.714 Sensitivity Afold: 0.821 RDfolder: 0.674 Positive Predictive Value Afold: 0.813 RDfolder: 0.772 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.590 PPfold(seed): 0.218 Sensitivity Afold: 0.610 PPfold(seed): 0.091 Positive Predictive Value Afold: 0.580 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.659 Mastr(seed): 0.358 Sensitivity Afold: 0.693 Mastr(seed): 0.144 Positive Predictive Value Afold: 0.633 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): N/A Afold: N/A Sensitivity CMfinder(seed): N/A Afold: N/A Positive Predictive Value CMfinder(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs Multilign(seed) Matthews Correlation Coefficient Afold: 0.856 Multilign(seed): 0.672 Sensitivity Afold: 0.817 Multilign(seed): 0.617 Positive Predictive Value Afold: 0.907 Multilign(seed): 0.755 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.627 Afold: 0.469 Sensitivity PETfold_pre2.0(seed): 0.547 Afold: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.725 Afold: 0.443 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.686 Afold: 0.671 Sensitivity TurboFold(20): 0.662 Afold: 0.701 Positive Predictive Value TurboFold(20): 0.718 Afold: 0.651 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: N/A CMfinder(20): N/A Sensitivity Afold: N/A CMfinder(20): N/A Positive Predictive Value Afold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.404 Afold: 0.398 Sensitivity PETfold_pre2.0(20): 0.371 Afold: 0.457 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.356 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.665 TurboFold(seed): 0.539 Sensitivity Afold: 0.684 TurboFold(seed): 0.537 Positive Predictive Value Afold: 0.657 TurboFold(seed): 0.554 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? Afold vs PPfold(20) Matthews Correlation Coefficient Afold: 0.671 PPfold(20): 0.611 Sensitivity Afold: 0.701 PPfold(20): 0.519 Positive Predictive Value Afold: 0.651 PPfold(20): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.765 NanoFolder: 0.610 Sensitivity Afold: 0.798 NanoFolder: 0.711 Positive Predictive Value Afold: 0.742 NanoFolder: 0.537 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.788 Carnac(seed): 0.352 Sensitivity Afold: 0.796 Carnac(seed): 0.126 Positive Predictive Value Afold: 0.786 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAsubopt	44 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.776 RNAsubopt: 0.664 Sensitivity MXScarna(seed): 0.736 RNAsubopt: 0.693 Positive Predictive Value MXScarna(seed): 0.824 RNAsubopt: 0.643 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RNAsubopt: 0.669 Sensitivity CentroidAlifold(20): 0.716 RNAsubopt: 0.690 Positive Predictive Value CentroidAlifold(20): 0.921 RNAsubopt: 0.654 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	104 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.780 RNAsubopt: 0.737 Sensitivity CentroidFold: 0.775 RNAsubopt: 0.758 Positive Predictive Value CentroidFold: 0.791 RNAsubopt: 0.724 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.782 RNAsubopt: 0.663 Sensitivity RNAalifold(20): 0.690 RNAsubopt: 0.686 Positive Predictive Value RNAalifold(20): 0.889 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	118 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.778 RNAsubopt: 0.738 Sensitivity Sfold: 0.768 RNAsubopt: 0.757 Positive Predictive Value Sfold: 0.793 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.777 RNAsubopt: 0.756 Sensitivity Fold: 0.796 RNAsubopt: 0.776 Positive Predictive Value Fold: 0.764 RNAsubopt: 0.742 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.765 RNAsubopt: 0.663 Sensitivity RNASampler(20): 0.671 RNAsubopt: 0.686 Positive Predictive Value RNASampler(20): 0.875 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.761 RNAsubopt: 0.663 Sensitivity MXScarna(20): 0.727 RNAsubopt: 0.686 Positive Predictive Value MXScarna(20): 0.800 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RNAsubopt: 0.709 Sensitivity CentroidHomfold‑LAST: 0.691 RNAsubopt: 0.720 Positive Predictive Value CentroidHomfold‑LAST: 0.893 RNAsubopt: 0.709 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.772 RNAsubopt: 0.738 Sensitivity HotKnots: 0.793 RNAsubopt: 0.757 Positive Predictive Value HotKnots: 0.757 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.775 RNAsubopt: 0.738 Sensitivity UNAFold: 0.786 RNAsubopt: 0.757 Positive Predictive Value UNAFold: 0.769 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.769 RNAsubopt: 0.738 Sensitivity Contrafold: 0.784 RNAsubopt: 0.757 Positive Predictive Value Contrafold: 0.761 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.782 RNAsubopt: 0.691 Sensitivity IPknot: 0.752 RNAsubopt: 0.703 Positive Predictive Value IPknot: 0.820 RNAsubopt: 0.692 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.816 RNAsubopt: 0.664 Sensitivity ContextFold: 0.780 RNAsubopt: 0.676 Positive Predictive Value ContextFold: 0.861 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs RNAsubopt Matthews Correlation Coefficient RNAshapes: 0.759 RNAsubopt: 0.738 Sensitivity RNAshapes: 0.770 RNAsubopt: 0.757 Positive Predictive Value RNAshapes: 0.755 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.754 RNAsubopt: 0.739 Sensitivity MaxExpect: 0.769 RNAsubopt: 0.759 Positive Predictive Value MaxExpect: 0.746 RNAsubopt: 0.725 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.752 RNAsubopt: 0.738 Sensitivity PknotsRG: 0.774 RNAsubopt: 0.757 Positive Predictive Value PknotsRG: 0.737 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.758 RNAsubopt: 0.738 Sensitivity RNAfold: 0.776 RNAsubopt: 0.757 Positive Predictive Value RNAfold: 0.748 RNAsubopt: 0.726 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.741 RNAsubopt: 0.736 Sensitivity ProbKnot: 0.774 RNAsubopt: 0.759 Positive Predictive Value ProbKnot: 0.715 RNAsubopt: 0.721 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 1.14023792096e-06	28 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.704 RNAsubopt: 0.663 Sensitivity Murlet(20): 0.596 RNAsubopt: 0.686 Positive Predictive Value Murlet(20): 0.837 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	43 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 RNAsubopt: 0.661 Sensitivity CentroidAlifold(seed): 0.552 RNAsubopt: 0.690 Positive Predictive Value CentroidAlifold(seed): 0.870 RNAsubopt: 0.640 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 4.1569883686e-08	92 Afold vs RNAsubopt Matthews Correlation Coefficient Afold: 0.747 RNAsubopt: 0.745 Sensitivity Afold: 0.774 RNAsubopt: 0.768 Positive Predictive Value Afold: 0.729 RNAsubopt: 0.729 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 0.0231119356319		- Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.696 RNAsubopt: 0.663 Sensitivity Carnac(20): 0.518 RNAsubopt: 0.686 Positive Predictive Value Carnac(20): 0.941 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.782 Cylofold: 0.741 Sensitivity RNAsubopt: 0.788 Cylofold: 0.724 Positive Predictive Value RNAsubopt: 0.785 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.736 McQFold: 0.718 Sensitivity RNAsubopt: 0.756 McQFold: 0.719 Positive Predictive Value RNAsubopt: 0.725 McQFold: 0.725 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.85233844192e-08	- CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.683 RNAsubopt: 0.666 Sensitivity CRWrnafold: 0.690 RNAsubopt: 0.682 Positive Predictive Value CRWrnafold: 0.689 RNAsubopt: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.676 RNAsubopt: 0.665 Sensitivity RNAalifold(seed): 0.525 RNAsubopt: 0.698 Positive Predictive Value RNAalifold(seed): 0.874 RNAsubopt: 0.639 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 6.27473311413e-06	+ RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.765 Pknots: 0.740 Sensitivity RNAsubopt: 0.775 Pknots: 0.763 Positive Predictive Value RNAsubopt: 0.764 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.765 RNAsubopt: 0.732 Sensitivity RNASampler(seed): 0.687 RNAsubopt: 0.765 Positive Predictive Value RNASampler(seed): 0.859 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.663 Mastr(20): 0.636 Sensitivity RNAsubopt: 0.686 Mastr(20): 0.483 Positive Predictive Value RNAsubopt: 0.647 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.27071136365e-07	+ RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.673 RSpredict(20): 0.663 Sensitivity RNAsubopt: 0.694 RSpredict(20): 0.593 Positive Predictive Value RNAsubopt: 0.659 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 2.71856013146e-06	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.795 Alterna: 0.767 Sensitivity RNAsubopt: 0.795 Alterna: 0.777 Positive Predictive Value RNAsubopt: 0.805 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.679 RNAsubopt: 0.664 Sensitivity RNASLOpt: 0.649 RNAsubopt: 0.676 Positive Predictive Value RNASLOpt: 0.721 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.39704516867e-06	+ RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.666 Multilign(20): 0.612 Sensitivity RNAsubopt: 0.668 Multilign(20): 0.581 Positive Predictive Value RNAsubopt: 0.674 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1568170475e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.738 Vsfold4: 0.650 Sensitivity RNAsubopt: 0.757 Vsfold4: 0.640 Positive Predictive Value RNAsubopt: 0.726 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.777 MCFold: 0.678 Sensitivity RNAsubopt: 0.787 MCFold: 0.717 Positive Predictive Value RNAsubopt: 0.775 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.691 RNAwolf: 0.594 Sensitivity RNAsubopt: 0.703 RNAwolf: 0.584 Positive Predictive Value RNAsubopt: 0.692 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.722 Murlet(seed): 0.620 Sensitivity RNAsubopt: 0.734 Murlet(seed): 0.442 Positive Predictive Value RNAsubopt: 0.719 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.737 Vsfold5: 0.612 Sensitivity RNAsubopt: 0.756 Vsfold5: 0.613 Positive Predictive Value RNAsubopt: 0.725 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.664 RSpredict(seed): 0.372 Sensitivity RNAsubopt: 0.693 RSpredict(seed): 0.222 Positive Predictive Value RNAsubopt: 0.643 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.792 RDfolder: 0.682 Sensitivity RNAsubopt: 0.790 RDfolder: 0.643 Positive Predictive Value RNAsubopt: 0.805 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.592 PPfold(seed): 0.122 Sensitivity RNAsubopt: 0.597 PPfold(seed): 0.029 Positive Predictive Value RNAsubopt: 0.599 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.53777893337e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.658 Mastr(seed): 0.306 Sensitivity RNAsubopt: 0.687 Mastr(seed): 0.105 Positive Predictive Value RNAsubopt: 0.636 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): N/A RNAsubopt: N/A Sensitivity CMfinder(seed): N/A RNAsubopt: N/A Positive Predictive Value CMfinder(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.683 RNAsubopt: 0.671 Sensitivity Multilign(seed): 0.636 RNAsubopt: 0.653 Positive Predictive Value Multilign(seed): 0.750 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAsubopt: 0.506 Sensitivity PETfold_pre2.0(seed): 0.772 RNAsubopt: 0.520 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAsubopt: 0.506 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.733 RNAsubopt: 0.694 Sensitivity TurboFold(20): 0.694 RNAsubopt: 0.699 Positive Predictive Value TurboFold(20): 0.781 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: N/A CMfinder(20): N/A Sensitivity RNAsubopt: N/A CMfinder(20): N/A Positive Predictive Value RNAsubopt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAsubopt: 0.583 Sensitivity PETfold_pre2.0(20): 0.707 RNAsubopt: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.650 RNAsubopt: 0.627 Sensitivity TurboFold(seed): 0.624 RNAsubopt: 0.629 Positive Predictive Value TurboFold(seed): 0.688 RNAsubopt: 0.635 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.780 RNAsubopt: 0.694 Sensitivity PPfold(20): 0.714 RNAsubopt: 0.699 Positive Predictive Value PPfold(20): 0.860 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.658 NanoFolder: 0.562 Sensitivity RNAsubopt: 0.677 NanoFolder: 0.656 Positive Predictive Value RNAsubopt: 0.650 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.745 Carnac(seed): 0.299 Sensitivity RNAsubopt: 0.757 Carnac(seed): 0.090 Positive Predictive Value RNAsubopt: 0.740 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08
Carnac(20)	27 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 Carnac(20): 0.695 Sensitivity MXScarna(seed): 0.743 Carnac(20): 0.518 Positive Predictive Value MXScarna(seed): 0.829 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Carnac(20): 0.694 Sensitivity CentroidAlifold(20): 0.716 Carnac(20): 0.516 Positive Predictive Value CentroidAlifold(20): 0.921 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.708 Carnac(20): 0.694 Sensitivity CentroidFold: 0.697 Carnac(20): 0.516 Positive Predictive Value CentroidFold: 0.724 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 1.43482349379e-06	28 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 Carnac(20): 0.696 Sensitivity RNAalifold(20): 0.690 Carnac(20): 0.518 Positive Predictive Value RNAalifold(20): 0.889 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.712 Carnac(20): 0.696 Sensitivity Sfold: 0.689 Carnac(20): 0.518 Positive Predictive Value Sfold: 0.742 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.83595875043e-07	18 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.720 Carnac(20): 0.647 Sensitivity Fold: 0.735 Carnac(20): 0.457 Positive Predictive Value Fold: 0.710 Carnac(20): 0.922 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.52609899389e-08	28 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.765 Carnac(20): 0.696 Sensitivity RNASampler(20): 0.671 Carnac(20): 0.518 Positive Predictive Value RNASampler(20): 0.875 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.761 Carnac(20): 0.696 Sensitivity MXScarna(20): 0.727 Carnac(20): 0.518 Positive Predictive Value MXScarna(20): 0.800 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	9 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Carnac(20): 0.632 Sensitivity CentroidHomfold‑LAST: 0.723 Carnac(20): 0.471 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	28 HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: 0.697 Carnac(20): 0.696 Sensitivity HotKnots: 0.718 Carnac(20): 0.518 Positive Predictive Value HotKnots: 0.682 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.51155202041	28 UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.711 Carnac(20): 0.696 Sensitivity UNAFold: 0.716 Carnac(20): 0.518 Positive Predictive Value UNAFold: 0.711 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 7.66564282849e-07	28 Carnac(20) vs Contrafold Matthews Correlation Coefficient Carnac(20): 0.696 Contrafold: 0.656 Sensitivity Carnac(20): 0.518 Contrafold: 0.675 Positive Predictive Value Carnac(20): 0.941 Contrafold: 0.643 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	8 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.684 Carnac(20): 0.662 Sensitivity IPknot: 0.654 Carnac(20): 0.516 Positive Predictive Value IPknot: 0.724 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.698 Carnac(20): 0.562 Sensitivity ContextFold: 0.638 Carnac(20): 0.397 Positive Predictive Value ContextFold: 0.771 Carnac(20): 0.807 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	28 RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.699 Carnac(20): 0.696 Sensitivity RNAshapes: 0.704 Carnac(20): 0.518 Positive Predictive Value RNAshapes: 0.699 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.233182913621	26 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.700 Carnac(20): 0.694 Sensitivity MaxExpect: 0.710 Carnac(20): 0.516 Positive Predictive Value MaxExpect: 0.696 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.000349666881076	28 PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.699 Carnac(20): 0.696 Sensitivity PknotsRG: 0.719 Carnac(20): 0.518 Positive Predictive Value PknotsRG: 0.684 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.00416853265544	28 Carnac(20) vs RNAfold Matthews Correlation Coefficient Carnac(20): 0.696 RNAfold: 0.687 Sensitivity Carnac(20): 0.518 RNAfold: 0.701 Positive Predictive Value Carnac(20): 0.941 RNAfold: 0.678 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 2.66698692294e-05	18 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.686 Carnac(20): 0.647 Sensitivity ProbKnot: 0.713 Carnac(20): 0.457 Positive Predictive Value ProbKnot: 0.665 Carnac(20): 0.922 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	28 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.704 Carnac(20): 0.696 Sensitivity Murlet(20): 0.596 Carnac(20): 0.518 Positive Predictive Value Murlet(20): 0.837 Carnac(20): 0.941 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 1.14354614608e-05	26 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Carnac(20): 0.694 Sensitivity CentroidAlifold(seed): 0.580 Carnac(20): 0.516 Positive Predictive Value CentroidAlifold(seed): 0.918 Carnac(20): 0.938 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.54865340847e-08	19 Carnac(20) vs Afold Matthews Correlation Coefficient Carnac(20): 0.694 Afold: 0.627 Sensitivity Carnac(20): 0.502 Afold: 0.650 Positive Predictive Value Carnac(20): 0.965 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.48055519165e-08	28 Carnac(20) vs RNAsubopt Matthews Correlation Coefficient Carnac(20): 0.696 RNAsubopt: 0.663 Sensitivity Carnac(20): 0.518 RNAsubopt: 0.686 Positive Predictive Value Carnac(20): 0.941 RNAsubopt: 0.647 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.06544643719e-08		- Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.703 Carnac(20): 0.687 Sensitivity Cylofold: 0.703 Carnac(20): 0.506 Positive Predictive Value Cylofold: 0.711 Carnac(20): 0.942 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.000351392923707	+ Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.696 McQFold: 0.625 Sensitivity Carnac(20): 0.518 McQFold: 0.638 Positive Predictive Value Carnac(20): 0.941 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Carnac(20): 0.620 Sensitivity CRWrnafold: 0.683 Carnac(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 Carnac(20): 0.828 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	- RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 Carnac(20): 0.612 Sensitivity RNAalifold(seed): 0.492 Carnac(20): 0.402 Positive Predictive Value RNAalifold(seed): 0.925 Carnac(20): 0.939 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.719 Pknots: 0.639 Sensitivity Carnac(20): 0.550 Pknots: 0.683 Positive Predictive Value Carnac(20): 0.946 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 4.98172311752e-08	? RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 Carnac(20): 0.701 Sensitivity RNASampler(seed): 0.658 Carnac(20): 0.513 Positive Predictive Value RNASampler(seed): 0.782 Carnac(20): 0.964 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.696 Mastr(20): 0.636 Sensitivity Carnac(20): 0.518 Mastr(20): 0.483 Positive Predictive Value Carnac(20): 0.941 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.695 RSpredict(20): 0.663 Sensitivity Carnac(20): 0.518 RSpredict(20): 0.593 Positive Predictive Value Carnac(20): 0.938 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.788 Alterna: 0.671 Sensitivity Carnac(20): 0.649 Alterna: 0.680 Positive Predictive Value Carnac(20): 0.966 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.27752322258e-08	? Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.562 RNASLOpt: 0.560 Sensitivity Carnac(20): 0.397 RNASLOpt: 0.543 Positive Predictive Value Carnac(20): 0.807 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.612 Carnac(20): 0.594 Sensitivity Multilign(20): 0.581 Carnac(20): 0.415 Positive Predictive Value Multilign(20): 0.657 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.000729039481942	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.696 Vsfold4: 0.531 Sensitivity Carnac(20): 0.518 Vsfold4: 0.528 Positive Predictive Value Carnac(20): 0.941 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.740 MCFold: 0.520 Sensitivity Carnac(20): 0.577 MCFold: 0.579 Positive Predictive Value Carnac(20): 0.955 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	? Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.662 RNAwolf: 0.453 Sensitivity Carnac(20): 0.516 RNAwolf: 0.447 Positive Predictive Value Carnac(20): 0.858 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.632 Murlet(seed): 0.587 Sensitivity Carnac(20): 0.424 Murlet(seed): 0.377 Positive Predictive Value Carnac(20): 0.950 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.696 Vsfold5: 0.484 Sensitivity Carnac(20): 0.518 Vsfold5: 0.488 Positive Predictive Value Carnac(20): 0.941 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.695 RSpredict(seed): 0.298 Sensitivity Carnac(20): 0.518 RSpredict(seed): 0.156 Positive Predictive Value Carnac(20): 0.938 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.731 RDfolder: 0.624 Sensitivity Carnac(20): 0.572 RDfolder: 0.591 Positive Predictive Value Carnac(20): 0.943 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.69132796717e-08	? Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.662 PPfold(seed): 0.031 Sensitivity Carnac(20): 0.516 PPfold(seed): 0.005 Positive Predictive Value Carnac(20): 0.858 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.696 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.941 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	? CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(20): N/A Sensitivity CMfinder(seed): N/A Carnac(20): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Carnac(20): 0.663 Sensitivity Multilign(seed): 0.750 Carnac(20): 0.500 Positive Predictive Value Multilign(seed): 0.852 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Carnac(20): 0.562 Sensitivity PETfold_pre2.0(seed): 0.784 Carnac(20): 0.397 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Carnac(20): 0.807 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Carnac(20): 0.632 Sensitivity TurboFold(20): 0.694 Carnac(20): 0.471 Positive Predictive Value TurboFold(20): 0.781 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): N/A CMfinder(20): N/A Sensitivity Carnac(20): N/A CMfinder(20): N/A Positive Predictive Value Carnac(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Carnac(20): 0.562 Sensitivity PETfold_pre2.0(20): 0.707 Carnac(20): 0.397 Positive Predictive Value PETfold_pre2.0(20): 0.796 Carnac(20): 0.807 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Carnac(20): 0.615 Sensitivity TurboFold(seed): 0.684 Carnac(20): 0.439 Positive Predictive Value TurboFold(seed): 0.749 Carnac(20): 0.872 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.780 Carnac(20): 0.632 Sensitivity PPfold(20): 0.714 Carnac(20): 0.471 Positive Predictive Value PPfold(20): 0.860 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.603 NanoFolder: 0.389 Sensitivity Carnac(20): 0.455 NanoFolder: 0.475 Positive Predictive Value Carnac(20): 0.807 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.693 Carnac(seed): 0.231 Sensitivity Carnac(20): 0.511 Carnac(seed): 0.054 Positive Predictive Value Carnac(20): 0.947 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08
Cylofold	21 MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.774 Cylofold: 0.732 Sensitivity MXScarna(seed): 0.730 Cylofold: 0.726 Positive Predictive Value MXScarna(seed): 0.827 Cylofold: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 2.87980998248e-07	14 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.823 Cylofold: 0.703 Sensitivity CentroidAlifold(20): 0.718 Cylofold: 0.703 Positive Predictive Value CentroidAlifold(20): 0.948 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.48055519165e-08	63 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.815 Cylofold: 0.741 Sensitivity CentroidFold: 0.796 Cylofold: 0.724 Positive Predictive Value CentroidFold: 0.841 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.787 Cylofold: 0.703 Sensitivity RNAalifold(20): 0.689 Cylofold: 0.703 Positive Predictive Value RNAalifold(20): 0.904 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.10198558684e-08	63 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.800 Cylofold: 0.741 Sensitivity Sfold: 0.781 Cylofold: 0.724 Positive Predictive Value Sfold: 0.826 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.806 Cylofold: 0.741 Sensitivity Fold: 0.813 Cylofold: 0.724 Positive Predictive Value Fold: 0.806 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.797 Cylofold: 0.703 Sensitivity RNASampler(20): 0.689 Cylofold: 0.703 Positive Predictive Value RNASampler(20): 0.928 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.06761512825e-08	14 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.804 Cylofold: 0.703 Sensitivity MXScarna(20): 0.757 Cylofold: 0.703 Positive Predictive Value MXScarna(20): 0.859 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.9966815982e-08	35 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.777 Cylofold: 0.685 Sensitivity CentroidHomfold‑LAST: 0.663 Cylofold: 0.673 Positive Predictive Value CentroidHomfold‑LAST: 0.919 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 5.23657817852e-08	63 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.800 Cylofold: 0.741 Sensitivity HotKnots: 0.814 Cylofold: 0.724 Positive Predictive Value HotKnots: 0.794 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.789 Cylofold: 0.741 Sensitivity UNAFold: 0.791 Cylofold: 0.724 Positive Predictive Value UNAFold: 0.794 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.800 Cylofold: 0.741 Sensitivity Contrafold: 0.804 Cylofold: 0.724 Positive Predictive Value Contrafold: 0.803 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.777 Cylofold: 0.676 Sensitivity IPknot: 0.738 Cylofold: 0.663 Positive Predictive Value IPknot: 0.826 Cylofold: 0.702 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.811 Cylofold: 0.666 Sensitivity ContextFold: 0.771 Cylofold: 0.646 Positive Predictive Value ContextFold: 0.861 Cylofold: 0.699 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	63 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.794 Cylofold: 0.741 Sensitivity RNAshapes: 0.796 Cylofold: 0.724 Positive Predictive Value RNAshapes: 0.800 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.791 Cylofold: 0.741 Sensitivity MaxExpect: 0.796 Cylofold: 0.724 Positive Predictive Value MaxExpect: 0.794 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.778 Cylofold: 0.741 Sensitivity PknotsRG: 0.790 Cylofold: 0.724 Positive Predictive Value PknotsRG: 0.774 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.774 Cylofold: 0.741 Sensitivity RNAfold: 0.779 Cylofold: 0.724 Positive Predictive Value RNAfold: 0.777 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.781 Cylofold: 0.738 Sensitivity ProbKnot: 0.804 Cylofold: 0.722 Positive Predictive Value ProbKnot: 0.767 Cylofold: 0.764 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.757 Cylofold: 0.703 Sensitivity Murlet(20): 0.653 Cylofold: 0.703 Positive Predictive Value Murlet(20): 0.885 Cylofold: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	21 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.734 Cylofold: 0.732 Sensitivity CentroidAlifold(seed): 0.575 Cylofold: 0.726 Positive Predictive Value CentroidAlifold(seed): 0.943 Cylofold: 0.747 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 0.011312336181	43 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.805 Cylofold: 0.752 Sensitivity Afold: 0.818 Cylofold: 0.731 Positive Predictive Value Afold: 0.800 Cylofold: 0.783 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	63 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.782 Cylofold: 0.741 Sensitivity RNAsubopt: 0.788 Cylofold: 0.724 Positive Predictive Value RNAsubopt: 0.785 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: 0.703 Carnac(20): 0.687 Sensitivity Cylofold: 0.703 Carnac(20): 0.506 Positive Predictive Value Cylofold: 0.711 Carnac(20): 0.942 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 0.000351392923707		- McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.795 Cylofold: 0.738 Sensitivity McQFold: 0.782 Cylofold: 0.721 Positive Predictive Value McQFold: 0.815 Cylofold: 0.764 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.663 Cylofold: 0.651 Sensitivity CRWrnafold: 0.661 Cylofold: 0.639 Positive Predictive Value CRWrnafold: 0.678 Cylofold: 0.677 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 7.14336419872e-05	+ Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.696 RNAalifold(seed): 0.635 Sensitivity Cylofold: 0.690 RNAalifold(seed): 0.480 Positive Predictive Value Cylofold: 0.712 RNAalifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	- Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.760 Cylofold: 0.741 Sensitivity Pknots: 0.777 Cylofold: 0.724 Positive Predictive Value Pknots: 0.752 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.775 RNASampler(seed): 0.678 Sensitivity Cylofold: 0.766 RNASampler(seed): 0.570 Positive Predictive Value Cylofold: 0.791 RNASampler(seed): 0.818 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.703 Mastr(20): 0.666 Sensitivity Cylofold: 0.703 Mastr(20): 0.503 Positive Predictive Value Cylofold: 0.711 Mastr(20): 0.890 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	+ Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.703 RSpredict(20): 0.692 Sensitivity Cylofold: 0.703 RSpredict(20): 0.619 Positive Predictive Value Cylofold: 0.711 RSpredict(20): 0.782 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.25083737045e-05	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.790 Alterna: 0.763 Sensitivity Cylofold: 0.770 Alterna: 0.779 Positive Predictive Value Cylofold: 0.821 Alterna: 0.759 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.666 RNASLOpt: 0.663 Sensitivity Cylofold: 0.646 RNASLOpt: 0.620 Positive Predictive Value Cylofold: 0.699 RNASLOpt: 0.723 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.209525580533	? Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.650 Multilign(20): 0.621 Sensitivity Cylofold: 0.641 Multilign(20): 0.560 Positive Predictive Value Cylofold: 0.674 Multilign(20): 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.741 Vsfold4: 0.672 Sensitivity Cylofold: 0.724 Vsfold4: 0.653 Positive Predictive Value Cylofold: 0.767 Vsfold4: 0.703 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.749 MCFold: 0.669 Sensitivity Cylofold: 0.732 MCFold: 0.700 Positive Predictive Value Cylofold: 0.776 MCFold: 0.652 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.676 RNAwolf: 0.590 Sensitivity Cylofold: 0.663 RNAwolf: 0.574 Positive Predictive Value Cylofold: 0.702 RNAwolf: 0.624 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.680 Murlet(seed): 0.571 Sensitivity Cylofold: 0.674 Murlet(seed): 0.390 Positive Predictive Value Cylofold: 0.696 Murlet(seed): 0.847 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.741 Vsfold5: 0.628 Sensitivity Cylofold: 0.724 Vsfold5: 0.625 Positive Predictive Value Cylofold: 0.767 Vsfold5: 0.644 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.732 RSpredict(seed): 0.315 Sensitivity Cylofold: 0.726 RSpredict(seed): 0.185 Positive Predictive Value Cylofold: 0.747 RSpredict(seed): 0.555 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.796 RDfolder: 0.662 Sensitivity Cylofold: 0.773 RDfolder: 0.627 Positive Predictive Value Cylofold: 0.830 RDfolder: 0.715 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.730 PPfold(seed): 0.153 Sensitivity Cylofold: 0.710 PPfold(seed): 0.032 Positive Predictive Value Cylofold: 0.763 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.732 Mastr(seed): 0.307 Sensitivity Cylofold: 0.726 Mastr(seed): 0.096 Positive Predictive Value Cylofold: 0.747 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.716 Multilign(seed): 0.683 Sensitivity Cylofold: 0.678 Multilign(seed): 0.636 Positive Predictive Value Cylofold: 0.769 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.773 Cylofold: 0.694 Sensitivity PETfold_pre2.0(seed): 0.702 Cylofold: 0.675 Positive Predictive Value PETfold_pre2.0(seed): 0.860 Cylofold: 0.726 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.787 TurboFold(20): 0.783 Sensitivity Cylofold: 0.765 TurboFold(20): 0.718 Positive Predictive Value Cylofold: 0.820 TurboFold(20): 0.863 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.763 Cylofold: 0.720 Sensitivity PETfold_pre2.0(20): 0.678 Cylofold: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.870 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.773 TurboFold(seed): 0.680 Sensitivity Cylofold: 0.743 TurboFold(seed): 0.622 Positive Predictive Value Cylofold: 0.815 TurboFold(seed): 0.760 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.811 Cylofold: 0.787 Sensitivity PPfold(20): 0.725 Cylofold: 0.765 Positive Predictive Value PPfold(20): 0.915 Cylofold: 0.820 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.705 NanoFolder: 0.616 Sensitivity Cylofold: 0.686 NanoFolder: 0.699 Positive Predictive Value Cylofold: 0.738 NanoFolder: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.713 Carnac(seed): 0.239 Sensitivity Cylofold: 0.702 Carnac(seed): 0.058 Positive Predictive Value Cylofold: 0.733 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08
McQFold	44 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.776 McQFold: 0.655 Sensitivity MXScarna(seed): 0.736 McQFold: 0.671 Positive Predictive Value MXScarna(seed): 0.824 McQFold: 0.646 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.810 McQFold: 0.629 Sensitivity CentroidAlifold(20): 0.716 McQFold: 0.641 Positive Predictive Value CentroidAlifold(20): 0.921 McQFold: 0.624 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.709 McQFold: 0.570 Sensitivity CentroidFold: 0.706 McQFold: 0.525 Positive Predictive Value CentroidFold: 0.714 McQFold: 0.620 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.782 McQFold: 0.625 Sensitivity RNAalifold(20): 0.690 McQFold: 0.638 Positive Predictive Value RNAalifold(20): 0.889 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	120 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.632 McQFold: 0.534 Sensitivity Sfold: 0.630 McQFold: 0.503 Positive Predictive Value Sfold: 0.635 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.775 McQFold: 0.733 Sensitivity Fold: 0.794 McQFold: 0.732 Positive Predictive Value Fold: 0.762 McQFold: 0.741 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.765 McQFold: 0.625 Sensitivity RNASampler(20): 0.671 McQFold: 0.638 Positive Predictive Value RNASampler(20): 0.875 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.761 McQFold: 0.625 Sensitivity MXScarna(20): 0.727 McQFold: 0.638 Positive Predictive Value MXScarna(20): 0.800 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	44 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 McQFold: 0.714 Sensitivity CentroidHomfold‑LAST: 0.691 McQFold: 0.706 Positive Predictive Value CentroidHomfold‑LAST: 0.893 McQFold: 0.733 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.770 McQFold: 0.718 Sensitivity HotKnots: 0.791 McQFold: 0.719 Positive Predictive Value HotKnots: 0.755 McQFold: 0.725 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.609 McQFold: 0.534 Sensitivity UNAFold: 0.640 McQFold: 0.503 Positive Predictive Value UNAFold: 0.580 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.698 McQFold: 0.534 Sensitivity Contrafold: 0.721 McQFold: 0.503 Positive Predictive Value Contrafold: 0.676 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.776 McQFold: 0.696 Sensitivity IPknot: 0.746 McQFold: 0.690 Positive Predictive Value IPknot: 0.815 McQFold: 0.713 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.810 McQFold: 0.662 Sensitivity ContextFold: 0.773 McQFold: 0.661 Positive Predictive Value ContextFold: 0.856 McQFold: 0.675 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	117 RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.758 McQFold: 0.718 Sensitivity RNAshapes: 0.768 McQFold: 0.719 Positive Predictive Value RNAshapes: 0.754 McQFold: 0.725 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.728 McQFold: 0.612 Sensitivity MaxExpect: 0.739 McQFold: 0.613 Positive Predictive Value MaxExpect: 0.718 McQFold: 0.613 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.591 McQFold: 0.534 Sensitivity PknotsRG: 0.629 McQFold: 0.503 Positive Predictive Value PknotsRG: 0.556 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.603 McQFold: 0.534 Sensitivity RNAfold: 0.639 McQFold: 0.503 Positive Predictive Value RNAfold: 0.569 McQFold: 0.569 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.738 McQFold: 0.720 Sensitivity ProbKnot: 0.772 McQFold: 0.728 Positive Predictive Value ProbKnot: 0.712 McQFold: 0.719 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 1.02208072244e-07	28 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.704 McQFold: 0.625 Sensitivity Murlet(20): 0.596 McQFold: 0.638 Positive Predictive Value Murlet(20): 0.837 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	43 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 McQFold: 0.652 Sensitivity CentroidAlifold(seed): 0.552 McQFold: 0.668 Positive Predictive Value CentroidAlifold(seed): 0.870 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	94 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.589 McQFold: 0.517 Sensitivity Afold: 0.629 McQFold: 0.484 Positive Predictive Value Afold: 0.552 McQFold: 0.553 Number of pairs reference - predicted secondary structure: 94 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.736 McQFold: 0.718 Sensitivity RNAsubopt: 0.756 McQFold: 0.719 Positive Predictive Value RNAsubopt: 0.725 McQFold: 0.725 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.85233844192e-08	28 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.696 McQFold: 0.625 Sensitivity Carnac(20): 0.518 McQFold: 0.638 Positive Predictive Value Carnac(20): 0.941 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	62 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.795 Cylofold: 0.738 Sensitivity McQFold: 0.782 Cylofold: 0.721 Positive Predictive Value McQFold: 0.815 Cylofold: 0.764 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08		= CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.674 McQFold: 0.669 Sensitivity CRWrnafold: 0.681 McQFold: 0.662 Positive Predictive Value CRWrnafold: 0.679 McQFold: 0.688 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.00659858700811	- RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.676 McQFold: 0.659 Sensitivity RNAalifold(seed): 0.525 McQFold: 0.684 Positive Predictive Value RNAalifold(seed): 0.874 McQFold: 0.642 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 1.62193520834e-06	+ McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.753 Pknots: 0.738 Sensitivity McQFold: 0.743 Pknots: 0.762 Positive Predictive Value McQFold: 0.772 Pknots: 0.724 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.776 RNASampler(seed): 0.765 Sensitivity McQFold: 0.797 RNASampler(seed): 0.687 Positive Predictive Value McQFold: 0.762 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.80024504584e-05	- Mastr(20) vs McQFold Matthews Correlation Coefficient Mastr(20): 0.636 McQFold: 0.625 Sensitivity Mastr(20): 0.483 McQFold: 0.638 Positive Predictive Value Mastr(20): 0.845 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000235226116958	- RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.663 McQFold: 0.634 Sensitivity RSpredict(20): 0.593 McQFold: 0.646 Positive Predictive Value RSpredict(20): 0.748 McQFold: 0.629 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 6.48688953717e-08	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.807 Alterna: 0.767 Sensitivity McQFold: 0.778 Alterna: 0.777 Positive Predictive Value McQFold: 0.848 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.668 McQFold: 0.662 Sensitivity RNASLOpt: 0.638 McQFold: 0.661 Positive Predictive Value RNASLOpt: 0.711 McQFold: 0.675 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 6.97652614729e-06	- Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.612 McQFold: 0.600 Sensitivity Multilign(20): 0.581 McQFold: 0.606 Positive Predictive Value Multilign(20): 0.657 McQFold: 0.606 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.68861226834e-05	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.718 Vsfold4: 0.647 Sensitivity McQFold: 0.719 Vsfold4: 0.637 Positive Predictive Value McQFold: 0.725 Vsfold4: 0.667 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.763 MCFold: 0.675 Sensitivity McQFold: 0.750 MCFold: 0.715 Positive Predictive Value McQFold: 0.785 MCFold: 0.650 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.696 RNAwolf: 0.585 Sensitivity McQFold: 0.690 RNAwolf: 0.575 Positive Predictive Value McQFold: 0.713 RNAwolf: 0.611 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.743 Murlet(seed): 0.620 Sensitivity McQFold: 0.744 Murlet(seed): 0.442 Positive Predictive Value McQFold: 0.749 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.717 Vsfold5: 0.610 Sensitivity McQFold: 0.717 Vsfold5: 0.610 Positive Predictive Value McQFold: 0.724 Vsfold5: 0.619 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.655 RSpredict(seed): 0.372 Sensitivity McQFold: 0.671 RSpredict(seed): 0.222 Positive Predictive Value McQFold: 0.646 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.809 RDfolder: 0.682 Sensitivity McQFold: 0.778 RDfolder: 0.643 Positive Predictive Value McQFold: 0.851 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.641 PPfold(seed): 0.122 Sensitivity McQFold: 0.654 PPfold(seed): 0.029 Positive Predictive Value McQFold: 0.639 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.649 Mastr(seed): 0.306 Sensitivity McQFold: 0.665 Mastr(seed): 0.105 Positive Predictive Value McQFold: 0.639 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.761 Multilign(seed): 0.683 Sensitivity McQFold: 0.737 Multilign(seed): 0.636 Positive Predictive Value McQFold: 0.798 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 McQFold: 0.558 Sensitivity PETfold_pre2.0(seed): 0.772 McQFold: 0.585 Positive Predictive Value PETfold_pre2.0(seed): 0.892 McQFold: 0.543 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.733 McQFold: 0.652 Sensitivity TurboFold(20): 0.694 McQFold: 0.665 Positive Predictive Value TurboFold(20): 0.781 McQFold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: N/A CMfinder(20): N/A Sensitivity McQFold: N/A CMfinder(20): N/A Positive Predictive Value McQFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 McQFold: 0.486 Sensitivity PETfold_pre2.0(20): 0.707 McQFold: 0.517 Positive Predictive Value PETfold_pre2.0(20): 0.796 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.650 McQFold: 0.634 Sensitivity TurboFold(seed): 0.624 McQFold: 0.649 Positive Predictive Value TurboFold(seed): 0.688 McQFold: 0.630 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.780 McQFold: 0.652 Sensitivity PPfold(20): 0.714 McQFold: 0.665 Positive Predictive Value PPfold(20): 0.860 McQFold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.659 NanoFolder: 0.543 Sensitivity McQFold: 0.671 NanoFolder: 0.639 Positive Predictive Value McQFold: 0.657 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.716 Carnac(seed): 0.299 Sensitivity McQFold: 0.723 Carnac(seed): 0.090 Positive Predictive Value McQFold: 0.716 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
CRWrnafold	9 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.705 CRWrnafold: 0.647 Sensitivity MXScarna(seed): 0.660 CRWrnafold: 0.655 Positive Predictive Value MXScarna(seed): 0.761 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.819 CRWrnafold: 0.668 Sensitivity CentroidAlifold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value CentroidAlifold(20): 0.930 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.737 CRWrnafold: 0.683 Sensitivity CentroidFold: 0.717 CRWrnafold: 0.690 Positive Predictive Value CentroidFold: 0.767 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.735 CRWrnafold: 0.668 Sensitivity RNAalifold(20): 0.677 CRWrnafold: 0.683 Positive Predictive Value RNAalifold(20): 0.804 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	32 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.711 CRWrnafold: 0.683 Sensitivity Sfold: 0.692 CRWrnafold: 0.690 Positive Predictive Value Sfold: 0.741 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.6410608252e-08	32 CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.683 Fold: 0.662 Sensitivity CRWrnafold: 0.690 Fold: 0.674 Positive Predictive Value CRWrnafold: 0.689 Fold: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.85233844192e-08	7 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.740 CRWrnafold: 0.668 Sensitivity RNASampler(20): 0.659 CRWrnafold: 0.683 Positive Predictive Value RNASampler(20): 0.837 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs MXScarna(20) Matthews Correlation Coefficient CRWrnafold: 0.668 MXScarna(20): 0.666 Sensitivity CRWrnafold: 0.683 MXScarna(20): 0.634 Positive Predictive Value CRWrnafold: 0.663 MXScarna(20): 0.707 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	31 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.758 CRWrnafold: 0.674 Sensitivity CentroidHomfold‑LAST: 0.670 CRWrnafold: 0.681 Positive Predictive Value CentroidHomfold‑LAST: 0.866 CRWrnafold: 0.679 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.725 CRWrnafold: 0.683 Sensitivity HotKnots: 0.747 CRWrnafold: 0.690 Positive Predictive Value HotKnots: 0.712 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.683 UNAFold: 0.683 Sensitivity CRWrnafold: 0.690 UNAFold: 0.694 Positive Predictive Value CRWrnafold: 0.689 UNAFold: 0.684 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.536377815296	32 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.733 CRWrnafold: 0.683 Sensitivity Contrafold: 0.731 CRWrnafold: 0.690 Positive Predictive Value Contrafold: 0.745 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.757 CRWrnafold: 0.683 Sensitivity IPknot: 0.731 CRWrnafold: 0.690 Positive Predictive Value IPknot: 0.793 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.799 CRWrnafold: 0.688 Sensitivity ContextFold: 0.762 CRWrnafold: 0.684 Positive Predictive Value ContextFold: 0.844 CRWrnafold: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	32 RNAshapes vs CRWrnafold Matthews Correlation Coefficient RNAshapes: 0.704 CRWrnafold: 0.683 Sensitivity RNAshapes: 0.710 CRWrnafold: 0.690 Positive Predictive Value RNAshapes: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 8.67590017402e-07	32 CRWrnafold vs MaxExpect Matthews Correlation Coefficient CRWrnafold: 0.683 MaxExpect: 0.662 Sensitivity CRWrnafold: 0.690 MaxExpect: 0.667 Positive Predictive Value CRWrnafold: 0.689 MaxExpect: 0.669 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 4.48494289621e-08	32 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.720 CRWrnafold: 0.683 Sensitivity PknotsRG: 0.743 CRWrnafold: 0.690 Positive Predictive Value PknotsRG: 0.708 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.706 CRWrnafold: 0.683 Sensitivity RNAfold: 0.715 CRWrnafold: 0.690 Positive Predictive Value RNAfold: 0.709 CRWrnafold: 0.689 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.5875416339e-07	32 CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.683 ProbKnot: 0.667 Sensitivity CRWrnafold: 0.690 ProbKnot: 0.692 Positive Predictive Value CRWrnafold: 0.689 ProbKnot: 0.654 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 1.97386617324e-07	7 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.677 CRWrnafold: 0.668 Sensitivity Murlet(20): 0.604 CRWrnafold: 0.683 Positive Predictive Value Murlet(20): 0.767 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.678 CRWrnafold: 0.647 Sensitivity CentroidAlifold(seed): 0.473 CRWrnafold: 0.655 Positive Predictive Value CentroidAlifold(seed): 0.980 CRWrnafold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.728 CRWrnafold: 0.652 Sensitivity Afold: 0.756 CRWrnafold: 0.669 Positive Predictive Value Afold: 0.710 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 2.66715895098e-08	32 CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.683 RNAsubopt: 0.666 Sensitivity CRWrnafold: 0.690 RNAsubopt: 0.682 Positive Predictive Value CRWrnafold: 0.689 RNAsubopt: 0.663 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Carnac(20): 0.620 Sensitivity CRWrnafold: 0.683 Carnac(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 Carnac(20): 0.828 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	25 CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.663 Cylofold: 0.651 Sensitivity CRWrnafold: 0.661 Cylofold: 0.639 Positive Predictive Value CRWrnafold: 0.678 Cylofold: 0.677 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 7.14336419872e-05	31 CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.674 McQFold: 0.669 Sensitivity CRWrnafold: 0.681 McQFold: 0.662 Positive Predictive Value CRWrnafold: 0.679 McQFold: 0.688 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 0.00659858700811		? RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.582 CRWrnafold: 0.513 Sensitivity RNAalifold(seed): 0.437 CRWrnafold: 0.524 Positive Predictive Value RNAalifold(seed): 0.786 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.683 Pknots: 0.631 Sensitivity CRWrnafold: 0.690 Pknots: 0.659 Positive Predictive Value CRWrnafold: 0.689 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.423 CRWrnafold: 0.322 Sensitivity RNASampler(seed): 0.358 CRWrnafold: 0.358 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.304 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Mastr(20): 0.649 Sensitivity CRWrnafold: 0.683 Mastr(20): 0.524 Positive Predictive Value CRWrnafold: 0.663 Mastr(20): 0.811 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.668 RSpredict(20): 0.535 Sensitivity CRWrnafold: 0.683 RSpredict(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 RSpredict(20): 0.621 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.673 Alterna: 0.669 Sensitivity CRWrnafold: 0.690 Alterna: 0.690 Positive Predictive Value CRWrnafold: 0.674 Alterna: 0.665 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 5.53672647526e-06	+ CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.688 RNASLOpt: 0.660 Sensitivity CRWrnafold: 0.684 RNASLOpt: 0.632 Positive Predictive Value CRWrnafold: 0.702 RNASLOpt: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	? CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Multilign(20): 0.617 Sensitivity CRWrnafold: 0.683 Multilign(20): 0.616 Positive Predictive Value CRWrnafold: 0.663 Multilign(20): 0.627 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.683 Vsfold4: 0.580 Sensitivity CRWrnafold: 0.690 Vsfold4: 0.571 Positive Predictive Value CRWrnafold: 0.689 Vsfold4: 0.604 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.682 MCFold: 0.639 Sensitivity CRWrnafold: 0.690 MCFold: 0.670 Positive Predictive Value CRWrnafold: 0.685 MCFold: 0.621 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.683 RNAwolf: 0.552 Sensitivity CRWrnafold: 0.690 RNAwolf: 0.546 Positive Predictive Value CRWrnafold: 0.689 RNAwolf: 0.575 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Murlet(seed): 0.510 Sensitivity CRWrnafold: 0.524 Murlet(seed): 0.349 Positive Predictive Value CRWrnafold: 0.516 Murlet(seed): 0.759 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.678 Vsfold5: 0.525 Sensitivity CRWrnafold: 0.685 Vsfold5: 0.528 Positive Predictive Value CRWrnafold: 0.683 Vsfold5: 0.538 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 RSpredict(seed): 0.126 Sensitivity CRWrnafold: 0.655 RSpredict(seed): 0.059 Positive Predictive Value CRWrnafold: 0.649 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.703 RDfolder: 0.530 Sensitivity CRWrnafold: 0.704 RDfolder: 0.479 Positive Predictive Value CRWrnafold: 0.717 RDfolder: 0.610 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	? CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 PPfold(seed): 0.134 Sensitivity CRWrnafold: 0.655 PPfold(seed): 0.034 Positive Predictive Value CRWrnafold: 0.649 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.655 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.649 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs CRWrnafold Matthews Correlation Coefficient CMfinder(seed): N/A CRWrnafold: N/A Sensitivity CMfinder(seed): N/A CRWrnafold: N/A Positive Predictive Value CMfinder(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): 0.540 CRWrnafold: 0.513 Sensitivity Multilign(seed): 0.500 CRWrnafold: 0.513 Positive Predictive Value Multilign(seed): 0.603 CRWrnafold: 0.534 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.816 CRWrnafold: 0.636 Sensitivity PETfold_pre2.0(seed): 0.761 CRWrnafold: 0.639 Positive Predictive Value PETfold_pre2.0(seed): 0.881 CRWrnafold: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.683 CRWrnafold: 0.668 Sensitivity TurboFold(20): 0.646 CRWrnafold: 0.683 Positive Predictive Value TurboFold(20): 0.731 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CRWrnafold: 0.663 Sensitivity PETfold_pre2.0(20): 0.707 CRWrnafold: 0.672 Positive Predictive Value PETfold_pre2.0(20): 0.796 CRWrnafold: 0.661 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 TurboFold(seed): 0.580 Sensitivity CRWrnafold: 0.595 TurboFold(seed): 0.558 Positive Predictive Value CRWrnafold: 0.591 TurboFold(seed): 0.615 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.780 CRWrnafold: 0.668 Sensitivity PPfold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value PPfold(20): 0.844 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.687 NanoFolder: 0.542 Sensitivity CRWrnafold: 0.694 NanoFolder: 0.635 Positive Predictive Value CRWrnafold: 0.689 NanoFolder: 0.478 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.59578924681e-08	? CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 Carnac(seed): 0.156 Sensitivity CRWrnafold: 0.595 Carnac(seed): 0.025 Positive Predictive Value CRWrnafold: 0.591 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0
RNAalifold(seed)	29 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.722 RNAalifold(seed): 0.676 Sensitivity MXScarna(seed): 0.677 RNAalifold(seed): 0.525 Positive Predictive Value MXScarna(seed): 0.776 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	17 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.748 RNAalifold(seed): 0.675 Sensitivity CentroidAlifold(20): 0.625 RNAalifold(seed): 0.496 Positive Predictive Value CentroidAlifold(20): 0.900 RNAalifold(seed): 0.924 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	28 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.712 RNAalifold(seed): 0.677 Sensitivity CentroidFold: 0.713 RNAalifold(seed): 0.528 Positive Predictive Value CentroidFold: 0.716 RNAalifold(seed): 0.873 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.699 RNAalifold(seed): 0.673 Sensitivity RNAalifold(20): 0.586 RNAalifold(seed): 0.492 Positive Predictive Value RNAalifold(20): 0.839 RNAalifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.78038963586e-08	29 Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.716 RNAalifold(seed): 0.676 Sensitivity Sfold: 0.710 RNAalifold(seed): 0.525 Positive Predictive Value Sfold: 0.727 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.667 RNAalifold(seed): 0.643 Sensitivity Fold: 0.701 RNAalifold(seed): 0.487 Positive Predictive Value Fold: 0.640 RNAalifold(seed): 0.855 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.27071136365e-07	18 RNASampler(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(20): 0.693 RNAalifold(seed): 0.673 Sensitivity RNASampler(20): 0.592 RNAalifold(seed): 0.492 Positive Predictive Value RNASampler(20): 0.815 RNAalifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.77512146924e-08	18 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.709 RNAalifold(seed): 0.673 Sensitivity MXScarna(20): 0.667 RNAalifold(seed): 0.492 Positive Predictive Value MXScarna(20): 0.758 RNAalifold(seed): 0.925 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	8 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.680 RNAalifold(seed): 0.606 Sensitivity CentroidHomfold‑LAST: 0.607 RNAalifold(seed): 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.773 RNAalifold(seed): 0.804 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	29 HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.704 RNAalifold(seed): 0.676 Sensitivity HotKnots: 0.743 RNAalifold(seed): 0.525 Positive Predictive Value HotKnots: 0.673 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	29 UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.696 RNAalifold(seed): 0.676 Sensitivity UNAFold: 0.721 RNAalifold(seed): 0.525 Positive Predictive Value UNAFold: 0.677 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 7.95107997107e-08	29 Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.693 RNAalifold(seed): 0.676 Sensitivity Contrafold: 0.718 RNAalifold(seed): 0.525 Positive Predictive Value Contrafold: 0.674 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 1.16758253407e-07	7 RNAalifold(seed) vs IPknot Matthews Correlation Coefficient RNAalifold(seed): 0.610 IPknot: 0.601 Sensitivity RNAalifold(seed): 0.473 IPknot: 0.560 Positive Predictive Value RNAalifold(seed): 0.798 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.570 RNAalifold(seed): 0.542 Sensitivity ContextFold: 0.515 RNAalifold(seed): 0.392 Positive Predictive Value ContextFold: 0.641 RNAalifold(seed): 0.760 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	29 RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.717 RNAalifold(seed): 0.676 Sensitivity RNAshapes: 0.742 RNAalifold(seed): 0.525 Positive Predictive Value RNAshapes: 0.698 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 RNAalifold(seed) vs MaxExpect Matthews Correlation Coefficient RNAalifold(seed): 0.672 MaxExpect: 0.668 Sensitivity RNAalifold(seed): 0.524 MaxExpect: 0.697 Positive Predictive Value RNAalifold(seed): 0.867 MaxExpect: 0.647 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.657358697881	29 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.707 RNAalifold(seed): 0.676 Sensitivity PknotsRG: 0.745 RNAalifold(seed): 0.525 Positive Predictive Value PknotsRG: 0.677 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	29 RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.707 RNAalifold(seed): 0.676 Sensitivity RNAfold: 0.739 RNAalifold(seed): 0.525 Positive Predictive Value RNAfold: 0.681 RNAalifold(seed): 0.874 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	18 ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.591 RNAalifold(seed): 0.586 Sensitivity ProbKnot: 0.635 RNAalifold(seed): 0.421 Positive Predictive Value ProbKnot: 0.556 RNAalifold(seed): 0.821 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 0.0153885189249	18 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 Murlet(20): 0.627 Sensitivity RNAalifold(seed): 0.492 Murlet(20): 0.498 Positive Predictive Value RNAalifold(seed): 0.925 Murlet(20): 0.795 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	28 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.740 RNAalifold(seed): 0.677 Sensitivity CentroidAlifold(seed): 0.648 RNAalifold(seed): 0.528 Positive Predictive Value CentroidAlifold(seed): 0.848 RNAalifold(seed): 0.873 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.681 RNAalifold(seed): 0.640 Sensitivity Afold: 0.724 RNAalifold(seed): 0.490 Positive Predictive Value Afold: 0.646 RNAalifold(seed): 0.843 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	29 RNAalifold(seed) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(seed): 0.676 RNAsubopt: 0.665 Sensitivity RNAalifold(seed): 0.525 RNAsubopt: 0.698 Positive Predictive Value RNAalifold(seed): 0.874 RNAsubopt: 0.639 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 6.27473311413e-06	18 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 Carnac(20): 0.612 Sensitivity RNAalifold(seed): 0.492 Carnac(20): 0.402 Positive Predictive Value RNAalifold(seed): 0.925 Carnac(20): 0.939 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.69132796717e-08	14 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: 0.696 RNAalifold(seed): 0.635 Sensitivity Cylofold: 0.690 RNAalifold(seed): 0.480 Positive Predictive Value Cylofold: 0.712 RNAalifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.80908287419e-08	29 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.676 McQFold: 0.659 Sensitivity RNAalifold(seed): 0.525 McQFold: 0.684 Positive Predictive Value RNAalifold(seed): 0.874 McQFold: 0.642 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 1.62193520834e-06	6 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.582 CRWrnafold: 0.513 Sensitivity RNAalifold(seed): 0.437 CRWrnafold: 0.524 Positive Predictive Value RNAalifold(seed): 0.786 CRWrnafold: 0.516 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0		= Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: 0.733 RNAalifold(seed): 0.727 Sensitivity Pknots: 0.766 RNAalifold(seed): 0.587 Positive Predictive Value Pknots: 0.711 RNAalifold(seed): 0.908 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.0529443953662	- RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 RNAalifold(seed): 0.730 Sensitivity RNASampler(seed): 0.687 RNAalifold(seed): 0.620 Positive Predictive Value RNASampler(seed): 0.859 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 Mastr(20): 0.486 Sensitivity RNAalifold(seed): 0.492 Mastr(20): 0.307 Positive Predictive Value RNAalifold(seed): 0.925 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 RSpredict(20): 0.576 Sensitivity RNAalifold(seed): 0.492 RSpredict(20): 0.504 Positive Predictive Value RNAalifold(seed): 0.925 RSpredict(20): 0.666 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	- Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.844 RNAalifold(seed): 0.743 Sensitivity Alterna: 0.833 RNAalifold(seed): 0.644 Positive Predictive Value Alterna: 0.863 RNAalifold(seed): 0.869 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	? RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.542 RNASLOpt: 0.461 Sensitivity RNAalifold(seed): 0.392 RNASLOpt: 0.443 Positive Predictive Value RNAalifold(seed): 0.760 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.656 Multilign(20): 0.545 Sensitivity RNAalifold(seed): 0.470 Multilign(20): 0.508 Positive Predictive Value RNAalifold(seed): 0.926 Multilign(20): 0.599 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.676 Vsfold4: 0.567 Sensitivity RNAalifold(seed): 0.525 Vsfold4: 0.569 Positive Predictive Value RNAalifold(seed): 0.874 Vsfold4: 0.571 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.718 MCFold: 0.648 Sensitivity RNAalifold(seed): 0.580 MCFold: 0.687 Positive Predictive Value RNAalifold(seed): 0.897 MCFold: 0.622 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNAwolf: 0.451 Sensitivity RNAalifold(seed): 0.473 RNAwolf: 0.447 Positive Predictive Value RNAalifold(seed): 0.798 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.737 Murlet(seed): 0.620 Sensitivity RNAalifold(seed): 0.603 Murlet(seed): 0.442 Positive Predictive Value RNAalifold(seed): 0.908 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.676 Vsfold5: 0.549 Sensitivity RNAalifold(seed): 0.525 Vsfold5: 0.553 Positive Predictive Value RNAalifold(seed): 0.874 Vsfold5: 0.553 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.676 RSpredict(seed): 0.471 Sensitivity RNAalifold(seed): 0.525 RSpredict(seed): 0.311 Positive Predictive Value RNAalifold(seed): 0.874 RSpredict(seed): 0.722 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.742 RDfolder: 0.671 Sensitivity RNAalifold(seed): 0.633 RDfolder: 0.616 Positive Predictive Value RNAalifold(seed): 0.883 RDfolder: 0.746 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	? RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 PPfold(seed): 0.155 Sensitivity RNAalifold(seed): 0.473 PPfold(seed): 0.047 Positive Predictive Value RNAalifold(seed): 0.798 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.676 Mastr(seed): 0.371 Sensitivity RNAalifold(seed): 0.525 Mastr(seed): 0.154 Positive Predictive Value RNAalifold(seed): 0.874 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	? RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 RNAalifold(seed): 0.620 Sensitivity Multilign(seed): 0.636 RNAalifold(seed): 0.517 Positive Predictive Value Multilign(seed): 0.750 RNAalifold(seed): 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAalifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.619 RNAalifold(seed): 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAalifold(seed): 0.760 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.690 RNAalifold(seed): 0.687 Sensitivity TurboFold(20): 0.647 RNAalifold(seed): 0.520 Positive Predictive Value TurboFold(20): 0.746 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(20): N/A Sensitivity RNAalifold(seed): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.691 PETfold_pre2.0(20): 0.619 Sensitivity RNAalifold(seed): 0.481 PETfold_pre2.0(20): 0.570 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.606 TurboFold(seed): 0.603 Sensitivity RNAalifold(seed): 0.464 TurboFold(seed): 0.577 Positive Predictive Value RNAalifold(seed): 0.804 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.709 RNAalifold(seed): 0.687 Sensitivity PPfold(20): 0.627 RNAalifold(seed): 0.520 Positive Predictive Value PPfold(20): 0.810 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.529 NanoFolder: 0.336 Sensitivity RNAalifold(seed): 0.390 NanoFolder: 0.415 Positive Predictive Value RNAalifold(seed): 0.727 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.737 Carnac(seed): 0.327 Sensitivity RNAalifold(seed): 0.603 Carnac(seed): 0.108 Positive Predictive Value RNAalifold(seed): 0.908 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08
Pknots	42 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.802 Pknots: 0.720 Sensitivity MXScarna(seed): 0.760 Pknots: 0.751 Positive Predictive Value MXScarna(seed): 0.852 Pknots: 0.698 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.830 Pknots: 0.647 Sensitivity CentroidAlifold(20): 0.748 Pknots: 0.688 Positive Predictive Value CentroidAlifold(20): 0.926 Pknots: 0.618 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	102 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.810 Pknots: 0.739 Sensitivity CentroidFold: 0.797 Pknots: 0.761 Positive Predictive Value CentroidFold: 0.831 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.800 Pknots: 0.639 Sensitivity RNAalifold(20): 0.721 Pknots: 0.683 Positive Predictive Value RNAalifold(20): 0.891 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	116 Sfold vs Pknots Matthews Correlation Coefficient Sfold: 0.807 Pknots: 0.740 Sensitivity Sfold: 0.790 Pknots: 0.763 Positive Predictive Value Sfold: 0.831 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	80 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.818 Pknots: 0.754 Sensitivity Fold: 0.826 Pknots: 0.770 Positive Predictive Value Fold: 0.817 Pknots: 0.747 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.798 Pknots: 0.639 Sensitivity RNASampler(20): 0.710 Pknots: 0.683 Positive Predictive Value RNASampler(20): 0.902 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.787 Pknots: 0.639 Sensitivity MXScarna(20): 0.755 Pknots: 0.683 Positive Predictive Value MXScarna(20): 0.824 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Pknots: 0.676 Sensitivity CentroidHomfold‑LAST: 0.691 Pknots: 0.693 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Pknots: 0.672 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: 0.804 Pknots: 0.740 Sensitivity HotKnots: 0.815 Pknots: 0.763 Positive Predictive Value HotKnots: 0.801 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: 0.806 Pknots: 0.740 Sensitivity UNAFold: 0.808 Pknots: 0.763 Positive Predictive Value UNAFold: 0.812 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.798 Pknots: 0.740 Sensitivity Contrafold: 0.805 Pknots: 0.763 Positive Predictive Value Contrafold: 0.799 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.782 Pknots: 0.663 Sensitivity IPknot: 0.752 Pknots: 0.683 Positive Predictive Value IPknot: 0.820 Pknots: 0.656 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.816 Pknots: 0.628 Sensitivity ContextFold: 0.780 Pknots: 0.649 Positive Predictive Value ContextFold: 0.861 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RNAshapes vs Pknots Matthews Correlation Coefficient RNAshapes: 0.792 Pknots: 0.740 Sensitivity RNAshapes: 0.793 Pknots: 0.763 Positive Predictive Value RNAshapes: 0.799 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	96 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.785 Pknots: 0.737 Sensitivity MaxExpect: 0.791 Pknots: 0.760 Positive Predictive Value MaxExpect: 0.787 Pknots: 0.723 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: 0.782 Pknots: 0.740 Sensitivity PknotsRG: 0.794 Pknots: 0.763 Positive Predictive Value PknotsRG: 0.779 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RNAfold vs Pknots Matthews Correlation Coefficient RNAfold: 0.790 Pknots: 0.740 Sensitivity RNAfold: 0.796 Pknots: 0.763 Positive Predictive Value RNAfold: 0.792 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	72 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.781 Pknots: 0.745 Sensitivity ProbKnot: 0.805 Pknots: 0.764 Positive Predictive Value ProbKnot: 0.765 Pknots: 0.737 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.735 Pknots: 0.639 Sensitivity Murlet(20): 0.636 Pknots: 0.683 Positive Predictive Value Murlet(20): 0.855 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	41 Pknots vs CentroidAlifold(seed) Matthews Correlation Coefficient Pknots: 0.717 CentroidAlifold(seed): 0.711 Sensitivity Pknots: 0.748 CentroidAlifold(seed): 0.564 Positive Predictive Value Pknots: 0.695 CentroidAlifold(seed): 0.904 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 0.103865234064	90 Afold vs Pknots Matthews Correlation Coefficient Afold: 0.790 Pknots: 0.774 Sensitivity Afold: 0.802 Pknots: 0.800 Positive Predictive Value Afold: 0.786 Pknots: 0.757 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 4.83792096436e-08	116 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.765 Pknots: 0.740 Sensitivity RNAsubopt: 0.775 Pknots: 0.763 Positive Predictive Value RNAsubopt: 0.764 Pknots: 0.726 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.719 Pknots: 0.639 Sensitivity Carnac(20): 0.550 Pknots: 0.683 Positive Predictive Value Carnac(20): 0.946 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 4.98172311752e-08	63 Pknots vs Cylofold Matthews Correlation Coefficient Pknots: 0.760 Cylofold: 0.741 Sensitivity Pknots: 0.777 Cylofold: 0.724 Positive Predictive Value Pknots: 0.752 Cylofold: 0.767 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	115 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.753 Pknots: 0.738 Sensitivity McQFold: 0.743 Pknots: 0.762 Positive Predictive Value McQFold: 0.772 Pknots: 0.724 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.683 Pknots: 0.631 Sensitivity CRWrnafold: 0.690 Pknots: 0.659 Positive Predictive Value CRWrnafold: 0.689 Pknots: 0.617 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: 0.733 RNAalifold(seed): 0.727 Sensitivity Pknots: 0.766 RNAalifold(seed): 0.587 Positive Predictive Value Pknots: 0.711 RNAalifold(seed): 0.908 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.0529443953662		+ Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.808 RNASampler(seed): 0.765 Sensitivity Pknots: 0.861 RNASampler(seed): 0.687 Positive Predictive Value Pknots: 0.763 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-08	- Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.682 Pknots: 0.639 Sensitivity Mastr(20): 0.555 Pknots: 0.683 Positive Predictive Value Mastr(20): 0.845 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	- RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.671 Pknots: 0.653 Sensitivity RSpredict(20): 0.596 Pknots: 0.693 Positive Predictive Value RSpredict(20): 0.762 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.000165943266419	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.812 Alterna: 0.767 Sensitivity Pknots: 0.820 Alterna: 0.777 Positive Predictive Value Pknots: 0.815 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.679 Pknots: 0.628 Sensitivity RNASLOpt: 0.649 Pknots: 0.649 Positive Predictive Value RNASLOpt: 0.721 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 7.03886575525e-08	- Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.612 Pknots: 0.588 Sensitivity Multilign(20): 0.581 Pknots: 0.606 Positive Predictive Value Multilign(20): 0.657 Pknots: 0.584 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.28825501566e-05	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.740 Vsfold4: 0.678 Sensitivity Pknots: 0.763 Vsfold4: 0.660 Positive Predictive Value Pknots: 0.726 Vsfold4: 0.707 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.751 MCFold: 0.678 Sensitivity Pknots: 0.774 MCFold: 0.717 Positive Predictive Value Pknots: 0.737 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.663 RNAwolf: 0.594 Sensitivity Pknots: 0.683 RNAwolf: 0.584 Positive Predictive Value Pknots: 0.656 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.727 Murlet(seed): 0.620 Sensitivity Pknots: 0.759 Murlet(seed): 0.442 Positive Predictive Value Pknots: 0.703 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.739 Vsfold5: 0.637 Sensitivity Pknots: 0.762 Vsfold5: 0.635 Positive Predictive Value Pknots: 0.725 Vsfold5: 0.652 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.720 RSpredict(seed): 0.393 Sensitivity Pknots: 0.751 RSpredict(seed): 0.240 Positive Predictive Value Pknots: 0.698 RSpredict(seed): 0.658 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.802 RDfolder: 0.682 Sensitivity Pknots: 0.809 RDfolder: 0.643 Positive Predictive Value Pknots: 0.804 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.630 PPfold(seed): 0.122 Sensitivity Pknots: 0.646 PPfold(seed): 0.029 Positive Predictive Value Pknots: 0.625 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.708 Mastr(seed): 0.328 Sensitivity Pknots: 0.743 Mastr(seed): 0.122 Positive Predictive Value Pknots: 0.684 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.694 Multilign(seed): 0.683 Sensitivity Pknots: 0.686 Multilign(seed): 0.636 Positive Predictive Value Pknots: 0.717 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Pknots: 0.531 Sensitivity PETfold_pre2.0(seed): 0.772 Pknots: 0.556 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Pknots: 0.519 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.733 Pknots: 0.634 Sensitivity TurboFold(20): 0.694 Pknots: 0.650 Positive Predictive Value TurboFold(20): 0.781 Pknots: 0.629 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Pknots: 0.446 Sensitivity PETfold_pre2.0(20): 0.707 Pknots: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.796 Pknots: 0.433 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.650 Pknots: 0.617 Sensitivity TurboFold(seed): 0.624 Pknots: 0.634 Positive Predictive Value TurboFold(seed): 0.688 Pknots: 0.613 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.780 Pknots: 0.634 Sensitivity PPfold(20): 0.714 Pknots: 0.650 Positive Predictive Value PPfold(20): 0.860 Pknots: 0.629 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.592 NanoFolder: 0.562 Sensitivity Pknots: 0.615 NanoFolder: 0.656 Positive Predictive Value Pknots: 0.583 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.34216867035e-07	+ Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.708 Carnac(seed): 0.299 Sensitivity Pknots: 0.744 Carnac(seed): 0.090 Positive Predictive Value Pknots: 0.682 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(seed)	17 RNASampler(seed) vs MXScarna(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 MXScarna(seed): 0.759 Sensitivity RNASampler(seed): 0.687 MXScarna(seed): 0.719 Positive Predictive Value RNASampler(seed): 0.859 MXScarna(seed): 0.808 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.38571919282e-05	7 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.714 RNASampler(seed): 0.694 Sensitivity CentroidAlifold(20): 0.628 RNASampler(seed): 0.635 Positive Predictive Value CentroidAlifold(20): 0.816 RNASampler(seed): 0.764 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	16 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.811 RNASampler(seed): 0.757 Sensitivity CentroidFold: 0.809 RNASampler(seed): 0.678 Positive Predictive Value CentroidFold: 0.819 RNASampler(seed): 0.853 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.10198558684e-08	8 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 RNAalifold(20): 0.636 Sensitivity RNASampler(seed): 0.658 RNAalifold(20): 0.608 Positive Predictive Value RNASampler(seed): 0.782 RNAalifold(20): 0.671 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	17 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.827 RNASampler(seed): 0.765 Sensitivity Sfold: 0.820 RNASampler(seed): 0.687 Positive Predictive Value Sfold: 0.840 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.78774507289e-09	12 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.734 Fold: 0.724 Sensitivity RNASampler(seed): 0.651 Fold: 0.758 Positive Predictive Value RNASampler(seed): 0.837 Fold: 0.700 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.000537170415527	8 RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): 0.720 RNASampler(seed): 0.715 Sensitivity RNASampler(20): 0.709 RNASampler(seed): 0.658 Positive Predictive Value RNASampler(20): 0.737 RNASampler(seed): 0.782 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 MXScarna(20): 0.687 Sensitivity RNASampler(seed): 0.658 MXScarna(20): 0.684 Positive Predictive Value RNASampler(seed): 0.782 MXScarna(20): 0.697 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.594 RNASampler(seed): 0.581 Sensitivity CentroidHomfold‑LAST: 0.541 RNASampler(seed): 0.495 Positive Predictive Value CentroidHomfold‑LAST: 0.663 RNASampler(seed): 0.692 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	17 HotKnots vs RNASampler(seed) Matthews Correlation Coefficient HotKnots: 0.803 RNASampler(seed): 0.765 Sensitivity HotKnots: 0.841 RNASampler(seed): 0.687 Positive Predictive Value HotKnots: 0.773 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	17 UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.794 RNASampler(seed): 0.765 Sensitivity UNAFold: 0.817 RNASampler(seed): 0.687 Positive Predictive Value UNAFold: 0.777 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.26346675981e-08	17 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.794 RNASampler(seed): 0.765 Sensitivity Contrafold: 0.812 RNASampler(seed): 0.687 Positive Predictive Value Contrafold: 0.782 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	4 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.597 RNASampler(seed): 0.559 Sensitivity IPknot: 0.560 RNASampler(seed): 0.484 Positive Predictive Value IPknot: 0.646 RNASampler(seed): 0.657 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.413 RNASampler(seed): 0.232 Sensitivity ContextFold: 0.395 RNASampler(seed): 0.211 Positive Predictive Value ContextFold: 0.441 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	17 RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.805 RNASampler(seed): 0.765 Sensitivity RNAshapes: 0.826 RNASampler(seed): 0.687 Positive Predictive Value RNAshapes: 0.789 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.64318034126e-08	15 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.757 MaxExpect: 0.742 Sensitivity RNASampler(seed): 0.685 MaxExpect: 0.777 Positive Predictive Value RNASampler(seed): 0.843 MaxExpect: 0.716 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.56588588961e-07	17 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.792 RNASampler(seed): 0.765 Sensitivity PknotsRG: 0.820 RNASampler(seed): 0.687 Positive Predictive Value PknotsRG: 0.771 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.77586369438e-08	17 RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.822 RNASampler(seed): 0.765 Sensitivity RNAfold: 0.849 RNASampler(seed): 0.687 Positive Predictive Value RNAfold: 0.801 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	8 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.640 ProbKnot: 0.621 Sensitivity RNASampler(seed): 0.551 ProbKnot: 0.680 Positive Predictive Value RNASampler(seed): 0.754 ProbKnot: 0.576 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 Murlet(20): 0.613 Sensitivity RNASampler(seed): 0.658 Murlet(20): 0.570 Positive Predictive Value RNASampler(seed): 0.782 Murlet(20): 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	16 RNASampler(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.757 CentroidAlifold(seed): 0.752 Sensitivity RNASampler(seed): 0.678 CentroidAlifold(seed): 0.678 Positive Predictive Value RNASampler(seed): 0.853 CentroidAlifold(seed): 0.841 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.0214507655873	16 Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.822 RNASampler(seed): 0.770 Sensitivity Afold: 0.851 RNASampler(seed): 0.699 Positive Predictive Value Afold: 0.798 RNASampler(seed): 0.853 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.86595104665e-08	17 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.765 RNAsubopt: 0.732 Sensitivity RNASampler(seed): 0.687 RNAsubopt: 0.765 Positive Predictive Value RNASampler(seed): 0.859 RNAsubopt: 0.708 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.28439804626e-08	8 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 Carnac(20): 0.701 Sensitivity RNASampler(seed): 0.658 Carnac(20): 0.513 Positive Predictive Value RNASampler(seed): 0.782 Carnac(20): 0.964 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs RNASampler(seed) Matthews Correlation Coefficient Cylofold: 0.775 RNASampler(seed): 0.678 Sensitivity Cylofold: 0.766 RNASampler(seed): 0.570 Positive Predictive Value Cylofold: 0.791 RNASampler(seed): 0.818 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	17 McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.776 RNASampler(seed): 0.765 Sensitivity McQFold: 0.797 RNASampler(seed): 0.687 Positive Predictive Value McQFold: 0.762 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.80024504584e-05	3 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.423 CRWrnafold: 0.322 Sensitivity RNASampler(seed): 0.358 CRWrnafold: 0.358 Positive Predictive Value RNASampler(seed): 0.511 CRWrnafold: 0.304 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	17 RNASampler(seed) vs RNAalifold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 RNAalifold(seed): 0.730 Sensitivity RNASampler(seed): 0.687 RNAalifold(seed): 0.620 Positive Predictive Value RNASampler(seed): 0.859 RNAalifold(seed): 0.866 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	17 Pknots vs RNASampler(seed) Matthews Correlation Coefficient Pknots: 0.808 RNASampler(seed): 0.765 Sensitivity Pknots: 0.861 RNASampler(seed): 0.687 Positive Predictive Value Pknots: 0.763 RNASampler(seed): 0.859 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-08		? RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 Mastr(20): 0.678 Sensitivity RNASampler(seed): 0.658 Mastr(20): 0.519 Positive Predictive Value RNASampler(seed): 0.782 Mastr(20): 0.891 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 RSpredict(20): 0.638 Sensitivity RNASampler(seed): 0.658 RSpredict(20): 0.690 Positive Predictive Value RNASampler(seed): 0.782 RSpredict(20): 0.596 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.874 RNASampler(seed): 0.818 Sensitivity Alterna: 0.859 RNASampler(seed): 0.715 Positive Predictive Value Alterna: 0.896 RNASampler(seed): 0.945 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.52609899389e-08	? RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.358 RNASampler(seed): 0.232 Sensitivity RNASLOpt: 0.395 RNASampler(seed): 0.211 Positive Predictive Value RNASLOpt: 0.333 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.683 Multilign(20): 0.667 Sensitivity RNASampler(seed): 0.593 Multilign(20): 0.703 Positive Predictive Value RNASampler(seed): 0.794 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.765 Vsfold4: 0.683 Sensitivity RNASampler(seed): 0.687 Vsfold4: 0.672 Positive Predictive Value RNASampler(seed): 0.859 Vsfold4: 0.703 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.765 MCFold: 0.700 Sensitivity RNASampler(seed): 0.687 MCFold: 0.751 Positive Predictive Value RNASampler(seed): 0.859 MCFold: 0.661 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.42071836373e-08	? RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.559 RNAwolf: 0.521 Sensitivity RNASampler(seed): 0.484 RNAwolf: 0.538 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.516 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 Murlet(seed): 0.639 Sensitivity RNASampler(seed): 0.687 Murlet(seed): 0.493 Positive Predictive Value RNASampler(seed): 0.859 Murlet(seed): 0.837 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.765 Vsfold5: 0.722 Sensitivity RNASampler(seed): 0.687 Vsfold5: 0.722 Positive Predictive Value RNASampler(seed): 0.859 Vsfold5: 0.730 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.01010269124e-08	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 RSpredict(seed): 0.631 Sensitivity RNASampler(seed): 0.687 RSpredict(seed): 0.501 Positive Predictive Value RNASampler(seed): 0.859 RSpredict(seed): 0.805 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.818 RDfolder: 0.731 Sensitivity RNASampler(seed): 0.715 RDfolder: 0.656 Positive Predictive Value RNASampler(seed): 0.945 RDfolder: 0.830 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.28439804626e-08	? RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.559 PPfold(seed): 0.200 Sensitivity RNASampler(seed): 0.484 PPfold(seed): 0.077 Positive Predictive Value RNASampler(seed): 0.657 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 Mastr(seed): 0.546 Sensitivity RNASampler(seed): 0.687 Mastr(seed): 0.336 Positive Predictive Value RNASampler(seed): 0.859 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	? 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	? Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.668 RNASampler(seed): 0.633 Sensitivity Multilign(seed): 0.629 RNASampler(seed): 0.517 Positive Predictive Value Multilign(seed): 0.727 RNASampler(seed): 0.793 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.630 RNASampler(seed): 0.232 Sensitivity PETfold_pre2.0(seed): 0.553 RNASampler(seed): 0.211 Positive Predictive Value PETfold_pre2.0(seed): 0.724 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.685 RNASampler(seed): 0.683 Sensitivity TurboFold(20): 0.681 RNASampler(seed): 0.593 Positive Predictive Value TurboFold(20): 0.697 RNASampler(seed): 0.794 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(seed): N/A CMfinder(20): N/A Sensitivity RNASampler(seed): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.397 PETfold_pre2.0(20): 0.247 Sensitivity RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Positive Predictive Value RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.581 TurboFold(seed): 0.560 Sensitivity RNASampler(seed): 0.495 TurboFold(seed): 0.569 Positive Predictive Value RNASampler(seed): 0.692 TurboFold(seed): 0.564 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.683 PPfold(20): 0.676 Sensitivity RNASampler(seed): 0.593 PPfold(20): 0.604 Positive Predictive Value RNASampler(seed): 0.794 PPfold(20): 0.764 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.232 NanoFolder: 0.207 Sensitivity RNASampler(seed): 0.211 NanoFolder: 0.289 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.159 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 Carnac(seed): 0.428 Sensitivity RNASampler(seed): 0.687 Carnac(seed): 0.186 Positive Predictive Value RNASampler(seed): 0.859 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08
Mastr(20)	27 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 Mastr(20): 0.635 Sensitivity MXScarna(seed): 0.743 Mastr(20): 0.478 Positive Predictive Value MXScarna(seed): 0.829 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Mastr(20): 0.628 Sensitivity CentroidAlifold(20): 0.716 Mastr(20): 0.471 Positive Predictive Value CentroidAlifold(20): 0.921 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.708 Mastr(20): 0.628 Sensitivity CentroidFold: 0.697 Mastr(20): 0.471 Positive Predictive Value CentroidFold: 0.724 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	28 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.782 Mastr(20): 0.636 Sensitivity RNAalifold(20): 0.690 Mastr(20): 0.483 Positive Predictive Value RNAalifold(20): 0.889 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.712 Mastr(20): 0.636 Sensitivity Sfold: 0.689 Mastr(20): 0.483 Positive Predictive Value Sfold: 0.742 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.720 Mastr(20): 0.582 Sensitivity Fold: 0.735 Mastr(20): 0.407 Positive Predictive Value Fold: 0.710 Mastr(20): 0.840 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.41358941668e-08	28 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.765 Mastr(20): 0.636 Sensitivity RNASampler(20): 0.671 Mastr(20): 0.483 Positive Predictive Value RNASampler(20): 0.875 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.761 Mastr(20): 0.636 Sensitivity MXScarna(20): 0.727 Mastr(20): 0.483 Positive Predictive Value MXScarna(20): 0.800 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	9 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Mastr(20): 0.694 Sensitivity CentroidHomfold‑LAST: 0.723 Mastr(20): 0.573 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	28 HotKnots vs Mastr(20) Matthews Correlation Coefficient HotKnots: 0.697 Mastr(20): 0.636 Sensitivity HotKnots: 0.718 Mastr(20): 0.483 Positive Predictive Value HotKnots: 0.682 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.711 Mastr(20): 0.636 Sensitivity UNAFold: 0.716 Mastr(20): 0.483 Positive Predictive Value UNAFold: 0.711 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.656 Mastr(20): 0.636 Sensitivity Contrafold: 0.675 Mastr(20): 0.483 Positive Predictive Value Contrafold: 0.643 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.0019918072826	8 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.684 Mastr(20): 0.674 Sensitivity IPknot: 0.654 Mastr(20): 0.548 Positive Predictive Value IPknot: 0.724 Mastr(20): 0.837 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.698 Mastr(20): 0.581 Sensitivity ContextFold: 0.638 Mastr(20): 0.431 Positive Predictive Value ContextFold: 0.771 Mastr(20): 0.794 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	28 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.699 Mastr(20): 0.636 Sensitivity RNAshapes: 0.704 Mastr(20): 0.483 Positive Predictive Value RNAshapes: 0.699 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.700 Mastr(20): 0.628 Sensitivity MaxExpect: 0.710 Mastr(20): 0.471 Positive Predictive Value MaxExpect: 0.696 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.59469103578e-08	28 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.699 Mastr(20): 0.636 Sensitivity PknotsRG: 0.719 Mastr(20): 0.483 Positive Predictive Value PknotsRG: 0.684 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.687 Mastr(20): 0.636 Sensitivity RNAfold: 0.701 Mastr(20): 0.483 Positive Predictive Value RNAfold: 0.678 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.686 Mastr(20): 0.582 Sensitivity ProbKnot: 0.713 Mastr(20): 0.407 Positive Predictive Value ProbKnot: 0.665 Mastr(20): 0.840 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.84041289224e-08	28 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.704 Mastr(20): 0.636 Sensitivity Murlet(20): 0.596 Mastr(20): 0.483 Positive Predictive Value Murlet(20): 0.837 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 Mastr(20): 0.628 Sensitivity CentroidAlifold(seed): 0.580 Mastr(20): 0.471 Positive Predictive Value CentroidAlifold(seed): 0.918 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	19 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.642 Afold: 0.627 Sensitivity Mastr(20): 0.478 Afold: 0.650 Positive Predictive Value Mastr(20): 0.868 Afold: 0.611 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.61352083003e-05	28 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.663 Mastr(20): 0.636 Sensitivity RNAsubopt: 0.686 Mastr(20): 0.483 Positive Predictive Value RNAsubopt: 0.647 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 4.27071136365e-07	28 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.696 Mastr(20): 0.636 Sensitivity Carnac(20): 0.518 Mastr(20): 0.483 Positive Predictive Value Carnac(20): 0.941 Mastr(20): 0.845 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	14 Cylofold vs Mastr(20) Matthews Correlation Coefficient Cylofold: 0.703 Mastr(20): 0.666 Sensitivity Cylofold: 0.703 Mastr(20): 0.503 Positive Predictive Value Cylofold: 0.711 Mastr(20): 0.890 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.20167918023e-08	28 Mastr(20) vs McQFold Matthews Correlation Coefficient Mastr(20): 0.636 McQFold: 0.625 Sensitivity Mastr(20): 0.483 McQFold: 0.638 Positive Predictive Value Mastr(20): 0.845 McQFold: 0.619 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.000235226116958	7 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Mastr(20): 0.649 Sensitivity CRWrnafold: 0.683 Mastr(20): 0.524 Positive Predictive Value CRWrnafold: 0.663 Mastr(20): 0.811 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	18 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 Mastr(20): 0.486 Sensitivity RNAalifold(seed): 0.492 Mastr(20): 0.307 Positive Predictive Value RNAalifold(seed): 0.925 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	27 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.682 Pknots: 0.639 Sensitivity Mastr(20): 0.555 Pknots: 0.683 Positive Predictive Value Mastr(20): 0.845 Pknots: 0.606 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	8 RNASampler(seed) vs Mastr(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 Mastr(20): 0.678 Sensitivity RNASampler(seed): 0.658 Mastr(20): 0.519 Positive Predictive Value RNASampler(seed): 0.782 Mastr(20): 0.891 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		- RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.663 Mastr(20): 0.635 Sensitivity RSpredict(20): 0.593 Mastr(20): 0.478 Positive Predictive Value RSpredict(20): 0.748 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 8.01557756351e-08	+ Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.824 Alterna: 0.671 Sensitivity Mastr(20): 0.761 Alterna: 0.680 Positive Predictive Value Mastr(20): 0.900 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	? Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.581 RNASLOpt: 0.560 Sensitivity Mastr(20): 0.431 RNASLOpt: 0.543 Positive Predictive Value Mastr(20): 0.794 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.663 Multilign(20): 0.612 Sensitivity Mastr(20): 0.519 Multilign(20): 0.581 Positive Predictive Value Mastr(20): 0.856 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	+ Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.636 Vsfold4: 0.531 Sensitivity Mastr(20): 0.483 Vsfold4: 0.528 Positive Predictive Value Mastr(20): 0.845 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.721 MCFold: 0.520 Sensitivity Mastr(20): 0.581 MCFold: 0.579 Positive Predictive Value Mastr(20): 0.901 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.674 RNAwolf: 0.453 Sensitivity Mastr(20): 0.548 RNAwolf: 0.447 Positive Predictive Value Mastr(20): 0.837 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.587 Mastr(20): 0.539 Sensitivity Murlet(seed): 0.377 Mastr(20): 0.380 Positive Predictive Value Murlet(seed): 0.921 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.636 Vsfold5: 0.484 Sensitivity Mastr(20): 0.483 Vsfold5: 0.488 Positive Predictive Value Mastr(20): 0.845 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.635 RSpredict(seed): 0.298 Sensitivity Mastr(20): 0.478 RSpredict(seed): 0.156 Positive Predictive Value Mastr(20): 0.849 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.765 RDfolder: 0.624 Sensitivity Mastr(20): 0.676 RDfolder: 0.591 Positive Predictive Value Mastr(20): 0.874 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.16131455263e-08	? Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.674 PPfold(seed): 0.031 Sensitivity Mastr(20): 0.548 PPfold(seed): 0.005 Positive Predictive Value Mastr(20): 0.837 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.636 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.483 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.845 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-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	? Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Mastr(20): 0.698 Sensitivity Multilign(seed): 0.750 Mastr(20): 0.630 Positive Predictive Value Multilign(seed): 0.852 Mastr(20): 0.788 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Mastr(20): 0.581 Sensitivity PETfold_pre2.0(seed): 0.784 Mastr(20): 0.431 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Mastr(20): 0.794 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Mastr(20): 0.694 Sensitivity TurboFold(20): 0.694 Mastr(20): 0.573 Positive Predictive Value TurboFold(20): 0.781 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(20): N/A Sensitivity Mastr(20): N/A CMfinder(20): N/A Positive Predictive Value Mastr(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Mastr(20): 0.581 Sensitivity PETfold_pre2.0(20): 0.707 Mastr(20): 0.431 Positive Predictive Value PETfold_pre2.0(20): 0.796 Mastr(20): 0.794 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Mastr(20): 0.673 Sensitivity TurboFold(seed): 0.684 Mastr(20): 0.551 Positive Predictive Value TurboFold(seed): 0.749 Mastr(20): 0.831 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.780 Mastr(20): 0.694 Sensitivity PPfold(20): 0.714 Mastr(20): 0.573 Positive Predictive Value PPfold(20): 0.860 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.601 NanoFolder: 0.389 Sensitivity Mastr(20): 0.465 NanoFolder: 0.475 Positive Predictive Value Mastr(20): 0.783 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.634 Carnac(seed): 0.231 Sensitivity Mastr(20): 0.495 Carnac(seed): 0.054 Positive Predictive Value Mastr(20): 0.819 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08
RSpredict(20)	27 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.783 RSpredict(20): 0.663 Sensitivity MXScarna(seed): 0.743 RSpredict(20): 0.593 Positive Predictive Value MXScarna(seed): 0.829 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RSpredict(20): 0.660 Sensitivity CentroidAlifold(20): 0.716 RSpredict(20): 0.590 Positive Predictive Value CentroidAlifold(20): 0.921 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	26 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.708 RSpredict(20): 0.660 Sensitivity CentroidFold: 0.697 RSpredict(20): 0.590 Positive Predictive Value CentroidFold: 0.724 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	27 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.775 RSpredict(20): 0.663 Sensitivity RNAalifold(20): 0.682 RSpredict(20): 0.593 Positive Predictive Value RNAalifold(20): 0.884 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.710 RSpredict(20): 0.663 Sensitivity Sfold: 0.686 RSpredict(20): 0.593 Positive Predictive Value Sfold: 0.739 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.720 RSpredict(20): 0.619 Sensitivity Fold: 0.735 RSpredict(20): 0.547 Positive Predictive Value Fold: 0.710 RSpredict(20): 0.707 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.51155234096e-08	27 RNASampler(20) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(20): 0.766 RSpredict(20): 0.663 Sensitivity RNASampler(20): 0.676 RSpredict(20): 0.593 Positive Predictive Value RNASampler(20): 0.872 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	27 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.760 RSpredict(20): 0.663 Sensitivity MXScarna(20): 0.726 RSpredict(20): 0.593 Positive Predictive Value MXScarna(20): 0.800 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	9 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 RSpredict(20): 0.582 Sensitivity CentroidHomfold‑LAST: 0.723 RSpredict(20): 0.519 Positive Predictive Value CentroidHomfold‑LAST: 0.851 RSpredict(20): 0.665 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	27 HotKnots vs RSpredict(20) Matthews Correlation Coefficient HotKnots: 0.694 RSpredict(20): 0.663 Sensitivity HotKnots: 0.716 RSpredict(20): 0.593 Positive Predictive Value HotKnots: 0.678 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.709 RSpredict(20): 0.663 Sensitivity UNAFold: 0.714 RSpredict(20): 0.593 Positive Predictive Value UNAFold: 0.708 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.664 RSpredict(20): 0.663 Sensitivity Contrafold: 0.682 RSpredict(20): 0.593 Positive Predictive Value Contrafold: 0.652 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 0.000632812409388	8 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.684 RSpredict(20): 0.586 Sensitivity IPknot: 0.654 RSpredict(20): 0.521 Positive Predictive Value IPknot: 0.724 RSpredict(20): 0.671 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.698 RSpredict(20): 0.428 Sensitivity ContextFold: 0.638 RSpredict(20): 0.362 Positive Predictive Value ContextFold: 0.771 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	27 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.703 RSpredict(20): 0.663 Sensitivity RNAshapes: 0.709 RSpredict(20): 0.593 Positive Predictive Value RNAshapes: 0.703 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.54865340847e-08	26 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.700 RSpredict(20): 0.660 Sensitivity MaxExpect: 0.710 RSpredict(20): 0.590 Positive Predictive Value MaxExpect: 0.696 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.59469103578e-08	27 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.694 RSpredict(20): 0.663 Sensitivity PknotsRG: 0.714 RSpredict(20): 0.593 Positive Predictive Value PknotsRG: 0.680 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 9.34100095224e-08	27 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.683 RSpredict(20): 0.663 Sensitivity RNAfold: 0.699 RSpredict(20): 0.593 Positive Predictive Value RNAfold: 0.674 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 1.43482349379e-06	18 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.686 RSpredict(20): 0.619 Sensitivity ProbKnot: 0.713 RSpredict(20): 0.547 Positive Predictive Value ProbKnot: 0.665 RSpredict(20): 0.707 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.34821445183e-08	27 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.698 RSpredict(20): 0.663 Sensitivity Murlet(20): 0.590 RSpredict(20): 0.593 Positive Predictive Value Murlet(20): 0.832 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.10776592382e-08	26 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 RSpredict(20): 0.660 Sensitivity CentroidAlifold(seed): 0.580 RSpredict(20): 0.590 Positive Predictive Value CentroidAlifold(seed): 0.918 RSpredict(20): 0.745 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	18 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.672 Afold: 0.622 Sensitivity RSpredict(20): 0.626 Afold: 0.647 Positive Predictive Value RSpredict(20): 0.727 Afold: 0.604 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	27 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.673 RSpredict(20): 0.663 Sensitivity RNAsubopt: 0.694 RSpredict(20): 0.593 Positive Predictive Value RNAsubopt: 0.659 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 2.71856013146e-06	27 Carnac(20) vs RSpredict(20) Matthews Correlation Coefficient Carnac(20): 0.695 RSpredict(20): 0.663 Sensitivity Carnac(20): 0.518 RSpredict(20): 0.593 Positive Predictive Value Carnac(20): 0.938 RSpredict(20): 0.748 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	14 Cylofold vs RSpredict(20) Matthews Correlation Coefficient Cylofold: 0.703 RSpredict(20): 0.692 Sensitivity Cylofold: 0.703 RSpredict(20): 0.619 Positive Predictive Value Cylofold: 0.711 RSpredict(20): 0.782 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.25083737045e-05	27 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.663 McQFold: 0.634 Sensitivity RSpredict(20): 0.593 McQFold: 0.646 Positive Predictive Value RSpredict(20): 0.748 McQFold: 0.629 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 6.48688953717e-08	7 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.668 RSpredict(20): 0.535 Sensitivity CRWrnafold: 0.683 RSpredict(20): 0.470 Positive Predictive Value CRWrnafold: 0.663 RSpredict(20): 0.621 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	18 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.673 RSpredict(20): 0.576 Sensitivity RNAalifold(seed): 0.492 RSpredict(20): 0.504 Positive Predictive Value RNAalifold(seed): 0.925 RSpredict(20): 0.666 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	26 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.671 Pknots: 0.653 Sensitivity RSpredict(20): 0.596 Pknots: 0.693 Positive Predictive Value RSpredict(20): 0.762 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.000165943266419	8 RNASampler(seed) vs RSpredict(20) Matthews Correlation Coefficient RNASampler(seed): 0.715 RSpredict(20): 0.638 Sensitivity RNASampler(seed): 0.658 RSpredict(20): 0.690 Positive Predictive Value RNASampler(seed): 0.782 RSpredict(20): 0.596 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	27 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.663 Mastr(20): 0.635 Sensitivity RSpredict(20): 0.593 Mastr(20): 0.478 Positive Predictive Value RSpredict(20): 0.748 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 8.01557756351e-08		+ RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.794 Alterna: 0.671 Sensitivity RSpredict(20): 0.718 Alterna: 0.680 Positive Predictive Value RSpredict(20): 0.886 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	? RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.560 RSpredict(20): 0.428 Sensitivity RNASLOpt: 0.543 RSpredict(20): 0.362 Positive Predictive Value RNASLOpt: 0.589 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.612 RSpredict(20): 0.568 Sensitivity Multilign(20): 0.581 RSpredict(20): 0.481 Positive Predictive Value Multilign(20): 0.657 RSpredict(20): 0.682 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.79167477826e-08	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.663 Vsfold4: 0.537 Sensitivity RSpredict(20): 0.593 Vsfold4: 0.530 Positive Predictive Value RSpredict(20): 0.748 Vsfold4: 0.551 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.712 MCFold: 0.520 Sensitivity RSpredict(20): 0.658 MCFold: 0.579 Positive Predictive Value RSpredict(20): 0.777 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.586 RNAwolf: 0.453 Sensitivity RSpredict(20): 0.521 RNAwolf: 0.447 Positive Predictive Value RSpredict(20): 0.671 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	- Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.587 RSpredict(20): 0.566 Sensitivity Murlet(seed): 0.377 RSpredict(20): 0.489 Positive Predictive Value Murlet(seed): 0.921 RSpredict(20): 0.666 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52316175909e-05	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.663 Vsfold5: 0.500 Sensitivity RSpredict(20): 0.593 Vsfold5: 0.501 Positive Predictive Value RSpredict(20): 0.748 Vsfold5: 0.509 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.663 RSpredict(seed): 0.298 Sensitivity RSpredict(20): 0.593 RSpredict(seed): 0.156 Positive Predictive Value RSpredict(20): 0.748 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.737 RDfolder: 0.624 Sensitivity RSpredict(20): 0.642 RDfolder: 0.591 Positive Predictive Value RSpredict(20): 0.857 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	? RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.586 PPfold(seed): 0.031 Sensitivity RSpredict(20): 0.521 PPfold(seed): 0.005 Positive Predictive Value RSpredict(20): 0.671 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.663 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.593 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	? RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.795 RSpredict(20): 0.675 Sensitivity Multilign(seed): 0.750 RSpredict(20): 0.610 Positive Predictive Value Multilign(seed): 0.852 RSpredict(20): 0.763 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RSpredict(20): 0.428 Sensitivity PETfold_pre2.0(seed): 0.784 RSpredict(20): 0.362 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.733 RSpredict(20): 0.582 Sensitivity TurboFold(20): 0.694 RSpredict(20): 0.519 Positive Predictive Value TurboFold(20): 0.781 RSpredict(20): 0.665 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(20): N/A Sensitivity RSpredict(20): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RSpredict(20): 0.428 Sensitivity PETfold_pre2.0(20): 0.707 RSpredict(20): 0.362 Positive Predictive Value PETfold_pre2.0(20): 0.796 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 RSpredict(20): 0.574 Sensitivity TurboFold(seed): 0.684 RSpredict(20): 0.519 Positive Predictive Value TurboFold(seed): 0.749 RSpredict(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.780 RSpredict(20): 0.582 Sensitivity PPfold(20): 0.714 RSpredict(20): 0.519 Positive Predictive Value PPfold(20): 0.860 RSpredict(20): 0.665 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.414 NanoFolder: 0.389 Sensitivity RSpredict(20): 0.356 NanoFolder: 0.475 Positive Predictive Value RSpredict(20): 0.493 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.628 Carnac(seed): 0.231 Sensitivity RSpredict(20): 0.553 Carnac(seed): 0.054 Positive Predictive Value RSpredict(20): 0.722 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08
Alterna	29 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.828 Alterna: 0.757 Sensitivity MXScarna(seed): 0.776 Alterna: 0.765 Positive Predictive Value MXScarna(seed): 0.892 Alterna: 0.760 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	12 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.886 Alterna: 0.658 Sensitivity CentroidAlifold(20): 0.823 Alterna: 0.667 Positive Predictive Value CentroidAlifold(20): 0.958 Alterna: 0.661 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.39551335374e-08	76 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.848 Alterna: 0.750 Sensitivity CentroidFold: 0.827 Alterna: 0.762 Positive Predictive Value CentroidFold: 0.877 Alterna: 0.750 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.865 Alterna: 0.671 Sensitivity RNAalifold(20): 0.803 Alterna: 0.680 Positive Predictive Value RNAalifold(20): 0.937 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	89 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.827 Alterna: 0.767 Sensitivity Sfold: 0.809 Alterna: 0.777 Positive Predictive Value Sfold: 0.854 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	56 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.845 Alterna: 0.788 Sensitivity Fold: 0.853 Alterna: 0.801 Positive Predictive Value Fold: 0.846 Alterna: 0.785 Number of pairs reference - predicted secondary structure: 56 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.912 Alterna: 0.671 Sensitivity RNASampler(20): 0.846 Alterna: 0.680 Positive Predictive Value RNASampler(20): 0.986 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.80908287419e-08	13 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.846 Alterna: 0.671 Sensitivity MXScarna(20): 0.803 Alterna: 0.680 Positive Predictive Value MXScarna(20): 0.897 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.34821445183e-08	29 CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.810 Alterna: 0.711 Sensitivity CentroidHomfold‑LAST: 0.719 Alterna: 0.734 Positive Predictive Value CentroidHomfold‑LAST: 0.922 Alterna: 0.704 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	89 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.830 Alterna: 0.767 Sensitivity HotKnots: 0.835 Alterna: 0.777 Positive Predictive Value HotKnots: 0.833 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.831 Alterna: 0.767 Sensitivity UNAFold: 0.829 Alterna: 0.777 Positive Predictive Value UNAFold: 0.842 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.845 Alterna: 0.767 Sensitivity Contrafold: 0.840 Alterna: 0.777 Positive Predictive Value Contrafold: 0.857 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.791 Alterna: 0.684 Sensitivity IPknot: 0.754 Alterna: 0.705 Positive Predictive Value IPknot: 0.840 Alterna: 0.679 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	14 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.782 Alterna: 0.691 Sensitivity ContextFold: 0.757 Alterna: 0.701 Positive Predictive Value ContextFold: 0.820 Alterna: 0.697 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.00627773251e-08	89 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.806 Alterna: 0.767 Sensitivity RNAshapes: 0.803 Alterna: 0.777 Positive Predictive Value RNAshapes: 0.819 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	70 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.815 Alterna: 0.750 Sensitivity MaxExpect: 0.815 Alterna: 0.764 Positive Predictive Value MaxExpect: 0.823 Alterna: 0.749 Number of pairs reference - predicted secondary structure: 70 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.803 Alterna: 0.767 Sensitivity PknotsRG: 0.808 Alterna: 0.777 Positive Predictive Value PknotsRG: 0.808 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.817 Alterna: 0.767 Sensitivity RNAfold: 0.820 Alterna: 0.777 Positive Predictive Value RNAfold: 0.824 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.819 Alterna: 0.781 Sensitivity ProbKnot: 0.847 Alterna: 0.798 Positive Predictive Value ProbKnot: 0.801 Alterna: 0.776 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.780 Alterna: 0.671 Sensitivity Murlet(20): 0.695 Alterna: 0.680 Positive Predictive Value Murlet(20): 0.882 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.02510705504e-08	28 Alterna vs CentroidAlifold(seed) Matthews Correlation Coefficient Alterna: 0.753 CentroidAlifold(seed): 0.673 Sensitivity Alterna: 0.761 CentroidAlifold(seed): 0.531 Positive Predictive Value Alterna: 0.756 CentroidAlifold(seed): 0.865 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	69 Afold vs Alterna Matthews Correlation Coefficient Afold: 0.810 Alterna: 0.778 Sensitivity Afold: 0.820 Alterna: 0.785 Positive Predictive Value Afold: 0.810 Alterna: 0.782 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.795 Alterna: 0.767 Sensitivity RNAsubopt: 0.795 Alterna: 0.777 Positive Predictive Value RNAsubopt: 0.805 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.788 Alterna: 0.671 Sensitivity Carnac(20): 0.649 Alterna: 0.680 Positive Predictive Value Carnac(20): 0.966 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.27752322258e-08	45 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.790 Alterna: 0.763 Sensitivity Cylofold: 0.770 Alterna: 0.779 Positive Predictive Value Cylofold: 0.821 Alterna: 0.759 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.807 Alterna: 0.767 Sensitivity McQFold: 0.778 Alterna: 0.777 Positive Predictive Value McQFold: 0.848 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	19 CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.673 Alterna: 0.669 Sensitivity CRWrnafold: 0.690 Alterna: 0.690 Positive Predictive Value CRWrnafold: 0.674 Alterna: 0.665 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 5.53672647526e-06	18 Alterna vs RNAalifold(seed) Matthews Correlation Coefficient Alterna: 0.844 RNAalifold(seed): 0.743 Sensitivity Alterna: 0.833 RNAalifold(seed): 0.644 Positive Predictive Value Alterna: 0.863 RNAalifold(seed): 0.869 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.61939086268e-08	89 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.812 Alterna: 0.767 Sensitivity Pknots: 0.820 Alterna: 0.777 Positive Predictive Value Pknots: 0.815 Alterna: 0.769 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 Alterna vs RNASampler(seed) Matthews Correlation Coefficient Alterna: 0.874 RNASampler(seed): 0.818 Sensitivity Alterna: 0.859 RNASampler(seed): 0.715 Positive Predictive Value Alterna: 0.896 RNASampler(seed): 0.945 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.52609899389e-08	13 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.824 Alterna: 0.671 Sensitivity Mastr(20): 0.761 Alterna: 0.680 Positive Predictive Value Mastr(20): 0.900 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.50323628132e-08	13 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.794 Alterna: 0.671 Sensitivity RSpredict(20): 0.718 Alterna: 0.680 Positive Predictive Value RSpredict(20): 0.886 Alterna: 0.674 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08		+ Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.691 RNASLOpt: 0.643 Sensitivity Alterna: 0.701 RNASLOpt: 0.597 Positive Predictive Value Alterna: 0.697 RNASLOpt: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08	? Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.811 Alterna: 0.750 Sensitivity Multilign(20): 0.811 Alterna: 0.756 Positive Predictive Value Multilign(20): 0.820 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs Vsfold4 Matthews Correlation Coefficient Alterna: 0.767 Vsfold4: 0.750 Sensitivity Alterna: 0.777 Vsfold4: 0.725 Positive Predictive Value Alterna: 0.769 Vsfold4: 0.788 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.780 MCFold: 0.706 Sensitivity Alterna: 0.789 MCFold: 0.741 Positive Predictive Value Alterna: 0.783 MCFold: 0.689 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.684 RNAwolf: 0.678 Sensitivity Alterna: 0.705 RNAwolf: 0.674 Positive Predictive Value Alterna: 0.679 RNAwolf: 0.698 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.00781880629872	+ Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.840 Murlet(seed): 0.656 Sensitivity Alterna: 0.828 Murlet(seed): 0.524 Positive Predictive Value Alterna: 0.860 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.767 Vsfold5: 0.714 Sensitivity Alterna: 0.777 Vsfold5: 0.705 Positive Predictive Value Alterna: 0.769 Vsfold5: 0.737 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.757 RSpredict(seed): 0.502 Sensitivity Alterna: 0.765 RSpredict(seed): 0.350 Positive Predictive Value Alterna: 0.760 RSpredict(seed): 0.739 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.768 RDfolder: 0.690 Sensitivity Alterna: 0.777 RDfolder: 0.652 Positive Predictive Value Alterna: 0.771 RDfolder: 0.745 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.671 PPfold(seed): 0.185 Sensitivity Alterna: 0.677 PPfold(seed): 0.047 Positive Predictive Value Alterna: 0.677 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.757 Mastr(seed): 0.421 Sensitivity Alterna: 0.765 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.760 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	? CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): N/A Alterna: N/A Sensitivity CMfinder(seed): N/A Alterna: N/A Positive Predictive Value CMfinder(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.702 Multilign(seed): 0.668 Sensitivity Alterna: 0.685 Multilign(seed): 0.629 Positive Predictive Value Alterna: 0.735 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.812 Alterna: 0.648 Sensitivity PETfold_pre2.0(seed): 0.745 Alterna: 0.655 Positive Predictive Value PETfold_pre2.0(seed): 0.891 Alterna: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.829 Alterna: 0.750 Sensitivity TurboFold(20): 0.800 Alterna: 0.756 Positive Predictive Value TurboFold(20): 0.867 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.702 TurboFold(seed): 0.667 Sensitivity Alterna: 0.685 TurboFold(seed): 0.640 Positive Predictive Value Alterna: 0.735 TurboFold(seed): 0.713 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.842 Alterna: 0.750 Sensitivity PPfold(20): 0.767 Alterna: 0.756 Positive Predictive Value PPfold(20): 0.932 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.756 NanoFolder: 0.610 Sensitivity Alterna: 0.753 NanoFolder: 0.706 Positive Predictive Value Alterna: 0.771 NanoFolder: 0.545 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.840 Carnac(seed): 0.420 Sensitivity Alterna: 0.828 Carnac(seed): 0.180 Positive Predictive Value Alterna: 0.860 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08
RNASLOpt	8 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.679 RNASLOpt: 0.560 Sensitivity MXScarna(seed): 0.620 RNASLOpt: 0.526 Positive Predictive Value MXScarna(seed): 0.752 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.779 RNASLOpt: 0.560 Sensitivity CentroidAlifold(20): 0.672 RNASLOpt: 0.543 Positive Predictive Value CentroidAlifold(20): 0.907 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.747 RNASLOpt: 0.679 Sensitivity CentroidFold: 0.721 RNASLOpt: 0.649 Positive Predictive Value CentroidFold: 0.783 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.656 RNASLOpt: 0.560 Sensitivity RNAalifold(20): 0.578 RNASLOpt: 0.543 Positive Predictive Value RNAalifold(20): 0.753 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.722 RNASLOpt: 0.679 Sensitivity Sfold: 0.697 RNASLOpt: 0.649 Positive Predictive Value Sfold: 0.758 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.696 RNASLOpt: 0.679 Sensitivity Fold: 0.699 RNASLOpt: 0.649 Positive Predictive Value Fold: 0.704 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.27481660653e-07	5 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.686 RNASLOpt: 0.560 Sensitivity RNASampler(20): 0.603 RNASLOpt: 0.543 Positive Predictive Value RNASampler(20): 0.787 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.586 RNASLOpt: 0.560 Sensitivity MXScarna(20): 0.543 RNASLOpt: 0.543 Positive Predictive Value MXScarna(20): 0.643 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	29 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.752 RNASLOpt: 0.668 Sensitivity CentroidHomfold‑LAST: 0.664 RNASLOpt: 0.638 Positive Predictive Value CentroidHomfold‑LAST: 0.861 RNASLOpt: 0.711 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.734 RNASLOpt: 0.679 Sensitivity HotKnots: 0.753 RNASLOpt: 0.649 Positive Predictive Value HotKnots: 0.725 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.690 RNASLOpt: 0.679 Sensitivity UNAFold: 0.697 RNASLOpt: 0.649 Positive Predictive Value UNAFold: 0.695 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.90626908729e-06	30 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.745 RNASLOpt: 0.679 Sensitivity Contrafold: 0.737 RNASLOpt: 0.649 Positive Predictive Value Contrafold: 0.763 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.765 RNASLOpt: 0.679 Sensitivity IPknot: 0.735 RNASLOpt: 0.649 Positive Predictive Value IPknot: 0.805 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.816 RNASLOpt: 0.679 Sensitivity ContextFold: 0.780 RNASLOpt: 0.649 Positive Predictive Value ContextFold: 0.861 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.713 RNASLOpt: 0.679 Sensitivity RNAshapes: 0.715 RNASLOpt: 0.649 Positive Predictive Value RNAshapes: 0.721 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.693 RNASLOpt: 0.679 Sensitivity MaxExpect: 0.690 RNASLOpt: 0.649 Positive Predictive Value MaxExpect: 0.707 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.06521910535e-06	30 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.735 RNASLOpt: 0.679 Sensitivity PknotsRG: 0.751 RNASLOpt: 0.649 Positive Predictive Value PknotsRG: 0.729 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.719 RNASLOpt: 0.679 Sensitivity RNAfold: 0.719 RNASLOpt: 0.649 Positive Predictive Value RNAfold: 0.729 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.696 RNASLOpt: 0.679 Sensitivity ProbKnot: 0.717 RNASLOpt: 0.649 Positive Predictive Value ProbKnot: 0.686 RNASLOpt: 0.721 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.02208072244e-07	5 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.594 RNASLOpt: 0.560 Sensitivity Murlet(20): 0.500 RNASLOpt: 0.543 Positive Predictive Value Murlet(20): 0.716 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.646 RNASLOpt: 0.560 Sensitivity CentroidAlifold(seed): 0.427 RNASLOpt: 0.526 Positive Predictive Value CentroidAlifold(seed): 0.986 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	18 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.764 RNASLOpt: 0.727 Sensitivity Afold: 0.781 RNASLOpt: 0.721 Positive Predictive Value Afold: 0.755 RNASLOpt: 0.743 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.69132796717e-08	30 RNASLOpt vs RNAsubopt Matthews Correlation Coefficient RNASLOpt: 0.679 RNAsubopt: 0.664 Sensitivity RNASLOpt: 0.649 RNAsubopt: 0.676 Positive Predictive Value RNASLOpt: 0.721 RNAsubopt: 0.664 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 1.39704516867e-06	5 Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.562 RNASLOpt: 0.560 Sensitivity Carnac(20): 0.397 RNASLOpt: 0.543 Positive Predictive Value Carnac(20): 0.807 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	23 Cylofold vs RNASLOpt Matthews Correlation Coefficient Cylofold: 0.666 RNASLOpt: 0.663 Sensitivity Cylofold: 0.646 RNASLOpt: 0.620 Positive Predictive Value Cylofold: 0.699 RNASLOpt: 0.723 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 0.209525580533	29 RNASLOpt vs McQFold Matthews Correlation Coefficient RNASLOpt: 0.668 McQFold: 0.662 Sensitivity RNASLOpt: 0.638 McQFold: 0.661 Positive Predictive Value RNASLOpt: 0.711 McQFold: 0.675 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 6.97652614729e-06	26 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.688 RNASLOpt: 0.660 Sensitivity CRWrnafold: 0.684 RNASLOpt: 0.632 Positive Predictive Value CRWrnafold: 0.702 RNASLOpt: 0.702 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	5 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.542 RNASLOpt: 0.461 Sensitivity RNAalifold(seed): 0.392 RNASLOpt: 0.443 Positive Predictive Value RNAalifold(seed): 0.760 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	30 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.679 Pknots: 0.628 Sensitivity RNASLOpt: 0.649 Pknots: 0.649 Positive Predictive Value RNASLOpt: 0.721 Pknots: 0.620 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 7.03886575525e-08	2 RNASLOpt vs RNASampler(seed) Matthews Correlation Coefficient RNASLOpt: 0.358 RNASampler(seed): 0.232 Sensitivity RNASLOpt: 0.395 RNASampler(seed): 0.211 Positive Predictive Value RNASLOpt: 0.333 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.581 RNASLOpt: 0.560 Sensitivity Mastr(20): 0.431 RNASLOpt: 0.543 Positive Predictive Value Mastr(20): 0.794 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.560 RSpredict(20): 0.428 Sensitivity RNASLOpt: 0.543 RSpredict(20): 0.362 Positive Predictive Value RNASLOpt: 0.589 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	14 Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: 0.691 RNASLOpt: 0.643 Sensitivity Alterna: 0.701 RNASLOpt: 0.597 Positive Predictive Value Alterna: 0.697 RNASLOpt: 0.711 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.43573297697e-08		? Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.583 RNASLOpt: 0.560 Sensitivity Multilign(20): 0.578 RNASLOpt: 0.543 Positive Predictive Value Multilign(20): 0.598 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.679 Vsfold4: 0.618 Sensitivity RNASLOpt: 0.649 Vsfold4: 0.602 Positive Predictive Value RNASLOpt: 0.721 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.707 MCFold: 0.683 Sensitivity RNASLOpt: 0.683 MCFold: 0.710 Positive Predictive Value RNASLOpt: 0.744 MCFold: 0.668 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.679 RNAwolf: 0.555 Sensitivity RNASLOpt: 0.649 RNAwolf: 0.544 Positive Predictive Value RNASLOpt: 0.721 RNAwolf: 0.583 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.495 RNASLOpt: 0.461 Sensitivity Murlet(seed): 0.340 RNASLOpt: 0.443 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.673 Vsfold5: 0.543 Sensitivity RNASLOpt: 0.643 Vsfold5: 0.547 Positive Predictive Value RNASLOpt: 0.715 Vsfold5: 0.556 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	? RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.560 RSpredict(seed): 0.131 Sensitivity RNASLOpt: 0.526 RSpredict(seed): 0.070 Positive Predictive Value RNASLOpt: 0.608 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.642 RDfolder: 0.537 Sensitivity RNASLOpt: 0.587 RDfolder: 0.485 Positive Predictive Value RNASLOpt: 0.723 RDfolder: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	? RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.560 PPfold(seed): 0.146 Sensitivity RNASLOpt: 0.526 PPfold(seed): 0.041 Positive Predictive Value RNASLOpt: 0.608 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.560 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.526 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.608 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): N/A RNASLOpt: N/A Sensitivity CMfinder(seed): N/A RNASLOpt: N/A Positive Predictive Value CMfinder(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.458 RNASLOpt: 0.375 Sensitivity Multilign(seed): 0.404 RNASLOpt: 0.319 Positive Predictive Value Multilign(seed): 0.543 RNASLOpt: 0.469 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNASLOpt: 0.560 Sensitivity PETfold_pre2.0(seed): 0.772 RNASLOpt: 0.526 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.655 RNASLOpt: 0.560 Sensitivity TurboFold(20): 0.612 RNASLOpt: 0.543 Positive Predictive Value TurboFold(20): 0.710 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: N/A CMfinder(20): N/A Sensitivity RNASLOpt: N/A CMfinder(20): N/A Positive Predictive Value RNASLOpt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNASLOpt: 0.560 Sensitivity PETfold_pre2.0(20): 0.707 RNASLOpt: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.552 RNASLOpt: 0.551 Sensitivity TurboFold(seed): 0.530 RNASLOpt: 0.522 Positive Predictive Value TurboFold(seed): 0.587 RNASLOpt: 0.593 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.732 RNASLOpt: 0.560 Sensitivity PPfold(20): 0.672 RNASLOpt: 0.543 Positive Predictive Value PPfold(20): 0.804 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.680 NanoFolder: 0.562 Sensitivity RNASLOpt: 0.663 NanoFolder: 0.656 Positive Predictive Value RNASLOpt: 0.707 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.95070920198e-08	? RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.551 Carnac(seed): 0.172 Sensitivity RNASLOpt: 0.522 Carnac(seed): 0.030 Positive Predictive Value RNASLOpt: 0.593 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
Multilign(20)	10 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.732 Multilign(20): 0.612 Sensitivity MXScarna(seed): 0.689 Multilign(20): 0.581 Positive Predictive Value MXScarna(seed): 0.787 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.16841705202e-08	10 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.762 Multilign(20): 0.612 Sensitivity CentroidAlifold(20): 0.639 Multilign(20): 0.581 Positive Predictive Value CentroidAlifold(20): 0.917 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.03576421863e-08	10 CentroidFold vs Multilign(20) Matthews Correlation Coefficient CentroidFold: 0.633 Multilign(20): 0.612 Sensitivity CentroidFold: 0.606 Multilign(20): 0.581 Positive Predictive Value CentroidFold: 0.673 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.60185372136e-08	10 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.689 Multilign(20): 0.612 Sensitivity RNAalifold(20): 0.598 Multilign(20): 0.581 Positive Predictive Value RNAalifold(20): 0.804 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.88760648134e-09	10 Sfold vs Multilign(20) Matthews Correlation Coefficient Sfold: 0.672 Multilign(20): 0.612 Sensitivity Sfold: 0.639 Multilign(20): 0.581 Positive Predictive Value Sfold: 0.716 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.06761512825e-08	10 Fold vs Multilign(20) Matthews Correlation Coefficient Fold: 0.702 Multilign(20): 0.612 Sensitivity Fold: 0.710 Multilign(20): 0.581 Positive Predictive Value Fold: 0.704 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.5161825748e-09	10 RNASampler(20) vs Multilign(20) Matthews Correlation Coefficient RNASampler(20): 0.731 Multilign(20): 0.612 Sensitivity RNASampler(20): 0.618 Multilign(20): 0.581 Positive Predictive Value RNASampler(20): 0.871 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.79651608537e-09	10 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.721 Multilign(20): 0.612 Sensitivity MXScarna(20): 0.685 Multilign(20): 0.581 Positive Predictive Value MXScarna(20): 0.767 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.53487163866e-09	9 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Multilign(20): 0.683 Sensitivity CentroidHomfold‑LAST: 0.723 Multilign(20): 0.680 Positive Predictive Value CentroidHomfold‑LAST: 0.851 Multilign(20): 0.697 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: 0.702 Multilign(20): 0.612 Sensitivity HotKnots: 0.710 Multilign(20): 0.581 Positive Predictive Value HotKnots: 0.704 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.84390417318e-09	10 UNAFold vs Multilign(20) Matthews Correlation Coefficient UNAFold: 0.656 Multilign(20): 0.612 Sensitivity UNAFold: 0.651 Multilign(20): 0.581 Positive Predictive Value UNAFold: 0.671 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.47941000302e-08	10 Contrafold vs Multilign(20) Matthews Correlation Coefficient Contrafold: 0.615 Multilign(20): 0.612 Sensitivity Contrafold: 0.614 Multilign(20): 0.581 Positive Predictive Value Contrafold: 0.627 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.323670796354	8 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.684 Multilign(20): 0.653 Sensitivity IPknot: 0.654 Multilign(20): 0.649 Positive Predictive Value IPknot: 0.724 Multilign(20): 0.667 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.698 Multilign(20): 0.583 Sensitivity ContextFold: 0.638 Multilign(20): 0.578 Positive Predictive Value ContextFold: 0.771 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 RNAshapes vs Multilign(20) Matthews Correlation Coefficient RNAshapes: 0.748 Multilign(20): 0.612 Sensitivity RNAshapes: 0.743 Multilign(20): 0.581 Positive Predictive Value RNAshapes: 0.762 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.02007144414e-09	10 MaxExpect vs Multilign(20) Matthews Correlation Coefficient MaxExpect: 0.617 Multilign(20): 0.612 Sensitivity MaxExpect: 0.622 Multilign(20): 0.581 Positive Predictive Value MaxExpect: 0.622 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.376887793106	10 PknotsRG vs Multilign(20) Matthews Correlation Coefficient PknotsRG: 0.689 Multilign(20): 0.612 Sensitivity PknotsRG: 0.701 Multilign(20): 0.581 Positive Predictive Value PknotsRG: 0.687 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 7.36926189455e-09	10 RNAfold vs Multilign(20) Matthews Correlation Coefficient RNAfold: 0.654 Multilign(20): 0.612 Sensitivity RNAfold: 0.651 Multilign(20): 0.581 Positive Predictive Value RNAfold: 0.668 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 4.09606974296e-09	10 ProbKnot vs Multilign(20) Matthews Correlation Coefficient ProbKnot: 0.621 Multilign(20): 0.612 Sensitivity ProbKnot: 0.643 Multilign(20): 0.581 Positive Predictive Value ProbKnot: 0.610 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 8.61569565073e-07	10 Murlet(20) vs Multilign(20) Matthews Correlation Coefficient Murlet(20): 0.647 Multilign(20): 0.612 Sensitivity Murlet(20): 0.544 Multilign(20): 0.581 Positive Predictive Value Murlet(20): 0.780 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.37002943053e-07	10 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.745 Multilign(20): 0.612 Sensitivity CentroidAlifold(seed): 0.602 Multilign(20): 0.581 Positive Predictive Value CentroidAlifold(seed): 0.929 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.75835195567e-08	5 Afold vs Multilign(20) Matthews Correlation Coefficient Afold: 0.576 Multilign(20): 0.474 Sensitivity Afold: 0.589 Multilign(20): 0.438 Positive Predictive Value Afold: 0.574 Multilign(20): 0.527 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	10 RNAsubopt vs Multilign(20) Matthews Correlation Coefficient RNAsubopt: 0.666 Multilign(20): 0.612 Sensitivity RNAsubopt: 0.668 Multilign(20): 0.581 Positive Predictive Value RNAsubopt: 0.674 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1568170475e-08	10 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.612 Carnac(20): 0.594 Sensitivity Multilign(20): 0.581 Carnac(20): 0.415 Positive Predictive Value Multilign(20): 0.657 Carnac(20): 0.862 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 0.000729039481942	8 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: 0.650 Multilign(20): 0.621 Sensitivity Cylofold: 0.641 Multilign(20): 0.560 Positive Predictive Value Cylofold: 0.674 Multilign(20): 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.612 McQFold: 0.600 Sensitivity Multilign(20): 0.581 McQFold: 0.606 Positive Predictive Value Multilign(20): 0.657 McQFold: 0.606 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 2.68861226834e-05	7 CRWrnafold vs Multilign(20) Matthews Correlation Coefficient CRWrnafold: 0.668 Multilign(20): 0.617 Sensitivity CRWrnafold: 0.683 Multilign(20): 0.616 Positive Predictive Value CRWrnafold: 0.663 Multilign(20): 0.627 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.656 Multilign(20): 0.545 Sensitivity RNAalifold(seed): 0.470 Multilign(20): 0.508 Positive Predictive Value RNAalifold(seed): 0.926 Multilign(20): 0.599 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.612 Pknots: 0.588 Sensitivity Multilign(20): 0.581 Pknots: 0.606 Positive Predictive Value Multilign(20): 0.657 Pknots: 0.584 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.28825501566e-05	4 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): 0.683 Multilign(20): 0.667 Sensitivity RNASampler(seed): 0.593 Multilign(20): 0.703 Positive Predictive Value RNASampler(seed): 0.794 Multilign(20): 0.640 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	10 Mastr(20) vs Multilign(20) Matthews Correlation Coefficient Mastr(20): 0.663 Multilign(20): 0.612 Sensitivity Mastr(20): 0.519 Multilign(20): 0.581 Positive Predictive Value Mastr(20): 0.856 Multilign(20): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.3551590886e-08	10 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.612 RSpredict(20): 0.568 Sensitivity Multilign(20): 0.581 RSpredict(20): 0.481 Positive Predictive Value Multilign(20): 0.657 RSpredict(20): 0.682 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.79167477826e-08	4 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.811 Alterna: 0.750 Sensitivity Multilign(20): 0.811 Alterna: 0.756 Positive Predictive Value Multilign(20): 0.820 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.583 RNASLOpt: 0.560 Sensitivity Multilign(20): 0.578 RNASLOpt: 0.543 Positive Predictive Value Multilign(20): 0.598 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.612 Vsfold4: 0.471 Sensitivity Multilign(20): 0.581 Vsfold4: 0.456 Positive Predictive Value Multilign(20): 0.657 Vsfold4: 0.502 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1568170475e-08	? Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.616 MCFold: 0.556 Sensitivity Multilign(20): 0.585 MCFold: 0.590 Positive Predictive Value Multilign(20): 0.660 MCFold: 0.536 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.653 RNAwolf: 0.453 Sensitivity Multilign(20): 0.649 RNAwolf: 0.447 Positive Predictive Value Multilign(20): 0.667 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.582 Multilign(20): 0.545 Sensitivity Murlet(seed): 0.373 Multilign(20): 0.508 Positive Predictive Value Murlet(seed): 0.920 Multilign(20): 0.599 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.612 Vsfold5: 0.463 Sensitivity Multilign(20): 0.581 Vsfold5: 0.469 Positive Predictive Value Multilign(20): 0.657 Vsfold5: 0.473 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.612 RSpredict(seed): 0.349 Sensitivity Multilign(20): 0.581 RSpredict(seed): 0.191 Positive Predictive Value Multilign(20): 0.657 RSpredict(seed): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.69265863073e-08	? Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.723 RDfolder: 0.548 Sensitivity Multilign(20): 0.691 RDfolder: 0.483 Positive Predictive Value Multilign(20): 0.769 RDfolder: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.653 PPfold(seed): 0.031 Sensitivity Multilign(20): 0.649 PPfold(seed): 0.005 Positive Predictive Value Multilign(20): 0.667 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.612 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.581 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.657 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.11462970451e-09	? 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(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Multilign(20): 0.768 Sensitivity Multilign(seed): 0.750 Multilign(20): 0.750 Positive Predictive Value Multilign(seed): 0.852 Multilign(20): 0.798 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Multilign(20): 0.583 Sensitivity PETfold_pre2.0(seed): 0.784 Multilign(20): 0.578 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Multilign(20): 0.683 Sensitivity TurboFold(20): 0.694 Multilign(20): 0.680 Positive Predictive Value TurboFold(20): 0.781 Multilign(20): 0.697 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): N/A CMfinder(20): N/A Sensitivity Multilign(20): N/A CMfinder(20): N/A Positive Predictive Value Multilign(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Multilign(20): 0.583 Sensitivity PETfold_pre2.0(20): 0.707 Multilign(20): 0.578 Positive Predictive Value PETfold_pre2.0(20): 0.796 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Multilign(20): 0.680 Sensitivity TurboFold(seed): 0.684 Multilign(20): 0.674 Positive Predictive Value TurboFold(seed): 0.749 Multilign(20): 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.780 Multilign(20): 0.683 Sensitivity PPfold(20): 0.714 Multilign(20): 0.680 Positive Predictive Value PPfold(20): 0.860 Multilign(20): 0.697 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.607 NanoFolder: 0.389 Sensitivity Multilign(20): 0.614 NanoFolder: 0.475 Positive Predictive Value Multilign(20): 0.608 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.603 Carnac(seed): 0.283 Sensitivity Multilign(20): 0.568 Carnac(seed): 0.081 Positive Predictive Value Multilign(20): 0.653 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
Vsfold4	44 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.776 Vsfold4: 0.595 Sensitivity MXScarna(seed): 0.736 Vsfold4: 0.595 Positive Predictive Value MXScarna(seed): 0.824 Vsfold4: 0.603 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Vsfold4: 0.530 Sensitivity CentroidAlifold(20): 0.716 Vsfold4: 0.524 Positive Predictive Value CentroidAlifold(20): 0.921 Vsfold4: 0.545 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	104 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.780 Vsfold4: 0.648 Sensitivity CentroidFold: 0.775 Vsfold4: 0.638 Positive Predictive Value CentroidFold: 0.791 Vsfold4: 0.667 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.782 Vsfold4: 0.531 Sensitivity RNAalifold(20): 0.690 Vsfold4: 0.528 Positive Predictive Value RNAalifold(20): 0.889 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	118 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.778 Vsfold4: 0.650 Sensitivity Sfold: 0.768 Vsfold4: 0.640 Positive Predictive Value Sfold: 0.793 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.777 Vsfold4: 0.648 Sensitivity Fold: 0.796 Vsfold4: 0.641 Positive Predictive Value Fold: 0.764 Vsfold4: 0.665 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold4: 0.531 Sensitivity RNASampler(20): 0.671 Vsfold4: 0.528 Positive Predictive Value RNASampler(20): 0.875 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	28 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.761 Vsfold4: 0.531 Sensitivity MXScarna(20): 0.727 Vsfold4: 0.528 Positive Predictive Value MXScarna(20): 0.800 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	44 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 Vsfold4: 0.636 Sensitivity CentroidHomfold‑LAST: 0.691 Vsfold4: 0.620 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Vsfold4: 0.667 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.772 Vsfold4: 0.650 Sensitivity HotKnots: 0.793 Vsfold4: 0.640 Positive Predictive Value HotKnots: 0.757 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.775 Vsfold4: 0.650 Sensitivity UNAFold: 0.786 Vsfold4: 0.640 Positive Predictive Value UNAFold: 0.769 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.769 Vsfold4: 0.650 Sensitivity Contrafold: 0.784 Vsfold4: 0.640 Positive Predictive Value Contrafold: 0.761 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.782 Vsfold4: 0.620 Sensitivity IPknot: 0.752 Vsfold4: 0.609 Positive Predictive Value IPknot: 0.820 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.816 Vsfold4: 0.618 Sensitivity ContextFold: 0.780 Vsfold4: 0.602 Positive Predictive Value ContextFold: 0.861 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.759 Vsfold4: 0.650 Sensitivity RNAshapes: 0.770 Vsfold4: 0.640 Positive Predictive Value RNAshapes: 0.755 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	98 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.754 Vsfold4: 0.643 Sensitivity MaxExpect: 0.769 Vsfold4: 0.634 Positive Predictive Value MaxExpect: 0.746 Vsfold4: 0.662 Number of pairs reference - predicted secondary structure: 98 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.752 Vsfold4: 0.650 Sensitivity PknotsRG: 0.774 Vsfold4: 0.640 Positive Predictive Value PknotsRG: 0.737 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.758 Vsfold4: 0.650 Sensitivity RNAfold: 0.776 Vsfold4: 0.640 Positive Predictive Value RNAfold: 0.748 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.741 Vsfold4: 0.623 Sensitivity ProbKnot: 0.774 Vsfold4: 0.617 Positive Predictive Value ProbKnot: 0.715 Vsfold4: 0.638 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.704 Vsfold4: 0.531 Sensitivity Murlet(20): 0.596 Vsfold4: 0.528 Positive Predictive Value Murlet(20): 0.837 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	43 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Vsfold4: 0.592 Sensitivity CentroidAlifold(seed): 0.552 Vsfold4: 0.591 Positive Predictive Value CentroidAlifold(seed): 0.870 Vsfold4: 0.600 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.747 Vsfold4: 0.656 Sensitivity Afold: 0.774 Vsfold4: 0.647 Positive Predictive Value Afold: 0.729 Vsfold4: 0.674 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.738 Vsfold4: 0.650 Sensitivity RNAsubopt: 0.757 Vsfold4: 0.640 Positive Predictive Value RNAsubopt: 0.726 Vsfold4: 0.669 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.696 Vsfold4: 0.531 Sensitivity Carnac(20): 0.518 Vsfold4: 0.528 Positive Predictive Value Carnac(20): 0.941 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	63 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.741 Vsfold4: 0.672 Sensitivity Cylofold: 0.724 Vsfold4: 0.653 Positive Predictive Value Cylofold: 0.767 Vsfold4: 0.703 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.718 Vsfold4: 0.647 Sensitivity McQFold: 0.719 Vsfold4: 0.637 Positive Predictive Value McQFold: 0.725 Vsfold4: 0.667 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.683 Vsfold4: 0.580 Sensitivity CRWrnafold: 0.690 Vsfold4: 0.571 Positive Predictive Value CRWrnafold: 0.689 Vsfold4: 0.604 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	29 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.676 Vsfold4: 0.567 Sensitivity RNAalifold(seed): 0.525 Vsfold4: 0.569 Positive Predictive Value RNAalifold(seed): 0.874 Vsfold4: 0.571 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	116 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.740 Vsfold4: 0.678 Sensitivity Pknots: 0.763 Vsfold4: 0.660 Positive Predictive Value Pknots: 0.726 Vsfold4: 0.707 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.765 Vsfold4: 0.683 Sensitivity RNASampler(seed): 0.687 Vsfold4: 0.672 Positive Predictive Value RNASampler(seed): 0.859 Vsfold4: 0.703 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	28 Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.636 Vsfold4: 0.531 Sensitivity Mastr(20): 0.483 Vsfold4: 0.528 Positive Predictive Value Mastr(20): 0.845 Vsfold4: 0.544 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.663 Vsfold4: 0.537 Sensitivity RSpredict(20): 0.593 Vsfold4: 0.530 Positive Predictive Value RSpredict(20): 0.748 Vsfold4: 0.551 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	89 Alterna vs Vsfold4 Matthews Correlation Coefficient Alterna: 0.767 Vsfold4: 0.750 Sensitivity Alterna: 0.777 Vsfold4: 0.725 Positive Predictive Value Alterna: 0.769 Vsfold4: 0.788 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 4.48494289621e-08	30 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.679 Vsfold4: 0.618 Sensitivity RNASLOpt: 0.649 Vsfold4: 0.602 Positive Predictive Value RNASLOpt: 0.721 Vsfold4: 0.647 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.85233844192e-08	10 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.612 Vsfold4: 0.471 Sensitivity Multilign(20): 0.581 Vsfold4: 0.456 Positive Predictive Value Multilign(20): 0.657 Vsfold4: 0.502 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.1568170475e-08		= Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.683 MCFold: 0.678 Sensitivity Vsfold4: 0.665 MCFold: 0.717 Positive Predictive Value Vsfold4: 0.714 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 0.0215355173778	+ Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.620 RNAwolf: 0.594 Sensitivity Vsfold4: 0.609 RNAwolf: 0.584 Positive Predictive Value Vsfold4: 0.647 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.05576593777e-07	= Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.621 Murlet(seed): 0.620 Sensitivity Vsfold4: 0.605 Murlet(seed): 0.442 Positive Predictive Value Vsfold4: 0.648 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.463852728543	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.648 Vsfold5: 0.612 Sensitivity Vsfold4: 0.639 Vsfold5: 0.613 Positive Predictive Value Vsfold4: 0.668 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.595 RSpredict(seed): 0.372 Sensitivity Vsfold4: 0.595 RSpredict(seed): 0.222 Positive Predictive Value Vsfold4: 0.603 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.749 RDfolder: 0.682 Sensitivity Vsfold4: 0.721 RDfolder: 0.643 Positive Predictive Value Vsfold4: 0.790 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.529 PPfold(seed): 0.122 Sensitivity Vsfold4: 0.514 PPfold(seed): 0.029 Positive Predictive Value Vsfold4: 0.558 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.3551590886e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.590 Mastr(seed): 0.306 Sensitivity Vsfold4: 0.592 Mastr(seed): 0.105 Positive Predictive Value Vsfold4: 0.597 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.683 Vsfold4: 0.503 Sensitivity Multilign(seed): 0.636 Vsfold4: 0.483 Positive Predictive Value Multilign(seed): 0.750 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Vsfold4: 0.508 Sensitivity PETfold_pre2.0(seed): 0.772 Vsfold4: 0.491 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.733 Vsfold4: 0.550 Sensitivity TurboFold(20): 0.694 Vsfold4: 0.534 Positive Predictive Value TurboFold(20): 0.781 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(20): N/A Sensitivity Vsfold4: N/A CMfinder(20): N/A Positive Predictive Value Vsfold4: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Vsfold4: 0.472 Sensitivity PETfold_pre2.0(20): 0.707 Vsfold4: 0.457 Positive Predictive Value PETfold_pre2.0(20): 0.796 Vsfold4: 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.650 Vsfold4: 0.487 Sensitivity TurboFold(seed): 0.624 Vsfold4: 0.468 Positive Predictive Value TurboFold(seed): 0.688 Vsfold4: 0.522 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.780 Vsfold4: 0.550 Sensitivity PPfold(20): 0.714 Vsfold4: 0.534 Positive Predictive Value PPfold(20): 0.860 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.609 NanoFolder: 0.562 Sensitivity Vsfold4: 0.608 NanoFolder: 0.656 Positive Predictive Value Vsfold4: 0.623 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.611 Carnac(seed): 0.299 Sensitivity Vsfold4: 0.597 Carnac(seed): 0.090 Positive Predictive Value Vsfold4: 0.636 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
MCFold	38 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.806 MCFold: 0.602 Sensitivity MXScarna(seed): 0.767 MCFold: 0.650 Positive Predictive Value MXScarna(seed): 0.854 MCFold: 0.568 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.831 MCFold: 0.512 Sensitivity CentroidAlifold(20): 0.752 MCFold: 0.571 Positive Predictive Value CentroidAlifold(20): 0.922 MCFold: 0.471 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	96 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.814 MCFold: 0.664 Sensitivity CentroidFold: 0.803 MCFold: 0.704 Positive Predictive Value CentroidFold: 0.833 MCFold: 0.637 Number of pairs reference - predicted secondary structure: 96 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.793 MCFold: 0.520 Sensitivity RNAalifold(20): 0.722 MCFold: 0.579 Positive Predictive Value RNAalifold(20): 0.876 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	109 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.818 MCFold: 0.678 Sensitivity Sfold: 0.805 MCFold: 0.717 Positive Predictive Value Sfold: 0.839 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.819 MCFold: 0.698 Sensitivity Fold: 0.830 MCFold: 0.729 Positive Predictive Value Fold: 0.815 MCFold: 0.679 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.810 MCFold: 0.520 Sensitivity RNASampler(20): 0.734 MCFold: 0.579 Positive Predictive Value RNASampler(20): 0.897 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.794 MCFold: 0.520 Sensitivity MXScarna(20): 0.760 MCFold: 0.579 Positive Predictive Value MXScarna(20): 0.833 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	41 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.786 MCFold: 0.669 Sensitivity CentroidHomfold‑LAST: 0.705 MCFold: 0.701 Positive Predictive Value CentroidHomfold‑LAST: 0.885 MCFold: 0.652 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.812 MCFold: 0.678 Sensitivity HotKnots: 0.826 MCFold: 0.717 Positive Predictive Value HotKnots: 0.806 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.815 MCFold: 0.678 Sensitivity UNAFold: 0.819 MCFold: 0.717 Positive Predictive Value UNAFold: 0.818 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.801 MCFold: 0.678 Sensitivity Contrafold: 0.809 MCFold: 0.717 Positive Predictive Value Contrafold: 0.801 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	36 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.792 MCFold: 0.668 Sensitivity IPknot: 0.763 MCFold: 0.698 Positive Predictive Value IPknot: 0.831 MCFold: 0.652 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.825 MCFold: 0.683 Sensitivity ContextFold: 0.790 MCFold: 0.710 Positive Predictive Value ContextFold: 0.868 MCFold: 0.668 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	109 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.808 MCFold: 0.678 Sensitivity RNAshapes: 0.810 MCFold: 0.717 Positive Predictive Value RNAshapes: 0.814 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.783 MCFold: 0.654 Sensitivity MaxExpect: 0.792 MCFold: 0.695 Positive Predictive Value MaxExpect: 0.782 MCFold: 0.627 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.796 MCFold: 0.678 Sensitivity PknotsRG: 0.810 MCFold: 0.717 Positive Predictive Value PknotsRG: 0.791 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.805 MCFold: 0.678 Sensitivity RNAfold: 0.814 MCFold: 0.717 Positive Predictive Value RNAfold: 0.805 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.782 MCFold: 0.681 Sensitivity ProbKnot: 0.809 MCFold: 0.714 Positive Predictive Value ProbKnot: 0.764 MCFold: 0.661 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.727 MCFold: 0.520 Sensitivity Murlet(20): 0.637 MCFold: 0.579 Positive Predictive Value Murlet(20): 0.837 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	37 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.711 MCFold: 0.597 Sensitivity CentroidAlifold(seed): 0.569 MCFold: 0.646 Positive Predictive Value CentroidAlifold(seed): 0.896 MCFold: 0.564 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.795 MCFold: 0.716 Sensitivity Afold: 0.811 MCFold: 0.756 Positive Predictive Value Afold: 0.787 MCFold: 0.690 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.777 MCFold: 0.678 Sensitivity RNAsubopt: 0.787 MCFold: 0.717 Positive Predictive Value RNAsubopt: 0.775 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.740 MCFold: 0.520 Sensitivity Carnac(20): 0.577 MCFold: 0.579 Positive Predictive Value Carnac(20): 0.955 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.1503931209e-08	59 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.749 MCFold: 0.669 Sensitivity Cylofold: 0.732 MCFold: 0.700 Positive Predictive Value Cylofold: 0.776 MCFold: 0.652 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	108 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.763 MCFold: 0.675 Sensitivity McQFold: 0.750 MCFold: 0.715 Positive Predictive Value McQFold: 0.785 MCFold: 0.650 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.682 MCFold: 0.639 Sensitivity CRWrnafold: 0.690 MCFold: 0.670 Positive Predictive Value CRWrnafold: 0.685 MCFold: 0.621 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.718 MCFold: 0.648 Sensitivity RNAalifold(seed): 0.580 MCFold: 0.687 Positive Predictive Value RNAalifold(seed): 0.897 MCFold: 0.622 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.19332990918e-08	109 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.751 MCFold: 0.678 Sensitivity Pknots: 0.774 MCFold: 0.717 Positive Predictive Value Pknots: 0.737 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.765 MCFold: 0.700 Sensitivity RNASampler(seed): 0.687 MCFold: 0.751 Positive Predictive Value RNASampler(seed): 0.859 MCFold: 0.661 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.42071836373e-08	24 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.721 MCFold: 0.520 Sensitivity Mastr(20): 0.581 MCFold: 0.579 Positive Predictive Value Mastr(20): 0.901 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.712 MCFold: 0.520 Sensitivity RSpredict(20): 0.658 MCFold: 0.579 Positive Predictive Value RSpredict(20): 0.777 MCFold: 0.479 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.19332990918e-08	86 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.780 MCFold: 0.706 Sensitivity Alterna: 0.789 MCFold: 0.741 Positive Predictive Value Alterna: 0.783 MCFold: 0.689 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.707 MCFold: 0.683 Sensitivity RNASLOpt: 0.683 MCFold: 0.710 Positive Predictive Value RNASLOpt: 0.744 MCFold: 0.668 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 3.85233844192e-08	9 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.616 MCFold: 0.556 Sensitivity Multilign(20): 0.585 MCFold: 0.590 Positive Predictive Value Multilign(20): 0.660 MCFold: 0.536 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	109 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.683 MCFold: 0.678 Sensitivity Vsfold4: 0.665 MCFold: 0.717 Positive Predictive Value Vsfold4: 0.714 MCFold: 0.653 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 0.0215355173778		+ MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.668 RNAwolf: 0.602 Sensitivity MCFold: 0.698 RNAwolf: 0.594 Positive Predictive Value MCFold: 0.652 RNAwolf: 0.624 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs Murlet(seed) Matthews Correlation Coefficient MCFold: 0.638 Murlet(seed): 0.619 Sensitivity MCFold: 0.677 Murlet(seed): 0.447 Positive Predictive Value MCFold: 0.612 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 2.45762693015e-06	+ MCFold vs Vsfold5 Matthews Correlation Coefficient MCFold: 0.676 Vsfold5: 0.662 Sensitivity MCFold: 0.716 Vsfold5: 0.657 Positive Predictive Value MCFold: 0.651 Vsfold5: 0.679 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 8.09943589199e-07	+ MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.602 RSpredict(seed): 0.415 Sensitivity MCFold: 0.650 RSpredict(seed): 0.261 Positive Predictive Value MCFold: 0.568 RSpredict(seed): 0.674 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MCFold vs RDfolder Matthews Correlation Coefficient MCFold: 0.705 RDfolder: 0.703 Sensitivity MCFold: 0.737 RDfolder: 0.660 Positive Predictive Value MCFold: 0.689 RDfolder: 0.764 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 0.154221523985	? MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.563 PPfold(seed): 0.135 Sensitivity MCFold: 0.596 PPfold(seed): 0.035 Positive Predictive Value MCFold: 0.544 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.602 Mastr(seed): 0.352 Sensitivity MCFold: 0.650 Mastr(seed): 0.140 Positive Predictive Value MCFold: 0.568 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MCFold vs Multilign(seed) Matthews Correlation Coefficient MCFold: 0.669 Multilign(seed): 0.668 Sensitivity MCFold: 0.674 Multilign(seed): 0.629 Positive Predictive Value MCFold: 0.682 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.808 MCFold: 0.546 Sensitivity PETfold_pre2.0(seed): 0.754 MCFold: 0.579 Positive Predictive Value PETfold_pre2.0(seed): 0.872 MCFold: 0.525 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.743 MCFold: 0.619 Sensitivity TurboFold(20): 0.712 MCFold: 0.655 Positive Predictive Value TurboFold(20): 0.783 MCFold: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.706 MCFold: 0.566 Sensitivity PETfold_pre2.0(20): 0.667 MCFold: 0.609 Positive Predictive Value PETfold_pre2.0(20): 0.753 MCFold: 0.535 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.648 MCFold: 0.617 Sensitivity TurboFold(seed): 0.631 MCFold: 0.642 Positive Predictive Value TurboFold(seed): 0.677 MCFold: 0.604 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.765 MCFold: 0.619 Sensitivity PPfold(20): 0.695 MCFold: 0.655 Positive Predictive Value PPfold(20): 0.848 MCFold: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.732 NanoFolder: 0.592 Sensitivity MCFold: 0.760 NanoFolder: 0.691 Positive Predictive Value MCFold: 0.714 NanoFolder: 0.521 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	+ MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.639 Carnac(seed): 0.314 Sensitivity MCFold: 0.684 Carnac(seed): 0.100 Positive Predictive Value MCFold: 0.606 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08
RNAwolf	11 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.728 RNAwolf: 0.499 Sensitivity MXScarna(seed): 0.675 RNAwolf: 0.490 Positive Predictive Value MXScarna(seed): 0.792 RNAwolf: 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.55268413083e-08	8 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.825 RNAwolf: 0.453 Sensitivity CentroidAlifold(20): 0.729 RNAwolf: 0.447 Positive Predictive Value CentroidAlifold(20): 0.938 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.766 RNAwolf: 0.594 Sensitivity CentroidFold: 0.743 RNAwolf: 0.584 Positive Predictive Value CentroidFold: 0.798 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.744 RNAwolf: 0.453 Sensitivity RNAalifold(20): 0.681 RNAwolf: 0.447 Positive Predictive Value RNAalifold(20): 0.821 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.736 RNAwolf: 0.594 Sensitivity Sfold: 0.713 RNAwolf: 0.584 Positive Predictive Value Sfold: 0.769 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.703 RNAwolf: 0.594 Sensitivity Fold: 0.712 RNAwolf: 0.584 Positive Predictive Value Fold: 0.707 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.762 RNAwolf: 0.453 Sensitivity RNASampler(20): 0.681 RNAwolf: 0.447 Positive Predictive Value RNASampler(20): 0.859 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.689 RNAwolf: 0.453 Sensitivity MXScarna(20): 0.649 RNAwolf: 0.447 Positive Predictive Value MXScarna(20): 0.739 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	37 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.783 RNAwolf: 0.585 Sensitivity CentroidHomfold‑LAST: 0.697 RNAwolf: 0.575 Positive Predictive Value CentroidHomfold‑LAST: 0.887 RNAwolf: 0.611 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.742 RNAwolf: 0.594 Sensitivity HotKnots: 0.759 RNAwolf: 0.584 Positive Predictive Value HotKnots: 0.735 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.706 RNAwolf: 0.594 Sensitivity UNAFold: 0.713 RNAwolf: 0.584 Positive Predictive Value UNAFold: 0.711 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.759 RNAwolf: 0.594 Sensitivity Contrafold: 0.756 RNAwolf: 0.584 Positive Predictive Value Contrafold: 0.772 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.782 RNAwolf: 0.594 Sensitivity IPknot: 0.752 RNAwolf: 0.584 Positive Predictive Value IPknot: 0.820 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.816 RNAwolf: 0.555 Sensitivity ContextFold: 0.780 RNAwolf: 0.544 Positive Predictive Value ContextFold: 0.861 RNAwolf: 0.583 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.722 RNAwolf: 0.594 Sensitivity RNAshapes: 0.727 RNAwolf: 0.584 Positive Predictive Value RNAshapes: 0.726 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.704 RNAwolf: 0.594 Sensitivity MaxExpect: 0.706 RNAwolf: 0.584 Positive Predictive Value MaxExpect: 0.713 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.738 RNAwolf: 0.594 Sensitivity PknotsRG: 0.756 RNAwolf: 0.584 Positive Predictive Value PknotsRG: 0.731 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.726 RNAwolf: 0.594 Sensitivity RNAfold: 0.731 RNAwolf: 0.584 Positive Predictive Value RNAfold: 0.732 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.701 RNAwolf: 0.594 Sensitivity ProbKnot: 0.724 RNAwolf: 0.584 Positive Predictive Value ProbKnot: 0.691 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.693 RNAwolf: 0.453 Sensitivity Murlet(20): 0.612 RNAwolf: 0.447 Positive Predictive Value Murlet(20): 0.793 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 RNAwolf: 0.499 Sensitivity CentroidAlifold(seed): 0.494 RNAwolf: 0.490 Positive Predictive Value CentroidAlifold(seed): 0.984 RNAwolf: 0.524 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.47941000302e-08	24 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.764 RNAwolf: 0.687 Sensitivity Afold: 0.783 RNAwolf: 0.668 Positive Predictive Value Afold: 0.754 RNAwolf: 0.719 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.691 RNAwolf: 0.594 Sensitivity RNAsubopt: 0.703 RNAwolf: 0.584 Positive Predictive Value RNAsubopt: 0.692 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.662 RNAwolf: 0.453 Sensitivity Carnac(20): 0.516 RNAwolf: 0.447 Positive Predictive Value Carnac(20): 0.858 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	30 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.676 RNAwolf: 0.590 Sensitivity Cylofold: 0.663 RNAwolf: 0.574 Positive Predictive Value Cylofold: 0.702 RNAwolf: 0.624 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.696 RNAwolf: 0.585 Sensitivity McQFold: 0.690 RNAwolf: 0.575 Positive Predictive Value McQFold: 0.713 RNAwolf: 0.611 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.683 RNAwolf: 0.552 Sensitivity CRWrnafold: 0.690 RNAwolf: 0.546 Positive Predictive Value CRWrnafold: 0.689 RNAwolf: 0.575 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNAwolf: 0.451 Sensitivity RNAalifold(seed): 0.473 RNAwolf: 0.447 Positive Predictive Value RNAalifold(seed): 0.798 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	38 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.663 RNAwolf: 0.594 Sensitivity Pknots: 0.683 RNAwolf: 0.584 Positive Predictive Value Pknots: 0.656 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	4 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.559 RNAwolf: 0.521 Sensitivity RNASampler(seed): 0.484 RNAwolf: 0.538 Positive Predictive Value RNASampler(seed): 0.657 RNAwolf: 0.516 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	8 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.674 RNAwolf: 0.453 Sensitivity Mastr(20): 0.548 RNAwolf: 0.447 Positive Predictive Value Mastr(20): 0.837 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.586 RNAwolf: 0.453 Sensitivity RSpredict(20): 0.521 RNAwolf: 0.447 Positive Predictive Value RSpredict(20): 0.671 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	22 Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.684 RNAwolf: 0.678 Sensitivity Alterna: 0.705 RNAwolf: 0.674 Positive Predictive Value Alterna: 0.679 RNAwolf: 0.698 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 0.00781880629872	30 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.679 RNAwolf: 0.555 Sensitivity RNASLOpt: 0.649 RNAwolf: 0.544 Positive Predictive Value RNASLOpt: 0.721 RNAwolf: 0.583 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.653 RNAwolf: 0.453 Sensitivity Multilign(20): 0.649 RNAwolf: 0.447 Positive Predictive Value Multilign(20): 0.667 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	38 Vsfold4 vs RNAwolf Matthews Correlation Coefficient Vsfold4: 0.620 RNAwolf: 0.594 Sensitivity Vsfold4: 0.609 RNAwolf: 0.584 Positive Predictive Value Vsfold4: 0.647 RNAwolf: 0.620 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.05576593777e-07	36 MCFold vs RNAwolf Matthews Correlation Coefficient MCFold: 0.668 RNAwolf: 0.602 Sensitivity MCFold: 0.698 RNAwolf: 0.594 Positive Predictive Value MCFold: 0.652 RNAwolf: 0.624 Number of pairs reference - predicted secondary structure: 36 Wilcoxon single-rank test P-value: 3.56938820447e-08		? Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.531 RNAwolf: 0.451 Sensitivity Murlet(seed): 0.373 RNAwolf: 0.447 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.589 Vsfold5: 0.558 Sensitivity RNAwolf: 0.578 Vsfold5: 0.566 Positive Predictive Value RNAwolf: 0.615 Vsfold5: 0.568 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.499 RSpredict(seed): 0.231 Sensitivity RNAwolf: 0.490 RSpredict(seed): 0.123 Positive Predictive Value RNAwolf: 0.524 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.1398907247e-09	+ RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.614 RDfolder: 0.567 Sensitivity RNAwolf: 0.604 RDfolder: 0.513 Positive Predictive Value RNAwolf: 0.643 RDfolder: 0.651 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.499 PPfold(seed): 0.122 Sensitivity RNAwolf: 0.490 PPfold(seed): 0.029 Positive Predictive Value RNAwolf: 0.524 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.18011954625e-08	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.499 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.490 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.524 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.02510705504e-08	? CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.629 RNAwolf: 0.552 Sensitivity Multilign(seed): 0.580 RNAwolf: 0.530 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.596 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAwolf: 0.401 Sensitivity PETfold_pre2.0(seed): 0.772 RNAwolf: 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAwolf: 0.427 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.712 RNAwolf: 0.453 Sensitivity TurboFold(20): 0.670 RNAwolf: 0.447 Positive Predictive Value TurboFold(20): 0.764 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs CMfinder(20) Matthews Correlation Coefficient RNAwolf: N/A CMfinder(20): N/A Sensitivity RNAwolf: N/A CMfinder(20): N/A Positive Predictive Value RNAwolf: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAwolf: 0.279 Sensitivity PETfold_pre2.0(20): 0.707 RNAwolf: 0.276 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAwolf: 0.299 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.621 RNAwolf: 0.426 Sensitivity TurboFold(seed): 0.594 RNAwolf: 0.417 Positive Predictive Value TurboFold(seed): 0.661 RNAwolf: 0.451 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.790 RNAwolf: 0.453 Sensitivity PPfold(20): 0.734 RNAwolf: 0.447 Positive Predictive Value PPfold(20): 0.857 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.598 NanoFolder: 0.562 Sensitivity RNAwolf: 0.584 NanoFolder: 0.656 Positive Predictive Value RNAwolf: 0.625 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.35936056444e-07	? RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.426 Carnac(seed): 0.145 Sensitivity RNAwolf: 0.417 Carnac(seed): 0.021 Positive Predictive Value RNAwolf: 0.451 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Murlet(seed)	26 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.761 Murlet(seed): 0.620 Sensitivity MXScarna(seed): 0.719 Murlet(seed): 0.442 Positive Predictive Value MXScarna(seed): 0.812 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.10776592382e-08	16 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.765 Murlet(seed): 0.588 Sensitivity CentroidAlifold(20): 0.651 Murlet(seed): 0.379 Positive Predictive Value CentroidAlifold(20): 0.905 Murlet(seed): 0.920 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.07760058607e-08	25 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.778 Murlet(seed): 0.621 Sensitivity CentroidFold: 0.757 Murlet(seed): 0.445 Positive Predictive Value CentroidFold: 0.806 Murlet(seed): 0.878 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	17 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.711 Murlet(seed): 0.587 Sensitivity RNAalifold(20): 0.610 Murlet(seed): 0.377 Positive Predictive Value RNAalifold(20): 0.834 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.24519439238e-08	26 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.787 Murlet(seed): 0.620 Sensitivity Sfold: 0.759 Murlet(seed): 0.442 Positive Predictive Value Sfold: 0.822 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	19 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.740 Murlet(seed): 0.614 Sensitivity Fold: 0.752 Murlet(seed): 0.435 Positive Predictive Value Fold: 0.736 Murlet(seed): 0.877 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 3.24519439238e-08	17 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.731 Murlet(seed): 0.587 Sensitivity RNASampler(20): 0.635 Murlet(seed): 0.377 Positive Predictive Value RNASampler(20): 0.848 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	17 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.738 Murlet(seed): 0.587 Sensitivity MXScarna(20): 0.697 Murlet(seed): 0.377 Positive Predictive Value MXScarna(20): 0.787 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.30280588002e-08	8 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.680 Murlet(seed): 0.535 Sensitivity CentroidHomfold‑LAST: 0.607 Murlet(seed): 0.375 Positive Predictive Value CentroidHomfold‑LAST: 0.773 Murlet(seed): 0.778 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.781 Murlet(seed): 0.620 Sensitivity HotKnots: 0.795 Murlet(seed): 0.442 Positive Predictive Value HotKnots: 0.774 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.767 Murlet(seed): 0.620 Sensitivity UNAFold: 0.766 Murlet(seed): 0.442 Positive Predictive Value UNAFold: 0.774 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	26 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.757 Murlet(seed): 0.620 Sensitivity Contrafold: 0.761 Murlet(seed): 0.442 Positive Predictive Value Contrafold: 0.761 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	7 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.601 Murlet(seed): 0.531 Sensitivity IPknot: 0.560 Murlet(seed): 0.373 Positive Predictive Value IPknot: 0.656 Murlet(seed): 0.767 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.570 Murlet(seed): 0.495 Sensitivity ContextFold: 0.515 Murlet(seed): 0.340 Positive Predictive Value ContextFold: 0.641 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	26 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.803 Murlet(seed): 0.620 Sensitivity RNAshapes: 0.803 Murlet(seed): 0.442 Positive Predictive Value RNAshapes: 0.809 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	24 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.726 Murlet(seed): 0.621 Sensitivity MaxExpect: 0.736 Murlet(seed): 0.447 Positive Predictive Value MaxExpect: 0.725 Murlet(seed): 0.872 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.786 Murlet(seed): 0.620 Sensitivity PknotsRG: 0.797 Murlet(seed): 0.442 Positive Predictive Value PknotsRG: 0.782 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	26 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.786 Murlet(seed): 0.620 Sensitivity RNAfold: 0.790 Murlet(seed): 0.442 Positive Predictive Value RNAfold: 0.788 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.639 Murlet(seed): 0.573 Sensitivity ProbKnot: 0.668 Murlet(seed): 0.384 Positive Predictive Value ProbKnot: 0.622 Murlet(seed): 0.866 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.28439804626e-08	17 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.661 Murlet(seed): 0.587 Sensitivity Murlet(20): 0.538 Murlet(seed): 0.377 Positive Predictive Value Murlet(20): 0.819 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	25 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.791 Murlet(seed): 0.621 Sensitivity CentroidAlifold(seed): 0.710 Murlet(seed): 0.445 Positive Predictive Value CentroidAlifold(seed): 0.886 Murlet(seed): 0.878 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	20 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.788 Murlet(seed): 0.624 Sensitivity Afold: 0.794 Murlet(seed): 0.463 Positive Predictive Value Afold: 0.789 Murlet(seed): 0.853 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.19332990918e-08	26 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.722 Murlet(seed): 0.620 Sensitivity RNAsubopt: 0.734 Murlet(seed): 0.442 Positive Predictive Value RNAsubopt: 0.719 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	17 Carnac(20) vs Murlet(seed) Matthews Correlation Coefficient Carnac(20): 0.632 Murlet(seed): 0.587 Sensitivity Carnac(20): 0.424 Murlet(seed): 0.377 Positive Predictive Value Carnac(20): 0.950 Murlet(seed): 0.921 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.30549897711e-08	13 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.680 Murlet(seed): 0.571 Sensitivity Cylofold: 0.674 Murlet(seed): 0.390 Positive Predictive Value Cylofold: 0.696 Murlet(seed): 0.847 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.30549897711e-08	26 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.743 Murlet(seed): 0.620 Sensitivity McQFold: 0.744 Murlet(seed): 0.442 Positive Predictive Value McQFold: 0.749 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	6 CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.513 Murlet(seed): 0.510 Sensitivity CRWrnafold: 0.524 Murlet(seed): 0.349 Positive Predictive Value CRWrnafold: 0.516 Murlet(seed): 0.759 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	26 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.737 Murlet(seed): 0.620 Sensitivity RNAalifold(seed): 0.603 Murlet(seed): 0.442 Positive Predictive Value RNAalifold(seed): 0.908 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	26 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: 0.727 Murlet(seed): 0.620 Sensitivity Pknots: 0.759 Murlet(seed): 0.442 Positive Predictive Value Pknots: 0.703 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	17 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 Murlet(seed): 0.639 Sensitivity RNASampler(seed): 0.687 Murlet(seed): 0.493 Positive Predictive Value RNASampler(seed): 0.859 Murlet(seed): 0.837 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.8150742666e-08	17 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.587 Mastr(20): 0.539 Sensitivity Murlet(seed): 0.377 Mastr(20): 0.380 Positive Predictive Value Murlet(seed): 0.921 Mastr(20): 0.777 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	17 Murlet(seed) vs RSpredict(20) Matthews Correlation Coefficient Murlet(seed): 0.587 RSpredict(20): 0.566 Sensitivity Murlet(seed): 0.377 RSpredict(20): 0.489 Positive Predictive Value Murlet(seed): 0.921 RSpredict(20): 0.666 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.52316175909e-05	17 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.840 Murlet(seed): 0.656 Sensitivity Alterna: 0.828 Murlet(seed): 0.524 Positive Predictive Value Alterna: 0.860 Murlet(seed): 0.838 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.45805449719e-08	5 Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.495 RNASLOpt: 0.461 Sensitivity Murlet(seed): 0.340 RNASLOpt: 0.443 Positive Predictive Value Murlet(seed): 0.733 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): 0.582 Multilign(20): 0.545 Sensitivity Murlet(seed): 0.373 Multilign(20): 0.508 Positive Predictive Value Murlet(seed): 0.920 Multilign(20): 0.599 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 Vsfold4 vs Murlet(seed) Matthews Correlation Coefficient Vsfold4: 0.621 Murlet(seed): 0.620 Sensitivity Vsfold4: 0.605 Murlet(seed): 0.442 Positive Predictive Value Vsfold4: 0.648 Murlet(seed): 0.879 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 0.463852728543	24 MCFold vs Murlet(seed) Matthews Correlation Coefficient MCFold: 0.638 Murlet(seed): 0.619 Sensitivity MCFold: 0.677 Murlet(seed): 0.447 Positive Predictive Value MCFold: 0.612 Murlet(seed): 0.867 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 2.45762693015e-06	7 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.531 RNAwolf: 0.451 Sensitivity Murlet(seed): 0.373 RNAwolf: 0.447 Positive Predictive Value Murlet(seed): 0.767 RNAwolf: 0.472 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		+ Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.620 Vsfold5: 0.603 Sensitivity Murlet(seed): 0.442 Vsfold5: 0.598 Positive Predictive Value Murlet(seed): 0.879 Vsfold5: 0.619 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 6.21280603249e-05	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.620 RSpredict(seed): 0.527 Sensitivity Murlet(seed): 0.442 RSpredict(seed): 0.371 Positive Predictive Value Murlet(seed): 0.879 RSpredict(seed): 0.760 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	= RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.660 Murlet(seed): 0.655 Sensitivity RDfolder: 0.606 Murlet(seed): 0.512 Positive Predictive Value RDfolder: 0.736 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.0625661724175	? Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.531 PPfold(seed): 0.155 Sensitivity Murlet(seed): 0.373 PPfold(seed): 0.047 Positive Predictive Value Murlet(seed): 0.767 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.620 Mastr(seed): 0.417 Sensitivity Murlet(seed): 0.442 Mastr(seed): 0.197 Positive Predictive Value Murlet(seed): 0.879 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-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 Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 Murlet(seed): 0.506 Sensitivity Multilign(seed): 0.636 Murlet(seed): 0.373 Positive Predictive Value Multilign(seed): 0.750 Murlet(seed): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Murlet(seed): 0.495 Sensitivity PETfold_pre2.0(seed): 0.619 Murlet(seed): 0.340 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.690 Murlet(seed): 0.616 Sensitivity TurboFold(20): 0.647 Murlet(seed): 0.420 Positive Predictive Value TurboFold(20): 0.746 Murlet(seed): 0.913 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Murlet(seed): 0.644 PETfold_pre2.0(20): 0.619 Sensitivity Murlet(seed): 0.418 PETfold_pre2.0(20): 0.570 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.603 Murlet(seed): 0.535 Sensitivity TurboFold(seed): 0.577 Murlet(seed): 0.375 Positive Predictive Value TurboFold(seed): 0.642 Murlet(seed): 0.778 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.709 Murlet(seed): 0.616 Sensitivity PPfold(20): 0.627 Murlet(seed): 0.420 Positive Predictive Value PPfold(20): 0.810 Murlet(seed): 0.913 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.473 NanoFolder: 0.336 Sensitivity Murlet(seed): 0.329 NanoFolder: 0.415 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.620 Carnac(seed): 0.327 Sensitivity Murlet(seed): 0.442 Carnac(seed): 0.108 Positive Predictive Value Murlet(seed): 0.879 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08
Vsfold5	44 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.776 Vsfold5: 0.570 Sensitivity MXScarna(seed): 0.736 Vsfold5: 0.575 Positive Predictive Value MXScarna(seed): 0.824 Vsfold5: 0.573 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Vsfold5: 0.494 Sensitivity CentroidAlifold(20): 0.716 Vsfold5: 0.495 Positive Predictive Value CentroidAlifold(20): 0.921 Vsfold5: 0.502 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.02343278931e-08	103 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.779 Vsfold5: 0.607 Sensitivity CentroidFold: 0.774 Vsfold5: 0.606 Positive Predictive Value CentroidFold: 0.790 Vsfold5: 0.617 Number of pairs reference - predicted secondary structure: 103 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.782 Vsfold5: 0.484 Sensitivity RNAalifold(20): 0.690 Vsfold5: 0.488 Positive Predictive Value RNAalifold(20): 0.889 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	117 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.777 Vsfold5: 0.612 Sensitivity Sfold: 0.767 Vsfold5: 0.613 Positive Predictive Value Sfold: 0.793 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	81 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.776 Vsfold5: 0.612 Sensitivity Fold: 0.795 Vsfold5: 0.613 Positive Predictive Value Fold: 0.763 Vsfold5: 0.620 Number of pairs reference - predicted secondary structure: 81 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.765 Vsfold5: 0.484 Sensitivity RNASampler(20): 0.671 Vsfold5: 0.488 Positive Predictive Value RNASampler(20): 0.875 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.761 Vsfold5: 0.484 Sensitivity MXScarna(20): 0.727 Vsfold5: 0.488 Positive Predictive Value MXScarna(20): 0.800 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	43 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.779 Vsfold5: 0.570 Sensitivity CentroidHomfold‑LAST: 0.687 Vsfold5: 0.575 Positive Predictive Value CentroidHomfold‑LAST: 0.891 Vsfold5: 0.580 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.771 Vsfold5: 0.612 Sensitivity HotKnots: 0.792 Vsfold5: 0.613 Positive Predictive Value HotKnots: 0.756 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.774 Vsfold5: 0.612 Sensitivity UNAFold: 0.786 Vsfold5: 0.613 Positive Predictive Value UNAFold: 0.768 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.768 Vsfold5: 0.612 Sensitivity Contrafold: 0.783 Vsfold5: 0.613 Positive Predictive Value Contrafold: 0.760 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.778 Vsfold5: 0.558 Sensitivity IPknot: 0.749 Vsfold5: 0.566 Positive Predictive Value IPknot: 0.818 Vsfold5: 0.568 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.813 Vsfold5: 0.543 Sensitivity ContextFold: 0.776 Vsfold5: 0.547 Positive Predictive Value ContextFold: 0.858 Vsfold5: 0.556 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	117 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.758 Vsfold5: 0.612 Sensitivity RNAshapes: 0.769 Vsfold5: 0.613 Positive Predictive Value RNAshapes: 0.754 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	97 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.753 Vsfold5: 0.599 Sensitivity MaxExpect: 0.767 Vsfold5: 0.598 Positive Predictive Value MaxExpect: 0.745 Vsfold5: 0.610 Number of pairs reference - predicted secondary structure: 97 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.751 Vsfold5: 0.612 Sensitivity PknotsRG: 0.773 Vsfold5: 0.613 Positive Predictive Value PknotsRG: 0.736 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.757 Vsfold5: 0.612 Sensitivity RNAfold: 0.775 Vsfold5: 0.613 Positive Predictive Value RNAfold: 0.747 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.739 Vsfold5: 0.589 Sensitivity ProbKnot: 0.773 Vsfold5: 0.592 Positive Predictive Value ProbKnot: 0.713 Vsfold5: 0.595 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.704 Vsfold5: 0.484 Sensitivity Murlet(20): 0.596 Vsfold5: 0.488 Positive Predictive Value Murlet(20): 0.837 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	43 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Vsfold5: 0.567 Sensitivity CentroidAlifold(seed): 0.552 Vsfold5: 0.572 Positive Predictive Value CentroidAlifold(seed): 0.870 Vsfold5: 0.569 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.746 Vsfold5: 0.624 Sensitivity Afold: 0.772 Vsfold5: 0.622 Positive Predictive Value Afold: 0.727 Vsfold5: 0.635 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.737 Vsfold5: 0.612 Sensitivity RNAsubopt: 0.756 Vsfold5: 0.613 Positive Predictive Value RNAsubopt: 0.725 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.696 Vsfold5: 0.484 Sensitivity Carnac(20): 0.518 Vsfold5: 0.488 Positive Predictive Value Carnac(20): 0.941 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	63 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.741 Vsfold5: 0.628 Sensitivity Cylofold: 0.724 Vsfold5: 0.625 Positive Predictive Value Cylofold: 0.767 Vsfold5: 0.644 Number of pairs reference - predicted secondary structure: 63 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.717 Vsfold5: 0.610 Sensitivity McQFold: 0.717 Vsfold5: 0.610 Positive Predictive Value McQFold: 0.724 Vsfold5: 0.619 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.678 Vsfold5: 0.525 Sensitivity CRWrnafold: 0.685 Vsfold5: 0.528 Positive Predictive Value CRWrnafold: 0.683 Vsfold5: 0.538 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.676 Vsfold5: 0.549 Sensitivity RNAalifold(seed): 0.525 Vsfold5: 0.553 Positive Predictive Value RNAalifold(seed): 0.874 Vsfold5: 0.553 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	115 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.739 Vsfold5: 0.637 Sensitivity Pknots: 0.762 Vsfold5: 0.635 Positive Predictive Value Pknots: 0.725 Vsfold5: 0.652 Number of pairs reference - predicted secondary structure: 115 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.765 Vsfold5: 0.722 Sensitivity RNASampler(seed): 0.687 Vsfold5: 0.722 Positive Predictive Value RNASampler(seed): 0.859 Vsfold5: 0.730 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.01010269124e-08	28 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.636 Vsfold5: 0.484 Sensitivity Mastr(20): 0.483 Vsfold5: 0.488 Positive Predictive Value Mastr(20): 0.845 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	27 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.663 Vsfold5: 0.500 Sensitivity RSpredict(20): 0.593 Vsfold5: 0.501 Positive Predictive Value RSpredict(20): 0.748 Vsfold5: 0.509 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	89 Alterna vs Vsfold5 Matthews Correlation Coefficient Alterna: 0.767 Vsfold5: 0.714 Sensitivity Alterna: 0.777 Vsfold5: 0.705 Positive Predictive Value Alterna: 0.769 Vsfold5: 0.737 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.673 Vsfold5: 0.543 Sensitivity RNASLOpt: 0.643 Vsfold5: 0.547 Positive Predictive Value RNASLOpt: 0.715 Vsfold5: 0.556 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	10 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.612 Vsfold5: 0.463 Sensitivity Multilign(20): 0.581 Vsfold5: 0.469 Positive Predictive Value Multilign(20): 0.657 Vsfold5: 0.473 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.13392142882e-08	117 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.648 Vsfold5: 0.612 Sensitivity Vsfold4: 0.639 Vsfold5: 0.613 Positive Predictive Value Vsfold4: 0.668 Vsfold5: 0.622 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	108 MCFold vs Vsfold5 Matthews Correlation Coefficient MCFold: 0.676 Vsfold5: 0.662 Sensitivity MCFold: 0.716 Vsfold5: 0.657 Positive Predictive Value MCFold: 0.651 Vsfold5: 0.679 Number of pairs reference - predicted secondary structure: 108 Wilcoxon single-rank test P-value: 8.09943589199e-07	37 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.589 Vsfold5: 0.558 Sensitivity RNAwolf: 0.578 Vsfold5: 0.566 Positive Predictive Value RNAwolf: 0.615 Vsfold5: 0.568 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 6.53888633552e-08	26 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.620 Vsfold5: 0.603 Sensitivity Murlet(seed): 0.442 Vsfold5: 0.598 Positive Predictive Value Murlet(seed): 0.879 Vsfold5: 0.619 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 6.21280603249e-05		+ Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.570 RSpredict(seed): 0.372 Sensitivity Vsfold5: 0.575 RSpredict(seed): 0.222 Positive Predictive Value Vsfold5: 0.573 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.720 RDfolder: 0.682 Sensitivity Vsfold5: 0.708 RDfolder: 0.643 Positive Predictive Value Vsfold5: 0.746 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.484 PPfold(seed): 0.122 Sensitivity Vsfold5: 0.498 PPfold(seed): 0.029 Positive Predictive Value Vsfold5: 0.486 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.557 Mastr(seed): 0.306 Sensitivity Vsfold5: 0.565 Mastr(seed): 0.105 Positive Predictive Value Vsfold5: 0.557 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(seed): N/A Sensitivity Vsfold5: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold5: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.683 Vsfold5: 0.427 Sensitivity Multilign(seed): 0.636 Vsfold5: 0.415 Positive Predictive Value Multilign(seed): 0.750 Vsfold5: 0.467 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Vsfold5: 0.451 Sensitivity PETfold_pre2.0(seed): 0.772 Vsfold5: 0.468 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.733 Vsfold5: 0.539 Sensitivity TurboFold(20): 0.694 Vsfold5: 0.549 Positive Predictive Value TurboFold(20): 0.781 Vsfold5: 0.543 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs CMfinder(20) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(20): N/A Sensitivity Vsfold5: N/A CMfinder(20): N/A Positive Predictive Value Vsfold5: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Vsfold5: 0.460 Sensitivity PETfold_pre2.0(20): 0.707 Vsfold5: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.796 Vsfold5: 0.458 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.650 Vsfold5: 0.475 Sensitivity TurboFold(seed): 0.624 Vsfold5: 0.478 Positive Predictive Value TurboFold(seed): 0.688 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.780 Vsfold5: 0.539 Sensitivity PPfold(20): 0.714 Vsfold5: 0.549 Positive Predictive Value PPfold(20): 0.860 Vsfold5: 0.543 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	= NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.551 Vsfold5: 0.545 Sensitivity NanoFolder: 0.647 Vsfold5: 0.558 Positive Predictive Value NanoFolder: 0.484 Vsfold5: 0.547 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.0284778450094	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.583 Carnac(seed): 0.299 Sensitivity Vsfold5: 0.581 Carnac(seed): 0.090 Positive Predictive Value Vsfold5: 0.597 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(seed)	44 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.776 RSpredict(seed): 0.372 Sensitivity MXScarna(seed): 0.736 RSpredict(seed): 0.222 Positive Predictive Value MXScarna(seed): 0.824 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 RSpredict(seed): 0.284 Sensitivity CentroidAlifold(20): 0.716 RSpredict(seed): 0.146 Positive Predictive Value CentroidAlifold(20): 0.921 RSpredict(seed): 0.564 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	43 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.724 RSpredict(seed): 0.365 Sensitivity CentroidFold: 0.727 RSpredict(seed): 0.216 Positive Predictive Value CentroidFold: 0.726 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.775 RSpredict(seed): 0.298 Sensitivity RNAalifold(20): 0.682 RSpredict(seed): 0.156 Positive Predictive Value RNAalifold(20): 0.884 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	44 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.709 RSpredict(seed): 0.372 Sensitivity Sfold: 0.701 RSpredict(seed): 0.222 Positive Predictive Value Sfold: 0.722 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.722 RSpredict(seed): 0.336 Sensitivity Fold: 0.750 RSpredict(seed): 0.196 Positive Predictive Value Fold: 0.700 RSpredict(seed): 0.585 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.766 RSpredict(seed): 0.298 Sensitivity RNASampler(20): 0.676 RSpredict(seed): 0.156 Positive Predictive Value RNASampler(20): 0.872 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.760 RSpredict(seed): 0.298 Sensitivity MXScarna(20): 0.726 RSpredict(seed): 0.156 Positive Predictive Value MXScarna(20): 0.800 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.1503931209e-08	12 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 RSpredict(seed): 0.264 Sensitivity CentroidHomfold‑LAST: 0.690 RSpredict(seed): 0.149 Positive Predictive Value CentroidHomfold‑LAST: 0.829 RSpredict(seed): 0.488 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.13392142882e-08	44 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.701 RSpredict(seed): 0.372 Sensitivity HotKnots: 0.732 RSpredict(seed): 0.222 Positive Predictive Value HotKnots: 0.676 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.700 RSpredict(seed): 0.372 Sensitivity UNAFold: 0.721 RSpredict(seed): 0.222 Positive Predictive Value UNAFold: 0.685 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.698 RSpredict(seed): 0.372 Sensitivity Contrafold: 0.726 RSpredict(seed): 0.222 Positive Predictive Value Contrafold: 0.677 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.701 RSpredict(seed): 0.231 Sensitivity IPknot: 0.658 RSpredict(seed): 0.123 Positive Predictive Value IPknot: 0.755 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.98760236454e-08	8 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.732 RSpredict(seed): 0.131 Sensitivity ContextFold: 0.673 RSpredict(seed): 0.070 Positive Predictive Value ContextFold: 0.804 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	44 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.699 RSpredict(seed): 0.372 Sensitivity RNAshapes: 0.720 RSpredict(seed): 0.222 Positive Predictive Value RNAshapes: 0.685 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.703 RSpredict(seed): 0.362 Sensitivity MaxExpect: 0.725 RSpredict(seed): 0.216 Positive Predictive Value MaxExpect: 0.687 RSpredict(seed): 0.620 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.703 RSpredict(seed): 0.372 Sensitivity PknotsRG: 0.732 RSpredict(seed): 0.222 Positive Predictive Value PknotsRG: 0.681 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.704 RSpredict(seed): 0.372 Sensitivity RNAfold: 0.730 RSpredict(seed): 0.222 Positive Predictive Value RNAfold: 0.685 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.657 RSpredict(seed): 0.267 Sensitivity ProbKnot: 0.701 RSpredict(seed): 0.145 Positive Predictive Value ProbKnot: 0.622 RSpredict(seed): 0.502 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	27 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.698 RSpredict(seed): 0.298 Sensitivity Murlet(20): 0.590 RSpredict(seed): 0.156 Positive Predictive Value Murlet(20): 0.832 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 RSpredict(seed): 0.365 Sensitivity CentroidAlifold(seed): 0.552 RSpredict(seed): 0.216 Positive Predictive Value CentroidAlifold(seed): 0.870 RSpredict(seed): 0.628 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.657 RSpredict(seed): 0.440 Sensitivity Afold: 0.693 RSpredict(seed): 0.281 Positive Predictive Value Afold: 0.629 RSpredict(seed): 0.697 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.664 RSpredict(seed): 0.372 Sensitivity RNAsubopt: 0.693 RSpredict(seed): 0.222 Positive Predictive Value RNAsubopt: 0.643 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	27 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.695 RSpredict(seed): 0.298 Sensitivity Carnac(20): 0.518 RSpredict(seed): 0.156 Positive Predictive Value Carnac(20): 0.938 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	21 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.732 RSpredict(seed): 0.315 Sensitivity Cylofold: 0.726 RSpredict(seed): 0.185 Positive Predictive Value Cylofold: 0.747 RSpredict(seed): 0.555 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	44 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.655 RSpredict(seed): 0.372 Sensitivity McQFold: 0.671 RSpredict(seed): 0.222 Positive Predictive Value McQFold: 0.646 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 RSpredict(seed): 0.126 Sensitivity CRWrnafold: 0.655 RSpredict(seed): 0.059 Positive Predictive Value CRWrnafold: 0.649 RSpredict(seed): 0.293 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	29 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.676 RSpredict(seed): 0.471 Sensitivity RNAalifold(seed): 0.525 RSpredict(seed): 0.311 Positive Predictive Value RNAalifold(seed): 0.874 RSpredict(seed): 0.722 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.720 RSpredict(seed): 0.393 Sensitivity Pknots: 0.751 RSpredict(seed): 0.240 Positive Predictive Value Pknots: 0.698 RSpredict(seed): 0.658 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 RSpredict(seed): 0.631 Sensitivity RNASampler(seed): 0.687 RSpredict(seed): 0.501 Positive Predictive Value RNASampler(seed): 0.859 RSpredict(seed): 0.805 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.57237423209e-08	27 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.635 RSpredict(seed): 0.298 Sensitivity Mastr(20): 0.478 RSpredict(seed): 0.156 Positive Predictive Value Mastr(20): 0.849 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.663 RSpredict(seed): 0.298 Sensitivity RSpredict(20): 0.593 RSpredict(seed): 0.156 Positive Predictive Value RSpredict(20): 0.748 RSpredict(seed): 0.582 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.19332990918e-08	29 Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.757 RSpredict(seed): 0.502 Sensitivity Alterna: 0.765 RSpredict(seed): 0.350 Positive Predictive Value Alterna: 0.760 RSpredict(seed): 0.739 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.560 RSpredict(seed): 0.131 Sensitivity RNASLOpt: 0.526 RSpredict(seed): 0.070 Positive Predictive Value RNASLOpt: 0.608 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.612 RSpredict(seed): 0.349 Sensitivity Multilign(20): 0.581 RSpredict(seed): 0.191 Positive Predictive Value Multilign(20): 0.657 RSpredict(seed): 0.657 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.69265863073e-08	44 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.595 RSpredict(seed): 0.372 Sensitivity Vsfold4: 0.595 RSpredict(seed): 0.222 Positive Predictive Value Vsfold4: 0.603 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.602 RSpredict(seed): 0.415 Sensitivity MCFold: 0.650 RSpredict(seed): 0.261 Positive Predictive Value MCFold: 0.568 RSpredict(seed): 0.674 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.499 RSpredict(seed): 0.231 Sensitivity RNAwolf: 0.490 RSpredict(seed): 0.123 Positive Predictive Value RNAwolf: 0.524 RSpredict(seed): 0.455 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 7.1398907247e-09	26 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.620 RSpredict(seed): 0.527 Sensitivity Murlet(seed): 0.442 RSpredict(seed): 0.371 Positive Predictive Value Murlet(seed): 0.879 RSpredict(seed): 0.760 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	44 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.570 RSpredict(seed): 0.372 Sensitivity Vsfold5: 0.575 RSpredict(seed): 0.222 Positive Predictive Value Vsfold5: 0.573 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.637 RSpredict(seed): 0.503 Sensitivity RDfolder: 0.604 RSpredict(seed): 0.345 Positive Predictive Value RDfolder: 0.687 RSpredict(seed): 0.753 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.231 PPfold(seed): 0.122 Sensitivity RSpredict(seed): 0.123 PPfold(seed): 0.029 Positive Predictive Value RSpredict(seed): 0.455 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.85438087962e-09	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.372 Mastr(seed): 0.310 Sensitivity RSpredict(seed): 0.222 Mastr(seed): 0.108 Positive Predictive Value RSpredict(seed): 0.636 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(seed): N/A Sensitivity RSpredict(seed): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 RSpredict(seed): 0.408 Sensitivity Multilign(seed): 0.636 RSpredict(seed): 0.280 Positive Predictive Value Multilign(seed): 0.750 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RSpredict(seed): 0.131 Sensitivity PETfold_pre2.0(seed): 0.772 RSpredict(seed): 0.070 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 RSpredict(seed): 0.346 Sensitivity TurboFold(20): 0.694 RSpredict(seed): 0.189 Positive Predictive Value TurboFold(20): 0.781 RSpredict(seed): 0.650 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(20): N/A Sensitivity RSpredict(seed): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RSpredict(seed): 0.219 Sensitivity PETfold_pre2.0(20): 0.707 RSpredict(seed): 0.103 Positive Predictive Value PETfold_pre2.0(20): 0.796 RSpredict(seed): 0.480 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.650 RSpredict(seed): 0.317 Sensitivity TurboFold(seed): 0.624 RSpredict(seed): 0.190 Positive Predictive Value TurboFold(seed): 0.688 RSpredict(seed): 0.549 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.780 RSpredict(seed): 0.346 Sensitivity PPfold(20): 0.714 RSpredict(seed): 0.189 Positive Predictive Value PPfold(20): 0.860 RSpredict(seed): 0.650 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.412 RSpredict(seed): 0.108 Sensitivity NanoFolder: 0.506 RSpredict(seed): 0.058 Positive Predictive Value NanoFolder: 0.350 RSpredict(seed): 0.225 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.467 Carnac(seed): 0.299 Sensitivity RSpredict(seed): 0.309 Carnac(seed): 0.090 Positive Predictive Value RSpredict(seed): 0.718 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08
RDfolder	31 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.809 RDfolder: 0.637 Sensitivity MXScarna(seed): 0.754 RDfolder: 0.604 Positive Predictive Value MXScarna(seed): 0.876 RDfolder: 0.687 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.872 RDfolder: 0.611 Sensitivity CentroidAlifold(20): 0.792 RDfolder: 0.578 Positive Predictive Value CentroidAlifold(20): 0.964 RDfolder: 0.662 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.1413769576e-08	79 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.840 RDfolder: 0.664 Sensitivity CentroidFold: 0.817 RDfolder: 0.625 Positive Predictive Value CentroidFold: 0.871 RDfolder: 0.721 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.840 RDfolder: 0.624 Sensitivity RNAalifold(20): 0.752 RDfolder: 0.591 Positive Predictive Value RNAalifold(20): 0.945 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 3.02344513449e-08	92 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.824 RDfolder: 0.682 Sensitivity Sfold: 0.803 RDfolder: 0.643 Positive Predictive Value Sfold: 0.853 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.821 RDfolder: 0.695 Sensitivity Fold: 0.825 RDfolder: 0.657 Positive Predictive Value Fold: 0.827 RDfolder: 0.752 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.881 RDfolder: 0.624 Sensitivity RNASampler(20): 0.799 RDfolder: 0.591 Positive Predictive Value RNASampler(20): 0.977 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.8150742666e-08	16 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.804 RDfolder: 0.624 Sensitivity MXScarna(20): 0.745 RDfolder: 0.591 Positive Predictive Value MXScarna(20): 0.875 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.20167918023e-08	32 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.815 RDfolder: 0.621 Sensitivity CentroidHomfold‑LAST: 0.721 RDfolder: 0.567 Positive Predictive Value CentroidHomfold‑LAST: 0.932 RDfolder: 0.700 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 5.23657817852e-08	92 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.833 RDfolder: 0.682 Sensitivity HotKnots: 0.838 RDfolder: 0.643 Positive Predictive Value HotKnots: 0.837 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.827 RDfolder: 0.682 Sensitivity UNAFold: 0.822 RDfolder: 0.643 Positive Predictive Value UNAFold: 0.841 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.838 RDfolder: 0.682 Sensitivity Contrafold: 0.831 RDfolder: 0.643 Positive Predictive Value Contrafold: 0.853 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.756 RDfolder: 0.567 Sensitivity IPknot: 0.718 RDfolder: 0.513 Positive Predictive Value IPknot: 0.808 RDfolder: 0.651 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	17 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.750 RDfolder: 0.537 Sensitivity ContextFold: 0.709 RDfolder: 0.485 Positive Predictive Value ContextFold: 0.808 RDfolder: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.76499031155e-08	92 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.805 RDfolder: 0.682 Sensitivity RNAshapes: 0.797 RDfolder: 0.643 Positive Predictive Value RNAshapes: 0.822 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	73 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.803 RDfolder: 0.674 Sensitivity MaxExpect: 0.801 RDfolder: 0.631 Positive Predictive Value MaxExpect: 0.815 RDfolder: 0.736 Number of pairs reference - predicted secondary structure: 73 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.808 RDfolder: 0.682 Sensitivity PknotsRG: 0.812 RDfolder: 0.643 Positive Predictive Value PknotsRG: 0.813 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.813 RDfolder: 0.682 Sensitivity RNAfold: 0.813 RDfolder: 0.643 Positive Predictive Value RNAfold: 0.823 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.804 RDfolder: 0.684 Sensitivity ProbKnot: 0.826 RDfolder: 0.650 Positive Predictive Value ProbKnot: 0.793 RDfolder: 0.738 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.768 RDfolder: 0.624 Sensitivity Murlet(20): 0.664 RDfolder: 0.591 Positive Predictive Value Murlet(20): 0.898 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.94377603181e-08	30 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 RDfolder: 0.630 Sensitivity CentroidAlifold(seed): 0.551 RDfolder: 0.597 Positive Predictive Value CentroidAlifold(seed): 0.877 RDfolder: 0.681 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	71 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.811 RDfolder: 0.714 Sensitivity Afold: 0.821 RDfolder: 0.674 Positive Predictive Value Afold: 0.813 RDfolder: 0.772 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.792 RDfolder: 0.682 Sensitivity RNAsubopt: 0.790 RDfolder: 0.643 Positive Predictive Value RNAsubopt: 0.805 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.731 RDfolder: 0.624 Sensitivity Carnac(20): 0.572 RDfolder: 0.591 Positive Predictive Value Carnac(20): 0.943 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.69132796717e-08	48 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.796 RDfolder: 0.662 Sensitivity Cylofold: 0.773 RDfolder: 0.627 Positive Predictive Value Cylofold: 0.830 RDfolder: 0.715 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	92 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.809 RDfolder: 0.682 Sensitivity McQFold: 0.778 RDfolder: 0.643 Positive Predictive Value McQFold: 0.851 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.703 RDfolder: 0.530 Sensitivity CRWrnafold: 0.704 RDfolder: 0.479 Positive Predictive Value CRWrnafold: 0.717 RDfolder: 0.610 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	21 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.742 RDfolder: 0.671 Sensitivity RNAalifold(seed): 0.633 RDfolder: 0.616 Positive Predictive Value RNAalifold(seed): 0.883 RDfolder: 0.746 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	92 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.802 RDfolder: 0.682 Sensitivity Pknots: 0.809 RDfolder: 0.643 Positive Predictive Value Pknots: 0.804 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.818 RDfolder: 0.731 Sensitivity RNASampler(seed): 0.715 RDfolder: 0.656 Positive Predictive Value RNASampler(seed): 0.945 RDfolder: 0.830 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.28439804626e-08	16 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.765 RDfolder: 0.624 Sensitivity Mastr(20): 0.676 RDfolder: 0.591 Positive Predictive Value Mastr(20): 0.874 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.16131455263e-08	16 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.737 RDfolder: 0.624 Sensitivity RSpredict(20): 0.642 RDfolder: 0.591 Positive Predictive Value RSpredict(20): 0.857 RDfolder: 0.674 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.61939086268e-08	88 Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.768 RDfolder: 0.690 Sensitivity Alterna: 0.777 RDfolder: 0.652 Positive Predictive Value Alterna: 0.771 RDfolder: 0.745 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.642 RDfolder: 0.537 Sensitivity RNASLOpt: 0.587 RDfolder: 0.485 Positive Predictive Value RNASLOpt: 0.723 RDfolder: 0.621 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.02344513449e-08	7 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.723 RDfolder: 0.548 Sensitivity Multilign(20): 0.691 RDfolder: 0.483 Positive Predictive Value Multilign(20): 0.769 RDfolder: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	92 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.749 RDfolder: 0.682 Sensitivity Vsfold4: 0.721 RDfolder: 0.643 Positive Predictive Value Vsfold4: 0.790 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 MCFold vs RDfolder Matthews Correlation Coefficient MCFold: 0.705 RDfolder: 0.703 Sensitivity MCFold: 0.737 RDfolder: 0.660 Positive Predictive Value MCFold: 0.689 RDfolder: 0.764 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 0.154221523985	25 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.614 RDfolder: 0.567 Sensitivity RNAwolf: 0.604 RDfolder: 0.513 Positive Predictive Value RNAwolf: 0.643 RDfolder: 0.651 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.23657817852e-08	20 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: 0.660 Murlet(seed): 0.655 Sensitivity RDfolder: 0.606 Murlet(seed): 0.512 Positive Predictive Value RDfolder: 0.736 Murlet(seed): 0.855 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 0.0625661724175	92 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.720 RDfolder: 0.682 Sensitivity Vsfold5: 0.708 RDfolder: 0.643 Positive Predictive Value Vsfold5: 0.746 RDfolder: 0.739 Number of pairs reference - predicted secondary structure: 92 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RDfolder vs RSpredict(seed) Matthews Correlation Coefficient RDfolder: 0.637 RSpredict(seed): 0.503 Sensitivity RDfolder: 0.604 RSpredict(seed): 0.345 Positive Predictive Value RDfolder: 0.687 RSpredict(seed): 0.753 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08		? RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.395 PPfold(seed): 0.160 Sensitivity RDfolder: 0.347 PPfold(seed): 0.035 Positive Predictive Value RDfolder: 0.476 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.637 Mastr(seed): 0.406 Sensitivity RDfolder: 0.604 Mastr(seed): 0.188 Positive Predictive Value RDfolder: 0.687 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RDfolder vs CMfinder(seed) Matthews Correlation Coefficient RDfolder: N/A CMfinder(seed): N/A Sensitivity RDfolder: N/A CMfinder(seed): N/A Positive Predictive Value RDfolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.683 RDfolder: 0.540 Sensitivity Multilign(seed): 0.636 RDfolder: 0.475 Positive Predictive Value Multilign(seed): 0.750 RDfolder: 0.636 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.745 RDfolder: 0.317 Sensitivity PETfold_pre2.0(seed): 0.673 RDfolder: 0.286 Positive Predictive Value PETfold_pre2.0(seed): 0.835 RDfolder: 0.384 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.783 RDfolder: 0.548 Sensitivity TurboFold(20): 0.718 RDfolder: 0.483 Positive Predictive Value TurboFold(20): 0.863 RDfolder: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.763 RDfolder: 0.445 Sensitivity PETfold_pre2.0(20): 0.678 RDfolder: 0.390 Positive Predictive Value PETfold_pre2.0(20): 0.870 RDfolder: 0.535 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.680 RDfolder: 0.528 Sensitivity TurboFold(seed): 0.622 RDfolder: 0.459 Positive Predictive Value TurboFold(seed): 0.760 RDfolder: 0.630 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.811 RDfolder: 0.548 Sensitivity PPfold(20): 0.725 RDfolder: 0.483 Positive Predictive Value PPfold(20): 0.915 RDfolder: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.626 RDfolder: 0.528 Sensitivity NanoFolder: 0.680 RDfolder: 0.492 Positive Predictive Value NanoFolder: 0.597 RDfolder: 0.594 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	+ RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.660 Carnac(seed): 0.389 Sensitivity RDfolder: 0.606 Carnac(seed): 0.155 Positive Predictive Value RDfolder: 0.736 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08
PPfold(seed)	11 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.728 PPfold(seed): 0.122 Sensitivity MXScarna(seed): 0.675 PPfold(seed): 0.029 Positive Predictive Value MXScarna(seed): 0.792 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.36849473644e-08	8 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.825 PPfold(seed): 0.031 Sensitivity CentroidAlifold(20): 0.729 PPfold(seed): 0.005 Positive Predictive Value CentroidAlifold(20): 0.938 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.682 PPfold(seed): 0.122 Sensitivity CentroidFold: 0.650 PPfold(seed): 0.029 Positive Predictive Value CentroidFold: 0.725 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.67657656842e-08	8 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.744 PPfold(seed): 0.031 Sensitivity RNAalifold(20): 0.681 PPfold(seed): 0.005 Positive Predictive Value RNAalifold(20): 0.821 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.641 PPfold(seed): 0.122 Sensitivity Sfold: 0.601 PPfold(seed): 0.029 Positive Predictive Value Sfold: 0.695 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.79203144115e-08	11 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.613 PPfold(seed): 0.122 Sensitivity Fold: 0.617 PPfold(seed): 0.029 Positive Predictive Value Fold: 0.620 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.93248927742e-08	8 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.762 PPfold(seed): 0.031 Sensitivity RNASampler(20): 0.681 PPfold(seed): 0.005 Positive Predictive Value RNASampler(20): 0.859 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 PPfold(seed): 0.031 Sensitivity MXScarna(20): 0.649 PPfold(seed): 0.005 Positive Predictive Value MXScarna(20): 0.739 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.738 PPfold(seed): 0.122 Sensitivity CentroidHomfold‑LAST: 0.671 PPfold(seed): 0.029 Positive Predictive Value CentroidHomfold‑LAST: 0.819 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.14531876181e-08	11 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.675 PPfold(seed): 0.122 Sensitivity HotKnots: 0.687 PPfold(seed): 0.029 Positive Predictive Value HotKnots: 0.673 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.91686328089e-09	11 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.584 PPfold(seed): 0.122 Sensitivity UNAFold: 0.584 PPfold(seed): 0.029 Positive Predictive Value UNAFold: 0.597 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.27752322258e-08	11 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.666 PPfold(seed): 0.122 Sensitivity Contrafold: 0.658 PPfold(seed): 0.029 Positive Predictive Value Contrafold: 0.684 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.75835195567e-08	11 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.701 PPfold(seed): 0.122 Sensitivity IPknot: 0.658 PPfold(seed): 0.029 Positive Predictive Value IPknot: 0.755 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 6.77162746897e-09	8 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.732 PPfold(seed): 0.146 Sensitivity ContextFold: 0.673 PPfold(seed): 0.041 Positive Predictive Value ContextFold: 0.804 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.648 PPfold(seed): 0.122 Sensitivity RNAshapes: 0.646 PPfold(seed): 0.029 Positive Predictive Value RNAshapes: 0.660 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.32883086441e-08	11 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.603 PPfold(seed): 0.122 Sensitivity MaxExpect: 0.601 PPfold(seed): 0.029 Positive Predictive Value MaxExpect: 0.616 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.52299983238e-08	11 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.714 PPfold(seed): 0.122 Sensitivity PknotsRG: 0.720 PPfold(seed): 0.029 Positive Predictive Value PknotsRG: 0.717 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.20383511129e-08	11 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.679 PPfold(seed): 0.122 Sensitivity RNAfold: 0.671 PPfold(seed): 0.029 Positive Predictive Value RNAfold: 0.697 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.04628667909e-08	11 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.604 PPfold(seed): 0.122 Sensitivity ProbKnot: 0.634 PPfold(seed): 0.029 Positive Predictive Value ProbKnot: 0.588 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.24019667966e-08	8 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.693 PPfold(seed): 0.031 Sensitivity Murlet(20): 0.612 PPfold(seed): 0.005 Positive Predictive Value Murlet(20): 0.793 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.694 PPfold(seed): 0.122 Sensitivity CentroidAlifold(seed): 0.494 PPfold(seed): 0.029 Positive Predictive Value CentroidAlifold(seed): 0.984 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.59816551561e-08	4 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.590 PPfold(seed): 0.218 Sensitivity Afold: 0.610 PPfold(seed): 0.091 Positive Predictive Value Afold: 0.580 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	11 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.592 PPfold(seed): 0.122 Sensitivity RNAsubopt: 0.597 PPfold(seed): 0.029 Positive Predictive Value RNAsubopt: 0.599 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.53777893337e-08	8 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.662 PPfold(seed): 0.031 Sensitivity Carnac(20): 0.516 PPfold(seed): 0.005 Positive Predictive Value Carnac(20): 0.858 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.730 PPfold(seed): 0.153 Sensitivity Cylofold: 0.710 PPfold(seed): 0.032 Positive Predictive Value Cylofold: 0.763 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.641 PPfold(seed): 0.122 Sensitivity McQFold: 0.654 PPfold(seed): 0.029 Positive Predictive Value McQFold: 0.639 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.39551335374e-08	9 CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 PPfold(seed): 0.134 Sensitivity CRWrnafold: 0.655 PPfold(seed): 0.034 Positive Predictive Value CRWrnafold: 0.649 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 PPfold(seed): 0.155 Sensitivity RNAalifold(seed): 0.473 PPfold(seed): 0.047 Positive Predictive Value RNAalifold(seed): 0.798 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	11 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.630 PPfold(seed): 0.122 Sensitivity Pknots: 0.646 PPfold(seed): 0.029 Positive Predictive Value Pknots: 0.625 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.98760236454e-08	4 RNASampler(seed) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.559 PPfold(seed): 0.200 Sensitivity RNASampler(seed): 0.484 PPfold(seed): 0.077 Positive Predictive Value RNASampler(seed): 0.657 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	8 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.674 PPfold(seed): 0.031 Sensitivity Mastr(20): 0.548 PPfold(seed): 0.005 Positive Predictive Value Mastr(20): 0.837 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.586 PPfold(seed): 0.031 Sensitivity RSpredict(20): 0.521 PPfold(seed): 0.005 Positive Predictive Value RSpredict(20): 0.671 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.671 PPfold(seed): 0.185 Sensitivity Alterna: 0.677 PPfold(seed): 0.047 Positive Predictive Value Alterna: 0.677 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.560 PPfold(seed): 0.146 Sensitivity RNASLOpt: 0.526 PPfold(seed): 0.041 Positive Predictive Value RNASLOpt: 0.608 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.653 PPfold(seed): 0.031 Sensitivity Multilign(20): 0.649 PPfold(seed): 0.005 Positive Predictive Value Multilign(20): 0.667 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	11 Vsfold4 vs PPfold(seed) Matthews Correlation Coefficient Vsfold4: 0.529 PPfold(seed): 0.122 Sensitivity Vsfold4: 0.514 PPfold(seed): 0.029 Positive Predictive Value Vsfold4: 0.558 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.3551590886e-08	9 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.563 PPfold(seed): 0.135 Sensitivity MCFold: 0.596 PPfold(seed): 0.035 Positive Predictive Value MCFold: 0.544 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	11 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.499 PPfold(seed): 0.122 Sensitivity RNAwolf: 0.490 PPfold(seed): 0.029 Positive Predictive Value RNAwolf: 0.524 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.18011954625e-08	7 Murlet(seed) vs PPfold(seed) Matthews Correlation Coefficient Murlet(seed): 0.531 PPfold(seed): 0.155 Sensitivity Murlet(seed): 0.373 PPfold(seed): 0.047 Positive Predictive Value Murlet(seed): 0.767 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	11 Vsfold5 vs PPfold(seed) Matthews Correlation Coefficient Vsfold5: 0.484 PPfold(seed): 0.122 Sensitivity Vsfold5: 0.498 PPfold(seed): 0.029 Positive Predictive Value Vsfold5: 0.486 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.50834591464e-08	11 RSpredict(seed) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(seed): 0.231 PPfold(seed): 0.122 Sensitivity RSpredict(seed): 0.123 PPfold(seed): 0.029 Positive Predictive Value RSpredict(seed): 0.455 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.85438087962e-09	8 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.395 PPfold(seed): 0.160 Sensitivity RDfolder: 0.347 PPfold(seed): 0.035 Positive Predictive Value RDfolder: 0.476 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.122 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.029 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.07842257011e-08	? PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(seed): N/A Sensitivity PPfold(seed): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.629 PPfold(seed): 0.208 Sensitivity Multilign(seed): 0.580 PPfold(seed): 0.060 Positive Predictive Value Multilign(seed): 0.699 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 PPfold(seed): 0.146 Sensitivity PETfold_pre2.0(seed): 0.772 PPfold(seed): 0.041 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.712 PPfold(seed): 0.031 Sensitivity TurboFold(20): 0.670 PPfold(seed): 0.005 Positive Predictive Value TurboFold(20): 0.764 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): N/A CMfinder(20): N/A Sensitivity PPfold(seed): N/A CMfinder(20): N/A Positive Predictive Value PPfold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 PPfold(seed): 0.039 Sensitivity PETfold_pre2.0(20): 0.707 PPfold(seed): 0.009 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.621 PPfold(seed): 0.139 Sensitivity TurboFold(seed): 0.594 PPfold(seed): 0.037 Positive Predictive Value TurboFold(seed): 0.661 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.790 PPfold(seed): 0.031 Sensitivity PPfold(20): 0.734 PPfold(seed): 0.005 Positive Predictive Value PPfold(20): 0.857 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.412 PPfold(seed): 0.153 Sensitivity NanoFolder: 0.506 PPfold(seed): 0.045 Positive Predictive Value NanoFolder: 0.350 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.145 PPfold(seed): 0.139 Sensitivity Carnac(seed): 0.021 PPfold(seed): 0.037 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
Mastr(seed)	44 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.776 Mastr(seed): 0.310 Sensitivity MXScarna(seed): 0.736 Mastr(seed): 0.108 Positive Predictive Value MXScarna(seed): 0.824 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.810 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.716 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.921 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.06544643719e-08	43 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.724 Mastr(seed): 0.311 Sensitivity CentroidFold: 0.727 Mastr(seed): 0.109 Positive Predictive Value CentroidFold: 0.726 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.782 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.690 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.889 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	45 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.710 Mastr(seed): 0.306 Sensitivity Sfold: 0.703 Mastr(seed): 0.105 Positive Predictive Value Sfold: 0.724 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.722 Mastr(seed): 0.326 Sensitivity Fold: 0.750 Mastr(seed): 0.121 Positive Predictive Value Fold: 0.700 Mastr(seed): 0.885 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.765 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.671 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.875 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	28 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.761 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.727 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.800 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	12 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.753 Mastr(seed): 0.000 Sensitivity CentroidHomfold‑LAST: 0.690 Mastr(seed): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.829 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.5677163434e-08	45 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.702 Mastr(seed): 0.306 Sensitivity HotKnots: 0.733 Mastr(seed): 0.105 Positive Predictive Value HotKnots: 0.679 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.701 Mastr(seed): 0.306 Sensitivity UNAFold: 0.722 Mastr(seed): 0.105 Positive Predictive Value UNAFold: 0.687 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.692 Mastr(seed): 0.306 Sensitivity Contrafold: 0.721 Mastr(seed): 0.105 Positive Predictive Value Contrafold: 0.670 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.701 Mastr(seed): 0.000 Sensitivity IPknot: 0.658 Mastr(seed): 0.000 Positive Predictive Value IPknot: 0.755 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.34193807955e-08	8 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.732 Mastr(seed): 0.000 Sensitivity ContextFold: 0.673 Mastr(seed): 0.000 Positive Predictive Value ContextFold: 0.804 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	45 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.697 Mastr(seed): 0.306 Sensitivity RNAshapes: 0.716 Mastr(seed): 0.105 Positive Predictive Value RNAshapes: 0.683 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.703 Mastr(seed): 0.322 Sensitivity MaxExpect: 0.725 Mastr(seed): 0.116 Positive Predictive Value MaxExpect: 0.687 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.706 Mastr(seed): 0.306 Sensitivity PknotsRG: 0.735 Mastr(seed): 0.105 Positive Predictive Value PknotsRG: 0.684 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	45 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.706 Mastr(seed): 0.306 Sensitivity RNAfold: 0.731 Mastr(seed): 0.105 Positive Predictive Value RNAfold: 0.688 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.657 Mastr(seed): 0.252 Sensitivity ProbKnot: 0.701 Mastr(seed): 0.064 Positive Predictive Value ProbKnot: 0.622 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.1503931209e-08	28 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.704 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.596 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.837 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	43 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.690 Mastr(seed): 0.311 Sensitivity CentroidAlifold(seed): 0.552 Mastr(seed): 0.109 Positive Predictive Value CentroidAlifold(seed): 0.870 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.659 Mastr(seed): 0.358 Sensitivity Afold: 0.693 Mastr(seed): 0.144 Positive Predictive Value Afold: 0.633 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	45 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.658 Mastr(seed): 0.306 Sensitivity RNAsubopt: 0.687 Mastr(seed): 0.105 Positive Predictive Value RNAsubopt: 0.636 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.696 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.518 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.941 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.732 Mastr(seed): 0.307 Sensitivity Cylofold: 0.726 Mastr(seed): 0.096 Positive Predictive Value Cylofold: 0.747 Mastr(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	45 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.649 Mastr(seed): 0.306 Sensitivity McQFold: 0.665 Mastr(seed): 0.105 Positive Predictive Value McQFold: 0.639 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.647 Mastr(seed): 0.000 Sensitivity CRWrnafold: 0.655 Mastr(seed): 0.000 Positive Predictive Value CRWrnafold: 0.649 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	29 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.676 Mastr(seed): 0.371 Sensitivity RNAalifold(seed): 0.525 Mastr(seed): 0.154 Positive Predictive Value RNAalifold(seed): 0.874 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.1503931209e-08	43 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.708 Mastr(seed): 0.328 Sensitivity Pknots: 0.743 Mastr(seed): 0.122 Positive Predictive Value Pknots: 0.684 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 Mastr(seed): 0.546 Sensitivity RNASampler(seed): 0.687 Mastr(seed): 0.336 Positive Predictive Value RNASampler(seed): 0.859 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	28 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.636 Mastr(seed): 0.000 Sensitivity Mastr(20): 0.483 Mastr(seed): 0.000 Positive Predictive Value Mastr(20): 0.845 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.23657817852e-08	27 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.663 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.593 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.748 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 27 Wilcoxon single-rank test P-value: 5.06544643719e-08	29 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.757 Mastr(seed): 0.421 Sensitivity Alterna: 0.765 Mastr(seed): 0.202 Positive Predictive Value Alterna: 0.760 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	8 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.560 Mastr(seed): 0.000 Sensitivity RNASLOpt: 0.526 Mastr(seed): 0.000 Positive Predictive Value RNASLOpt: 0.608 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	10 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.612 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.581 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.657 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.11462970451e-09	45 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.590 Mastr(seed): 0.306 Sensitivity Vsfold4: 0.592 Mastr(seed): 0.105 Positive Predictive Value Vsfold4: 0.597 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.602 Mastr(seed): 0.352 Sensitivity MCFold: 0.650 Mastr(seed): 0.140 Positive Predictive Value MCFold: 0.568 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.499 Mastr(seed): 0.000 Sensitivity RNAwolf: 0.490 Mastr(seed): 0.000 Positive Predictive Value RNAwolf: 0.524 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.02510705504e-08	26 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.620 Mastr(seed): 0.417 Sensitivity Murlet(seed): 0.442 Mastr(seed): 0.197 Positive Predictive Value Murlet(seed): 0.879 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	45 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.557 Mastr(seed): 0.306 Sensitivity Vsfold5: 0.565 Mastr(seed): 0.105 Positive Predictive Value Vsfold5: 0.557 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.372 Mastr(seed): 0.310 Sensitivity RSpredict(seed): 0.222 Mastr(seed): 0.108 Positive Predictive Value RSpredict(seed): 0.636 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.637 Mastr(seed): 0.406 Sensitivity RDfolder: 0.604 Mastr(seed): 0.188 Positive Predictive Value RDfolder: 0.687 Mastr(seed): 0.899 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.122 Mastr(seed): 0.000 Sensitivity PPfold(seed): 0.029 Mastr(seed): 0.000 Positive Predictive Value PPfold(seed): 0.538 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.07842257011e-08		? Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.636 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.750 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.772 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.781 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Mastr(seed) vs CMfinder(20) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(20): N/A Sensitivity Mastr(seed): N/A CMfinder(20): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.707 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.796 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.650 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.624 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.688 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.780 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.714 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.860 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.412 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.506 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.350 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.381 Carnac(seed): 0.299 Sensitivity Mastr(seed): 0.164 Carnac(seed): 0.090 Positive Predictive Value Mastr(seed): 0.899 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08
CMfinder(seed)	0 CMfinder(seed) vs MXScarna(seed) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(seed): N/A Sensitivity CMfinder(seed): N/A MXScarna(seed): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CentroidFold Matthews Correlation Coefficient CMfinder(seed): N/A CentroidFold: N/A Sensitivity CMfinder(seed): N/A CentroidFold: N/A Positive Predictive Value CMfinder(seed): N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): N/A Sfold: N/A Sensitivity CMfinder(seed): N/A Sfold: N/A Positive Predictive Value CMfinder(seed): N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: N/A CMfinder(seed): N/A Sensitivity Fold: N/A CMfinder(seed): N/A Positive Predictive Value Fold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Sensitivity CMfinder(seed): N/A CentroidHomfold‑LAST: N/A Positive Predictive Value CMfinder(seed): 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 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 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: N/A CMfinder(seed): N/A Sensitivity UNAFold: N/A CMfinder(seed): N/A Positive Predictive Value UNAFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: N/A CMfinder(seed): N/A Sensitivity Contrafold: N/A CMfinder(seed): N/A Positive Predictive Value Contrafold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs IPknot Matthews Correlation Coefficient CMfinder(seed): N/A IPknot: N/A Sensitivity CMfinder(seed): N/A IPknot: N/A Positive Predictive Value CMfinder(seed): N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: N/A CMfinder(seed): N/A Sensitivity ContextFold: N/A CMfinder(seed): N/A Positive Predictive Value ContextFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): N/A RNAshapes: N/A Sensitivity CMfinder(seed): N/A RNAshapes: N/A Positive Predictive Value CMfinder(seed): N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(seed): N/A Sensitivity MaxExpect: N/A CMfinder(seed): N/A Positive Predictive Value MaxExpect: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(seed): N/A Sensitivity PknotsRG: N/A CMfinder(seed): N/A Positive Predictive Value PknotsRG: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): N/A RNAfold: N/A Sensitivity CMfinder(seed): N/A RNAfold: N/A Positive Predictive Value CMfinder(seed): N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(seed): N/A Sensitivity ProbKnot: N/A CMfinder(seed): N/A Positive Predictive Value ProbKnot: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(seed): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): N/A Afold: N/A Sensitivity CMfinder(seed): N/A Afold: N/A Positive Predictive Value CMfinder(seed): N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): N/A RNAsubopt: N/A Sensitivity CMfinder(seed): N/A RNAsubopt: N/A Positive Predictive Value CMfinder(seed): N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(20): N/A Sensitivity CMfinder(seed): N/A Carnac(20): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: N/A CMfinder(seed): N/A Sensitivity McQFold: N/A CMfinder(seed): N/A Positive Predictive Value McQFold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CRWrnafold Matthews Correlation Coefficient CMfinder(seed): N/A CRWrnafold: N/A Sensitivity CMfinder(seed): N/A CRWrnafold: N/A Positive Predictive Value CMfinder(seed): N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(seed): N/A Sensitivity RNAalifold(seed): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): N/A RNASLOpt: N/A Sensitivity CMfinder(seed): N/A RNASLOpt: N/A Positive Predictive Value CMfinder(seed): N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(seed): N/A Sensitivity Vsfold4: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold4: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): N/A RNAwolf: N/A Sensitivity CMfinder(seed): N/A RNAwolf: N/A Positive Predictive Value CMfinder(seed): N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Murlet(seed): N/A Sensitivity CMfinder(seed): N/A Murlet(seed): N/A Positive Predictive Value CMfinder(seed): N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs CMfinder(seed) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(seed): N/A Sensitivity Vsfold5: N/A CMfinder(seed): N/A Positive Predictive Value Vsfold5: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(seed): N/A Sensitivity RSpredict(seed): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 Mastr(seed) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(seed): N/A Sensitivity Mastr(seed): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(seed): N/A Sensitivity TurboFold(seed): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Multilign(seed)	5 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 MXScarna(seed): 0.630 Sensitivity Multilign(seed): 0.636 MXScarna(seed): 0.593 Positive Predictive Value Multilign(seed): 0.750 MXScarna(seed): 0.686 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.818 Multilign(seed): 0.795 Sensitivity CentroidAlifold(20): 0.730 Multilign(seed): 0.750 Positive Predictive Value CentroidAlifold(20): 0.924 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.704 Multilign(seed): 0.683 Sensitivity CentroidFold: 0.661 Multilign(seed): 0.636 Positive Predictive Value CentroidFold: 0.765 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RNAalifold(20) Matthews Correlation Coefficient Multilign(seed): 0.795 RNAalifold(20): 0.776 Sensitivity Multilign(seed): 0.750 RNAalifold(20): 0.720 Positive Predictive Value Multilign(seed): 0.852 RNAalifold(20): 0.847 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Sfold vs Multilign(seed) Matthews Correlation Coefficient Sfold: 0.751 Multilign(seed): 0.683 Sensitivity Sfold: 0.703 Multilign(seed): 0.636 Positive Predictive Value Sfold: 0.814 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.683 Fold: 0.653 Sensitivity Multilign(seed): 0.636 Fold: 0.636 Positive Predictive Value Multilign(seed): 0.750 Fold: 0.688 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.829 Multilign(seed): 0.795 Sensitivity RNASampler(20): 0.740 Multilign(seed): 0.750 Positive Predictive Value RNASampler(20): 0.937 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): 0.795 MXScarna(20): 0.747 Sensitivity Multilign(seed): 0.750 MXScarna(20): 0.730 Positive Predictive Value Multilign(seed): 0.852 MXScarna(20): 0.777 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.726 Multilign(seed): 0.683 Sensitivity CentroidHomfold‑LAST: 0.636 Multilign(seed): 0.636 Positive Predictive Value CentroidHomfold‑LAST: 0.843 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.770 Multilign(seed): 0.683 Sensitivity HotKnots: 0.746 Multilign(seed): 0.636 Positive Predictive Value HotKnots: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.683 UNAFold: 0.674 Sensitivity Multilign(seed): 0.636 UNAFold: 0.653 Positive Predictive Value Multilign(seed): 0.750 UNAFold: 0.713 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.693 Multilign(seed): 0.683 Sensitivity Contrafold: 0.669 Multilign(seed): 0.636 Positive Predictive Value Contrafold: 0.731 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.656 Multilign(seed): 0.629 Sensitivity IPknot: 0.600 Multilign(seed): 0.580 Positive Predictive Value IPknot: 0.732 Multilign(seed): 0.699 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.606 Multilign(seed): 0.458 Sensitivity ContextFold: 0.574 Multilign(seed): 0.404 Positive Predictive Value ContextFold: 0.659 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 RNAshapes vs Multilign(seed) Matthews Correlation Coefficient RNAshapes: 0.770 Multilign(seed): 0.683 Sensitivity RNAshapes: 0.746 Multilign(seed): 0.636 Positive Predictive Value RNAshapes: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.683 MaxExpect: 0.656 Sensitivity Multilign(seed): 0.636 MaxExpect: 0.636 Positive Predictive Value Multilign(seed): 0.750 MaxExpect: 0.694 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.765 Multilign(seed): 0.683 Sensitivity PknotsRG: 0.737 Multilign(seed): 0.636 Positive Predictive Value PknotsRG: 0.806 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 RNAfold vs Multilign(seed) Matthews Correlation Coefficient RNAfold: 0.770 Multilign(seed): 0.683 Sensitivity RNAfold: 0.746 Multilign(seed): 0.636 Positive Predictive Value RNAfold: 0.807 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.683 ProbKnot: 0.641 Sensitivity Multilign(seed): 0.636 ProbKnot: 0.636 Positive Predictive Value Multilign(seed): 0.750 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Murlet(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Murlet(20): 0.775 Sensitivity Multilign(seed): 0.750 Murlet(20): 0.710 Positive Predictive Value Multilign(seed): 0.852 Murlet(20): 0.855 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.747 Multilign(seed): 0.683 Sensitivity CentroidAlifold(seed): 0.627 Multilign(seed): 0.636 Positive Predictive Value CentroidAlifold(seed): 0.902 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Afold vs Multilign(seed) Matthews Correlation Coefficient Afold: 0.856 Multilign(seed): 0.672 Sensitivity Afold: 0.817 Multilign(seed): 0.617 Positive Predictive Value Afold: 0.907 Multilign(seed): 0.755 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.683 RNAsubopt: 0.671 Sensitivity Multilign(seed): 0.636 RNAsubopt: 0.653 Positive Predictive Value Multilign(seed): 0.750 RNAsubopt: 0.706 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Carnac(20): 0.663 Sensitivity Multilign(seed): 0.750 Carnac(20): 0.500 Positive Predictive Value Multilign(seed): 0.852 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.716 Multilign(seed): 0.683 Sensitivity Cylofold: 0.678 Multilign(seed): 0.636 Positive Predictive Value Cylofold: 0.769 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.761 Multilign(seed): 0.683 Sensitivity McQFold: 0.737 Multilign(seed): 0.636 Positive Predictive Value McQFold: 0.798 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.540 CRWrnafold: 0.513 Sensitivity Multilign(seed): 0.500 CRWrnafold: 0.513 Positive Predictive Value Multilign(seed): 0.603 CRWrnafold: 0.534 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 RNAalifold(seed): 0.620 Sensitivity Multilign(seed): 0.636 RNAalifold(seed): 0.517 Positive Predictive Value Multilign(seed): 0.750 RNAalifold(seed): 0.763 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.694 Multilign(seed): 0.683 Sensitivity Pknots: 0.686 Multilign(seed): 0.636 Positive Predictive Value Pknots: 0.717 Multilign(seed): 0.750 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.668 RNASampler(seed): 0.633 Sensitivity Multilign(seed): 0.629 RNASampler(seed): 0.517 Positive Predictive Value Multilign(seed): 0.727 RNASampler(seed): 0.793 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Mastr(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Mastr(20): 0.698 Sensitivity Multilign(seed): 0.750 Mastr(20): 0.630 Positive Predictive Value Multilign(seed): 0.852 Mastr(20): 0.788 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RSpredict(20) Matthews Correlation Coefficient Multilign(seed): 0.795 RSpredict(20): 0.675 Sensitivity Multilign(seed): 0.750 RSpredict(20): 0.610 Positive Predictive Value Multilign(seed): 0.852 RSpredict(20): 0.763 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Alterna vs Multilign(seed) Matthews Correlation Coefficient Alterna: 0.702 Multilign(seed): 0.668 Sensitivity Alterna: 0.685 Multilign(seed): 0.629 Positive Predictive Value Alterna: 0.735 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	2 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.458 RNASLOpt: 0.375 Sensitivity Multilign(seed): 0.404 RNASLOpt: 0.319 Positive Predictive Value Multilign(seed): 0.543 RNASLOpt: 0.469 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): 0.795 Multilign(20): 0.768 Sensitivity Multilign(seed): 0.750 Multilign(20): 0.750 Positive Predictive Value Multilign(seed): 0.852 Multilign(20): 0.798 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.683 Vsfold4: 0.503 Sensitivity Multilign(seed): 0.636 Vsfold4: 0.483 Positive Predictive Value Multilign(seed): 0.750 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 MCFold vs Multilign(seed) Matthews Correlation Coefficient MCFold: 0.669 Multilign(seed): 0.668 Sensitivity MCFold: 0.674 Multilign(seed): 0.629 Positive Predictive Value MCFold: 0.682 Multilign(seed): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.629 RNAwolf: 0.552 Sensitivity Multilign(seed): 0.580 RNAwolf: 0.530 Positive Predictive Value Multilign(seed): 0.699 RNAwolf: 0.596 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 Murlet(seed): 0.506 Sensitivity Multilign(seed): 0.636 Murlet(seed): 0.373 Positive Predictive Value Multilign(seed): 0.750 Murlet(seed): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.683 Vsfold5: 0.427 Sensitivity Multilign(seed): 0.636 Vsfold5: 0.415 Positive Predictive Value Multilign(seed): 0.750 Vsfold5: 0.467 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 RSpredict(seed): 0.408 Sensitivity Multilign(seed): 0.636 RSpredict(seed): 0.280 Positive Predictive Value Multilign(seed): 0.750 RSpredict(seed): 0.623 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.683 RDfolder: 0.540 Sensitivity Multilign(seed): 0.636 RDfolder: 0.475 Positive Predictive Value Multilign(seed): 0.750 RDfolder: 0.636 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Multilign(seed) vs PPfold(seed) Matthews Correlation Coefficient Multilign(seed): 0.629 PPfold(seed): 0.208 Sensitivity Multilign(seed): 0.580 PPfold(seed): 0.060 Positive Predictive Value Multilign(seed): 0.699 PPfold(seed): 0.750 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 Mastr(seed): 0.000 Sensitivity Multilign(seed): 0.636 Mastr(seed): 0.000 Positive Predictive Value Multilign(seed): 0.750 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(seed): N/A Sensitivity Multilign(seed): N/A CMfinder(seed): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.699 Multilign(seed): 0.458 Sensitivity PETfold_pre2.0(seed): 0.617 Multilign(seed): 0.404 Positive Predictive Value PETfold_pre2.0(seed): 0.806 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.795 TurboFold(20): 0.789 Sensitivity Multilign(seed): 0.750 TurboFold(20): 0.740 Positive Predictive Value Multilign(seed): 0.852 TurboFold(20): 0.851 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.872 Multilign(seed): 0.731 Sensitivity PETfold_pre2.0(20): 0.828 Multilign(seed): 0.655 Positive Predictive Value PETfold_pre2.0(20): 0.923 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs TurboFold(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 TurboFold(seed): 0.667 Sensitivity Multilign(seed): 0.636 TurboFold(seed): 0.627 Positive Predictive Value Multilign(seed): 0.750 TurboFold(seed): 0.725 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.818 Multilign(seed): 0.795 Sensitivity PPfold(20): 0.740 Multilign(seed): 0.750 Positive Predictive Value PPfold(20): 0.914 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.458 NanoFolder: 0.447 Sensitivity Multilign(seed): 0.404 NanoFolder: 0.489 Positive Predictive Value Multilign(seed): 0.543 NanoFolder: 0.434 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 Carnac(seed): 0.427 Sensitivity Multilign(seed): 0.636 Carnac(seed): 0.186 Positive Predictive Value Multilign(seed): 0.750 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
PETfold_pre2.0(seed)	8 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 MXScarna(seed): 0.679 Sensitivity PETfold_pre2.0(seed): 0.772 MXScarna(seed): 0.620 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MXScarna(seed): 0.752 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 CentroidAlifold(20): 0.779 Sensitivity PETfold_pre2.0(seed): 0.784 CentroidAlifold(20): 0.672 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidAlifold(20): 0.907 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 CentroidFold: 0.634 Sensitivity PETfold_pre2.0(seed): 0.772 CentroidFold: 0.602 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidFold: 0.678 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RNAalifold(20): 0.656 Sensitivity PETfold_pre2.0(seed): 0.784 RNAalifold(20): 0.578 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAalifold(20): 0.753 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Sfold: 0.562 Sensitivity PETfold_pre2.0(seed): 0.772 Sfold: 0.526 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Sfold: 0.612 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Fold: 0.550 Sensitivity PETfold_pre2.0(seed): 0.772 Fold: 0.556 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Fold: 0.556 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RNASampler(20): 0.686 Sensitivity PETfold_pre2.0(seed): 0.784 RNASampler(20): 0.603 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNASampler(20): 0.787 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 MXScarna(20): 0.586 Sensitivity PETfold_pre2.0(seed): 0.784 MXScarna(20): 0.543 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MXScarna(20): 0.643 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 CentroidHomfold‑LAST: 0.692 Sensitivity PETfold_pre2.0(seed): 0.772 CentroidHomfold‑LAST: 0.632 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidHomfold‑LAST: 0.766 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 HotKnots: 0.618 Sensitivity PETfold_pre2.0(seed): 0.772 HotKnots: 0.643 Positive Predictive Value PETfold_pre2.0(seed): 0.892 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 UNAFold: 0.489 Sensitivity PETfold_pre2.0(seed): 0.772 UNAFold: 0.497 Positive Predictive Value PETfold_pre2.0(seed): 0.892 UNAFold: 0.494 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Contrafold: 0.626 Sensitivity PETfold_pre2.0(seed): 0.772 Contrafold: 0.614 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Contrafold: 0.648 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 IPknot: 0.653 Sensitivity PETfold_pre2.0(seed): 0.772 IPknot: 0.614 Positive Predictive Value PETfold_pre2.0(seed): 0.892 IPknot: 0.705 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 ContextFold: 0.732 Sensitivity PETfold_pre2.0(seed): 0.772 ContextFold: 0.673 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ContextFold: 0.804 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAshapes: 0.577 Sensitivity PETfold_pre2.0(seed): 0.772 RNAshapes: 0.585 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAshapes: 0.581 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 MaxExpect: 0.532 Sensitivity PETfold_pre2.0(seed): 0.772 MaxExpect: 0.532 Positive Predictive Value PETfold_pre2.0(seed): 0.892 MaxExpect: 0.545 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 PknotsRG: 0.678 Sensitivity PETfold_pre2.0(seed): 0.772 PknotsRG: 0.696 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PknotsRG: 0.669 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAfold: 0.620 Sensitivity PETfold_pre2.0(seed): 0.772 RNAfold: 0.620 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAfold: 0.631 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 ProbKnot: 0.544 Sensitivity PETfold_pre2.0(seed): 0.772 ProbKnot: 0.579 Positive Predictive Value PETfold_pre2.0(seed): 0.892 ProbKnot: 0.524 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Murlet(20): 0.594 Sensitivity PETfold_pre2.0(seed): 0.784 Murlet(20): 0.500 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Murlet(20): 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 CentroidAlifold(seed): 0.646 Sensitivity PETfold_pre2.0(seed): 0.772 CentroidAlifold(seed): 0.427 Positive Predictive Value PETfold_pre2.0(seed): 0.892 CentroidAlifold(seed): 0.986 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.627 Afold: 0.469 Sensitivity PETfold_pre2.0(seed): 0.547 Afold: 0.509 Positive Predictive Value PETfold_pre2.0(seed): 0.725 Afold: 0.443 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAsubopt: 0.506 Sensitivity PETfold_pre2.0(seed): 0.772 RNAsubopt: 0.520 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAsubopt: 0.506 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Carnac(20): 0.562 Sensitivity PETfold_pre2.0(seed): 0.784 Carnac(20): 0.397 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Carnac(20): 0.807 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.773 Cylofold: 0.694 Sensitivity PETfold_pre2.0(seed): 0.702 Cylofold: 0.675 Positive Predictive Value PETfold_pre2.0(seed): 0.860 Cylofold: 0.726 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 McQFold: 0.558 Sensitivity PETfold_pre2.0(seed): 0.772 McQFold: 0.585 Positive Predictive Value PETfold_pre2.0(seed): 0.892 McQFold: 0.543 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.816 CRWrnafold: 0.636 Sensitivity PETfold_pre2.0(seed): 0.761 CRWrnafold: 0.639 Positive Predictive Value PETfold_pre2.0(seed): 0.881 CRWrnafold: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 RNAalifold(seed): 0.542 Sensitivity PETfold_pre2.0(seed): 0.619 RNAalifold(seed): 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.789 RNAalifold(seed): 0.760 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Pknots: 0.531 Sensitivity PETfold_pre2.0(seed): 0.772 Pknots: 0.556 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Pknots: 0.519 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.630 RNASampler(seed): 0.232 Sensitivity PETfold_pre2.0(seed): 0.553 RNASampler(seed): 0.211 Positive Predictive Value PETfold_pre2.0(seed): 0.724 RNASampler(seed): 0.267 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Mastr(20): 0.581 Sensitivity PETfold_pre2.0(seed): 0.784 Mastr(20): 0.431 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Mastr(20): 0.794 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 RSpredict(20): 0.428 Sensitivity PETfold_pre2.0(seed): 0.784 RSpredict(20): 0.362 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.812 Alterna: 0.648 Sensitivity PETfold_pre2.0(seed): 0.745 Alterna: 0.655 Positive Predictive Value PETfold_pre2.0(seed): 0.891 Alterna: 0.655 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNASLOpt: 0.560 Sensitivity PETfold_pre2.0(seed): 0.772 RNASLOpt: 0.526 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNASLOpt: 0.608 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 Multilign(20): 0.583 Sensitivity PETfold_pre2.0(seed): 0.784 Multilign(20): 0.578 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Vsfold4: 0.508 Sensitivity PETfold_pre2.0(seed): 0.772 Vsfold4: 0.491 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.808 MCFold: 0.546 Sensitivity PETfold_pre2.0(seed): 0.754 MCFold: 0.579 Positive Predictive Value PETfold_pre2.0(seed): 0.872 MCFold: 0.525 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RNAwolf: 0.401 Sensitivity PETfold_pre2.0(seed): 0.772 RNAwolf: 0.392 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RNAwolf: 0.427 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.695 Murlet(seed): 0.495 Sensitivity PETfold_pre2.0(seed): 0.619 Murlet(seed): 0.340 Positive Predictive Value PETfold_pre2.0(seed): 0.789 Murlet(seed): 0.733 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Vsfold5: 0.451 Sensitivity PETfold_pre2.0(seed): 0.772 Vsfold5: 0.468 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Vsfold5: 0.449 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 RSpredict(seed): 0.131 Sensitivity PETfold_pre2.0(seed): 0.772 RSpredict(seed): 0.070 Positive Predictive Value PETfold_pre2.0(seed): 0.892 RSpredict(seed): 0.267 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.745 RDfolder: 0.317 Sensitivity PETfold_pre2.0(seed): 0.673 RDfolder: 0.286 Positive Predictive Value PETfold_pre2.0(seed): 0.835 RDfolder: 0.384 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 PPfold(seed): 0.146 Sensitivity PETfold_pre2.0(seed): 0.772 PPfold(seed): 0.041 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.828 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(seed): 0.772 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.892 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 CMfinder(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Sensitivity CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Positive Predictive Value CMfinder(seed): N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.699 Multilign(seed): 0.458 Sensitivity PETfold_pre2.0(seed): 0.617 Multilign(seed): 0.404 Positive Predictive Value PETfold_pre2.0(seed): 0.806 Multilign(seed): 0.543 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0		? PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 TurboFold(20): 0.655 Sensitivity PETfold_pre2.0(seed): 0.784 TurboFold(20): 0.612 Positive Predictive Value PETfold_pre2.0(seed): 0.892 TurboFold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(seed): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 PETfold_pre2.0(20): 0.747 Sensitivity PETfold_pre2.0(seed): 0.784 PETfold_pre2.0(20): 0.707 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.786 TurboFold(seed): 0.552 Sensitivity PETfold_pre2.0(seed): 0.724 TurboFold(seed): 0.530 Positive Predictive Value PETfold_pre2.0(seed): 0.858 TurboFold(seed): 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 PPfold(20): 0.732 Sensitivity PETfold_pre2.0(seed): 0.784 PPfold(20): 0.672 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PPfold(20): 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.846 NanoFolder: 0.412 Sensitivity PETfold_pre2.0(seed): 0.795 NanoFolder: 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.905 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.786 Carnac(seed): 0.172 Sensitivity PETfold_pre2.0(seed): 0.724 Carnac(seed): 0.030 Positive Predictive Value PETfold_pre2.0(seed): 0.858 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0
TurboFold(20)	9 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 MXScarna(seed): 0.732 Sensitivity TurboFold(20): 0.694 MXScarna(seed): 0.689 Positive Predictive Value TurboFold(20): 0.781 MXScarna(seed): 0.785 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(20) vs TurboFold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 TurboFold(20): 0.733 Sensitivity CentroidAlifold(20): 0.714 TurboFold(20): 0.694 Positive Predictive Value CentroidAlifold(20): 0.913 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.733 CentroidFold: 0.708 Sensitivity TurboFold(20): 0.694 CentroidFold: 0.689 Positive Predictive Value TurboFold(20): 0.781 CentroidFold: 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.733 RNAalifold(20): 0.724 Sensitivity TurboFold(20): 0.694 RNAalifold(20): 0.665 Positive Predictive Value TurboFold(20): 0.781 RNAalifold(20): 0.797 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.733 Sfold: 0.721 Sensitivity TurboFold(20): 0.694 Sfold: 0.689 Positive Predictive Value TurboFold(20): 0.781 Sfold: 0.763 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.733 Fold: 0.652 Sensitivity TurboFold(20): 0.694 Fold: 0.660 Positive Predictive Value TurboFold(20): 0.781 Fold: 0.654 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNASampler(20) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(20): 0.779 TurboFold(20): 0.733 Sensitivity RNASampler(20): 0.704 TurboFold(20): 0.694 Positive Predictive Value RNASampler(20): 0.868 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.733 MXScarna(20): 0.693 Sensitivity TurboFold(20): 0.694 MXScarna(20): 0.655 Positive Predictive Value TurboFold(20): 0.781 MXScarna(20): 0.742 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs TurboFold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 TurboFold(20): 0.733 Sensitivity CentroidHomfold‑LAST: 0.723 TurboFold(20): 0.694 Positive Predictive Value CentroidHomfold‑LAST: 0.851 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: 0.759 TurboFold(20): 0.733 Sensitivity HotKnots: 0.772 TurboFold(20): 0.694 Positive Predictive Value HotKnots: 0.754 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.733 UNAFold: 0.706 Sensitivity TurboFold(20): 0.694 UNAFold: 0.704 Positive Predictive Value TurboFold(20): 0.781 UNAFold: 0.718 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.733 Contrafold: 0.700 Sensitivity TurboFold(20): 0.694 Contrafold: 0.699 Positive Predictive Value TurboFold(20): 0.781 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.712 IPknot: 0.684 Sensitivity TurboFold(20): 0.670 IPknot: 0.654 Positive Predictive Value TurboFold(20): 0.764 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.698 TurboFold(20): 0.655 Sensitivity ContextFold: 0.638 TurboFold(20): 0.612 Positive Predictive Value ContextFold: 0.771 TurboFold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.733 RNAshapes: 0.705 Sensitivity TurboFold(20): 0.694 RNAshapes: 0.699 Positive Predictive Value TurboFold(20): 0.781 RNAshapes: 0.720 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.733 MaxExpect: 0.681 Sensitivity TurboFold(20): 0.694 MaxExpect: 0.684 Positive Predictive Value TurboFold(20): 0.781 MaxExpect: 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs TurboFold(20) Matthews Correlation Coefficient PknotsRG: 0.744 TurboFold(20): 0.733 Sensitivity PknotsRG: 0.762 TurboFold(20): 0.694 Positive Predictive Value PknotsRG: 0.734 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.733 RNAfold: 0.705 Sensitivity TurboFold(20): 0.694 RNAfold: 0.704 Positive Predictive Value TurboFold(20): 0.781 RNAfold: 0.714 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.733 ProbKnot: 0.681 Sensitivity TurboFold(20): 0.694 ProbKnot: 0.709 Positive Predictive Value TurboFold(20): 0.781 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Murlet(20): 0.677 Sensitivity TurboFold(20): 0.694 Murlet(20): 0.602 Positive Predictive Value TurboFold(20): 0.781 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 CentroidAlifold(seed): 0.730 Sensitivity TurboFold(20): 0.694 CentroidAlifold(seed): 0.578 Positive Predictive Value TurboFold(20): 0.781 CentroidAlifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.686 Afold: 0.671 Sensitivity TurboFold(20): 0.662 Afold: 0.701 Positive Predictive Value TurboFold(20): 0.718 Afold: 0.651 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.733 RNAsubopt: 0.694 Sensitivity TurboFold(20): 0.694 RNAsubopt: 0.699 Positive Predictive Value TurboFold(20): 0.781 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Carnac(20): 0.632 Sensitivity TurboFold(20): 0.694 Carnac(20): 0.471 Positive Predictive Value TurboFold(20): 0.781 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: 0.787 TurboFold(20): 0.783 Sensitivity Cylofold: 0.765 TurboFold(20): 0.718 Positive Predictive Value Cylofold: 0.820 TurboFold(20): 0.863 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.733 McQFold: 0.652 Sensitivity TurboFold(20): 0.694 McQFold: 0.665 Positive Predictive Value TurboFold(20): 0.781 McQFold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.683 CRWrnafold: 0.668 Sensitivity TurboFold(20): 0.646 CRWrnafold: 0.683 Positive Predictive Value TurboFold(20): 0.731 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.690 RNAalifold(seed): 0.687 Sensitivity TurboFold(20): 0.647 RNAalifold(seed): 0.520 Positive Predictive Value TurboFold(20): 0.746 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.733 Pknots: 0.634 Sensitivity TurboFold(20): 0.694 Pknots: 0.650 Positive Predictive Value TurboFold(20): 0.781 Pknots: 0.629 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.685 RNASampler(seed): 0.683 Sensitivity TurboFold(20): 0.681 RNASampler(seed): 0.593 Positive Predictive Value TurboFold(20): 0.697 RNASampler(seed): 0.794 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Mastr(20): 0.694 Sensitivity TurboFold(20): 0.694 Mastr(20): 0.573 Positive Predictive Value TurboFold(20): 0.781 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.733 RSpredict(20): 0.582 Sensitivity TurboFold(20): 0.694 RSpredict(20): 0.519 Positive Predictive Value TurboFold(20): 0.781 RSpredict(20): 0.665 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.829 Alterna: 0.750 Sensitivity TurboFold(20): 0.800 Alterna: 0.756 Positive Predictive Value TurboFold(20): 0.867 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.655 RNASLOpt: 0.560 Sensitivity TurboFold(20): 0.612 RNASLOpt: 0.543 Positive Predictive Value TurboFold(20): 0.710 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.733 Multilign(20): 0.683 Sensitivity TurboFold(20): 0.694 Multilign(20): 0.680 Positive Predictive Value TurboFold(20): 0.781 Multilign(20): 0.697 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.733 Vsfold4: 0.550 Sensitivity TurboFold(20): 0.694 Vsfold4: 0.534 Positive Predictive Value TurboFold(20): 0.781 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.743 MCFold: 0.619 Sensitivity TurboFold(20): 0.712 MCFold: 0.655 Positive Predictive Value TurboFold(20): 0.783 MCFold: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.712 RNAwolf: 0.453 Sensitivity TurboFold(20): 0.670 RNAwolf: 0.447 Positive Predictive Value TurboFold(20): 0.764 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.690 Murlet(seed): 0.616 Sensitivity TurboFold(20): 0.647 Murlet(seed): 0.420 Positive Predictive Value TurboFold(20): 0.746 Murlet(seed): 0.913 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.733 Vsfold5: 0.539 Sensitivity TurboFold(20): 0.694 Vsfold5: 0.549 Positive Predictive Value TurboFold(20): 0.781 Vsfold5: 0.543 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 RSpredict(seed): 0.346 Sensitivity TurboFold(20): 0.694 RSpredict(seed): 0.189 Positive Predictive Value TurboFold(20): 0.781 RSpredict(seed): 0.650 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.783 RDfolder: 0.548 Sensitivity TurboFold(20): 0.718 RDfolder: 0.483 Positive Predictive Value TurboFold(20): 0.863 RDfolder: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.712 PPfold(seed): 0.031 Sensitivity TurboFold(20): 0.670 PPfold(seed): 0.005 Positive Predictive Value TurboFold(20): 0.764 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.733 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.694 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.781 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 Multilign(seed) vs TurboFold(20) Matthews Correlation Coefficient Multilign(seed): 0.795 TurboFold(20): 0.789 Sensitivity Multilign(seed): 0.750 TurboFold(20): 0.740 Positive Predictive Value Multilign(seed): 0.852 TurboFold(20): 0.851 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 TurboFold(20): 0.655 Sensitivity PETfold_pre2.0(seed): 0.784 TurboFold(20): 0.612 Positive Predictive Value PETfold_pre2.0(seed): 0.892 TurboFold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(20): N/A Sensitivity TurboFold(20): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 TurboFold(20): 0.655 Sensitivity PETfold_pre2.0(20): 0.707 TurboFold(20): 0.612 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.725 TurboFold(seed): 0.712 Sensitivity TurboFold(20): 0.684 TurboFold(seed): 0.684 Positive Predictive Value TurboFold(20): 0.776 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.780 TurboFold(20): 0.733 Sensitivity PPfold(20): 0.714 TurboFold(20): 0.694 Positive Predictive Value PPfold(20): 0.860 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.643 NanoFolder: 0.389 Sensitivity TurboFold(20): 0.614 NanoFolder: 0.475 Positive Predictive Value TurboFold(20): 0.681 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.725 Carnac(seed): 0.308 Sensitivity TurboFold(20): 0.684 Carnac(seed): 0.096 Positive Predictive Value TurboFold(20): 0.776 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
CMfinder(20)	0 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): N/A CMfinder(20): N/A Sensitivity MXScarna(seed): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(20): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: N/A CMfinder(20): N/A Sensitivity CentroidFold: N/A CMfinder(20): N/A Positive Predictive Value CentroidFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(20): N/A Sensitivity RNAalifold(20): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: N/A CMfinder(20): N/A Sensitivity Sfold: N/A CMfinder(20): N/A Positive Predictive Value Sfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: N/A CMfinder(20): N/A Sensitivity Fold: N/A CMfinder(20): N/A Positive Predictive Value Fold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(20): N/A Sensitivity RNASampler(20): N/A CMfinder(20): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): N/A CMfinder(20): N/A Sensitivity MXScarna(20): N/A CMfinder(20): N/A Positive Predictive Value MXScarna(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A CMfinder(20): N/A Sensitivity CentroidHomfold‑LAST: N/A CMfinder(20): N/A Positive Predictive Value CentroidHomfold‑LAST: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: N/A CMfinder(20): N/A Sensitivity UNAFold: N/A CMfinder(20): N/A Positive Predictive Value UNAFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: N/A CMfinder(20): N/A Sensitivity Contrafold: N/A CMfinder(20): N/A Positive Predictive Value Contrafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: N/A CMfinder(20): N/A Sensitivity IPknot: N/A CMfinder(20): N/A Positive Predictive Value IPknot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: N/A CMfinder(20): N/A Sensitivity ContextFold: N/A CMfinder(20): N/A Positive Predictive Value ContextFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs CMfinder(20) Matthews Correlation Coefficient RNAshapes: N/A CMfinder(20): N/A Sensitivity RNAshapes: N/A CMfinder(20): N/A Positive Predictive Value RNAshapes: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: N/A CMfinder(20): N/A Sensitivity MaxExpect: N/A CMfinder(20): N/A Positive Predictive Value MaxExpect: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: N/A CMfinder(20): N/A Sensitivity PknotsRG: N/A CMfinder(20): N/A Positive Predictive Value PknotsRG: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: N/A CMfinder(20): N/A Sensitivity RNAfold: N/A CMfinder(20): N/A Positive Predictive Value RNAfold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: N/A CMfinder(20): N/A Sensitivity ProbKnot: N/A CMfinder(20): N/A Positive Predictive Value ProbKnot: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(20): N/A Sensitivity Murlet(20): N/A CMfinder(20): N/A Positive Predictive Value Murlet(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): N/A CMfinder(20): N/A Sensitivity CentroidAlifold(seed): N/A CMfinder(20): N/A Positive Predictive Value CentroidAlifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: N/A CMfinder(20): N/A Sensitivity Afold: N/A CMfinder(20): N/A Positive Predictive Value Afold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: N/A CMfinder(20): N/A Sensitivity RNAsubopt: N/A CMfinder(20): N/A Positive Predictive Value RNAsubopt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs CMfinder(20) Matthews Correlation Coefficient Carnac(20): N/A CMfinder(20): N/A Sensitivity Carnac(20): N/A CMfinder(20): N/A Positive Predictive Value Carnac(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 McQFold vs CMfinder(20) Matthews Correlation Coefficient McQFold: N/A CMfinder(20): N/A Sensitivity McQFold: N/A CMfinder(20): N/A Positive Predictive Value McQFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: N/A CMfinder(20): N/A Sensitivity CRWrnafold: N/A CMfinder(20): N/A Positive Predictive Value CRWrnafold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(seed): N/A CMfinder(20): N/A Sensitivity RNAalifold(seed): N/A CMfinder(20): N/A Positive Predictive Value RNAalifold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 Mastr(20) vs CMfinder(20) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(20): N/A Sensitivity Mastr(20): N/A CMfinder(20): N/A Positive Predictive Value Mastr(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(20): N/A Sensitivity RSpredict(20): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 RNASLOpt vs CMfinder(20) Matthews Correlation Coefficient RNASLOpt: N/A CMfinder(20): N/A Sensitivity RNASLOpt: N/A CMfinder(20): N/A Positive Predictive Value RNASLOpt: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): N/A CMfinder(20): N/A Sensitivity Multilign(20): N/A CMfinder(20): N/A Positive Predictive Value Multilign(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs CMfinder(20) Matthews Correlation Coefficient Vsfold4: N/A CMfinder(20): N/A Sensitivity Vsfold4: N/A CMfinder(20): N/A Positive Predictive Value Vsfold4: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 RNAwolf vs CMfinder(20) Matthews Correlation Coefficient RNAwolf: N/A CMfinder(20): N/A Sensitivity RNAwolf: N/A CMfinder(20): N/A Positive Predictive Value RNAwolf: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): N/A CMfinder(20): N/A Sensitivity Murlet(seed): N/A CMfinder(20): N/A Positive Predictive Value Murlet(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs CMfinder(20) Matthews Correlation Coefficient Vsfold5: N/A CMfinder(20): N/A Sensitivity Vsfold5: N/A CMfinder(20): N/A Positive Predictive Value Vsfold5: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(seed): N/A CMfinder(20): N/A Sensitivity RSpredict(seed): N/A CMfinder(20): N/A Positive Predictive Value RSpredict(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 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 Mastr(seed) vs CMfinder(20) Matthews Correlation Coefficient Mastr(seed): N/A CMfinder(20): N/A Sensitivity Mastr(seed): N/A CMfinder(20): N/A Positive Predictive Value Mastr(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs CMfinder(20) Matthews Correlation Coefficient Multilign(seed): N/A CMfinder(20): N/A Sensitivity Multilign(seed): N/A CMfinder(20): N/A Positive Predictive Value Multilign(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(seed): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(20): N/A Sensitivity TurboFold(20): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(20): N/A Sensitivity PPfold(20): N/A CMfinder(20): N/A Positive Predictive Value PPfold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs CMfinder(20) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(20): N/A Sensitivity NanoFolder: N/A CMfinder(20): N/A Positive Predictive Value NanoFolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(seed) vs CMfinder(20) Matthews Correlation Coefficient Carnac(seed): N/A CMfinder(20): N/A Sensitivity Carnac(seed): N/A CMfinder(20): N/A Positive Predictive Value Carnac(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
PETfold_pre2.0(20)	5 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 MXScarna(seed): 0.691 Sensitivity PETfold_pre2.0(20): 0.707 MXScarna(seed): 0.638 Positive Predictive Value PETfold_pre2.0(20): 0.796 MXScarna(seed): 0.755 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.779 PETfold_pre2.0(20): 0.747 Sensitivity CentroidAlifold(20): 0.672 PETfold_pre2.0(20): 0.707 Positive Predictive Value CentroidAlifold(20): 0.907 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CentroidFold: 0.618 Sensitivity PETfold_pre2.0(20): 0.707 CentroidFold: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 CentroidFold: 0.642 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAalifold(20): 0.656 Sensitivity PETfold_pre2.0(20): 0.707 RNAalifold(20): 0.578 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAalifold(20): 0.753 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Sfold: 0.612 Sensitivity PETfold_pre2.0(20): 0.707 Sfold: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.796 Sfold: 0.648 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Fold: 0.531 Sensitivity PETfold_pre2.0(20): 0.707 Fold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 Fold: 0.529 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNASampler(20): 0.686 Sensitivity PETfold_pre2.0(20): 0.707 RNASampler(20): 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNASampler(20): 0.787 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 MXScarna(20): 0.586 Sensitivity PETfold_pre2.0(20): 0.707 MXScarna(20): 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 MXScarna(20): 0.643 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CentroidHomfold‑LAST: 0.715 Sensitivity PETfold_pre2.0(20): 0.707 CentroidHomfold‑LAST: 0.664 Positive Predictive Value PETfold_pre2.0(20): 0.796 CentroidHomfold‑LAST: 0.778 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 HotKnots: 0.688 Sensitivity PETfold_pre2.0(20): 0.707 HotKnots: 0.724 Positive Predictive Value PETfold_pre2.0(20): 0.796 HotKnots: 0.661 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 UNAFold: 0.593 Sensitivity PETfold_pre2.0(20): 0.707 UNAFold: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 UNAFold: 0.593 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Contrafold: 0.624 Sensitivity PETfold_pre2.0(20): 0.707 Contrafold: 0.621 Positive Predictive Value PETfold_pre2.0(20): 0.796 Contrafold: 0.637 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 IPknot: 0.606 Sensitivity PETfold_pre2.0(20): 0.707 IPknot: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.796 IPknot: 0.636 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs ContextFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 ContextFold: 0.698 Sensitivity PETfold_pre2.0(20): 0.707 ContextFold: 0.638 Positive Predictive Value PETfold_pre2.0(20): 0.796 ContextFold: 0.771 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAshapes: 0.590 Sensitivity PETfold_pre2.0(20): 0.707 RNAshapes: 0.595 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAshapes: 0.595 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 MaxExpect: 0.579 Sensitivity PETfold_pre2.0(20): 0.707 MaxExpect: 0.586 Positive Predictive Value PETfold_pre2.0(20): 0.796 MaxExpect: 0.581 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 PknotsRG: 0.672 Sensitivity PETfold_pre2.0(20): 0.707 PknotsRG: 0.716 Positive Predictive Value PETfold_pre2.0(20): 0.796 PknotsRG: 0.638 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAfold: 0.591 Sensitivity PETfold_pre2.0(20): 0.707 RNAfold: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAfold: 0.588 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 ProbKnot: 0.592 Sensitivity PETfold_pre2.0(20): 0.707 ProbKnot: 0.629 Positive Predictive Value PETfold_pre2.0(20): 0.796 ProbKnot: 0.566 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Murlet(20): 0.594 Sensitivity PETfold_pre2.0(20): 0.707 Murlet(20): 0.500 Positive Predictive Value PETfold_pre2.0(20): 0.796 Murlet(20): 0.716 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CentroidAlifold(seed): 0.729 Sensitivity PETfold_pre2.0(20): 0.707 CentroidAlifold(seed): 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 CentroidAlifold(seed): 0.984 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	2 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.404 Afold: 0.398 Sensitivity PETfold_pre2.0(20): 0.371 Afold: 0.457 Positive Predictive Value PETfold_pre2.0(20): 0.448 Afold: 0.356 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAsubopt: 0.583 Sensitivity PETfold_pre2.0(20): 0.707 RNAsubopt: 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAsubopt: 0.574 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Carnac(20): 0.562 Sensitivity PETfold_pre2.0(20): 0.707 Carnac(20): 0.397 Positive Predictive Value PETfold_pre2.0(20): 0.796 Carnac(20): 0.807 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.763 Cylofold: 0.720 Sensitivity PETfold_pre2.0(20): 0.678 Cylofold: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.870 Cylofold: 0.759 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 McQFold: 0.486 Sensitivity PETfold_pre2.0(20): 0.707 McQFold: 0.517 Positive Predictive Value PETfold_pre2.0(20): 0.796 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 CRWrnafold: 0.663 Sensitivity PETfold_pre2.0(20): 0.707 CRWrnafold: 0.672 Positive Predictive Value PETfold_pre2.0(20): 0.796 CRWrnafold: 0.661 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 RNAalifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNAalifold(seed): 0.691 PETfold_pre2.0(20): 0.619 Sensitivity RNAalifold(seed): 0.481 PETfold_pre2.0(20): 0.570 Positive Predictive Value RNAalifold(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Pknots: 0.446 Sensitivity PETfold_pre2.0(20): 0.707 Pknots: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.796 Pknots: 0.433 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	1 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): 0.397 PETfold_pre2.0(20): 0.247 Sensitivity RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Positive Predictive Value RNASampler(seed): 0.400 PETfold_pre2.0(20): 0.250 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Mastr(20): 0.581 Sensitivity PETfold_pre2.0(20): 0.707 Mastr(20): 0.431 Positive Predictive Value PETfold_pre2.0(20): 0.796 Mastr(20): 0.794 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RSpredict(20): 0.428 Sensitivity PETfold_pre2.0(20): 0.707 RSpredict(20): 0.362 Positive Predictive Value PETfold_pre2.0(20): 0.796 RSpredict(20): 0.519 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNASLOpt: 0.560 Sensitivity PETfold_pre2.0(20): 0.707 RNASLOpt: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Multilign(20): 0.583 Sensitivity PETfold_pre2.0(20): 0.707 Multilign(20): 0.578 Positive Predictive Value PETfold_pre2.0(20): 0.796 Multilign(20): 0.598 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Vsfold4: 0.472 Sensitivity PETfold_pre2.0(20): 0.707 Vsfold4: 0.457 Positive Predictive Value PETfold_pre2.0(20): 0.796 Vsfold4: 0.500 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.706 MCFold: 0.566 Sensitivity PETfold_pre2.0(20): 0.667 MCFold: 0.609 Positive Predictive Value PETfold_pre2.0(20): 0.753 MCFold: 0.535 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RNAwolf: 0.279 Sensitivity PETfold_pre2.0(20): 0.707 RNAwolf: 0.276 Positive Predictive Value PETfold_pre2.0(20): 0.796 RNAwolf: 0.299 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 Murlet(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient Murlet(seed): 0.644 PETfold_pre2.0(20): 0.619 Sensitivity Murlet(seed): 0.418 PETfold_pre2.0(20): 0.570 Positive Predictive Value Murlet(seed): 1.000 PETfold_pre2.0(20): 0.682 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Vsfold5: 0.460 Sensitivity PETfold_pre2.0(20): 0.707 Vsfold5: 0.474 Positive Predictive Value PETfold_pre2.0(20): 0.796 Vsfold5: 0.458 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 RSpredict(seed): 0.219 Sensitivity PETfold_pre2.0(20): 0.707 RSpredict(seed): 0.103 Positive Predictive Value PETfold_pre2.0(20): 0.796 RSpredict(seed): 0.480 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.763 RDfolder: 0.445 Sensitivity PETfold_pre2.0(20): 0.678 RDfolder: 0.390 Positive Predictive Value PETfold_pre2.0(20): 0.870 RDfolder: 0.535 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 PPfold(seed): 0.039 Sensitivity PETfold_pre2.0(20): 0.707 PPfold(seed): 0.009 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.707 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.796 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.872 Multilign(seed): 0.731 Sensitivity PETfold_pre2.0(20): 0.828 Multilign(seed): 0.655 Positive Predictive Value PETfold_pre2.0(20): 0.923 Multilign(seed): 0.826 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 PETfold_pre2.0(20): 0.747 Sensitivity PETfold_pre2.0(seed): 0.784 PETfold_pre2.0(20): 0.707 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PETfold_pre2.0(20): 0.796 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(20) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 TurboFold(20): 0.655 Sensitivity PETfold_pre2.0(20): 0.707 TurboFold(20): 0.612 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(20): 0.710 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(20): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(20): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 TurboFold(seed): 0.636 Sensitivity PETfold_pre2.0(20): 0.707 TurboFold(seed): 0.612 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(seed): 0.670 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 PPfold(20): 0.732 Sensitivity PETfold_pre2.0(20): 0.707 PPfold(20): 0.672 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(20): 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 NanoFolder: 0.389 Sensitivity PETfold_pre2.0(20): 0.733 NanoFolder: 0.475 Positive Predictive Value PETfold_pre2.0(20): 0.787 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.707 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.796 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
TurboFold(seed)	9 MXScarna(seed) vs TurboFold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.653 TurboFold(seed): 0.650 Sensitivity MXScarna(seed): 0.605 TurboFold(seed): 0.624 Positive Predictive Value MXScarna(seed): 0.717 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 CentroidAlifold(20) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.783 TurboFold(seed): 0.712 Sensitivity CentroidAlifold(20): 0.684 TurboFold(seed): 0.684 Positive Predictive Value CentroidAlifold(20): 0.901 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 CentroidFold vs TurboFold(seed) Matthews Correlation Coefficient CentroidFold: 0.683 TurboFold(seed): 0.650 Sensitivity CentroidFold: 0.654 TurboFold(seed): 0.624 Positive Predictive Value CentroidFold: 0.724 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 RNAalifold(20): 0.694 Sensitivity TurboFold(seed): 0.684 RNAalifold(20): 0.631 Positive Predictive Value TurboFold(seed): 0.749 RNAalifold(20): 0.771 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 Sfold vs TurboFold(seed) Matthews Correlation Coefficient Sfold: 0.693 TurboFold(seed): 0.650 Sensitivity Sfold: 0.654 TurboFold(seed): 0.624 Positive Predictive Value Sfold: 0.744 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.650 Fold: 0.590 Sensitivity TurboFold(seed): 0.624 Fold: 0.590 Positive Predictive Value TurboFold(seed): 0.688 Fold: 0.602 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 RNASampler(20) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(20): 0.760 TurboFold(seed): 0.712 Sensitivity RNASampler(20): 0.679 TurboFold(seed): 0.684 Positive Predictive Value RNASampler(20): 0.858 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 MXScarna(20): 0.660 Sensitivity TurboFold(seed): 0.684 MXScarna(20): 0.620 Positive Predictive Value TurboFold(seed): 0.749 MXScarna(20): 0.712 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs TurboFold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.704 TurboFold(seed): 0.650 Sensitivity CentroidHomfold‑LAST: 0.639 TurboFold(seed): 0.624 Positive Predictive Value CentroidHomfold‑LAST: 0.784 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 HotKnots vs TurboFold(seed) Matthews Correlation Coefficient HotKnots: 0.745 TurboFold(seed): 0.650 Sensitivity HotKnots: 0.756 TurboFold(seed): 0.624 Positive Predictive Value HotKnots: 0.742 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.650 UNAFold: 0.638 Sensitivity TurboFold(seed): 0.624 UNAFold: 0.634 Positive Predictive Value TurboFold(seed): 0.688 UNAFold: 0.653 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 Contrafold vs TurboFold(seed) Matthews Correlation Coefficient Contrafold: 0.677 TurboFold(seed): 0.650 Sensitivity Contrafold: 0.663 TurboFold(seed): 0.624 Positive Predictive Value Contrafold: 0.701 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 IPknot vs TurboFold(seed) Matthews Correlation Coefficient IPknot: 0.648 TurboFold(seed): 0.621 Sensitivity IPknot: 0.610 TurboFold(seed): 0.594 Positive Predictive Value IPknot: 0.699 TurboFold(seed): 0.661 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.682 TurboFold(seed): 0.552 Sensitivity ContextFold: 0.627 TurboFold(seed): 0.530 Positive Predictive Value ContextFold: 0.750 TurboFold(seed): 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 RNAshapes vs TurboFold(seed) Matthews Correlation Coefficient RNAshapes: 0.690 TurboFold(seed): 0.650 Sensitivity RNAshapes: 0.683 TurboFold(seed): 0.624 Positive Predictive Value RNAshapes: 0.707 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.650 MaxExpect: 0.620 Sensitivity TurboFold(seed): 0.624 MaxExpect: 0.615 Positive Predictive Value TurboFold(seed): 0.688 MaxExpect: 0.636 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.731 TurboFold(seed): 0.650 Sensitivity PknotsRG: 0.746 TurboFold(seed): 0.624 Positive Predictive Value PknotsRG: 0.725 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 RNAfold vs TurboFold(seed) Matthews Correlation Coefficient RNAfold: 0.690 TurboFold(seed): 0.650 Sensitivity RNAfold: 0.688 TurboFold(seed): 0.624 Positive Predictive Value RNAfold: 0.701 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.650 ProbKnot: 0.618 Sensitivity TurboFold(seed): 0.624 ProbKnot: 0.639 Positive Predictive Value TurboFold(seed): 0.688 ProbKnot: 0.609 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Murlet(20): 0.652 Sensitivity TurboFold(seed): 0.684 Murlet(20): 0.572 Positive Predictive Value TurboFold(seed): 0.749 Murlet(20): 0.754 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.715 TurboFold(seed): 0.650 Sensitivity CentroidAlifold(seed): 0.556 TurboFold(seed): 0.624 Positive Predictive Value CentroidAlifold(seed): 0.927 TurboFold(seed): 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 Afold vs TurboFold(seed) Matthews Correlation Coefficient Afold: 0.665 TurboFold(seed): 0.539 Sensitivity Afold: 0.684 TurboFold(seed): 0.537 Positive Predictive Value Afold: 0.657 TurboFold(seed): 0.554 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.650 RNAsubopt: 0.627 Sensitivity TurboFold(seed): 0.624 RNAsubopt: 0.629 Positive Predictive Value TurboFold(seed): 0.688 RNAsubopt: 0.635 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Carnac(20): 0.615 Sensitivity TurboFold(seed): 0.684 Carnac(20): 0.439 Positive Predictive Value TurboFold(seed): 0.749 Carnac(20): 0.872 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 Cylofold vs TurboFold(seed) Matthews Correlation Coefficient Cylofold: 0.773 TurboFold(seed): 0.680 Sensitivity Cylofold: 0.743 TurboFold(seed): 0.622 Positive Predictive Value Cylofold: 0.815 TurboFold(seed): 0.760 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.650 McQFold: 0.634 Sensitivity TurboFold(seed): 0.624 McQFold: 0.649 Positive Predictive Value TurboFold(seed): 0.688 McQFold: 0.630 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 CRWrnafold vs TurboFold(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 TurboFold(seed): 0.580 Sensitivity CRWrnafold: 0.595 TurboFold(seed): 0.558 Positive Predictive Value CRWrnafold: 0.591 TurboFold(seed): 0.615 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 RNAalifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.606 TurboFold(seed): 0.603 Sensitivity RNAalifold(seed): 0.464 TurboFold(seed): 0.577 Positive Predictive Value RNAalifold(seed): 0.804 TurboFold(seed): 0.642 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.650 Pknots: 0.617 Sensitivity TurboFold(seed): 0.624 Pknots: 0.634 Positive Predictive Value TurboFold(seed): 0.688 Pknots: 0.613 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	5 RNASampler(seed) vs TurboFold(seed) Matthews Correlation Coefficient RNASampler(seed): 0.581 TurboFold(seed): 0.560 Sensitivity RNASampler(seed): 0.495 TurboFold(seed): 0.569 Positive Predictive Value RNASampler(seed): 0.692 TurboFold(seed): 0.564 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Mastr(20): 0.673 Sensitivity TurboFold(seed): 0.684 Mastr(20): 0.551 Positive Predictive Value TurboFold(seed): 0.749 Mastr(20): 0.831 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 RSpredict(20): 0.574 Sensitivity TurboFold(seed): 0.684 RSpredict(20): 0.519 Positive Predictive Value TurboFold(seed): 0.749 RSpredict(20): 0.647 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	4 Alterna vs TurboFold(seed) Matthews Correlation Coefficient Alterna: 0.702 TurboFold(seed): 0.667 Sensitivity Alterna: 0.685 TurboFold(seed): 0.640 Positive Predictive Value Alterna: 0.735 TurboFold(seed): 0.713 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.552 RNASLOpt: 0.551 Sensitivity TurboFold(seed): 0.530 RNASLOpt: 0.522 Positive Predictive Value TurboFold(seed): 0.587 RNASLOpt: 0.593 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.712 Multilign(20): 0.680 Sensitivity TurboFold(seed): 0.684 Multilign(20): 0.674 Positive Predictive Value TurboFold(seed): 0.749 Multilign(20): 0.696 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.650 Vsfold4: 0.487 Sensitivity TurboFold(seed): 0.624 Vsfold4: 0.468 Positive Predictive Value TurboFold(seed): 0.688 Vsfold4: 0.522 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.648 MCFold: 0.617 Sensitivity TurboFold(seed): 0.631 MCFold: 0.642 Positive Predictive Value TurboFold(seed): 0.677 MCFold: 0.604 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.621 RNAwolf: 0.426 Sensitivity TurboFold(seed): 0.594 RNAwolf: 0.417 Positive Predictive Value TurboFold(seed): 0.661 RNAwolf: 0.451 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.603 Murlet(seed): 0.535 Sensitivity TurboFold(seed): 0.577 Murlet(seed): 0.375 Positive Predictive Value TurboFold(seed): 0.642 Murlet(seed): 0.778 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.650 Vsfold5: 0.475 Sensitivity TurboFold(seed): 0.624 Vsfold5: 0.478 Positive Predictive Value TurboFold(seed): 0.688 Vsfold5: 0.488 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.650 RSpredict(seed): 0.317 Sensitivity TurboFold(seed): 0.624 RSpredict(seed): 0.190 Positive Predictive Value TurboFold(seed): 0.688 RSpredict(seed): 0.549 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.680 RDfolder: 0.528 Sensitivity TurboFold(seed): 0.622 RDfolder: 0.459 Positive Predictive Value TurboFold(seed): 0.760 RDfolder: 0.630 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.621 PPfold(seed): 0.139 Sensitivity TurboFold(seed): 0.594 PPfold(seed): 0.037 Positive Predictive Value TurboFold(seed): 0.661 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.650 Mastr(seed): 0.000 Sensitivity TurboFold(seed): 0.624 Mastr(seed): 0.000 Positive Predictive Value TurboFold(seed): 0.688 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 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	5 Multilign(seed) vs TurboFold(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 TurboFold(seed): 0.667 Sensitivity Multilign(seed): 0.636 TurboFold(seed): 0.627 Positive Predictive Value Multilign(seed): 0.750 TurboFold(seed): 0.725 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.786 TurboFold(seed): 0.552 Sensitivity PETfold_pre2.0(seed): 0.724 TurboFold(seed): 0.530 Positive Predictive Value PETfold_pre2.0(seed): 0.858 TurboFold(seed): 0.587 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.725 TurboFold(seed): 0.712 Sensitivity TurboFold(20): 0.684 TurboFold(seed): 0.684 Positive Predictive Value TurboFold(20): 0.776 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): N/A CMfinder(20): N/A Sensitivity TurboFold(seed): N/A CMfinder(20): N/A Positive Predictive Value TurboFold(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs TurboFold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 TurboFold(seed): 0.636 Sensitivity PETfold_pre2.0(20): 0.707 TurboFold(seed): 0.612 Positive Predictive Value PETfold_pre2.0(20): 0.796 TurboFold(seed): 0.670 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.756 TurboFold(seed): 0.712 Sensitivity PPfold(20): 0.684 TurboFold(seed): 0.684 Positive Predictive Value PPfold(20): 0.842 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.532 NanoFolder: 0.410 Sensitivity TurboFold(seed): 0.521 NanoFolder: 0.496 Positive Predictive Value TurboFold(seed): 0.554 NanoFolder: 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.650 Carnac(seed): 0.325 Sensitivity TurboFold(seed): 0.624 Carnac(seed): 0.107 Positive Predictive Value TurboFold(seed): 0.688 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0
PPfold(20)	9 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.780 MXScarna(seed): 0.732 Sensitivity PPfold(20): 0.714 MXScarna(seed): 0.689 Positive Predictive Value PPfold(20): 0.860 MXScarna(seed): 0.785 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 PPfold(20): 0.780 Sensitivity CentroidAlifold(20): 0.714 PPfold(20): 0.714 Positive Predictive Value CentroidAlifold(20): 0.913 PPfold(20): 0.860 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.780 CentroidFold: 0.708 Sensitivity PPfold(20): 0.714 CentroidFold: 0.689 Positive Predictive Value PPfold(20): 0.860 CentroidFold: 0.736 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.780 RNAalifold(20): 0.724 Sensitivity PPfold(20): 0.714 RNAalifold(20): 0.665 Positive Predictive Value PPfold(20): 0.860 RNAalifold(20): 0.797 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.780 Sfold: 0.721 Sensitivity PPfold(20): 0.714 Sfold: 0.689 Positive Predictive Value PPfold(20): 0.860 Sfold: 0.763 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.780 Fold: 0.652 Sensitivity PPfold(20): 0.714 Fold: 0.660 Positive Predictive Value PPfold(20): 0.860 Fold: 0.654 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.780 RNASampler(20): 0.779 Sensitivity PPfold(20): 0.714 RNASampler(20): 0.704 Positive Predictive Value PPfold(20): 0.860 RNASampler(20): 0.868 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.780 MXScarna(20): 0.693 Sensitivity PPfold(20): 0.714 MXScarna(20): 0.655 Positive Predictive Value PPfold(20): 0.860 MXScarna(20): 0.742 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.782 PPfold(20): 0.780 Sensitivity CentroidHomfold‑LAST: 0.723 PPfold(20): 0.714 Positive Predictive Value CentroidHomfold‑LAST: 0.851 PPfold(20): 0.860 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.780 HotKnots: 0.759 Sensitivity PPfold(20): 0.714 HotKnots: 0.772 Positive Predictive Value PPfold(20): 0.860 HotKnots: 0.754 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.780 UNAFold: 0.706 Sensitivity PPfold(20): 0.714 UNAFold: 0.704 Positive Predictive Value PPfold(20): 0.860 UNAFold: 0.718 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.780 Contrafold: 0.700 Sensitivity PPfold(20): 0.714 Contrafold: 0.699 Positive Predictive Value PPfold(20): 0.860 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.790 IPknot: 0.684 Sensitivity PPfold(20): 0.734 IPknot: 0.654 Positive Predictive Value PPfold(20): 0.857 IPknot: 0.724 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs ContextFold Matthews Correlation Coefficient PPfold(20): 0.732 ContextFold: 0.698 Sensitivity PPfold(20): 0.672 ContextFold: 0.638 Positive Predictive Value PPfold(20): 0.804 ContextFold: 0.771 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.780 RNAshapes: 0.705 Sensitivity PPfold(20): 0.714 RNAshapes: 0.699 Positive Predictive Value PPfold(20): 0.860 RNAshapes: 0.720 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.780 MaxExpect: 0.681 Sensitivity PPfold(20): 0.714 MaxExpect: 0.684 Positive Predictive Value PPfold(20): 0.860 MaxExpect: 0.688 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.780 PknotsRG: 0.744 Sensitivity PPfold(20): 0.714 PknotsRG: 0.762 Positive Predictive Value PPfold(20): 0.860 PknotsRG: 0.734 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.780 RNAfold: 0.705 Sensitivity PPfold(20): 0.714 RNAfold: 0.704 Positive Predictive Value PPfold(20): 0.860 RNAfold: 0.714 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.780 ProbKnot: 0.681 Sensitivity PPfold(20): 0.714 ProbKnot: 0.709 Positive Predictive Value PPfold(20): 0.860 ProbKnot: 0.664 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.780 Murlet(20): 0.677 Sensitivity PPfold(20): 0.714 Murlet(20): 0.602 Positive Predictive Value PPfold(20): 0.860 Murlet(20): 0.770 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.780 CentroidAlifold(seed): 0.730 Sensitivity PPfold(20): 0.714 CentroidAlifold(seed): 0.578 Positive Predictive Value PPfold(20): 0.860 CentroidAlifold(seed): 0.930 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 Afold vs PPfold(20) Matthews Correlation Coefficient Afold: 0.671 PPfold(20): 0.611 Sensitivity Afold: 0.701 PPfold(20): 0.519 Positive Predictive Value Afold: 0.651 PPfold(20): 0.727 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.780 RNAsubopt: 0.694 Sensitivity PPfold(20): 0.714 RNAsubopt: 0.699 Positive Predictive Value PPfold(20): 0.860 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.780 Carnac(20): 0.632 Sensitivity PPfold(20): 0.714 Carnac(20): 0.471 Positive Predictive Value PPfold(20): 0.860 Carnac(20): 0.858 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.811 Cylofold: 0.787 Sensitivity PPfold(20): 0.725 Cylofold: 0.765 Positive Predictive Value PPfold(20): 0.915 Cylofold: 0.820 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.780 McQFold: 0.652 Sensitivity PPfold(20): 0.714 McQFold: 0.665 Positive Predictive Value PPfold(20): 0.860 McQFold: 0.649 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.780 CRWrnafold: 0.668 Sensitivity PPfold(20): 0.726 CRWrnafold: 0.683 Positive Predictive Value PPfold(20): 0.844 CRWrnafold: 0.663 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.709 RNAalifold(seed): 0.687 Sensitivity PPfold(20): 0.627 RNAalifold(seed): 0.520 Positive Predictive Value PPfold(20): 0.810 RNAalifold(seed): 0.918 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.780 Pknots: 0.634 Sensitivity PPfold(20): 0.714 Pknots: 0.650 Positive Predictive Value PPfold(20): 0.860 Pknots: 0.629 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): 0.683 PPfold(20): 0.676 Sensitivity RNASampler(seed): 0.593 PPfold(20): 0.604 Positive Predictive Value RNASampler(seed): 0.794 PPfold(20): 0.764 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.780 Mastr(20): 0.694 Sensitivity PPfold(20): 0.714 Mastr(20): 0.573 Positive Predictive Value PPfold(20): 0.860 Mastr(20): 0.849 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.780 RSpredict(20): 0.582 Sensitivity PPfold(20): 0.714 RSpredict(20): 0.519 Positive Predictive Value PPfold(20): 0.860 RSpredict(20): 0.665 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.842 Alterna: 0.750 Sensitivity PPfold(20): 0.767 Alterna: 0.756 Positive Predictive Value PPfold(20): 0.932 Alterna: 0.756 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.732 RNASLOpt: 0.560 Sensitivity PPfold(20): 0.672 RNASLOpt: 0.543 Positive Predictive Value PPfold(20): 0.804 RNASLOpt: 0.589 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.780 Multilign(20): 0.683 Sensitivity PPfold(20): 0.714 Multilign(20): 0.680 Positive Predictive Value PPfold(20): 0.860 Multilign(20): 0.697 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.780 Vsfold4: 0.550 Sensitivity PPfold(20): 0.714 Vsfold4: 0.534 Positive Predictive Value PPfold(20): 0.860 Vsfold4: 0.579 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.765 MCFold: 0.619 Sensitivity PPfold(20): 0.695 MCFold: 0.655 Positive Predictive Value PPfold(20): 0.848 MCFold: 0.595 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.790 RNAwolf: 0.453 Sensitivity PPfold(20): 0.734 RNAwolf: 0.447 Positive Predictive Value PPfold(20): 0.857 RNAwolf: 0.475 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.709 Murlet(seed): 0.616 Sensitivity PPfold(20): 0.627 Murlet(seed): 0.420 Positive Predictive Value PPfold(20): 0.810 Murlet(seed): 0.913 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.780 Vsfold5: 0.539 Sensitivity PPfold(20): 0.714 Vsfold5: 0.549 Positive Predictive Value PPfold(20): 0.860 Vsfold5: 0.543 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.780 RSpredict(seed): 0.346 Sensitivity PPfold(20): 0.714 RSpredict(seed): 0.189 Positive Predictive Value PPfold(20): 0.860 RSpredict(seed): 0.650 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	7 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.811 RDfolder: 0.548 Sensitivity PPfold(20): 0.725 RDfolder: 0.483 Positive Predictive Value PPfold(20): 0.915 RDfolder: 0.643 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.790 PPfold(seed): 0.031 Sensitivity PPfold(20): 0.734 PPfold(seed): 0.005 Positive Predictive Value PPfold(20): 0.857 PPfold(seed): 0.200 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.780 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.714 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.860 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.818 Multilign(seed): 0.795 Sensitivity PPfold(20): 0.740 Multilign(seed): 0.750 Positive Predictive Value PPfold(20): 0.914 Multilign(seed): 0.852 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.835 PPfold(20): 0.732 Sensitivity PETfold_pre2.0(seed): 0.784 PPfold(20): 0.672 Positive Predictive Value PETfold_pre2.0(seed): 0.892 PPfold(20): 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 PPfold(20) vs TurboFold(20) Matthews Correlation Coefficient PPfold(20): 0.780 TurboFold(20): 0.733 Sensitivity PPfold(20): 0.714 TurboFold(20): 0.694 Positive Predictive Value PPfold(20): 0.860 TurboFold(20): 0.781 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(20): N/A Sensitivity PPfold(20): N/A CMfinder(20): N/A Positive Predictive Value PPfold(20): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 PPfold(20): 0.732 Sensitivity PETfold_pre2.0(20): 0.707 PPfold(20): 0.672 Positive Predictive Value PETfold_pre2.0(20): 0.796 PPfold(20): 0.804 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs TurboFold(seed) Matthews Correlation Coefficient PPfold(20): 0.756 TurboFold(seed): 0.712 Sensitivity PPfold(20): 0.684 TurboFold(seed): 0.684 Positive Predictive Value PPfold(20): 0.842 TurboFold(seed): 0.749 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0		? PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.746 NanoFolder: 0.389 Sensitivity PPfold(20): 0.703 NanoFolder: 0.475 Positive Predictive Value PPfold(20): 0.798 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	? PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.756 Carnac(seed): 0.308 Sensitivity PPfold(20): 0.684 Carnac(seed): 0.096 Positive Predictive Value PPfold(20): 0.842 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0
NanoFolder	7 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.691 NanoFolder: 0.412 Sensitivity MXScarna(seed): 0.641 NanoFolder: 0.506 Positive Predictive Value MXScarna(seed): 0.752 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.780 NanoFolder: 0.389 Sensitivity CentroidAlifold(20): 0.683 NanoFolder: 0.475 Positive Predictive Value CentroidAlifold(20): 0.896 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.768 NanoFolder: 0.562 Sensitivity CentroidFold: 0.746 NanoFolder: 0.656 Positive Predictive Value CentroidFold: 0.798 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.10499527239e-08	4 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.677 NanoFolder: 0.389 Sensitivity RNAalifold(20): 0.624 NanoFolder: 0.475 Positive Predictive Value RNAalifold(20): 0.741 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.707 NanoFolder: 0.562 Sensitivity Sfold: 0.687 NanoFolder: 0.656 Positive Predictive Value Sfold: 0.738 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.86595104665e-08	17 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.722 NanoFolder: 0.562 Sensitivity Fold: 0.732 NanoFolder: 0.656 Positive Predictive Value Fold: 0.722 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.48055519165e-08	4 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.689 NanoFolder: 0.389 Sensitivity RNASampler(20): 0.624 NanoFolder: 0.475 Positive Predictive Value RNASampler(20): 0.768 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.619 NanoFolder: 0.389 Sensitivity MXScarna(20): 0.604 NanoFolder: 0.475 Positive Predictive Value MXScarna(20): 0.642 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	16 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 NanoFolder: 0.543 Sensitivity CentroidHomfold‑LAST: 0.650 NanoFolder: 0.639 Positive Predictive Value CentroidHomfold‑LAST: 0.818 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.18141491686e-08	17 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.728 NanoFolder: 0.562 Sensitivity HotKnots: 0.749 NanoFolder: 0.656 Positive Predictive Value HotKnots: 0.717 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	17 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.663 NanoFolder: 0.562 Sensitivity UNAFold: 0.677 NanoFolder: 0.656 Positive Predictive Value UNAFold: 0.661 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.33194562506e-08	17 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.761 NanoFolder: 0.562 Sensitivity Contrafold: 0.756 NanoFolder: 0.656 Positive Predictive Value Contrafold: 0.775 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	17 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.785 NanoFolder: 0.562 Sensitivity IPknot: 0.759 NanoFolder: 0.656 Positive Predictive Value IPknot: 0.819 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.08252958266e-08	17 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.823 NanoFolder: 0.562 Sensitivity ContextFold: 0.784 NanoFolder: 0.656 Positive Predictive Value ContextFold: 0.870 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.1413769576e-08	17 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.715 NanoFolder: 0.562 Sensitivity RNAshapes: 0.729 NanoFolder: 0.656 Positive Predictive Value RNAshapes: 0.711 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	17 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.687 NanoFolder: 0.562 Sensitivity MaxExpect: 0.691 NanoFolder: 0.656 Positive Predictive Value MaxExpect: 0.693 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.06323189071e-08	17 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.745 NanoFolder: 0.562 Sensitivity PknotsRG: 0.766 NanoFolder: 0.656 Positive Predictive Value PknotsRG: 0.734 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.54914456376e-08	17 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.741 NanoFolder: 0.562 Sensitivity RNAfold: 0.749 NanoFolder: 0.656 Positive Predictive Value RNAfold: 0.741 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.43573297697e-08	17 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.694 NanoFolder: 0.562 Sensitivity ProbKnot: 0.722 NanoFolder: 0.656 Positive Predictive Value ProbKnot: 0.677 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.18846395401e-08	4 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.609 NanoFolder: 0.389 Sensitivity Murlet(20): 0.535 NanoFolder: 0.475 Positive Predictive Value Murlet(20): 0.701 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	7 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.638 NanoFolder: 0.412 Sensitivity CentroidAlifold(seed): 0.417 NanoFolder: 0.506 Positive Predictive Value CentroidAlifold(seed): 0.985 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	12 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.765 NanoFolder: 0.610 Sensitivity Afold: 0.798 NanoFolder: 0.711 Positive Predictive Value Afold: 0.742 NanoFolder: 0.537 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.04409141234e-08	17 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.658 NanoFolder: 0.562 Sensitivity RNAsubopt: 0.677 NanoFolder: 0.656 Positive Predictive Value RNAsubopt: 0.650 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.7402423548e-08	4 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.603 NanoFolder: 0.389 Sensitivity Carnac(20): 0.455 NanoFolder: 0.475 Positive Predictive Value Carnac(20): 0.807 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	14 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.705 NanoFolder: 0.616 Sensitivity Cylofold: 0.686 NanoFolder: 0.699 Positive Predictive Value Cylofold: 0.738 NanoFolder: 0.560 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.91441904741e-08	16 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.659 NanoFolder: 0.543 Sensitivity McQFold: 0.671 NanoFolder: 0.639 Positive Predictive Value McQFold: 0.657 NanoFolder: 0.476 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.32677072069e-08	14 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.687 NanoFolder: 0.542 Sensitivity CRWrnafold: 0.694 NanoFolder: 0.635 Positive Predictive Value CRWrnafold: 0.689 NanoFolder: 0.478 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.59578924681e-08	4 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.529 NanoFolder: 0.336 Sensitivity RNAalifold(seed): 0.390 NanoFolder: 0.415 Positive Predictive Value RNAalifold(seed): 0.727 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.592 NanoFolder: 0.562 Sensitivity Pknots: 0.615 NanoFolder: 0.656 Positive Predictive Value Pknots: 0.583 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.34216867035e-07	2 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.232 NanoFolder: 0.207 Sensitivity RNASampler(seed): 0.211 NanoFolder: 0.289 Positive Predictive Value RNASampler(seed): 0.267 NanoFolder: 0.159 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	4 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.601 NanoFolder: 0.389 Sensitivity Mastr(20): 0.465 NanoFolder: 0.475 Positive Predictive Value Mastr(20): 0.783 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	4 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.414 NanoFolder: 0.389 Sensitivity RSpredict(20): 0.356 NanoFolder: 0.475 Positive Predictive Value RSpredict(20): 0.493 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	6 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.756 NanoFolder: 0.610 Sensitivity Alterna: 0.753 NanoFolder: 0.706 Positive Predictive Value Alterna: 0.771 NanoFolder: 0.545 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	17 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.680 NanoFolder: 0.562 Sensitivity RNASLOpt: 0.663 NanoFolder: 0.656 Positive Predictive Value RNASLOpt: 0.707 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.95070920198e-08	4 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.607 NanoFolder: 0.389 Sensitivity Multilign(20): 0.614 NanoFolder: 0.475 Positive Predictive Value Multilign(20): 0.608 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	17 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.609 NanoFolder: 0.562 Sensitivity Vsfold4: 0.608 NanoFolder: 0.656 Positive Predictive Value Vsfold4: 0.623 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.97012568641e-08	15 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.732 NanoFolder: 0.592 Sensitivity MCFold: 0.760 NanoFolder: 0.691 Positive Predictive Value MCFold: 0.714 NanoFolder: 0.521 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 2.69132796717e-08	17 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.598 NanoFolder: 0.562 Sensitivity RNAwolf: 0.584 NanoFolder: 0.656 Positive Predictive Value RNAwolf: 0.625 NanoFolder: 0.495 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.35936056444e-07	4 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.473 NanoFolder: 0.336 Sensitivity Murlet(seed): 0.329 NanoFolder: 0.415 Positive Predictive Value Murlet(seed): 0.692 NanoFolder: 0.288 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	16 NanoFolder vs Vsfold5 Matthews Correlation Coefficient NanoFolder: 0.551 Vsfold5: 0.545 Sensitivity NanoFolder: 0.647 Vsfold5: 0.558 Positive Predictive Value NanoFolder: 0.484 Vsfold5: 0.547 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 0.0284778450094	7 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.412 RSpredict(seed): 0.108 Sensitivity NanoFolder: 0.506 RSpredict(seed): 0.058 Positive Predictive Value NanoFolder: 0.350 RSpredict(seed): 0.225 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	8 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: 0.626 RDfolder: 0.528 Sensitivity NanoFolder: 0.680 RDfolder: 0.492 Positive Predictive Value NanoFolder: 0.597 RDfolder: 0.594 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	7 NanoFolder vs PPfold(seed) Matthews Correlation Coefficient NanoFolder: 0.412 PPfold(seed): 0.153 Sensitivity NanoFolder: 0.506 PPfold(seed): 0.045 Positive Predictive Value NanoFolder: 0.350 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	7 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.412 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.506 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.350 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	0 NanoFolder vs CMfinder(seed) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(seed): N/A Sensitivity NanoFolder: N/A CMfinder(seed): N/A Positive Predictive Value NanoFolder: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 0.458 NanoFolder: 0.447 Sensitivity Multilign(seed): 0.404 NanoFolder: 0.489 Positive Predictive Value Multilign(seed): 0.543 NanoFolder: 0.434 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	7 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.846 NanoFolder: 0.412 Sensitivity PETfold_pre2.0(seed): 0.795 NanoFolder: 0.506 Positive Predictive Value PETfold_pre2.0(seed): 0.905 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	4 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.643 NanoFolder: 0.389 Sensitivity TurboFold(20): 0.614 NanoFolder: 0.475 Positive Predictive Value TurboFold(20): 0.681 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	0 NanoFolder vs CMfinder(20) Matthews Correlation Coefficient NanoFolder: N/A CMfinder(20): N/A Sensitivity NanoFolder: N/A CMfinder(20): N/A Positive Predictive Value NanoFolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	4 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 NanoFolder: 0.389 Sensitivity PETfold_pre2.0(20): 0.733 NanoFolder: 0.475 Positive Predictive Value PETfold_pre2.0(20): 0.787 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0	5 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.532 NanoFolder: 0.410 Sensitivity TurboFold(seed): 0.521 NanoFolder: 0.496 Positive Predictive Value TurboFold(seed): 0.554 NanoFolder: 0.353 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	4 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.746 NanoFolder: 0.389 Sensitivity PPfold(20): 0.703 NanoFolder: 0.475 Positive Predictive Value PPfold(20): 0.798 NanoFolder: 0.331 Number of pairs reference - predicted secondary structure: 4 Wilcoxon single-rank test P-value: 0.0		? NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.410 Carnac(seed): 0.182 Sensitivity NanoFolder: 0.496 Carnac(seed): 0.034 Positive Predictive Value NanoFolder: 0.353 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0
Carnac(seed)	30 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.781 Carnac(seed): 0.299 Sensitivity MXScarna(seed): 0.746 Carnac(seed): 0.090 Positive Predictive Value MXScarna(seed): 0.825 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.801 Carnac(seed): 0.187 Sensitivity CentroidAlifold(20): 0.708 Carnac(seed): 0.035 Positive Predictive Value CentroidAlifold(20): 0.910 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 4.94031556815e-08	29 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.779 Carnac(seed): 0.276 Sensitivity CentroidFold: 0.768 Carnac(seed): 0.077 Positive Predictive Value CentroidFold: 0.796 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	21 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.756 Carnac(seed): 0.231 Sensitivity RNAalifold(20): 0.668 Carnac(seed): 0.054 Positive Predictive Value RNAalifold(20): 0.861 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.23657817852e-08	30 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.798 Carnac(seed): 0.299 Sensitivity Sfold: 0.777 Carnac(seed): 0.090 Positive Predictive Value Sfold: 0.826 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.763 Carnac(seed): 0.312 Sensitivity Fold: 0.773 Carnac(seed): 0.099 Positive Predictive Value Fold: 0.759 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	21 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.769 Carnac(seed): 0.231 Sensitivity RNASampler(20): 0.676 Carnac(seed): 0.054 Positive Predictive Value RNASampler(20): 0.880 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	21 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.763 Carnac(seed): 0.231 Sensitivity MXScarna(20): 0.729 Carnac(seed): 0.054 Positive Predictive Value MXScarna(20): 0.803 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	9 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.704 Carnac(seed): 0.325 Sensitivity CentroidHomfold‑LAST: 0.639 Carnac(seed): 0.107 Positive Predictive Value CentroidHomfold‑LAST: 0.784 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	30 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.795 Carnac(seed): 0.299 Sensitivity HotKnots: 0.808 Carnac(seed): 0.090 Positive Predictive Value HotKnots: 0.788 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.783 Carnac(seed): 0.299 Sensitivity UNAFold: 0.784 Carnac(seed): 0.090 Positive Predictive Value UNAFold: 0.788 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.760 Carnac(seed): 0.299 Sensitivity Contrafold: 0.773 Carnac(seed): 0.090 Positive Predictive Value Contrafold: 0.754 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.648 Carnac(seed): 0.145 Sensitivity IPknot: 0.610 Carnac(seed): 0.021 Positive Predictive Value IPknot: 0.699 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	6 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.682 Carnac(seed): 0.172 Sensitivity ContextFold: 0.627 Carnac(seed): 0.030 Positive Predictive Value ContextFold: 0.750 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	30 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.800 Carnac(seed): 0.299 Sensitivity RNAshapes: 0.801 Carnac(seed): 0.090 Positive Predictive Value RNAshapes: 0.804 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.750 Carnac(seed): 0.283 Sensitivity MaxExpect: 0.760 Carnac(seed): 0.081 Positive Predictive Value MaxExpect: 0.747 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	30 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.784 Carnac(seed): 0.299 Sensitivity PknotsRG: 0.795 Carnac(seed): 0.090 Positive Predictive Value PknotsRG: 0.779 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.785 Carnac(seed): 0.299 Sensitivity RNAfold: 0.791 Carnac(seed): 0.090 Positive Predictive Value RNAfold: 0.785 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.694 Carnac(seed): 0.214 Sensitivity ProbKnot: 0.719 Carnac(seed): 0.047 Positive Predictive Value ProbKnot: 0.677 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.27388928538e-08	21 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.707 Carnac(seed): 0.231 Sensitivity Murlet(20): 0.595 Carnac(seed): 0.054 Positive Predictive Value Murlet(20): 0.847 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.06544643719e-08	29 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.772 Carnac(seed): 0.276 Sensitivity CentroidAlifold(seed): 0.670 Carnac(seed): 0.077 Positive Predictive Value CentroidAlifold(seed): 0.895 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.788 Carnac(seed): 0.352 Sensitivity Afold: 0.796 Carnac(seed): 0.126 Positive Predictive Value Afold: 0.786 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.745 Carnac(seed): 0.299 Sensitivity RNAsubopt: 0.757 Carnac(seed): 0.090 Positive Predictive Value RNAsubopt: 0.740 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	21 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.693 Carnac(seed): 0.231 Sensitivity Carnac(20): 0.511 Carnac(seed): 0.054 Positive Predictive Value Carnac(20): 0.947 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.19332990918e-08	15 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.713 Carnac(seed): 0.239 Sensitivity Cylofold: 0.702 Carnac(seed): 0.058 Positive Predictive Value Cylofold: 0.733 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.91441904741e-08	30 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.716 Carnac(seed): 0.299 Sensitivity McQFold: 0.723 Carnac(seed): 0.090 Positive Predictive Value McQFold: 0.716 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.588 Carnac(seed): 0.156 Sensitivity CRWrnafold: 0.595 Carnac(seed): 0.025 Positive Predictive Value CRWrnafold: 0.591 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	26 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.737 Carnac(seed): 0.327 Sensitivity RNAalifold(seed): 0.603 Carnac(seed): 0.108 Positive Predictive Value RNAalifold(seed): 0.908 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	30 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: 0.708 Carnac(seed): 0.299 Sensitivity Pknots: 0.744 Carnac(seed): 0.090 Positive Predictive Value Pknots: 0.682 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.765 Carnac(seed): 0.428 Sensitivity RNASampler(seed): 0.687 Carnac(seed): 0.186 Positive Predictive Value RNASampler(seed): 0.859 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.59578924681e-08	21 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.634 Carnac(seed): 0.231 Sensitivity Mastr(20): 0.495 Carnac(seed): 0.054 Positive Predictive Value Mastr(20): 0.819 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	21 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.628 Carnac(seed): 0.231 Sensitivity RSpredict(20): 0.553 Carnac(seed): 0.054 Positive Predictive Value RSpredict(20): 0.722 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.1503931209e-08	17 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.840 Carnac(seed): 0.420 Sensitivity Alterna: 0.828 Carnac(seed): 0.180 Positive Predictive Value Alterna: 0.860 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.66715895098e-08	6 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.551 Carnac(seed): 0.172 Sensitivity RNASLOpt: 0.522 Carnac(seed): 0.030 Positive Predictive Value RNASLOpt: 0.593 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	9 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.603 Carnac(seed): 0.283 Sensitivity Multilign(20): 0.568 Carnac(seed): 0.081 Positive Predictive Value Multilign(20): 0.653 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	30 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.611 Carnac(seed): 0.299 Sensitivity Vsfold4: 0.597 Carnac(seed): 0.090 Positive Predictive Value Vsfold4: 0.636 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.639 Carnac(seed): 0.314 Sensitivity MCFold: 0.684 Carnac(seed): 0.100 Positive Predictive Value MCFold: 0.606 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.19332990918e-08	8 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.426 Carnac(seed): 0.145 Sensitivity RNAwolf: 0.417 Carnac(seed): 0.021 Positive Predictive Value RNAwolf: 0.451 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	26 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.620 Carnac(seed): 0.327 Sensitivity Murlet(seed): 0.442 Carnac(seed): 0.108 Positive Predictive Value Murlet(seed): 0.879 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	30 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.583 Carnac(seed): 0.299 Sensitivity Vsfold5: 0.581 Carnac(seed): 0.090 Positive Predictive Value Vsfold5: 0.597 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.467 Carnac(seed): 0.299 Sensitivity RSpredict(seed): 0.309 Carnac(seed): 0.090 Positive Predictive Value RSpredict(seed): 0.718 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	20 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: 0.660 Carnac(seed): 0.389 Sensitivity RDfolder: 0.606 Carnac(seed): 0.155 Positive Predictive Value RDfolder: 0.736 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 20 Wilcoxon single-rank test P-value: 5.23657817852e-08	8 Carnac(seed) vs PPfold(seed) Matthews Correlation Coefficient Carnac(seed): 0.145 PPfold(seed): 0.139 Sensitivity Carnac(seed): 0.021 PPfold(seed): 0.037 Positive Predictive Value Carnac(seed): 1.000 PPfold(seed): 0.538 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	30 Mastr(seed) vs Carnac(seed) Matthews Correlation Coefficient Mastr(seed): 0.381 Carnac(seed): 0.299 Sensitivity Mastr(seed): 0.164 Carnac(seed): 0.090 Positive Predictive Value Mastr(seed): 0.899 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 5.23657817852e-08	0 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): N/A Carnac(seed): N/A Sensitivity CMfinder(seed): N/A Carnac(seed): N/A Positive Predictive Value CMfinder(seed): N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.683 Carnac(seed): 0.427 Sensitivity Multilign(seed): 0.636 Carnac(seed): 0.186 Positive Predictive Value Multilign(seed): 0.750 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	6 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.786 Carnac(seed): 0.172 Sensitivity PETfold_pre2.0(seed): 0.724 Carnac(seed): 0.030 Positive Predictive Value PETfold_pre2.0(seed): 0.858 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	8 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.725 Carnac(seed): 0.308 Sensitivity TurboFold(20): 0.684 Carnac(seed): 0.096 Positive Predictive Value TurboFold(20): 0.776 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	0 Carnac(seed) vs CMfinder(20) Matthews Correlation Coefficient Carnac(seed): N/A CMfinder(20): N/A Sensitivity Carnac(seed): N/A CMfinder(20): N/A Positive Predictive Value Carnac(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	5 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.747 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.707 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.796 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	9 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.650 Carnac(seed): 0.325 Sensitivity TurboFold(seed): 0.624 Carnac(seed): 0.107 Positive Predictive Value TurboFold(seed): 0.688 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	8 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.756 Carnac(seed): 0.308 Sensitivity PPfold(20): 0.684 Carnac(seed): 0.096 Positive Predictive Value PPfold(20): 0.842 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	5 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.410 Carnac(seed): 0.182 Sensitivity NanoFolder: 0.496 Carnac(seed): 0.034 Positive Predictive Value NanoFolder: 0.353 Carnac(seed): 1.000 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0

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

All RNAs from the PDB datasetstandard base pair definition

Summary of pairwise comparisons

Detailed results of pairwise comparisons between methods

All RNAs from the PDB dataset
standard base pair definition