CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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All medium-sized RNAs from RNAstrand dataset

	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 201, 800
Number of RNA sequences: 818
Robustness test: no

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

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

Summary of pairwise comparisons

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

Legend:

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

Rank	Method Name	Trained	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	PETfold_pre2.0(seed)	no	44	2	0	7	658	643
2	ContextFold	yes	44	3	0	6	818	818
3	TurboFold(20)	no	39	2	0	12	245	245
4	CentroidAlifold(seed)	yes	39	6	1	7	658	426
5	PETfold_pre2.0(20)	no	38	3	0	12	245	242
6	PPfold(20)	yes	37	4	0	12	245	238
7	CentroidHomfold‑LAST	yes	37	10	0	6	818	759
8	CentroidAlifold(20)	yes	35	5	1	12	245	245
9	MXScarna(seed)	no	35	11	0	7	658	431
10	IPknot	yes	33	13	1	6	818	818
11	RNAalifold(20)	no	32	9	0	12	245	245
12	TurboFold(seed)	no	30	0	0	23	658	18
13	Multilign(20)	no	29	11	0	13	245	223
14	MXScarna(20)	no	29	11	1	12	245	245
15	CentroidFold	yes	29	17	1	6	818	818
16	Contrafold	yes	28	19	0	6	818	818
17	PPfold(seed)	yes	26	4	0	23	658	23
18	Sfold	no	26	20	1	6	818	818
19	MaxExpect	yes	26	21	0	6	818	818
20	ProbKnot	yes	25	22	0	6	818	818
21	RNASampler(seed)	no	24	6	0	23	658	12
22	Fold	no	23	24	0	6	818	818
23	RNASampler(20)	no	22	17	1	13	245	78
24	Murlet(20)	yes	22	17	2	12	245	176
25	UNAFold	no	22	25	0	6	818	818
26	PknotsRG	no	20	26	1	6	818	818
26	RNAfold	no	20	26	1	6	818	818
28	Afold	no	19	26	1	7	818	525
29	RNAsubopt	no	19	28	0	6	818	759
30	RNAalifold(seed)	no	18	28	0	7	658	427
31	CMfinder(20)	yes	15	26	0	12	245	245
32	McQFold	yes	14	33	0	6	818	818
33	CRWrnafold	yes	12	34	1	6	818	818
33	RNASLOpt	no	12	34	1	6	818	660
35	RNAshapes	no	11	34	1	7	818	706
36	Murlet(seed)	yes	10	21	1	21	658	31
37	RSpredict(20)	no	10	31	0	12	245	245
38	Carnac(20)	no	8	33	0	12	245	245
39	RNAwolf	yes	7	40	0	6	818	818
40	CMfinder(seed)	yes	6	25	0	22	658	51
41	RSpredict(seed)	no	6	40	0	7	658	429
42	Vsfold4	no	6	41	0	6	818	730
43	Vsfold5	no	5	42	0	6	818	720
44	NanoFolder	yes	3	39	0	11	818	134
45	Carnac(seed)	no	1	42	1	9	658	145
46	Mastr(seed)	yes	1	45	0	7	658	407
47	Mastr(20)	yes	0	40	1	12	245	245
N/A	Multilign(seed)	no	19	0	0	34	658	10
N/A	Cylofold	no	0	0	0	53	818	2
N/A	HotKnots	no	0	0	0	53	818	1
N/A	MCFold	yes	0	0	0	53	818	0
N/A	RDfolder	no	0	0	0	53	818	0
N/A	Pknots	no	0	0	0	53	818	0
N/A	Alterna	no	0	0	0	53	818	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.


PETfold_pre2.0(seed)		- ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.741 PETfold_pre2.0(seed): 0.701 Sensitivity ContextFold: 0.702 PETfold_pre2.0(seed): 0.612 Positive Predictive Value ContextFold: 0.782 PETfold_pre2.0(seed): 0.803 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 TurboFold(20): 0.752 Sensitivity PETfold_pre2.0(seed): 0.693 TurboFold(20): 0.698 Positive Predictive Value PETfold_pre2.0(seed): 0.854 TurboFold(20): 0.811 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 CentroidAlifold(seed): 0.714 Sensitivity PETfold_pre2.0(seed): 0.654 CentroidAlifold(seed): 0.564 Positive Predictive Value PETfold_pre2.0(seed): 0.834 CentroidAlifold(seed): 0.905 Number of pairs reference - predicted secondary structure: 411 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 PETfold_pre2.0(20): 0.747 Sensitivity PETfold_pre2.0(seed): 0.693 PETfold_pre2.0(20): 0.669 Positive Predictive Value PETfold_pre2.0(seed): 0.854 PETfold_pre2.0(20): 0.835 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.770 PPfold(20): 0.744 Sensitivity PETfold_pre2.0(seed): 0.694 PPfold(20): 0.648 Positive Predictive Value PETfold_pre2.0(seed): 0.855 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 CentroidHomfold‑LAST: 0.665 Sensitivity PETfold_pre2.0(seed): 0.618 CentroidHomfold‑LAST: 0.511 Positive Predictive Value PETfold_pre2.0(seed): 0.802 CentroidHomfold‑LAST: 0.868 Number of pairs reference - predicted secondary structure: 630 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 CentroidAlifold(20): 0.729 Sensitivity PETfold_pre2.0(seed): 0.693 CentroidAlifold(20): 0.581 Positive Predictive Value PETfold_pre2.0(seed): 0.854 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 MXScarna(seed): 0.632 Sensitivity PETfold_pre2.0(seed): 0.654 MXScarna(seed): 0.530 Positive Predictive Value PETfold_pre2.0(seed): 0.834 MXScarna(seed): 0.756 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 IPknot: 0.619 Sensitivity PETfold_pre2.0(seed): 0.612 IPknot: 0.566 Positive Predictive Value PETfold_pre2.0(seed): 0.803 IPknot: 0.678 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 RNAalifold(20): 0.673 Sensitivity PETfold_pre2.0(seed): 0.693 RNAalifold(20): 0.550 Positive Predictive Value PETfold_pre2.0(seed): 0.854 RNAalifold(20): 0.825 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.789 PETfold_pre2.0(seed): 0.764 Sensitivity TurboFold(seed): 0.762 PETfold_pre2.0(seed): 0.719 Positive Predictive Value TurboFold(seed): 0.818 PETfold_pre2.0(seed): 0.813 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.73923511064e-08	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.765 Multilign(20): 0.655 Sensitivity PETfold_pre2.0(seed): 0.687 Multilign(20): 0.596 Positive Predictive Value PETfold_pre2.0(seed): 0.852 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 MXScarna(20): 0.647 Sensitivity PETfold_pre2.0(seed): 0.693 MXScarna(20): 0.576 Positive Predictive Value PETfold_pre2.0(seed): 0.854 MXScarna(20): 0.729 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 CentroidFold: 0.587 Sensitivity PETfold_pre2.0(seed): 0.612 CentroidFold: 0.536 Positive Predictive Value PETfold_pre2.0(seed): 0.803 CentroidFold: 0.645 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 Contrafold: 0.571 Sensitivity PETfold_pre2.0(seed): 0.612 Contrafold: 0.559 Positive Predictive Value PETfold_pre2.0(seed): 0.803 Contrafold: 0.584 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.740 PPfold(seed): 0.716 Sensitivity PETfold_pre2.0(seed): 0.706 PPfold(seed): 0.652 Positive Predictive Value PETfold_pre2.0(seed): 0.776 PPfold(seed): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 Sfold: 0.542 Sensitivity PETfold_pre2.0(seed): 0.612 Sfold: 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.803 Sfold: 0.597 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 MaxExpect: 0.543 Sensitivity PETfold_pre2.0(seed): 0.612 MaxExpect: 0.531 Positive Predictive Value PETfold_pre2.0(seed): 0.803 MaxExpect: 0.557 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 ProbKnot: 0.541 Sensitivity PETfold_pre2.0(seed): 0.612 ProbKnot: 0.537 Positive Predictive Value PETfold_pre2.0(seed): 0.803 ProbKnot: 0.547 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.955 RNASampler(seed): 0.779 Sensitivity PETfold_pre2.0(seed): 0.915 RNASampler(seed): 0.659 Positive Predictive Value PETfold_pre2.0(seed): 0.997 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 6.70002765408e-09	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 Fold: 0.520 Sensitivity PETfold_pre2.0(seed): 0.612 Fold: 0.522 Positive Predictive Value PETfold_pre2.0(seed): 0.803 Fold: 0.519 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.756 RNASampler(20): 0.594 Sensitivity PETfold_pre2.0(seed): 0.682 RNASampler(20): 0.461 Positive Predictive Value PETfold_pre2.0(seed): 0.840 RNASampler(20): 0.766 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.770 Murlet(20): 0.574 Sensitivity PETfold_pre2.0(seed): 0.697 Murlet(20): 0.444 Positive Predictive Value PETfold_pre2.0(seed): 0.852 Murlet(20): 0.744 Number of pairs reference - predicted secondary structure: 171 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 UNAFold: 0.506 Sensitivity PETfold_pre2.0(seed): 0.612 UNAFold: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.803 UNAFold: 0.511 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 PknotsRG: 0.503 Sensitivity PETfold_pre2.0(seed): 0.612 PknotsRG: 0.504 Positive Predictive Value PETfold_pre2.0(seed): 0.803 PknotsRG: 0.503 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 RNAfold: 0.507 Sensitivity PETfold_pre2.0(seed): 0.612 RNAfold: 0.508 Positive Predictive Value PETfold_pre2.0(seed): 0.803 RNAfold: 0.507 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.806 Multilign(seed): 0.759 Sensitivity PETfold_pre2.0(seed): 0.781 Multilign(seed): 0.752 Positive Predictive Value PETfold_pre2.0(seed): 0.832 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.721 Afold: 0.529 Sensitivity PETfold_pre2.0(seed): 0.632 Afold: 0.525 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Afold: 0.535 Number of pairs reference - predicted secondary structure: 387 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 RNAsubopt: 0.495 Sensitivity PETfold_pre2.0(seed): 0.618 RNAsubopt: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.802 RNAsubopt: 0.490 Number of pairs reference - predicted secondary structure: 630 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 RNAalifold(seed): 0.541 Sensitivity PETfold_pre2.0(seed): 0.654 RNAalifold(seed): 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.834 RNAalifold(seed): 0.848 Number of pairs reference - predicted secondary structure: 412 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 CMfinder(20): 0.482 Sensitivity PETfold_pre2.0(seed): 0.693 CMfinder(20): 0.314 Positive Predictive Value PETfold_pre2.0(seed): 0.854 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 McQFold: 0.448 Sensitivity PETfold_pre2.0(seed): 0.612 McQFold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.803 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 CRWrnafold: 0.436 Sensitivity PETfold_pre2.0(seed): 0.612 CRWrnafold: 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.803 CRWrnafold: 0.436 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 RNASLOpt: 0.445 Sensitivity PETfold_pre2.0(seed): 0.635 RNASLOpt: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.808 RNASLOpt: 0.471 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.706 RNAshapes: 0.425 Sensitivity PETfold_pre2.0(seed): 0.622 RNAshapes: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.801 RNAshapes: 0.430 Number of pairs reference - predicted secondary structure: 597 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.825 Murlet(seed): 0.569 Sensitivity PETfold_pre2.0(seed): 0.790 Murlet(seed): 0.383 Positive Predictive Value PETfold_pre2.0(seed): 0.863 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 RSpredict(20): 0.402 Sensitivity PETfold_pre2.0(seed): 0.693 RSpredict(20): 0.269 Positive Predictive Value PETfold_pre2.0(seed): 0.854 RSpredict(20): 0.602 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Carnac(20): 0.386 Sensitivity PETfold_pre2.0(seed): 0.693 Carnac(20): 0.173 Positive Predictive Value PETfold_pre2.0(seed): 0.854 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 RNAwolf: 0.349 Sensitivity PETfold_pre2.0(seed): 0.612 RNAwolf: 0.364 Positive Predictive Value PETfold_pre2.0(seed): 0.803 RNAwolf: 0.337 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 CMfinder(seed): 0.454 Sensitivity PETfold_pre2.0(seed): 0.667 CMfinder(seed): 0.271 Positive Predictive Value PETfold_pre2.0(seed): 0.888 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 RSpredict(seed): 0.194 Sensitivity PETfold_pre2.0(seed): 0.654 RSpredict(seed): 0.077 Positive Predictive Value PETfold_pre2.0(seed): 0.834 RSpredict(seed): 0.494 Number of pairs reference - predicted secondary structure: 414 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.705 Vsfold4: 0.307 Sensitivity PETfold_pre2.0(seed): 0.621 Vsfold4: 0.282 Positive Predictive Value PETfold_pre2.0(seed): 0.801 Vsfold4: 0.336 Number of pairs reference - predicted secondary structure: 615 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.705 Vsfold5: 0.300 Sensitivity PETfold_pre2.0(seed): 0.622 Vsfold5: 0.285 Positive Predictive Value PETfold_pre2.0(seed): 0.801 Vsfold5: 0.318 Number of pairs reference - predicted secondary structure: 608 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 NanoFolder: 0.174 Sensitivity PETfold_pre2.0(seed): 0.634 NanoFolder: 0.205 Positive Predictive Value PETfold_pre2.0(seed): 0.824 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.711 Carnac(seed): 0.151 Sensitivity PETfold_pre2.0(seed): 0.608 Carnac(seed): 0.028 Positive Predictive Value PETfold_pre2.0(seed): 0.832 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.739 Mastr(seed): 0.074 Sensitivity PETfold_pre2.0(seed): 0.656 Mastr(seed): 0.006 Positive Predictive Value PETfold_pre2.0(seed): 0.834 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 392 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.891 HotKnots: 0.640 Sensitivity PETfold_pre2.0(seed): 0.795 HotKnots: 0.615 Positive Predictive Value PETfold_pre2.0(seed): 1.000 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(seed): N/A Sensitivity Pknots: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A MCFold: N/A Sensitivity PETfold_pre2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_pre2.0(seed): N/A Sensitivity Alterna: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(seed): 0.693 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.854 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08
ContextFold	643 ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.741 PETfold_pre2.0(seed): 0.701 Sensitivity ContextFold: 0.702 PETfold_pre2.0(seed): 0.612 Positive Predictive Value ContextFold: 0.782 PETfold_pre2.0(seed): 0.803 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.843 TurboFold(20): 0.752 Sensitivity ContextFold: 0.799 TurboFold(20): 0.701 Positive Predictive Value ContextFold: 0.891 TurboFold(20): 0.809 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.802 CentroidAlifold(seed): 0.709 Sensitivity ContextFold: 0.766 CentroidAlifold(seed): 0.556 Positive Predictive Value ContextFold: 0.841 CentroidAlifold(seed): 0.906 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.844 PETfold_pre2.0(20): 0.739 Sensitivity ContextFold: 0.798 PETfold_pre2.0(20): 0.654 Positive Predictive Value ContextFold: 0.892 PETfold_pre2.0(20): 0.836 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.844 PPfold(20): 0.733 Sensitivity ContextFold: 0.799 PPfold(20): 0.629 Positive Predictive Value ContextFold: 0.892 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.741 CentroidHomfold‑LAST: 0.650 Sensitivity ContextFold: 0.704 CentroidHomfold‑LAST: 0.491 Positive Predictive Value ContextFold: 0.780 CentroidHomfold‑LAST: 0.862 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.843 CentroidAlifold(20): 0.725 Sensitivity ContextFold: 0.799 CentroidAlifold(20): 0.574 Positive Predictive Value ContextFold: 0.891 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.802 MXScarna(seed): 0.637 Sensitivity ContextFold: 0.766 MXScarna(seed): 0.535 Positive Predictive Value ContextFold: 0.841 MXScarna(seed): 0.759 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.720 IPknot: 0.612 Sensitivity ContextFold: 0.687 IPknot: 0.561 Positive Predictive Value ContextFold: 0.756 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.843 RNAalifold(20): 0.668 Sensitivity ContextFold: 0.799 RNAalifold(20): 0.540 Positive Predictive Value ContextFold: 0.891 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.787 ContextFold: 0.723 Sensitivity TurboFold(seed): 0.760 ContextFold: 0.702 Positive Predictive Value TurboFold(seed): 0.815 ContextFold: 0.747 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.846 Multilign(20): 0.651 Sensitivity ContextFold: 0.803 Multilign(20): 0.590 Positive Predictive Value ContextFold: 0.893 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.843 MXScarna(20): 0.654 Sensitivity ContextFold: 0.799 MXScarna(20): 0.584 Positive Predictive Value ContextFold: 0.891 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.720 CentroidFold: 0.583 Sensitivity ContextFold: 0.687 CentroidFold: 0.533 Positive Predictive Value ContextFold: 0.756 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.720 Contrafold: 0.567 Sensitivity ContextFold: 0.687 Contrafold: 0.558 Positive Predictive Value ContextFold: 0.756 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.728 PPfold(seed): 0.716 Sensitivity ContextFold: 0.712 PPfold(seed): 0.652 Positive Predictive Value ContextFold: 0.745 PPfold(seed): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 1.41743914454e-05	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.720 Sfold: 0.538 Sensitivity ContextFold: 0.687 Sfold: 0.491 Positive Predictive Value ContextFold: 0.756 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.720 MaxExpect: 0.536 Sensitivity ContextFold: 0.687 MaxExpect: 0.527 Positive Predictive Value ContextFold: 0.756 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.720 ProbKnot: 0.534 Sensitivity ContextFold: 0.687 ProbKnot: 0.534 Positive Predictive Value ContextFold: 0.756 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): 0.779 ContextFold: 0.694 Sensitivity RNASampler(seed): 0.659 ContextFold: 0.680 Positive Predictive Value RNASampler(seed): 0.921 ContextFold: 0.709 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.720 Fold: 0.511 Sensitivity ContextFold: 0.687 Fold: 0.517 Positive Predictive Value ContextFold: 0.756 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.790 RNASampler(20): 0.565 Sensitivity ContextFold: 0.750 RNASampler(20): 0.413 Positive Predictive Value ContextFold: 0.832 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.829 Murlet(20): 0.573 Sensitivity ContextFold: 0.784 Murlet(20): 0.441 Positive Predictive Value ContextFold: 0.878 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.720 UNAFold: 0.501 Sensitivity ContextFold: 0.687 UNAFold: 0.501 Positive Predictive Value ContextFold: 0.756 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.720 PknotsRG: 0.499 Sensitivity ContextFold: 0.687 PknotsRG: 0.504 Positive Predictive Value ContextFold: 0.756 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.720 RNAfold: 0.499 Sensitivity ContextFold: 0.687 RNAfold: 0.504 Positive Predictive Value ContextFold: 0.756 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.734 ContextFold: 0.624 Sensitivity Multilign(seed): 0.733 ContextFold: 0.618 Positive Predictive Value Multilign(seed): 0.737 ContextFold: 0.631 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.742 Afold: 0.516 Sensitivity ContextFold: 0.711 Afold: 0.517 Positive Predictive Value ContextFold: 0.776 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.741 RNAsubopt: 0.501 Sensitivity ContextFold: 0.704 RNAsubopt: 0.510 Positive Predictive Value ContextFold: 0.780 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.802 RNAalifold(seed): 0.541 Sensitivity ContextFold: 0.765 RNAalifold(seed): 0.344 Positive Predictive Value ContextFold: 0.840 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.843 CMfinder(20): 0.478 Sensitivity ContextFold: 0.799 CMfinder(20): 0.309 Positive Predictive Value ContextFold: 0.891 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.720 McQFold: 0.443 Sensitivity ContextFold: 0.687 McQFold: 0.435 Positive Predictive Value ContextFold: 0.756 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.720 CRWrnafold: 0.432 Sensitivity ContextFold: 0.687 CRWrnafold: 0.438 Positive Predictive Value ContextFold: 0.756 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.747 RNASLOpt: 0.442 Sensitivity ContextFold: 0.711 RNASLOpt: 0.419 Positive Predictive Value ContextFold: 0.787 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.746 RNAshapes: 0.438 Sensitivity ContextFold: 0.708 RNAshapes: 0.434 Positive Predictive Value ContextFold: 0.786 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.780 Murlet(seed): 0.569 Sensitivity ContextFold: 0.764 Murlet(seed): 0.383 Positive Predictive Value ContextFold: 0.798 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.843 RSpredict(20): 0.418 Sensitivity ContextFold: 0.799 RSpredict(20): 0.285 Positive Predictive Value ContextFold: 0.891 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.843 Carnac(20): 0.378 Sensitivity ContextFold: 0.799 Carnac(20): 0.166 Positive Predictive Value ContextFold: 0.891 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.720 RNAwolf: 0.339 Sensitivity ContextFold: 0.687 RNAwolf: 0.355 Positive Predictive Value ContextFold: 0.756 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.800 CMfinder(seed): 0.454 Sensitivity ContextFold: 0.774 CMfinder(seed): 0.271 Positive Predictive Value ContextFold: 0.827 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.802 RSpredict(seed): 0.214 Sensitivity ContextFold: 0.766 RSpredict(seed): 0.089 Positive Predictive Value ContextFold: 0.841 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.743 Vsfold4: 0.306 Sensitivity ContextFold: 0.706 Vsfold4: 0.282 Positive Predictive Value ContextFold: 0.782 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.745 Vsfold5: 0.300 Sensitivity ContextFold: 0.707 Vsfold5: 0.286 Positive Predictive Value ContextFold: 0.785 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.778 NanoFolder: 0.166 Sensitivity ContextFold: 0.738 NanoFolder: 0.197 Positive Predictive Value ContextFold: 0.820 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.719 Carnac(seed): 0.150 Sensitivity ContextFold: 0.697 Carnac(seed): 0.028 Positive Predictive Value ContextFold: 0.742 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.796 Mastr(seed): 0.073 Sensitivity ContextFold: 0.761 Mastr(seed): 0.006 Positive Predictive Value ContextFold: 0.833 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: 0.640 ContextFold: 0.576 Sensitivity HotKnots: 0.615 ContextFold: 0.538 Positive Predictive Value HotKnots: 0.667 ContextFold: 0.618 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: N/A Pknots: N/A Sensitivity ContextFold: N/A Pknots: N/A Positive Predictive Value ContextFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.944 Cylofold: 0.271 Sensitivity ContextFold: 0.905 Cylofold: 0.241 Positive Predictive Value ContextFold: 0.984 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: N/A MCFold: N/A Sensitivity ContextFold: N/A MCFold: N/A Positive Predictive Value ContextFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: N/A ContextFold: N/A Sensitivity RDfolder: N/A ContextFold: N/A Positive Predictive Value RDfolder: N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: N/A Alterna: N/A Sensitivity ContextFold: N/A Alterna: N/A Positive Predictive Value ContextFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.843 Mastr(20): 0.000 Sensitivity ContextFold: 0.799 Mastr(20): 0.000 Positive Predictive Value ContextFold: 0.891 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(20)	230 PETfold_pre2.0(seed) vs TurboFold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 TurboFold(20): 0.752 Sensitivity PETfold_pre2.0(seed): 0.693 TurboFold(20): 0.698 Positive Predictive Value PETfold_pre2.0(seed): 0.854 TurboFold(20): 0.811 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.843 TurboFold(20): 0.752 Sensitivity ContextFold: 0.799 TurboFold(20): 0.701 Positive Predictive Value ContextFold: 0.891 TurboFold(20): 0.809 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 CentroidAlifold(seed): 0.733 Sensitivity TurboFold(20): 0.718 CentroidAlifold(seed): 0.564 Positive Predictive Value TurboFold(20): 0.828 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.753 PETfold_pre2.0(20): 0.739 Sensitivity TurboFold(20): 0.700 PETfold_pre2.0(20): 0.654 Positive Predictive Value TurboFold(20): 0.810 PETfold_pre2.0(20): 0.836 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.752 PPfold(20): 0.733 Sensitivity TurboFold(20): 0.700 PPfold(20): 0.629 Positive Predictive Value TurboFold(20): 0.808 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.752 CentroidHomfold‑LAST: 0.710 Sensitivity TurboFold(20): 0.701 CentroidHomfold‑LAST: 0.561 Positive Predictive Value TurboFold(20): 0.809 CentroidHomfold‑LAST: 0.898 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.752 CentroidAlifold(20): 0.725 Sensitivity TurboFold(20): 0.701 CentroidAlifold(20): 0.574 Positive Predictive Value TurboFold(20): 0.809 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 MXScarna(seed): 0.684 Sensitivity TurboFold(20): 0.718 MXScarna(seed): 0.582 Positive Predictive Value TurboFold(20): 0.828 MXScarna(seed): 0.805 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.752 IPknot: 0.655 Sensitivity TurboFold(20): 0.701 IPknot: 0.586 Positive Predictive Value TurboFold(20): 0.809 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.752 RNAalifold(20): 0.668 Sensitivity TurboFold(20): 0.701 RNAalifold(20): 0.540 Positive Predictive Value TurboFold(20): 0.809 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.767 TurboFold(seed): 0.755 Sensitivity TurboFold(20): 0.750 TurboFold(seed): 0.739 Positive Predictive Value TurboFold(20): 0.786 TurboFold(seed): 0.774 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.749 Multilign(20): 0.651 Sensitivity TurboFold(20): 0.697 Multilign(20): 0.590 Positive Predictive Value TurboFold(20): 0.806 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.752 MXScarna(20): 0.654 Sensitivity TurboFold(20): 0.701 MXScarna(20): 0.584 Positive Predictive Value TurboFold(20): 0.809 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.752 CentroidFold: 0.621 Sensitivity TurboFold(20): 0.701 CentroidFold: 0.557 Positive Predictive Value TurboFold(20): 0.809 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.752 Contrafold: 0.606 Sensitivity TurboFold(20): 0.701 Contrafold: 0.585 Positive Predictive Value TurboFold(20): 0.809 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.882 PPfold(seed): 0.847 Sensitivity TurboFold(20): 0.842 PPfold(seed): 0.782 Positive Predictive Value TurboFold(20): 0.924 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.752 Sfold: 0.584 Sensitivity TurboFold(20): 0.701 Sfold: 0.522 Positive Predictive Value TurboFold(20): 0.809 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.752 MaxExpect: 0.592 Sensitivity TurboFold(20): 0.701 MaxExpect: 0.569 Positive Predictive Value TurboFold(20): 0.809 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.752 ProbKnot: 0.590 Sensitivity TurboFold(20): 0.701 ProbKnot: 0.572 Positive Predictive Value TurboFold(20): 0.809 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): N/A TurboFold(20): N/A Sensitivity RNASampler(seed): N/A TurboFold(20): N/A Positive Predictive Value RNASampler(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.752 Fold: 0.562 Sensitivity TurboFold(20): 0.701 Fold: 0.555 Positive Predictive Value TurboFold(20): 0.809 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.734 RNASampler(20): 0.565 Sensitivity TurboFold(20): 0.691 RNASampler(20): 0.413 Positive Predictive Value TurboFold(20): 0.781 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.747 Murlet(20): 0.573 Sensitivity TurboFold(20): 0.695 Murlet(20): 0.441 Positive Predictive Value TurboFold(20): 0.804 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.752 UNAFold: 0.547 Sensitivity TurboFold(20): 0.701 UNAFold: 0.535 Positive Predictive Value TurboFold(20): 0.809 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.752 PknotsRG: 0.525 Sensitivity TurboFold(20): 0.701 PknotsRG: 0.518 Positive Predictive Value TurboFold(20): 0.809 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.752 RNAfold: 0.544 Sensitivity TurboFold(20): 0.701 RNAfold: 0.536 Positive Predictive Value TurboFold(20): 0.809 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): N/A Multilign(seed): N/A Sensitivity TurboFold(20): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.762 Afold: 0.556 Sensitivity TurboFold(20): 0.709 Afold: 0.544 Positive Predictive Value TurboFold(20): 0.819 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.752 RNAsubopt: 0.530 Sensitivity TurboFold(20): 0.701 RNAsubopt: 0.529 Positive Predictive Value TurboFold(20): 0.809 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 RNAalifold(seed): 0.492 Sensitivity TurboFold(20): 0.718 RNAalifold(seed): 0.290 Positive Predictive Value TurboFold(20): 0.828 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.752 CMfinder(20): 0.478 Sensitivity TurboFold(20): 0.701 CMfinder(20): 0.309 Positive Predictive Value TurboFold(20): 0.809 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.752 McQFold: 0.442 Sensitivity TurboFold(20): 0.701 McQFold: 0.424 Positive Predictive Value TurboFold(20): 0.809 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.752 CRWrnafold: 0.464 Sensitivity TurboFold(20): 0.701 CRWrnafold: 0.456 Positive Predictive Value TurboFold(20): 0.809 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.750 RNASLOpt: 0.450 Sensitivity TurboFold(20): 0.699 RNASLOpt: 0.417 Positive Predictive Value TurboFold(20): 0.805 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.751 RNAshapes: 0.468 Sensitivity TurboFold(20): 0.700 RNAshapes: 0.454 Positive Predictive Value TurboFold(20): 0.808 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.882 Murlet(seed): 0.588 Sensitivity TurboFold(20): 0.842 Murlet(seed): 0.347 Positive Predictive Value TurboFold(20): 0.924 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.752 RSpredict(20): 0.418 Sensitivity TurboFold(20): 0.701 RSpredict(20): 0.285 Positive Predictive Value TurboFold(20): 0.809 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.752 Carnac(20): 0.378 Sensitivity TurboFold(20): 0.701 Carnac(20): 0.166 Positive Predictive Value TurboFold(20): 0.809 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.752 RNAwolf: 0.367 Sensitivity TurboFold(20): 0.701 RNAwolf: 0.377 Positive Predictive Value TurboFold(20): 0.809 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 RSpredict(seed): 0.197 Sensitivity TurboFold(20): 0.718 RSpredict(seed): 0.077 Positive Predictive Value TurboFold(20): 0.828 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.751 Vsfold4: 0.352 Sensitivity TurboFold(20): 0.700 Vsfold4: 0.319 Positive Predictive Value TurboFold(20): 0.808 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.751 Vsfold5: 0.333 Sensitivity TurboFold(20): 0.699 Vsfold5: 0.308 Positive Predictive Value TurboFold(20): 0.807 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.735 NanoFolder: 0.150 Sensitivity TurboFold(20): 0.684 NanoFolder: 0.173 Positive Predictive Value TurboFold(20): 0.791 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.851 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.825 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.878 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.772 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.721 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.828 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: N/A TurboFold(20): N/A Sensitivity HotKnots: N/A TurboFold(20): N/A Positive Predictive Value HotKnots: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): N/A Pknots: N/A Sensitivity TurboFold(20): N/A Pknots: N/A Positive Predictive Value TurboFold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: N/A TurboFold(20): N/A Sensitivity Cylofold: N/A TurboFold(20): N/A Positive Predictive Value Cylofold: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): N/A MCFold: N/A Sensitivity TurboFold(20): N/A MCFold: N/A Positive Predictive Value TurboFold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs TurboFold(20) Matthews Correlation Coefficient RDfolder: N/A TurboFold(20): N/A Sensitivity RDfolder: N/A TurboFold(20): N/A Positive Predictive Value RDfolder: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): N/A Alterna: N/A Sensitivity TurboFold(20): N/A Alterna: N/A Positive Predictive Value TurboFold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.752 Mastr(20): 0.000 Sensitivity TurboFold(20): 0.701 Mastr(20): 0.000 Positive Predictive Value TurboFold(20): 0.809 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	411 PETfold_pre2.0(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 CentroidAlifold(seed): 0.714 Sensitivity PETfold_pre2.0(seed): 0.654 CentroidAlifold(seed): 0.564 Positive Predictive Value PETfold_pre2.0(seed): 0.834 CentroidAlifold(seed): 0.905 Number of pairs reference - predicted secondary structure: 411 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.802 CentroidAlifold(seed): 0.709 Sensitivity ContextFold: 0.766 CentroidAlifold(seed): 0.556 Positive Predictive Value ContextFold: 0.841 CentroidAlifold(seed): 0.906 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 CentroidAlifold(seed): 0.733 Sensitivity TurboFold(20): 0.718 CentroidAlifold(seed): 0.564 Positive Predictive Value TurboFold(20): 0.828 CentroidAlifold(seed): 0.953 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08		- PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.756 CentroidAlifold(seed): 0.735 Sensitivity PETfold_pre2.0(20): 0.670 CentroidAlifold(seed): 0.567 Positive Predictive Value PETfold_pre2.0(20): 0.855 CentroidAlifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 200 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.748 CentroidAlifold(seed): 0.734 Sensitivity PPfold(20): 0.646 CentroidAlifold(seed): 0.565 Positive Predictive Value PPfold(20): 0.866 CentroidAlifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.713 CentroidHomfold‑LAST: 0.686 Sensitivity CentroidAlifold(seed): 0.562 CentroidHomfold‑LAST: 0.539 Positive Predictive Value CentroidAlifold(seed): 0.906 CentroidHomfold‑LAST: 0.874 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 CentroidAlifold(20): 0.732 Sensitivity CentroidAlifold(seed): 0.564 CentroidAlifold(20): 0.578 Positive Predictive Value CentroidAlifold(seed): 0.953 CentroidAlifold(20): 0.929 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 0.00419655428257	+ CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 MXScarna(seed): 0.637 Sensitivity CentroidAlifold(seed): 0.556 MXScarna(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.906 MXScarna(seed): 0.759 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 IPknot: 0.654 Sensitivity CentroidAlifold(seed): 0.556 IPknot: 0.599 Positive Predictive Value CentroidAlifold(seed): 0.906 IPknot: 0.715 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 RNAalifold(20): 0.676 Sensitivity CentroidAlifold(seed): 0.564 RNAalifold(20): 0.542 Positive Predictive Value CentroidAlifold(seed): 0.953 RNAalifold(20): 0.843 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 CentroidAlifold(seed): 0.751 Sensitivity TurboFold(seed): 0.760 CentroidAlifold(seed): 0.665 Positive Predictive Value TurboFold(seed): 0.815 CentroidAlifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 Multilign(20): 0.658 Sensitivity CentroidAlifold(seed): 0.553 Multilign(20): 0.593 Positive Predictive Value CentroidAlifold(seed): 0.955 Multilign(20): 0.731 Number of pairs reference - predicted secondary structure: 184 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 MXScarna(20): 0.679 Sensitivity CentroidAlifold(seed): 0.564 MXScarna(20): 0.599 Positive Predictive Value CentroidAlifold(seed): 0.953 MXScarna(20): 0.772 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 CentroidFold: 0.633 Sensitivity CentroidAlifold(seed): 0.556 CentroidFold: 0.580 Positive Predictive Value CentroidAlifold(seed): 0.906 CentroidFold: 0.692 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Contrafold: 0.620 Sensitivity CentroidAlifold(seed): 0.556 Contrafold: 0.605 Positive Predictive Value CentroidAlifold(seed): 0.906 Contrafold: 0.637 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.731 PPfold(seed): 0.716 Sensitivity CentroidAlifold(seed): 0.667 PPfold(seed): 0.652 Positive Predictive Value CentroidAlifold(seed): 0.802 PPfold(seed): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Sfold: 0.612 Sensitivity CentroidAlifold(seed): 0.556 Sfold: 0.558 Positive Predictive Value CentroidAlifold(seed): 0.906 Sfold: 0.673 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 MaxExpect: 0.598 Sensitivity CentroidAlifold(seed): 0.556 MaxExpect: 0.581 Positive Predictive Value CentroidAlifold(seed): 0.906 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 ProbKnot: 0.597 Sensitivity CentroidAlifold(seed): 0.556 ProbKnot: 0.585 Positive Predictive Value CentroidAlifold(seed): 0.906 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.946 RNASampler(seed): 0.779 Sensitivity CentroidAlifold(seed): 0.900 RNASampler(seed): 0.659 Positive Predictive Value CentroidAlifold(seed): 0.995 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Fold: 0.573 Sensitivity CentroidAlifold(seed): 0.556 Fold: 0.570 Positive Predictive Value CentroidAlifold(seed): 0.906 Fold: 0.577 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.769 RNASampler(20): 0.578 Sensitivity CentroidAlifold(seed): 0.615 RNASampler(20): 0.384 Positive Predictive Value CentroidAlifold(seed): 0.961 RNASampler(20): 0.871 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.750 Murlet(20): 0.568 Sensitivity CentroidAlifold(seed): 0.590 Murlet(20): 0.427 Positive Predictive Value CentroidAlifold(seed): 0.954 Murlet(20): 0.758 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 UNAFold: 0.576 Sensitivity CentroidAlifold(seed): 0.556 UNAFold: 0.566 Positive Predictive Value CentroidAlifold(seed): 0.906 UNAFold: 0.588 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 PknotsRG: 0.560 Sensitivity CentroidAlifold(seed): 0.556 PknotsRG: 0.554 Positive Predictive Value CentroidAlifold(seed): 0.906 PknotsRG: 0.567 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNAfold: 0.569 Sensitivity CentroidAlifold(seed): 0.556 RNAfold: 0.563 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAfold: 0.577 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.806 Multilign(seed): 0.759 Sensitivity CentroidAlifold(seed): 0.767 Multilign(seed): 0.752 Positive Predictive Value CentroidAlifold(seed): 0.848 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.704 Afold: 0.558 Sensitivity CentroidAlifold(seed): 0.546 Afold: 0.551 Positive Predictive Value CentroidAlifold(seed): 0.909 Afold: 0.566 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.713 RNAsubopt: 0.559 Sensitivity CentroidAlifold(seed): 0.562 RNAsubopt: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAsubopt: 0.559 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNAalifold(seed): 0.541 Sensitivity CentroidAlifold(seed): 0.556 RNAalifold(seed): 0.344 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 CMfinder(20): 0.497 Sensitivity CentroidAlifold(seed): 0.564 CMfinder(20): 0.327 Positive Predictive Value CentroidAlifold(seed): 0.953 CMfinder(20): 0.758 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 McQFold: 0.465 Sensitivity CentroidAlifold(seed): 0.556 McQFold: 0.449 Positive Predictive Value CentroidAlifold(seed): 0.906 McQFold: 0.484 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 CRWrnafold: 0.482 Sensitivity CentroidAlifold(seed): 0.556 CRWrnafold: 0.477 Positive Predictive Value CentroidAlifold(seed): 0.906 CRWrnafold: 0.488 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 RNASLOpt: 0.465 Sensitivity CentroidAlifold(seed): 0.581 RNASLOpt: 0.433 Positive Predictive Value CentroidAlifold(seed): 0.912 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 365 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.717 RNAshapes: 0.507 Sensitivity CentroidAlifold(seed): 0.567 RNAshapes: 0.495 Positive Predictive Value CentroidAlifold(seed): 0.908 RNAshapes: 0.521 Number of pairs reference - predicted secondary structure: 388 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.814 Murlet(seed): 0.569 Sensitivity CentroidAlifold(seed): 0.748 Murlet(seed): 0.383 Positive Predictive Value CentroidAlifold(seed): 0.886 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 RSpredict(20): 0.404 Sensitivity CentroidAlifold(seed): 0.564 RSpredict(20): 0.260 Positive Predictive Value CentroidAlifold(seed): 0.953 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Carnac(20): 0.361 Sensitivity CentroidAlifold(seed): 0.564 Carnac(20): 0.148 Positive Predictive Value CentroidAlifold(seed): 0.953 Carnac(20): 0.881 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNAwolf: 0.379 Sensitivity CentroidAlifold(seed): 0.556 RNAwolf: 0.389 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.753 CMfinder(seed): 0.454 Sensitivity CentroidAlifold(seed): 0.625 CMfinder(seed): 0.271 Positive Predictive Value CentroidAlifold(seed): 0.909 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RSpredict(seed): 0.215 Sensitivity CentroidAlifold(seed): 0.556 RSpredict(seed): 0.090 Positive Predictive Value CentroidAlifold(seed): 0.906 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.717 Vsfold4: 0.336 Sensitivity CentroidAlifold(seed): 0.568 Vsfold4: 0.304 Positive Predictive Value CentroidAlifold(seed): 0.906 Vsfold4: 0.372 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.718 Vsfold5: 0.314 Sensitivity CentroidAlifold(seed): 0.569 Vsfold5: 0.293 Positive Predictive Value CentroidAlifold(seed): 0.907 Vsfold5: 0.339 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 NanoFolder: 0.176 Sensitivity CentroidAlifold(seed): 0.560 NanoFolder: 0.203 Positive Predictive Value CentroidAlifold(seed): 0.929 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.708 Carnac(seed): 0.150 Sensitivity CentroidAlifold(seed): 0.578 Carnac(seed): 0.028 Positive Predictive Value CentroidAlifold(seed): 0.869 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.712 Mastr(seed): 0.074 Sensitivity CentroidAlifold(seed): 0.560 Mastr(seed): 0.006 Positive Predictive Value CentroidAlifold(seed): 0.905 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.906 HotKnots: 0.640 Sensitivity CentroidAlifold(seed): 0.821 HotKnots: 0.615 Positive Predictive Value CentroidAlifold(seed): 1.000 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): N/A Pknots: N/A Sensitivity CentroidAlifold(seed): N/A Pknots: N/A Positive Predictive Value CentroidAlifold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): N/A Cylofold: N/A Sensitivity CentroidAlifold(seed): N/A Cylofold: N/A Positive Predictive Value CentroidAlifold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): N/A MCFold: N/A Sensitivity CentroidAlifold(seed): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): N/A RDfolder: N/A Sensitivity CentroidAlifold(seed): N/A RDfolder: N/A Positive Predictive Value CentroidAlifold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): N/A Alterna: N/A Sensitivity CentroidAlifold(seed): N/A Alterna: N/A Positive Predictive Value CentroidAlifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Mastr(20): 0.000 Sensitivity CentroidAlifold(seed): 0.564 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.953 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(20)	230 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 PETfold_pre2.0(20): 0.747 Sensitivity PETfold_pre2.0(seed): 0.693 PETfold_pre2.0(20): 0.669 Positive Predictive Value PETfold_pre2.0(seed): 0.854 PETfold_pre2.0(20): 0.835 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.844 PETfold_pre2.0(20): 0.739 Sensitivity ContextFold: 0.798 PETfold_pre2.0(20): 0.654 Positive Predictive Value ContextFold: 0.892 PETfold_pre2.0(20): 0.836 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.753 PETfold_pre2.0(20): 0.739 Sensitivity TurboFold(20): 0.700 PETfold_pre2.0(20): 0.654 Positive Predictive Value TurboFold(20): 0.810 PETfold_pre2.0(20): 0.836 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	200 PETfold_pre2.0(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.756 CentroidAlifold(seed): 0.735 Sensitivity PETfold_pre2.0(20): 0.670 CentroidAlifold(seed): 0.567 Positive Predictive Value PETfold_pre2.0(20): 0.855 CentroidAlifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 200 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 PPfold(20): 0.735 Sensitivity PETfold_pre2.0(20): 0.654 PPfold(20): 0.633 Positive Predictive Value PETfold_pre2.0(20): 0.836 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CentroidHomfold‑LAST: 0.711 Sensitivity PETfold_pre2.0(20): 0.654 CentroidHomfold‑LAST: 0.563 Positive Predictive Value PETfold_pre2.0(20): 0.836 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CentroidAlifold(20): 0.726 Sensitivity PETfold_pre2.0(20): 0.654 CentroidAlifold(20): 0.576 Positive Predictive Value PETfold_pre2.0(20): 0.836 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.756 MXScarna(seed): 0.684 Sensitivity PETfold_pre2.0(20): 0.670 MXScarna(seed): 0.581 Positive Predictive Value PETfold_pre2.0(20): 0.855 MXScarna(seed): 0.806 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 IPknot: 0.654 Sensitivity PETfold_pre2.0(20): 0.654 IPknot: 0.585 Positive Predictive Value PETfold_pre2.0(20): 0.836 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAalifold(20): 0.669 Sensitivity PETfold_pre2.0(20): 0.654 RNAalifold(20): 0.542 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 PETfold_pre2.0(20): 0.341 Sensitivity TurboFold(seed): 0.739 PETfold_pre2.0(20): 0.136 Positive Predictive Value TurboFold(seed): 0.774 PETfold_pre2.0(20): 0.857 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Multilign(20): 0.652 Sensitivity PETfold_pre2.0(20): 0.649 Multilign(20): 0.590 Positive Predictive Value PETfold_pre2.0(20): 0.835 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 MXScarna(20): 0.654 Sensitivity PETfold_pre2.0(20): 0.654 MXScarna(20): 0.583 Positive Predictive Value PETfold_pre2.0(20): 0.836 MXScarna(20): 0.734 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CentroidFold: 0.621 Sensitivity PETfold_pre2.0(20): 0.654 CentroidFold: 0.556 Positive Predictive Value PETfold_pre2.0(20): 0.836 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Contrafold: 0.606 Sensitivity PETfold_pre2.0(20): 0.654 Contrafold: 0.584 Positive Predictive Value PETfold_pre2.0(20): 0.836 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.919 PPfold(seed): 0.847 Sensitivity PETfold_pre2.0(20): 0.901 PPfold(seed): 0.782 Positive Predictive Value PETfold_pre2.0(20): 0.938 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Sfold: 0.583 Sensitivity PETfold_pre2.0(20): 0.654 Sfold: 0.521 Positive Predictive Value PETfold_pre2.0(20): 0.836 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 MaxExpect: 0.591 Sensitivity PETfold_pre2.0(20): 0.654 MaxExpect: 0.568 Positive Predictive Value PETfold_pre2.0(20): 0.836 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 ProbKnot: 0.589 Sensitivity PETfold_pre2.0(20): 0.654 ProbKnot: 0.571 Positive Predictive Value PETfold_pre2.0(20): 0.836 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Fold: 0.561 Sensitivity PETfold_pre2.0(20): 0.654 Fold: 0.553 Positive Predictive Value PETfold_pre2.0(20): 0.836 Fold: 0.570 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.700 RNASampler(20): 0.566 Sensitivity PETfold_pre2.0(20): 0.610 RNASampler(20): 0.417 Positive Predictive Value PETfold_pre2.0(20): 0.805 RNASampler(20): 0.771 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.738 Murlet(20): 0.573 Sensitivity PETfold_pre2.0(20): 0.660 Murlet(20): 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.827 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 UNAFold: 0.546 Sensitivity PETfold_pre2.0(20): 0.654 UNAFold: 0.534 Positive Predictive Value PETfold_pre2.0(20): 0.836 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 PknotsRG: 0.525 Sensitivity PETfold_pre2.0(20): 0.654 PknotsRG: 0.517 Positive Predictive Value PETfold_pre2.0(20): 0.836 PknotsRG: 0.534 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAfold: 0.543 Sensitivity PETfold_pre2.0(20): 0.654 RNAfold: 0.534 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAfold: 0.552 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Multilign(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Multilign(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 Afold: 0.555 Sensitivity PETfold_pre2.0(20): 0.656 Afold: 0.542 Positive Predictive Value PETfold_pre2.0(20): 0.848 Afold: 0.570 Number of pairs reference - predicted secondary structure: 182 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAsubopt: 0.531 Sensitivity PETfold_pre2.0(20): 0.654 RNAsubopt: 0.530 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAsubopt: 0.533 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.756 RNAalifold(seed): 0.491 Sensitivity PETfold_pre2.0(20): 0.670 RNAalifold(seed): 0.289 Positive Predictive Value PETfold_pre2.0(20): 0.855 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 200 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CMfinder(20): 0.479 Sensitivity PETfold_pre2.0(20): 0.654 CMfinder(20): 0.310 Positive Predictive Value PETfold_pre2.0(20): 0.836 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 McQFold: 0.442 Sensitivity PETfold_pre2.0(20): 0.654 McQFold: 0.423 Positive Predictive Value PETfold_pre2.0(20): 0.836 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CRWrnafold: 0.462 Sensitivity PETfold_pre2.0(20): 0.654 CRWrnafold: 0.454 Positive Predictive Value PETfold_pre2.0(20): 0.836 CRWrnafold: 0.472 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 RNASLOpt: 0.449 Sensitivity PETfold_pre2.0(20): 0.658 RNASLOpt: 0.415 Positive Predictive Value PETfold_pre2.0(20): 0.835 RNASLOpt: 0.487 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 RNAshapes: 0.467 Sensitivity PETfold_pre2.0(20): 0.656 RNAshapes: 0.453 Positive Predictive Value PETfold_pre2.0(20): 0.838 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 232 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.919 Murlet(seed): 0.588 Sensitivity PETfold_pre2.0(20): 0.901 Murlet(seed): 0.347 Positive Predictive Value PETfold_pre2.0(20): 0.938 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RSpredict(20): 0.416 Sensitivity PETfold_pre2.0(20): 0.654 RSpredict(20): 0.284 Positive Predictive Value PETfold_pre2.0(20): 0.836 RSpredict(20): 0.613 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Carnac(20): 0.380 Sensitivity PETfold_pre2.0(20): 0.654 Carnac(20): 0.167 Positive Predictive Value PETfold_pre2.0(20): 0.836 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAwolf: 0.367 Sensitivity PETfold_pre2.0(20): 0.654 RNAwolf: 0.376 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 RSpredict(seed): 0.191 Sensitivity PETfold_pre2.0(20): 0.670 RSpredict(seed): 0.073 Positive Predictive Value PETfold_pre2.0(20): 0.855 RSpredict(seed): 0.505 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.740 Vsfold4: 0.355 Sensitivity PETfold_pre2.0(20): 0.656 Vsfold4: 0.321 Positive Predictive Value PETfold_pre2.0(20): 0.837 Vsfold4: 0.395 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 Vsfold5: 0.336 Sensitivity PETfold_pre2.0(20): 0.657 Vsfold5: 0.311 Positive Predictive Value PETfold_pre2.0(20): 0.837 Vsfold5: 0.365 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.731 NanoFolder: 0.151 Sensitivity PETfold_pre2.0(20): 0.643 NanoFolder: 0.174 Positive Predictive Value PETfold_pre2.0(20): 0.831 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.767 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.894 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.26497248087e-08	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.759 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.674 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.855 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs PETfold_pre2.0(20) Matthews Correlation Coefficient HotKnots: N/A PETfold_pre2.0(20): N/A Sensitivity HotKnots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value HotKnots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs PETfold_pre2.0(20) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(20): N/A Sensitivity Pknots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PETfold_pre2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(20): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): N/A MCFold: N/A Sensitivity PETfold_pre2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PETfold_pre2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(20): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(20): 0.654 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.836 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(20)	223 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.770 PPfold(20): 0.744 Sensitivity PETfold_pre2.0(seed): 0.694 PPfold(20): 0.648 Positive Predictive Value PETfold_pre2.0(seed): 0.855 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.844 PPfold(20): 0.733 Sensitivity ContextFold: 0.799 PPfold(20): 0.629 Positive Predictive Value ContextFold: 0.892 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.752 PPfold(20): 0.733 Sensitivity TurboFold(20): 0.700 PPfold(20): 0.629 Positive Predictive Value TurboFold(20): 0.808 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 PPfold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient PPfold(20): 0.748 CentroidAlifold(seed): 0.734 Sensitivity PPfold(20): 0.646 CentroidAlifold(seed): 0.565 Positive Predictive Value PPfold(20): 0.866 CentroidAlifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 PPfold(20): 0.735 Sensitivity PETfold_pre2.0(20): 0.654 PPfold(20): 0.633 Positive Predictive Value PETfold_pre2.0(20): 0.836 PPfold(20): 0.855 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.733 CentroidHomfold‑LAST: 0.710 Sensitivity PPfold(20): 0.629 CentroidHomfold‑LAST: 0.560 Positive Predictive Value PPfold(20): 0.855 CentroidHomfold‑LAST: 0.900 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.733 CentroidAlifold(20): 0.725 Sensitivity PPfold(20): 0.629 CentroidAlifold(20): 0.575 Positive Predictive Value PPfold(20): 0.855 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.748 MXScarna(seed): 0.687 Sensitivity PPfold(20): 0.647 MXScarna(seed): 0.585 Positive Predictive Value PPfold(20): 0.867 MXScarna(seed): 0.808 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.733 IPknot: 0.656 Sensitivity PPfold(20): 0.629 IPknot: 0.587 Positive Predictive Value PPfold(20): 0.855 IPknot: 0.735 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.733 RNAalifold(20): 0.669 Sensitivity PPfold(20): 0.629 RNAalifold(20): 0.541 Positive Predictive Value PPfold(20): 0.855 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 PPfold(20): 0.293 Sensitivity TurboFold(seed): 0.739 PPfold(20): 0.125 Positive Predictive Value TurboFold(seed): 0.774 PPfold(20): 0.688 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.732 Multilign(20): 0.652 Sensitivity PPfold(20): 0.627 Multilign(20): 0.590 Positive Predictive Value PPfold(20): 0.855 Multilign(20): 0.722 Number of pairs reference - predicted secondary structure: 217 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.733 MXScarna(20): 0.655 Sensitivity PPfold(20): 0.629 MXScarna(20): 0.585 Positive Predictive Value PPfold(20): 0.855 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.733 CentroidFold: 0.620 Sensitivity PPfold(20): 0.629 CentroidFold: 0.556 Positive Predictive Value PPfold(20): 0.855 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.733 Contrafold: 0.606 Sensitivity PPfold(20): 0.629 Contrafold: 0.584 Positive Predictive Value PPfold(20): 0.855 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.886 PPfold(seed): 0.847 Sensitivity PPfold(20): 0.842 PPfold(seed): 0.782 Positive Predictive Value PPfold(20): 0.934 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.733 Sfold: 0.583 Sensitivity PPfold(20): 0.629 Sfold: 0.521 Positive Predictive Value PPfold(20): 0.855 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.733 MaxExpect: 0.590 Sensitivity PPfold(20): 0.629 MaxExpect: 0.567 Positive Predictive Value PPfold(20): 0.855 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.733 ProbKnot: 0.588 Sensitivity PPfold(20): 0.629 ProbKnot: 0.570 Positive Predictive Value PPfold(20): 0.855 ProbKnot: 0.608 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(20): N/A Sensitivity RNASampler(seed): N/A PPfold(20): N/A Positive Predictive Value RNASampler(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.733 Fold: 0.562 Sensitivity PPfold(20): 0.629 Fold: 0.554 Positive Predictive Value PPfold(20): 0.855 Fold: 0.571 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.689 RNASampler(20): 0.565 Sensitivity PPfold(20): 0.567 RNASampler(20): 0.413 Positive Predictive Value PPfold(20): 0.838 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.735 Murlet(20): 0.576 Sensitivity PPfold(20): 0.637 Murlet(20): 0.445 Positive Predictive Value PPfold(20): 0.849 Murlet(20): 0.749 Number of pairs reference - predicted secondary structure: 174 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.733 UNAFold: 0.547 Sensitivity PPfold(20): 0.629 UNAFold: 0.535 Positive Predictive Value PPfold(20): 0.855 UNAFold: 0.561 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.733 PknotsRG: 0.524 Sensitivity PPfold(20): 0.629 PknotsRG: 0.517 Positive Predictive Value PPfold(20): 0.855 PknotsRG: 0.534 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.733 RNAfold: 0.544 Sensitivity PPfold(20): 0.629 RNAfold: 0.537 Positive Predictive Value PPfold(20): 0.855 RNAfold: 0.554 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): N/A Multilign(seed): N/A Sensitivity PPfold(20): N/A Multilign(seed): N/A Positive Predictive Value PPfold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.737 Afold: 0.557 Sensitivity PPfold(20): 0.632 Afold: 0.545 Positive Predictive Value PPfold(20): 0.861 Afold: 0.572 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.733 RNAsubopt: 0.530 Sensitivity PPfold(20): 0.629 RNAsubopt: 0.530 Positive Predictive Value PPfold(20): 0.855 RNAsubopt: 0.533 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.748 RNAalifold(seed): 0.492 Sensitivity PPfold(20): 0.646 RNAalifold(seed): 0.290 Positive Predictive Value PPfold(20): 0.866 RNAalifold(seed): 0.837 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.733 CMfinder(20): 0.479 Sensitivity PPfold(20): 0.629 CMfinder(20): 0.310 Positive Predictive Value PPfold(20): 0.855 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.733 McQFold: 0.442 Sensitivity PPfold(20): 0.629 McQFold: 0.423 Positive Predictive Value PPfold(20): 0.855 McQFold: 0.463 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.733 CRWrnafold: 0.463 Sensitivity PPfold(20): 0.629 CRWrnafold: 0.455 Positive Predictive Value PPfold(20): 0.855 CRWrnafold: 0.473 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.736 RNASLOpt: 0.450 Sensitivity PPfold(20): 0.633 RNASLOpt: 0.417 Positive Predictive Value PPfold(20): 0.856 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 222 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.736 RNAshapes: 0.467 Sensitivity PPfold(20): 0.632 RNAshapes: 0.454 Positive Predictive Value PPfold(20): 0.858 RNAshapes: 0.482 Number of pairs reference - predicted secondary structure: 229 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.886 Murlet(seed): 0.588 Sensitivity PPfold(20): 0.842 Murlet(seed): 0.347 Positive Predictive Value PPfold(20): 0.934 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.733 RSpredict(20): 0.421 Sensitivity PPfold(20): 0.629 RSpredict(20): 0.289 Positive Predictive Value PPfold(20): 0.855 RSpredict(20): 0.616 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.733 Carnac(20): 0.383 Sensitivity PPfold(20): 0.629 Carnac(20): 0.170 Positive Predictive Value PPfold(20): 0.855 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.733 RNAwolf: 0.369 Sensitivity PPfold(20): 0.629 RNAwolf: 0.378 Positive Predictive Value PPfold(20): 0.855 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.749 RSpredict(seed): 0.201 Sensitivity PPfold(20): 0.647 RSpredict(seed): 0.079 Positive Predictive Value PPfold(20): 0.867 RSpredict(seed): 0.514 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.735 Vsfold4: 0.351 Sensitivity PPfold(20): 0.632 Vsfold4: 0.318 Positive Predictive Value PPfold(20): 0.856 Vsfold4: 0.390 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.736 Vsfold5: 0.331 Sensitivity PPfold(20): 0.632 Vsfold5: 0.306 Positive Predictive Value PPfold(20): 0.857 Vsfold5: 0.360 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.722 NanoFolder: 0.152 Sensitivity PPfold(20): 0.614 NanoFolder: 0.176 Positive Predictive Value PPfold(20): 0.849 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.803 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.725 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.890 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.750 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.649 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.868 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 183 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs PPfold(20) Matthews Correlation Coefficient HotKnots: N/A PPfold(20): N/A Sensitivity HotKnots: N/A PPfold(20): N/A Positive Predictive Value HotKnots: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): N/A Pknots: N/A Sensitivity PPfold(20): N/A Pknots: N/A Positive Predictive Value PPfold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PPfold(20) Matthews Correlation Coefficient Cylofold: N/A PPfold(20): N/A Sensitivity Cylofold: N/A PPfold(20): N/A Positive Predictive Value Cylofold: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): N/A MCFold: N/A Sensitivity PPfold(20): N/A MCFold: N/A Positive Predictive Value PPfold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): N/A RDfolder: N/A Sensitivity PPfold(20): N/A RDfolder: N/A Positive Predictive Value PPfold(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): N/A Alterna: N/A Sensitivity PPfold(20): N/A Alterna: N/A Positive Predictive Value PPfold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.733 Mastr(20): 0.000 Sensitivity PPfold(20): 0.629 Mastr(20): 0.000 Positive Predictive Value PPfold(20): 0.855 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidHomfold‑LAST	630 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 CentroidHomfold‑LAST: 0.665 Sensitivity PETfold_pre2.0(seed): 0.618 CentroidHomfold‑LAST: 0.511 Positive Predictive Value PETfold_pre2.0(seed): 0.802 CentroidHomfold‑LAST: 0.868 Number of pairs reference - predicted secondary structure: 630 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.741 CentroidHomfold‑LAST: 0.650 Sensitivity ContextFold: 0.704 CentroidHomfold‑LAST: 0.491 Positive Predictive Value ContextFold: 0.780 CentroidHomfold‑LAST: 0.862 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.752 CentroidHomfold‑LAST: 0.710 Sensitivity TurboFold(20): 0.701 CentroidHomfold‑LAST: 0.561 Positive Predictive Value TurboFold(20): 0.809 CentroidHomfold‑LAST: 0.898 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	413 CentroidAlifold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(seed): 0.713 CentroidHomfold‑LAST: 0.686 Sensitivity CentroidAlifold(seed): 0.562 CentroidHomfold‑LAST: 0.539 Positive Predictive Value CentroidAlifold(seed): 0.906 CentroidHomfold‑LAST: 0.874 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CentroidHomfold‑LAST: 0.711 Sensitivity PETfold_pre2.0(20): 0.654 CentroidHomfold‑LAST: 0.563 Positive Predictive Value PETfold_pre2.0(20): 0.836 CentroidHomfold‑LAST: 0.899 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(20): 0.733 CentroidHomfold‑LAST: 0.710 Sensitivity PPfold(20): 0.629 CentroidHomfold‑LAST: 0.560 Positive Predictive Value PPfold(20): 0.855 CentroidHomfold‑LAST: 0.900 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CentroidHomfold‑LAST: 0.710 Sensitivity CentroidAlifold(20): 0.574 CentroidHomfold‑LAST: 0.561 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidHomfold‑LAST: 0.898 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.686 MXScarna(seed): 0.641 Sensitivity CentroidHomfold‑LAST: 0.539 MXScarna(seed): 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.874 MXScarna(seed): 0.762 Number of pairs reference - predicted secondary structure: 418 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 IPknot: 0.619 Sensitivity CentroidHomfold‑LAST: 0.491 IPknot: 0.569 Positive Predictive Value CentroidHomfold‑LAST: 0.862 IPknot: 0.675 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 RNAalifold(20): 0.668 Sensitivity CentroidHomfold‑LAST: 0.561 RNAalifold(20): 0.540 Positive Predictive Value CentroidHomfold‑LAST: 0.898 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.776 CentroidHomfold‑LAST: 0.747 Sensitivity TurboFold(seed): 0.753 CentroidHomfold‑LAST: 0.652 Positive Predictive Value TurboFold(seed): 0.802 CentroidHomfold‑LAST: 0.858 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.704 Multilign(20): 0.651 Sensitivity CentroidHomfold‑LAST: 0.553 Multilign(20): 0.590 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 MXScarna(20): 0.654 Sensitivity CentroidHomfold‑LAST: 0.561 MXScarna(20): 0.584 Positive Predictive Value CentroidHomfold‑LAST: 0.898 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 CentroidFold: 0.589 Sensitivity CentroidHomfold‑LAST: 0.491 CentroidFold: 0.540 Positive Predictive Value CentroidHomfold‑LAST: 0.862 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 Contrafold: 0.574 Sensitivity CentroidHomfold‑LAST: 0.491 Contrafold: 0.564 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): 0.735 CentroidHomfold‑LAST: 0.723 Sensitivity PPfold(seed): 0.691 CentroidHomfold‑LAST: 0.641 Positive Predictive Value PPfold(seed): 0.783 CentroidHomfold‑LAST: 0.817 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 6.02521692575e-08	+ CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 Sfold: 0.546 Sensitivity CentroidHomfold‑LAST: 0.491 Sfold: 0.498 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Sfold: 0.600 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 MaxExpect: 0.544 Sensitivity CentroidHomfold‑LAST: 0.491 MaxExpect: 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.862 MaxExpect: 0.556 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 ProbKnot: 0.542 Sensitivity CentroidHomfold‑LAST: 0.491 ProbKnot: 0.539 Positive Predictive Value CentroidHomfold‑LAST: 0.862 ProbKnot: 0.547 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.807 RNASampler(seed): 0.779 Sensitivity CentroidHomfold‑LAST: 0.729 RNASampler(seed): 0.659 Positive Predictive Value CentroidHomfold‑LAST: 0.894 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.69265863073e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 Fold: 0.521 Sensitivity CentroidHomfold‑LAST: 0.491 Fold: 0.525 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Fold: 0.519 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.717 RNASampler(20): 0.565 Sensitivity CentroidHomfold‑LAST: 0.582 RNASampler(20): 0.413 Positive Predictive Value CentroidHomfold‑LAST: 0.885 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.713 Murlet(20): 0.573 Sensitivity CentroidHomfold‑LAST: 0.569 Murlet(20): 0.441 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 UNAFold: 0.510 Sensitivity CentroidHomfold‑LAST: 0.491 UNAFold: 0.507 Positive Predictive Value CentroidHomfold‑LAST: 0.862 UNAFold: 0.514 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 PknotsRG: 0.506 Sensitivity CentroidHomfold‑LAST: 0.491 PknotsRG: 0.509 Positive Predictive Value CentroidHomfold‑LAST: 0.862 PknotsRG: 0.506 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 RNAfold: 0.510 Sensitivity CentroidHomfold‑LAST: 0.491 RNAfold: 0.512 Positive Predictive Value CentroidHomfold‑LAST: 0.862 RNAfold: 0.509 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Multilign(seed): 0.734 CentroidHomfold‑LAST: 0.710 Sensitivity Multilign(seed): 0.733 CentroidHomfold‑LAST: 0.608 Positive Predictive Value Multilign(seed): 0.737 CentroidHomfold‑LAST: 0.831 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.661 Afold: 0.532 Sensitivity CentroidHomfold‑LAST: 0.508 Afold: 0.529 Positive Predictive Value CentroidHomfold‑LAST: 0.863 Afold: 0.536 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 RNAsubopt: 0.501 Sensitivity CentroidHomfold‑LAST: 0.491 RNAsubopt: 0.510 Positive Predictive Value CentroidHomfold‑LAST: 0.862 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.686 RNAalifold(seed): 0.542 Sensitivity CentroidHomfold‑LAST: 0.539 RNAalifold(seed): 0.345 Positive Predictive Value CentroidHomfold‑LAST: 0.874 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 414 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 CMfinder(20): 0.478 Sensitivity CentroidHomfold‑LAST: 0.561 CMfinder(20): 0.309 Positive Predictive Value CentroidHomfold‑LAST: 0.898 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 McQFold: 0.452 Sensitivity CentroidHomfold‑LAST: 0.491 McQFold: 0.442 Positive Predictive Value CentroidHomfold‑LAST: 0.862 McQFold: 0.463 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 CRWrnafold: 0.442 Sensitivity CentroidHomfold‑LAST: 0.491 CRWrnafold: 0.445 Positive Predictive Value CentroidHomfold‑LAST: 0.862 CRWrnafold: 0.440 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.659 RNASLOpt: 0.442 Sensitivity CentroidHomfold‑LAST: 0.506 RNASLOpt: 0.419 Positive Predictive Value CentroidHomfold‑LAST: 0.860 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RNAshapes: 0.438 Sensitivity CentroidHomfold‑LAST: 0.496 RNAshapes: 0.434 Positive Predictive Value CentroidHomfold‑LAST: 0.863 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 Murlet(seed): 0.556 Sensitivity CentroidHomfold‑LAST: 0.611 Murlet(seed): 0.366 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 RSpredict(20): 0.418 Sensitivity CentroidHomfold‑LAST: 0.561 RSpredict(20): 0.285 Positive Predictive Value CentroidHomfold‑LAST: 0.898 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 Carnac(20): 0.378 Sensitivity CentroidHomfold‑LAST: 0.561 Carnac(20): 0.166 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 RNAwolf: 0.349 Sensitivity CentroidHomfold‑LAST: 0.491 RNAwolf: 0.364 Positive Predictive Value CentroidHomfold‑LAST: 0.862 RNAwolf: 0.336 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.731 CMfinder(seed): 0.454 Sensitivity CentroidHomfold‑LAST: 0.587 CMfinder(seed): 0.271 Positive Predictive Value CentroidHomfold‑LAST: 0.911 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.686 RSpredict(seed): 0.212 Sensitivity CentroidHomfold‑LAST: 0.539 RSpredict(seed): 0.087 Positive Predictive Value CentroidHomfold‑LAST: 0.874 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.655 Vsfold4: 0.306 Sensitivity CentroidHomfold‑LAST: 0.497 Vsfold4: 0.282 Positive Predictive Value CentroidHomfold‑LAST: 0.863 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.655 Vsfold5: 0.300 Sensitivity CentroidHomfold‑LAST: 0.497 Vsfold5: 0.286 Positive Predictive Value CentroidHomfold‑LAST: 0.864 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.660 NanoFolder: 0.170 Sensitivity CentroidHomfold‑LAST: 0.493 NanoFolder: 0.201 Positive Predictive Value CentroidHomfold‑LAST: 0.886 NanoFolder: 0.146 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Carnac(seed): 0.154 Sensitivity CentroidHomfold‑LAST: 0.550 Carnac(seed): 0.027 Positive Predictive Value CentroidHomfold‑LAST: 0.817 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.687 Mastr(seed): 0.075 Sensitivity CentroidHomfold‑LAST: 0.543 Mastr(seed): 0.006 Positive Predictive Value CentroidHomfold‑LAST: 0.871 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 394 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.640 CentroidHomfold‑LAST: 0.232 Sensitivity HotKnots: 0.615 CentroidHomfold‑LAST: 0.154 Positive Predictive Value HotKnots: 0.667 CentroidHomfold‑LAST: 0.353 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: N/A CentroidHomfold‑LAST: N/A Sensitivity Pknots: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Pknots: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Cylofold: 0.271 Sensitivity CentroidHomfold‑LAST: 0.613 Cylofold: 0.241 Positive Predictive Value CentroidHomfold‑LAST: 0.808 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A MCFold: N/A Sensitivity CentroidHomfold‑LAST: N/A MCFold: N/A Positive Predictive Value CentroidHomfold‑LAST: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CentroidHomfold‑LAST Matthews Correlation Coefficient RDfolder: N/A CentroidHomfold‑LAST: N/A Sensitivity RDfolder: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value RDfolder: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CentroidHomfold‑LAST Matthews Correlation Coefficient Alterna: N/A CentroidHomfold‑LAST: N/A Sensitivity Alterna: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Alterna: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 Mastr(20): 0.000 Sensitivity CentroidHomfold‑LAST: 0.561 Mastr(20): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(20)	230 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 CentroidAlifold(20): 0.729 Sensitivity PETfold_pre2.0(seed): 0.693 CentroidAlifold(20): 0.581 Positive Predictive Value PETfold_pre2.0(seed): 0.854 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.843 CentroidAlifold(20): 0.725 Sensitivity ContextFold: 0.799 CentroidAlifold(20): 0.574 Positive Predictive Value ContextFold: 0.891 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.752 CentroidAlifold(20): 0.725 Sensitivity TurboFold(20): 0.701 CentroidAlifold(20): 0.574 Positive Predictive Value TurboFold(20): 0.809 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 CentroidAlifold(20): 0.732 Sensitivity CentroidAlifold(seed): 0.564 CentroidAlifold(20): 0.578 Positive Predictive Value CentroidAlifold(seed): 0.953 CentroidAlifold(20): 0.929 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 0.00419655428257	242 PETfold_pre2.0(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CentroidAlifold(20): 0.726 Sensitivity PETfold_pre2.0(20): 0.654 CentroidAlifold(20): 0.576 Positive Predictive Value PETfold_pre2.0(20): 0.836 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient PPfold(20): 0.733 CentroidAlifold(20): 0.725 Sensitivity PPfold(20): 0.629 CentroidAlifold(20): 0.575 Positive Predictive Value PPfold(20): 0.855 CentroidAlifold(20): 0.916 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CentroidHomfold‑LAST: 0.710 Sensitivity CentroidAlifold(20): 0.574 CentroidHomfold‑LAST: 0.561 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidHomfold‑LAST: 0.898 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.732 MXScarna(seed): 0.684 Sensitivity CentroidAlifold(20): 0.577 MXScarna(seed): 0.582 Positive Predictive Value CentroidAlifold(20): 0.929 MXScarna(seed): 0.805 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.725 IPknot: 0.655 Sensitivity CentroidAlifold(20): 0.574 IPknot: 0.586 Positive Predictive Value CentroidAlifold(20): 0.916 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAalifold(20): 0.668 Sensitivity CentroidAlifold(20): 0.574 RNAalifold(20): 0.540 Positive Predictive Value CentroidAlifold(20): 0.916 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 CentroidAlifold(20): 0.642 Sensitivity TurboFold(seed): 0.739 CentroidAlifold(20): 0.455 Positive Predictive Value TurboFold(seed): 0.774 CentroidAlifold(20): 0.909 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.721 Multilign(20): 0.651 Sensitivity CentroidAlifold(20): 0.567 Multilign(20): 0.590 Positive Predictive Value CentroidAlifold(20): 0.916 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 MXScarna(20): 0.654 Sensitivity CentroidAlifold(20): 0.574 MXScarna(20): 0.584 Positive Predictive Value CentroidAlifold(20): 0.916 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CentroidFold: 0.621 Sensitivity CentroidAlifold(20): 0.574 CentroidFold: 0.557 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Contrafold: 0.606 Sensitivity CentroidAlifold(20): 0.574 Contrafold: 0.585 Positive Predictive Value CentroidAlifold(20): 0.916 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.908 PPfold(seed): 0.847 Sensitivity CentroidAlifold(20): 0.871 PPfold(seed): 0.782 Positive Predictive Value CentroidAlifold(20): 0.946 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Sfold: 0.584 Sensitivity CentroidAlifold(20): 0.574 Sfold: 0.522 Positive Predictive Value CentroidAlifold(20): 0.916 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.725 MaxExpect: 0.592 Sensitivity CentroidAlifold(20): 0.574 MaxExpect: 0.569 Positive Predictive Value CentroidAlifold(20): 0.916 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.725 ProbKnot: 0.590 Sensitivity CentroidAlifold(20): 0.574 ProbKnot: 0.572 Positive Predictive Value CentroidAlifold(20): 0.916 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(20): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Fold: 0.562 Sensitivity CentroidAlifold(20): 0.574 Fold: 0.555 Positive Predictive Value CentroidAlifold(20): 0.916 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.719 RNASampler(20): 0.565 Sensitivity CentroidAlifold(20): 0.588 RNASampler(20): 0.413 Positive Predictive Value CentroidAlifold(20): 0.880 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.732 Murlet(20): 0.573 Sensitivity CentroidAlifold(20): 0.591 Murlet(20): 0.441 Positive Predictive Value CentroidAlifold(20): 0.908 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 UNAFold: 0.547 Sensitivity CentroidAlifold(20): 0.574 UNAFold: 0.535 Positive Predictive Value CentroidAlifold(20): 0.916 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.725 PknotsRG: 0.525 Sensitivity CentroidAlifold(20): 0.574 PknotsRG: 0.518 Positive Predictive Value CentroidAlifold(20): 0.916 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAfold: 0.544 Sensitivity CentroidAlifold(20): 0.574 RNAfold: 0.536 Positive Predictive Value CentroidAlifold(20): 0.916 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient Multilign(seed): N/A CentroidAlifold(20): N/A Sensitivity Multilign(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value Multilign(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Afold: 0.556 Sensitivity CentroidAlifold(20): 0.566 Afold: 0.544 Positive Predictive Value CentroidAlifold(20): 0.924 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAsubopt: 0.530 Sensitivity CentroidAlifold(20): 0.574 RNAsubopt: 0.529 Positive Predictive Value CentroidAlifold(20): 0.916 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.732 RNAalifold(seed): 0.492 Sensitivity CentroidAlifold(20): 0.578 RNAalifold(seed): 0.290 Positive Predictive Value CentroidAlifold(20): 0.929 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CMfinder(20): 0.478 Sensitivity CentroidAlifold(20): 0.574 CMfinder(20): 0.309 Positive Predictive Value CentroidAlifold(20): 0.916 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 McQFold: 0.442 Sensitivity CentroidAlifold(20): 0.574 McQFold: 0.424 Positive Predictive Value CentroidAlifold(20): 0.916 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CRWrnafold: 0.464 Sensitivity CentroidAlifold(20): 0.574 CRWrnafold: 0.456 Positive Predictive Value CentroidAlifold(20): 0.916 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.726 RNASLOpt: 0.450 Sensitivity CentroidAlifold(20): 0.577 RNASLOpt: 0.417 Positive Predictive Value CentroidAlifold(20): 0.914 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAshapes: 0.468 Sensitivity CentroidAlifold(20): 0.575 RNAshapes: 0.454 Positive Predictive Value CentroidAlifold(20): 0.916 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.908 Murlet(seed): 0.588 Sensitivity CentroidAlifold(20): 0.871 Murlet(seed): 0.347 Positive Predictive Value CentroidAlifold(20): 0.946 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RSpredict(20): 0.418 Sensitivity CentroidAlifold(20): 0.574 RSpredict(20): 0.285 Positive Predictive Value CentroidAlifold(20): 0.916 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Carnac(20): 0.378 Sensitivity CentroidAlifold(20): 0.574 Carnac(20): 0.166 Positive Predictive Value CentroidAlifold(20): 0.916 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAwolf: 0.367 Sensitivity CentroidAlifold(20): 0.574 RNAwolf: 0.377 Positive Predictive Value CentroidAlifold(20): 0.916 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CMfinder(seed): N/A CentroidAlifold(20): N/A Sensitivity CMfinder(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value CMfinder(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.733 RSpredict(seed): 0.197 Sensitivity CentroidAlifold(20): 0.578 RSpredict(seed): 0.077 Positive Predictive Value CentroidAlifold(20): 0.930 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Vsfold4: 0.352 Sensitivity CentroidAlifold(20): 0.575 Vsfold4: 0.319 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.726 Vsfold5: 0.333 Sensitivity CentroidAlifold(20): 0.575 Vsfold5: 0.308 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.714 NanoFolder: 0.150 Sensitivity CentroidAlifold(20): 0.562 NanoFolder: 0.173 Positive Predictive Value CentroidAlifold(20): 0.908 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.846 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.773 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.927 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.736 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.583 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.930 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CentroidAlifold(20) Matthews Correlation Coefficient HotKnots: N/A CentroidAlifold(20): N/A Sensitivity HotKnots: N/A CentroidAlifold(20): N/A Positive Predictive Value HotKnots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CentroidAlifold(20) Matthews Correlation Coefficient Pknots: N/A CentroidAlifold(20): N/A Sensitivity Pknots: N/A CentroidAlifold(20): N/A Positive Predictive Value Pknots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs CentroidAlifold(20) Matthews Correlation Coefficient Cylofold: N/A CentroidAlifold(20): N/A Sensitivity Cylofold: N/A CentroidAlifold(20): N/A Positive Predictive Value Cylofold: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): N/A MCFold: N/A Sensitivity CentroidAlifold(20): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CentroidAlifold(20) Matthews Correlation Coefficient RDfolder: N/A CentroidAlifold(20): N/A Sensitivity RDfolder: N/A CentroidAlifold(20): N/A Positive Predictive Value RDfolder: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CentroidAlifold(20) Matthews Correlation Coefficient Alterna: N/A CentroidAlifold(20): N/A Sensitivity Alterna: N/A CentroidAlifold(20): N/A Positive Predictive Value Alterna: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Mastr(20): 0.000 Sensitivity CentroidAlifold(20): 0.574 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(20): 0.916 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(seed)	416 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 MXScarna(seed): 0.632 Sensitivity PETfold_pre2.0(seed): 0.654 MXScarna(seed): 0.530 Positive Predictive Value PETfold_pre2.0(seed): 0.834 MXScarna(seed): 0.756 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.802 MXScarna(seed): 0.637 Sensitivity ContextFold: 0.766 MXScarna(seed): 0.535 Positive Predictive Value ContextFold: 0.841 MXScarna(seed): 0.759 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 MXScarna(seed): 0.684 Sensitivity TurboFold(20): 0.718 MXScarna(seed): 0.582 Positive Predictive Value TurboFold(20): 0.828 MXScarna(seed): 0.805 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 MXScarna(seed): 0.637 Sensitivity CentroidAlifold(seed): 0.556 MXScarna(seed): 0.536 Positive Predictive Value CentroidAlifold(seed): 0.906 MXScarna(seed): 0.759 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PETfold_pre2.0(20) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.756 MXScarna(seed): 0.684 Sensitivity PETfold_pre2.0(20): 0.670 MXScarna(seed): 0.581 Positive Predictive Value PETfold_pre2.0(20): 0.855 MXScarna(seed): 0.806 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	198 PPfold(20) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(20): 0.748 MXScarna(seed): 0.687 Sensitivity PPfold(20): 0.647 MXScarna(seed): 0.585 Positive Predictive Value PPfold(20): 0.867 MXScarna(seed): 0.808 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	418 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.686 MXScarna(seed): 0.641 Sensitivity CentroidHomfold‑LAST: 0.539 MXScarna(seed): 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.874 MXScarna(seed): 0.762 Number of pairs reference - predicted secondary structure: 418 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 CentroidAlifold(20) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.732 MXScarna(seed): 0.684 Sensitivity CentroidAlifold(20): 0.577 MXScarna(seed): 0.582 Positive Predictive Value CentroidAlifold(20): 0.929 MXScarna(seed): 0.805 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08		- IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.654 MXScarna(seed): 0.637 Sensitivity IPknot: 0.599 MXScarna(seed): 0.535 Positive Predictive Value IPknot: 0.716 MXScarna(seed): 0.759 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 RNAalifold(20): 0.675 Sensitivity MXScarna(seed): 0.582 RNAalifold(20): 0.541 Positive Predictive Value MXScarna(seed): 0.805 RNAalifold(20): 0.843 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 MXScarna(seed): 0.737 Sensitivity TurboFold(seed): 0.760 MXScarna(seed): 0.692 Positive Predictive Value TurboFold(seed): 0.815 MXScarna(seed): 0.785 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.678 Multilign(20): 0.658 Sensitivity MXScarna(seed): 0.572 Multilign(20): 0.594 Positive Predictive Value MXScarna(seed): 0.806 Multilign(20): 0.731 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 MXScarna(20): 0.680 Sensitivity MXScarna(seed): 0.582 MXScarna(20): 0.599 Positive Predictive Value MXScarna(seed): 0.805 MXScarna(20): 0.772 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.637 CentroidFold: 0.633 Sensitivity MXScarna(seed): 0.535 CentroidFold: 0.580 Positive Predictive Value MXScarna(seed): 0.759 CentroidFold: 0.693 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.637 Contrafold: 0.620 Sensitivity MXScarna(seed): 0.535 Contrafold: 0.605 Positive Predictive Value MXScarna(seed): 0.759 Contrafold: 0.637 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 MXScarna(seed): 0.699 Sensitivity PPfold(seed): 0.652 MXScarna(seed): 0.671 Positive Predictive Value PPfold(seed): 0.787 MXScarna(seed): 0.730 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.637 Sfold: 0.612 Sensitivity MXScarna(seed): 0.535 Sfold: 0.558 Positive Predictive Value MXScarna(seed): 0.759 Sfold: 0.673 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.637 MaxExpect: 0.598 Sensitivity MXScarna(seed): 0.535 MaxExpect: 0.581 Positive Predictive Value MXScarna(seed): 0.759 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.637 ProbKnot: 0.597 Sensitivity MXScarna(seed): 0.535 ProbKnot: 0.585 Positive Predictive Value MXScarna(seed): 0.759 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.813 RNASampler(seed): 0.779 Sensitivity MXScarna(seed): 0.782 RNASampler(seed): 0.659 Positive Predictive Value MXScarna(seed): 0.845 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.637 Fold: 0.573 Sensitivity MXScarna(seed): 0.535 Fold: 0.570 Positive Predictive Value MXScarna(seed): 0.759 Fold: 0.577 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.778 RNASampler(20): 0.578 Sensitivity MXScarna(seed): 0.721 RNASampler(20): 0.384 Positive Predictive Value MXScarna(seed): 0.841 RNASampler(20): 0.871 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.696 Murlet(20): 0.568 Sensitivity MXScarna(seed): 0.600 Murlet(20): 0.427 Positive Predictive Value MXScarna(seed): 0.807 Murlet(20): 0.758 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.637 UNAFold: 0.576 Sensitivity MXScarna(seed): 0.535 UNAFold: 0.566 Positive Predictive Value MXScarna(seed): 0.759 UNAFold: 0.588 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.637 PknotsRG: 0.559 Sensitivity MXScarna(seed): 0.535 PknotsRG: 0.554 Positive Predictive Value MXScarna(seed): 0.759 PknotsRG: 0.566 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.637 RNAfold: 0.569 Sensitivity MXScarna(seed): 0.535 RNAfold: 0.563 Positive Predictive Value MXScarna(seed): 0.759 RNAfold: 0.577 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 MXScarna(seed): 0.729 Sensitivity Multilign(seed): 0.752 MXScarna(seed): 0.703 Positive Predictive Value Multilign(seed): 0.767 MXScarna(seed): 0.756 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.631 Afold: 0.558 Sensitivity MXScarna(seed): 0.526 Afold: 0.551 Positive Predictive Value MXScarna(seed): 0.757 Afold: 0.567 Number of pairs reference - predicted secondary structure: 356 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.641 RNAsubopt: 0.559 Sensitivity MXScarna(seed): 0.541 RNAsubopt: 0.560 Positive Predictive Value MXScarna(seed): 0.762 RNAsubopt: 0.560 Number of pairs reference - predicted secondary structure: 418 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.637 RNAalifold(seed): 0.541 Sensitivity MXScarna(seed): 0.536 RNAalifold(seed): 0.344 Positive Predictive Value MXScarna(seed): 0.759 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 CMfinder(20): 0.497 Sensitivity MXScarna(seed): 0.582 CMfinder(20): 0.327 Positive Predictive Value MXScarna(seed): 0.805 CMfinder(20): 0.758 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.637 McQFold: 0.466 Sensitivity MXScarna(seed): 0.535 McQFold: 0.450 Positive Predictive Value MXScarna(seed): 0.759 McQFold: 0.485 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.637 CRWrnafold: 0.482 Sensitivity MXScarna(seed): 0.535 CRWrnafold: 0.478 Positive Predictive Value MXScarna(seed): 0.759 CRWrnafold: 0.488 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.662 RNASLOpt: 0.465 Sensitivity MXScarna(seed): 0.567 RNASLOpt: 0.434 Positive Predictive Value MXScarna(seed): 0.775 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 370 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.648 RNAshapes: 0.506 Sensitivity MXScarna(seed): 0.549 RNAshapes: 0.495 Positive Predictive Value MXScarna(seed): 0.766 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.742 Murlet(seed): 0.569 Sensitivity MXScarna(seed): 0.721 Murlet(seed): 0.383 Positive Predictive Value MXScarna(seed): 0.765 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 RSpredict(20): 0.402 Sensitivity MXScarna(seed): 0.582 RSpredict(20): 0.258 Positive Predictive Value MXScarna(seed): 0.805 RSpredict(20): 0.629 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 Carnac(20): 0.360 Sensitivity MXScarna(seed): 0.582 Carnac(20): 0.147 Positive Predictive Value MXScarna(seed): 0.805 Carnac(20): 0.880 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.637 RNAwolf: 0.379 Sensitivity MXScarna(seed): 0.535 RNAwolf: 0.389 Positive Predictive Value MXScarna(seed): 0.759 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(seed): 0.696 CMfinder(seed): 0.454 Sensitivity MXScarna(seed): 0.605 CMfinder(seed): 0.271 Positive Predictive Value MXScarna(seed): 0.802 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.637 RSpredict(seed): 0.215 Sensitivity MXScarna(seed): 0.536 RSpredict(seed): 0.090 Positive Predictive Value MXScarna(seed): 0.759 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 428 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.649 Vsfold4: 0.337 Sensitivity MXScarna(seed): 0.550 Vsfold4: 0.305 Positive Predictive Value MXScarna(seed): 0.766 Vsfold4: 0.373 Number of pairs reference - predicted secondary structure: 403 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.649 Vsfold5: 0.316 Sensitivity MXScarna(seed): 0.550 Vsfold5: 0.295 Positive Predictive Value MXScarna(seed): 0.766 Vsfold5: 0.341 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.646 NanoFolder: 0.176 Sensitivity MXScarna(seed): 0.540 NanoFolder: 0.203 Positive Predictive Value MXScarna(seed): 0.773 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.643 Carnac(seed): 0.150 Sensitivity MXScarna(seed): 0.553 Carnac(seed): 0.028 Positive Predictive Value MXScarna(seed): 0.749 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.641 Mastr(seed): 0.073 Sensitivity MXScarna(seed): 0.541 Mastr(seed): 0.006 Positive Predictive Value MXScarna(seed): 0.760 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 404 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: 0.640 MXScarna(seed): 0.203 Sensitivity HotKnots: 0.615 MXScarna(seed): 0.179 Positive Predictive Value HotKnots: 0.667 MXScarna(seed): 0.233 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: N/A MXScarna(seed): N/A Sensitivity Pknots: N/A MXScarna(seed): N/A Positive Predictive Value Pknots: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: N/A MXScarna(seed): N/A Sensitivity Cylofold: N/A MXScarna(seed): N/A Positive Predictive Value Cylofold: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): N/A MCFold: N/A Sensitivity MXScarna(seed): N/A MCFold: N/A Positive Predictive Value MXScarna(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: N/A MXScarna(seed): N/A Sensitivity RDfolder: N/A MXScarna(seed): N/A Positive Predictive Value RDfolder: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs MXScarna(seed) Matthews Correlation Coefficient Alterna: N/A MXScarna(seed): N/A Sensitivity Alterna: N/A MXScarna(seed): N/A Positive Predictive Value Alterna: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 Mastr(20): 0.000 Sensitivity MXScarna(seed): 0.582 Mastr(20): 0.000 Positive Predictive Value MXScarna(seed): 0.805 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08
IPknot	643 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 IPknot: 0.619 Sensitivity PETfold_pre2.0(seed): 0.612 IPknot: 0.566 Positive Predictive Value PETfold_pre2.0(seed): 0.803 IPknot: 0.678 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.720 IPknot: 0.612 Sensitivity ContextFold: 0.687 IPknot: 0.561 Positive Predictive Value ContextFold: 0.756 IPknot: 0.667 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.752 IPknot: 0.655 Sensitivity TurboFold(20): 0.701 IPknot: 0.586 Positive Predictive Value TurboFold(20): 0.809 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 IPknot: 0.654 Sensitivity CentroidAlifold(seed): 0.556 IPknot: 0.599 Positive Predictive Value CentroidAlifold(seed): 0.906 IPknot: 0.715 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 IPknot: 0.654 Sensitivity PETfold_pre2.0(20): 0.654 IPknot: 0.585 Positive Predictive Value PETfold_pre2.0(20): 0.836 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.733 IPknot: 0.656 Sensitivity PPfold(20): 0.629 IPknot: 0.587 Positive Predictive Value PPfold(20): 0.855 IPknot: 0.735 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 IPknot: 0.619 Sensitivity CentroidHomfold‑LAST: 0.491 IPknot: 0.569 Positive Predictive Value CentroidHomfold‑LAST: 0.862 IPknot: 0.675 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.725 IPknot: 0.655 Sensitivity CentroidAlifold(20): 0.574 IPknot: 0.586 Positive Predictive Value CentroidAlifold(20): 0.916 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 IPknot vs MXScarna(seed) Matthews Correlation Coefficient IPknot: 0.654 MXScarna(seed): 0.637 Sensitivity IPknot: 0.599 MXScarna(seed): 0.535 Positive Predictive Value IPknot: 0.716 MXScarna(seed): 0.759 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.668 IPknot: 0.655 Sensitivity RNAalifold(20): 0.540 IPknot: 0.586 Positive Predictive Value RNAalifold(20): 0.827 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.787 IPknot: 0.698 Sensitivity TurboFold(seed): 0.760 IPknot: 0.678 Positive Predictive Value TurboFold(seed): 0.815 IPknot: 0.719 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.657 Multilign(20): 0.651 Sensitivity IPknot: 0.588 Multilign(20): 0.590 Positive Predictive Value IPknot: 0.735 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 5.62644058675e-08	= IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.655 MXScarna(20): 0.654 Sensitivity IPknot: 0.586 MXScarna(20): 0.584 Positive Predictive Value IPknot: 0.732 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 0.0274981398492	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.612 CentroidFold: 0.583 Sensitivity IPknot: 0.561 CentroidFold: 0.533 Positive Predictive Value IPknot: 0.667 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.612 Contrafold: 0.567 Sensitivity IPknot: 0.561 Contrafold: 0.558 Positive Predictive Value IPknot: 0.667 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs IPknot Matthews Correlation Coefficient PPfold(seed): 0.716 IPknot: 0.688 Sensitivity PPfold(seed): 0.652 IPknot: 0.673 Positive Predictive Value PPfold(seed): 0.787 IPknot: 0.705 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 7.95107997107e-08	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.612 Sfold: 0.538 Sensitivity IPknot: 0.561 Sfold: 0.491 Positive Predictive Value IPknot: 0.667 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.612 MaxExpect: 0.536 Sensitivity IPknot: 0.561 MaxExpect: 0.527 Positive Predictive Value IPknot: 0.667 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.612 ProbKnot: 0.534 Sensitivity IPknot: 0.561 ProbKnot: 0.534 Positive Predictive Value IPknot: 0.667 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): 0.779 IPknot: 0.757 Sensitivity RNASampler(seed): 0.659 IPknot: 0.738 Positive Predictive Value RNASampler(seed): 0.921 IPknot: 0.778 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.51046461328e-06	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.612 Fold: 0.511 Sensitivity IPknot: 0.561 Fold: 0.517 Positive Predictive Value IPknot: 0.667 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.631 RNASampler(20): 0.565 Sensitivity IPknot: 0.577 RNASampler(20): 0.413 Positive Predictive Value IPknot: 0.690 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.649 Murlet(20): 0.573 Sensitivity IPknot: 0.580 Murlet(20): 0.441 Positive Predictive Value IPknot: 0.728 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.612 UNAFold: 0.501 Sensitivity IPknot: 0.561 UNAFold: 0.501 Positive Predictive Value IPknot: 0.667 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.612 PknotsRG: 0.499 Sensitivity IPknot: 0.561 PknotsRG: 0.504 Positive Predictive Value IPknot: 0.667 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.612 RNAfold: 0.499 Sensitivity IPknot: 0.561 RNAfold: 0.504 Positive Predictive Value IPknot: 0.667 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs IPknot Matthews Correlation Coefficient Multilign(seed): 0.734 IPknot: 0.660 Sensitivity Multilign(seed): 0.733 IPknot: 0.664 Positive Predictive Value Multilign(seed): 0.737 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.34341160367e-09	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.628 Afold: 0.516 Sensitivity IPknot: 0.577 Afold: 0.517 Positive Predictive Value IPknot: 0.684 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.619 RNAsubopt: 0.501 Sensitivity IPknot: 0.569 RNAsubopt: 0.510 Positive Predictive Value IPknot: 0.675 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.654 RNAalifold(seed): 0.541 Sensitivity IPknot: 0.599 RNAalifold(seed): 0.344 Positive Predictive Value IPknot: 0.715 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.655 CMfinder(20): 0.478 Sensitivity IPknot: 0.586 CMfinder(20): 0.309 Positive Predictive Value IPknot: 0.732 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.612 McQFold: 0.443 Sensitivity IPknot: 0.561 McQFold: 0.435 Positive Predictive Value IPknot: 0.667 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.612 CRWrnafold: 0.432 Sensitivity IPknot: 0.561 CRWrnafold: 0.438 Positive Predictive Value IPknot: 0.667 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.621 RNASLOpt: 0.442 Sensitivity IPknot: 0.571 RNASLOpt: 0.419 Positive Predictive Value IPknot: 0.678 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.620 RNAshapes: 0.438 Sensitivity IPknot: 0.569 RNAshapes: 0.434 Positive Predictive Value IPknot: 0.678 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.718 Murlet(seed): 0.569 Sensitivity IPknot: 0.699 Murlet(seed): 0.383 Positive Predictive Value IPknot: 0.738 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.655 RSpredict(20): 0.418 Sensitivity IPknot: 0.586 RSpredict(20): 0.285 Positive Predictive Value IPknot: 0.732 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.655 Carnac(20): 0.378 Sensitivity IPknot: 0.586 Carnac(20): 0.166 Positive Predictive Value IPknot: 0.732 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.612 RNAwolf: 0.339 Sensitivity IPknot: 0.561 RNAwolf: 0.355 Positive Predictive Value IPknot: 0.667 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.725 CMfinder(seed): 0.454 Sensitivity IPknot: 0.696 CMfinder(seed): 0.271 Positive Predictive Value IPknot: 0.756 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.654 RSpredict(seed): 0.214 Sensitivity IPknot: 0.599 RSpredict(seed): 0.089 Positive Predictive Value IPknot: 0.715 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.619 Vsfold4: 0.306 Sensitivity IPknot: 0.568 Vsfold4: 0.282 Positive Predictive Value IPknot: 0.675 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.619 Vsfold5: 0.300 Sensitivity IPknot: 0.568 Vsfold5: 0.286 Positive Predictive Value IPknot: 0.676 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.659 NanoFolder: 0.166 Sensitivity IPknot: 0.600 NanoFolder: 0.197 Positive Predictive Value IPknot: 0.725 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.625 Carnac(seed): 0.150 Sensitivity IPknot: 0.597 Carnac(seed): 0.028 Positive Predictive Value IPknot: 0.655 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.653 Mastr(seed): 0.073 Sensitivity IPknot: 0.600 Mastr(seed): 0.006 Positive Predictive Value IPknot: 0.711 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs IPknot Matthews Correlation Coefficient HotKnots: 0.640 IPknot: 0.597 Sensitivity HotKnots: 0.615 IPknot: 0.590 Positive Predictive Value HotKnots: 0.667 IPknot: 0.605 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs IPknot Matthews Correlation Coefficient Pknots: N/A IPknot: N/A Sensitivity Pknots: N/A IPknot: N/A Positive Predictive Value Pknots: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.648 Cylofold: 0.271 Sensitivity IPknot: 0.584 Cylofold: 0.241 Positive Predictive Value IPknot: 0.721 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MCFold vs IPknot Matthews Correlation Coefficient MCFold: N/A IPknot: N/A Sensitivity MCFold: N/A IPknot: N/A Positive Predictive Value MCFold: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs IPknot Matthews Correlation Coefficient RDfolder: N/A IPknot: N/A Sensitivity RDfolder: N/A IPknot: N/A Positive Predictive Value RDfolder: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs IPknot Matthews Correlation Coefficient Alterna: N/A IPknot: N/A Sensitivity Alterna: N/A IPknot: N/A Positive Predictive Value Alterna: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.655 Mastr(20): 0.000 Sensitivity IPknot: 0.586 Mastr(20): 0.000 Positive Predictive Value IPknot: 0.732 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(20)	230 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 RNAalifold(20): 0.673 Sensitivity PETfold_pre2.0(seed): 0.693 RNAalifold(20): 0.550 Positive Predictive Value PETfold_pre2.0(seed): 0.854 RNAalifold(20): 0.825 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.843 RNAalifold(20): 0.668 Sensitivity ContextFold: 0.799 RNAalifold(20): 0.540 Positive Predictive Value ContextFold: 0.891 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.752 RNAalifold(20): 0.668 Sensitivity TurboFold(20): 0.701 RNAalifold(20): 0.540 Positive Predictive Value TurboFold(20): 0.809 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 RNAalifold(20): 0.676 Sensitivity CentroidAlifold(seed): 0.564 RNAalifold(20): 0.542 Positive Predictive Value CentroidAlifold(seed): 0.953 RNAalifold(20): 0.843 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAalifold(20): 0.669 Sensitivity PETfold_pre2.0(20): 0.654 RNAalifold(20): 0.542 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.733 RNAalifold(20): 0.669 Sensitivity PPfold(20): 0.629 RNAalifold(20): 0.541 Positive Predictive Value PPfold(20): 0.855 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 RNAalifold(20): 0.668 Sensitivity CentroidHomfold‑LAST: 0.561 RNAalifold(20): 0.540 Positive Predictive Value CentroidHomfold‑LAST: 0.898 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAalifold(20): 0.668 Sensitivity CentroidAlifold(20): 0.574 RNAalifold(20): 0.540 Positive Predictive Value CentroidAlifold(20): 0.916 RNAalifold(20): 0.827 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 RNAalifold(20): 0.675 Sensitivity MXScarna(seed): 0.582 RNAalifold(20): 0.541 Positive Predictive Value MXScarna(seed): 0.805 RNAalifold(20): 0.843 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.668 IPknot: 0.655 Sensitivity RNAalifold(20): 0.540 IPknot: 0.586 Positive Predictive Value RNAalifold(20): 0.827 IPknot: 0.732 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08		? TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 RNAalifold(20): 0.483 Sensitivity TurboFold(seed): 0.739 RNAalifold(20): 0.318 Positive Predictive Value TurboFold(seed): 0.774 RNAalifold(20): 0.737 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.664 Multilign(20): 0.651 Sensitivity RNAalifold(20): 0.534 Multilign(20): 0.590 Positive Predictive Value RNAalifold(20): 0.827 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 MXScarna(20): 0.654 Sensitivity RNAalifold(20): 0.540 MXScarna(20): 0.584 Positive Predictive Value RNAalifold(20): 0.827 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.668 CentroidFold: 0.621 Sensitivity RNAalifold(20): 0.540 CentroidFold: 0.557 Positive Predictive Value RNAalifold(20): 0.827 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.668 Contrafold: 0.606 Sensitivity RNAalifold(20): 0.540 Contrafold: 0.585 Positive Predictive Value RNAalifold(20): 0.827 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.886 PPfold(seed): 0.847 Sensitivity RNAalifold(20): 0.832 PPfold(seed): 0.782 Positive Predictive Value RNAalifold(20): 0.944 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.668 Sfold: 0.584 Sensitivity RNAalifold(20): 0.540 Sfold: 0.522 Positive Predictive Value RNAalifold(20): 0.827 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.668 MaxExpect: 0.592 Sensitivity RNAalifold(20): 0.540 MaxExpect: 0.569 Positive Predictive Value RNAalifold(20): 0.827 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.668 ProbKnot: 0.590 Sensitivity RNAalifold(20): 0.540 ProbKnot: 0.572 Positive Predictive Value RNAalifold(20): 0.827 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(20): N/A Sensitivity RNASampler(seed): N/A RNAalifold(20): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.668 Fold: 0.562 Sensitivity RNAalifold(20): 0.540 Fold: 0.555 Positive Predictive Value RNAalifold(20): 0.827 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.661 RNASampler(20): 0.565 Sensitivity RNAalifold(20): 0.546 RNASampler(20): 0.413 Positive Predictive Value RNAalifold(20): 0.802 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.679 Murlet(20): 0.573 Sensitivity RNAalifold(20): 0.560 Murlet(20): 0.441 Positive Predictive Value RNAalifold(20): 0.823 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.668 UNAFold: 0.547 Sensitivity RNAalifold(20): 0.540 UNAFold: 0.535 Positive Predictive Value RNAalifold(20): 0.827 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.668 PknotsRG: 0.525 Sensitivity RNAalifold(20): 0.540 PknotsRG: 0.518 Positive Predictive Value RNAalifold(20): 0.827 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAfold: 0.544 Sensitivity RNAalifold(20): 0.540 RNAfold: 0.536 Positive Predictive Value RNAalifold(20): 0.827 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Multilign(seed): N/A Sensitivity RNAalifold(20): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.665 Afold: 0.556 Sensitivity RNAalifold(20): 0.531 Afold: 0.544 Positive Predictive Value RNAalifold(20): 0.836 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAsubopt: 0.530 Sensitivity RNAalifold(20): 0.540 RNAsubopt: 0.529 Positive Predictive Value RNAalifold(20): 0.827 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.676 RNAalifold(seed): 0.492 Sensitivity RNAalifold(20): 0.542 RNAalifold(seed): 0.290 Positive Predictive Value RNAalifold(20): 0.843 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 CMfinder(20): 0.478 Sensitivity RNAalifold(20): 0.540 CMfinder(20): 0.309 Positive Predictive Value RNAalifold(20): 0.827 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.668 McQFold: 0.442 Sensitivity RNAalifold(20): 0.540 McQFold: 0.424 Positive Predictive Value RNAalifold(20): 0.827 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.668 CRWrnafold: 0.464 Sensitivity RNAalifold(20): 0.540 CRWrnafold: 0.456 Positive Predictive Value RNAalifold(20): 0.827 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.670 RNASLOpt: 0.450 Sensitivity RNAalifold(20): 0.544 RNASLOpt: 0.417 Positive Predictive Value RNAalifold(20): 0.827 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.670 RNAshapes: 0.468 Sensitivity RNAalifold(20): 0.542 RNAshapes: 0.454 Positive Predictive Value RNAalifold(20): 0.830 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.886 Murlet(seed): 0.588 Sensitivity RNAalifold(20): 0.832 Murlet(seed): 0.347 Positive Predictive Value RNAalifold(20): 0.944 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 RSpredict(20): 0.418 Sensitivity RNAalifold(20): 0.540 RSpredict(20): 0.285 Positive Predictive Value RNAalifold(20): 0.827 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 Carnac(20): 0.378 Sensitivity RNAalifold(20): 0.540 Carnac(20): 0.166 Positive Predictive Value RNAalifold(20): 0.827 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAwolf: 0.367 Sensitivity RNAalifold(20): 0.540 RNAwolf: 0.377 Positive Predictive Value RNAalifold(20): 0.827 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.676 RSpredict(seed): 0.197 Sensitivity RNAalifold(20): 0.543 RSpredict(seed): 0.077 Positive Predictive Value RNAalifold(20): 0.844 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.669 Vsfold4: 0.352 Sensitivity RNAalifold(20): 0.542 Vsfold4: 0.319 Positive Predictive Value RNAalifold(20): 0.828 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.670 Vsfold5: 0.333 Sensitivity RNAalifold(20): 0.542 Vsfold5: 0.308 Positive Predictive Value RNAalifold(20): 0.828 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.662 NanoFolder: 0.150 Sensitivity RNAalifold(20): 0.538 NanoFolder: 0.173 Positive Predictive Value RNAalifold(20): 0.817 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.737 Carnac(seed): 0.000 Sensitivity RNAalifold(20): 0.627 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.868 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.677 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.545 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs RNAalifold(20) Matthews Correlation Coefficient HotKnots: N/A RNAalifold(20): N/A Sensitivity HotKnots: N/A RNAalifold(20): N/A Positive Predictive Value HotKnots: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): N/A Pknots: N/A Sensitivity RNAalifold(20): N/A Pknots: N/A Positive Predictive Value RNAalifold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs RNAalifold(20) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(20): N/A Sensitivity Cylofold: N/A RNAalifold(20): N/A Positive Predictive Value Cylofold: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): N/A MCFold: N/A Sensitivity RNAalifold(20): N/A MCFold: N/A Positive Predictive Value RNAalifold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAalifold(20) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(20): N/A Sensitivity RDfolder: N/A RNAalifold(20): N/A Positive Predictive Value RDfolder: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): N/A Alterna: N/A Sensitivity RNAalifold(20): N/A Alterna: N/A Positive Predictive Value RNAalifold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 Mastr(20): 0.000 Sensitivity RNAalifold(20): 0.540 Mastr(20): 0.000 Positive Predictive Value RNAalifold(20): 0.827 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(seed)	17 TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.789 PETfold_pre2.0(seed): 0.764 Sensitivity TurboFold(seed): 0.762 PETfold_pre2.0(seed): 0.719 Positive Predictive Value TurboFold(seed): 0.818 PETfold_pre2.0(seed): 0.813 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.73923511064e-08	18 TurboFold(seed) vs ContextFold Matthews Correlation Coefficient TurboFold(seed): 0.787 ContextFold: 0.723 Sensitivity TurboFold(seed): 0.760 ContextFold: 0.702 Positive Predictive Value TurboFold(seed): 0.815 ContextFold: 0.747 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.45805449719e-08	1 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.767 TurboFold(seed): 0.755 Sensitivity TurboFold(20): 0.750 TurboFold(seed): 0.739 Positive Predictive Value TurboFold(20): 0.786 TurboFold(seed): 0.774 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	18 TurboFold(seed) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 CentroidAlifold(seed): 0.751 Sensitivity TurboFold(seed): 0.760 CentroidAlifold(seed): 0.665 Positive Predictive Value TurboFold(seed): 0.815 CentroidAlifold(seed): 0.849 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.18846395401e-08	1 TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 PETfold_pre2.0(20): 0.341 Sensitivity TurboFold(seed): 0.739 PETfold_pre2.0(20): 0.136 Positive Predictive Value TurboFold(seed): 0.774 PETfold_pre2.0(20): 0.857 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 PPfold(20): 0.293 Sensitivity TurboFold(seed): 0.739 PPfold(20): 0.125 Positive Predictive Value TurboFold(seed): 0.774 PPfold(20): 0.688 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	17 TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.776 CentroidHomfold‑LAST: 0.747 Sensitivity TurboFold(seed): 0.753 CentroidHomfold‑LAST: 0.652 Positive Predictive Value TurboFold(seed): 0.802 CentroidHomfold‑LAST: 0.858 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.39090039918e-08	1 TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 CentroidAlifold(20): 0.642 Sensitivity TurboFold(seed): 0.739 CentroidAlifold(20): 0.455 Positive Predictive Value TurboFold(seed): 0.774 CentroidAlifold(20): 0.909 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	18 TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 MXScarna(seed): 0.737 Sensitivity TurboFold(seed): 0.760 MXScarna(seed): 0.692 Positive Predictive Value TurboFold(seed): 0.815 MXScarna(seed): 0.785 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.30280588002e-08	18 TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.787 IPknot: 0.698 Sensitivity TurboFold(seed): 0.760 IPknot: 0.678 Positive Predictive Value TurboFold(seed): 0.815 IPknot: 0.719 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	1 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 RNAalifold(20): 0.483 Sensitivity TurboFold(seed): 0.739 RNAalifold(20): 0.318 Positive Predictive Value TurboFold(seed): 0.774 RNAalifold(20): 0.737 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0		? TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 Multilign(20): 0.653 Sensitivity TurboFold(seed): 0.739 Multilign(20): 0.477 Positive Predictive Value TurboFold(seed): 0.774 Multilign(20): 0.894 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 MXScarna(20): 0.731 Sensitivity TurboFold(seed): 0.739 MXScarna(20): 0.727 Positive Predictive Value TurboFold(seed): 0.774 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.787 CentroidFold: 0.684 Sensitivity TurboFold(seed): 0.760 CentroidFold: 0.654 Positive Predictive Value TurboFold(seed): 0.815 CentroidFold: 0.717 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.787 Contrafold: 0.678 Sensitivity TurboFold(seed): 0.760 Contrafold: 0.684 Positive Predictive Value TurboFold(seed): 0.815 Contrafold: 0.672 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.793 PPfold(seed): 0.740 Sensitivity TurboFold(seed): 0.766 PPfold(seed): 0.659 Positive Predictive Value TurboFold(seed): 0.821 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	+ TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.787 Sfold: 0.671 Sensitivity TurboFold(seed): 0.760 Sfold: 0.644 Positive Predictive Value TurboFold(seed): 0.815 Sfold: 0.701 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.787 MaxExpect: 0.641 Sensitivity TurboFold(seed): 0.760 MaxExpect: 0.652 Positive Predictive Value TurboFold(seed): 0.815 MaxExpect: 0.631 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	+ TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.787 ProbKnot: 0.651 Sensitivity TurboFold(seed): 0.760 ProbKnot: 0.668 Positive Predictive Value TurboFold(seed): 0.815 ProbKnot: 0.635 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.66062906821e-08	? TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.900 RNASampler(seed): 0.811 Sensitivity TurboFold(seed): 0.862 RNASampler(seed): 0.687 Positive Predictive Value TurboFold(seed): 0.939 RNASampler(seed): 0.959 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.787 Fold: 0.643 Sensitivity TurboFold(seed): 0.760 Fold: 0.658 Positive Predictive Value TurboFold(seed): 0.815 Fold: 0.630 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.41358941668e-08	? TurboFold(seed) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 RNASampler(20): 0.282 Sensitivity TurboFold(seed): 0.739 RNASampler(20): 0.080 Positive Predictive Value TurboFold(seed): 0.774 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(20): N/A Sensitivity TurboFold(seed): N/A Murlet(20): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.787 UNAFold: 0.651 Sensitivity TurboFold(seed): 0.760 UNAFold: 0.659 Positive Predictive Value TurboFold(seed): 0.815 UNAFold: 0.644 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	+ TurboFold(seed) vs PknotsRG Matthews Correlation Coefficient TurboFold(seed): 0.787 PknotsRG: 0.605 Sensitivity TurboFold(seed): 0.760 PknotsRG: 0.616 Positive Predictive Value TurboFold(seed): 0.815 PknotsRG: 0.594 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	+ TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.787 RNAfold: 0.671 Sensitivity TurboFold(seed): 0.760 RNAfold: 0.682 Positive Predictive Value TurboFold(seed): 0.815 RNAfold: 0.662 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.64318034126e-08	? TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.782 Multilign(seed): 0.759 Sensitivity TurboFold(seed): 0.767 Multilign(seed): 0.752 Positive Predictive Value TurboFold(seed): 0.799 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.799 Afold: 0.632 Sensitivity TurboFold(seed): 0.774 Afold: 0.646 Positive Predictive Value TurboFold(seed): 0.826 Afold: 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.776 RNAsubopt: 0.590 Sensitivity TurboFold(seed): 0.753 RNAsubopt: 0.604 Positive Predictive Value TurboFold(seed): 0.802 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	+ TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 RNAalifold(seed): 0.726 Sensitivity TurboFold(seed): 0.760 RNAalifold(seed): 0.595 Positive Predictive Value TurboFold(seed): 0.815 RNAalifold(seed): 0.888 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	? TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 CMfinder(20): 0.414 Sensitivity TurboFold(seed): 0.739 CMfinder(20): 0.261 Positive Predictive Value TurboFold(seed): 0.774 CMfinder(20): 0.657 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.787 McQFold: 0.461 Sensitivity TurboFold(seed): 0.760 McQFold: 0.452 Positive Predictive Value TurboFold(seed): 0.815 McQFold: 0.471 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	+ TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.787 CRWrnafold: 0.508 Sensitivity TurboFold(seed): 0.760 CRWrnafold: 0.517 Positive Predictive Value TurboFold(seed): 0.815 CRWrnafold: 0.500 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	+ TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.776 RNASLOpt: 0.463 Sensitivity TurboFold(seed): 0.753 RNASLOpt: 0.454 Positive Predictive Value TurboFold(seed): 0.802 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.772 RNAshapes: 0.593 Sensitivity TurboFold(seed): 0.750 RNAshapes: 0.603 Positive Predictive Value TurboFold(seed): 0.796 RNAshapes: 0.585 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.58287649515e-08	+ TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.794 Murlet(seed): 0.703 Sensitivity TurboFold(seed): 0.773 Murlet(seed): 0.540 Positive Predictive Value TurboFold(seed): 0.815 Murlet(seed): 0.916 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.10032755566e-08	? TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 RSpredict(20): 0.617 Sensitivity TurboFold(seed): 0.739 RSpredict(20): 0.523 Positive Predictive Value TurboFold(seed): 0.774 RSpredict(20): 0.730 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 Carnac(20): 0.303 Sensitivity TurboFold(seed): 0.739 Carnac(20): 0.102 Positive Predictive Value TurboFold(seed): 0.774 Carnac(20): 0.900 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.787 RNAwolf: 0.369 Sensitivity TurboFold(seed): 0.760 RNAwolf: 0.385 Positive Predictive Value TurboFold(seed): 0.815 RNAwolf: 0.355 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	? TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): 0.900 CMfinder(seed): 0.558 Sensitivity TurboFold(seed): 0.862 CMfinder(seed): 0.422 Positive Predictive Value TurboFold(seed): 0.939 CMfinder(seed): 0.740 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 RSpredict(seed): 0.510 Sensitivity TurboFold(seed): 0.760 RSpredict(seed): 0.389 Positive Predictive Value TurboFold(seed): 0.815 RSpredict(seed): 0.670 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.84041289224e-08	+ TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.776 Vsfold4: 0.171 Sensitivity TurboFold(seed): 0.753 Vsfold4: 0.159 Positive Predictive Value TurboFold(seed): 0.802 Vsfold4: 0.188 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	+ TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.776 Vsfold5: 0.241 Sensitivity TurboFold(seed): 0.753 Vsfold5: 0.240 Positive Predictive Value TurboFold(seed): 0.802 Vsfold5: 0.245 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	? TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.834 NanoFolder: 0.088 Sensitivity TurboFold(seed): 0.822 NanoFolder: 0.116 Positive Predictive Value TurboFold(seed): 0.848 NanoFolder: 0.070 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 Carnac(seed): 0.435 Sensitivity TurboFold(seed): 0.760 Carnac(seed): 0.217 Positive Predictive Value TurboFold(seed): 0.815 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	+ TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 Mastr(seed): 0.393 Sensitivity TurboFold(seed): 0.760 Mastr(seed): 0.173 Positive Predictive Value TurboFold(seed): 0.815 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	? TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): N/A HotKnots: N/A Sensitivity TurboFold(seed): N/A HotKnots: N/A Positive Predictive Value TurboFold(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): N/A Pknots: N/A Sensitivity TurboFold(seed): N/A Pknots: N/A Positive Predictive Value TurboFold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): N/A Cylofold: N/A Sensitivity TurboFold(seed): N/A Cylofold: N/A Positive Predictive Value TurboFold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): N/A MCFold: N/A Sensitivity TurboFold(seed): N/A MCFold: N/A Positive Predictive Value TurboFold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): N/A RDfolder: N/A Sensitivity TurboFold(seed): N/A RDfolder: N/A Positive Predictive Value TurboFold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): N/A Alterna: N/A Sensitivity TurboFold(seed): N/A Alterna: N/A Positive Predictive Value TurboFold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 Mastr(20): 0.000 Sensitivity TurboFold(seed): 0.739 Mastr(20): 0.000 Positive Predictive Value TurboFold(seed): 0.774 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0
Multilign(20)	209 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.765 Multilign(20): 0.655 Sensitivity PETfold_pre2.0(seed): 0.687 Multilign(20): 0.596 Positive Predictive Value PETfold_pre2.0(seed): 0.852 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	223 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.846 Multilign(20): 0.651 Sensitivity ContextFold: 0.803 Multilign(20): 0.590 Positive Predictive Value ContextFold: 0.893 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	223 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.749 Multilign(20): 0.651 Sensitivity TurboFold(20): 0.697 Multilign(20): 0.590 Positive Predictive Value TurboFold(20): 0.806 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	184 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.726 Multilign(20): 0.658 Sensitivity CentroidAlifold(seed): 0.553 Multilign(20): 0.593 Positive Predictive Value CentroidAlifold(seed): 0.955 Multilign(20): 0.731 Number of pairs reference - predicted secondary structure: 184 Wilcoxon single-rank test P-value: 3.56938820447e-08	220 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.736 Multilign(20): 0.652 Sensitivity PETfold_pre2.0(20): 0.649 Multilign(20): 0.590 Positive Predictive Value PETfold_pre2.0(20): 0.835 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 220 Wilcoxon single-rank test P-value: 3.56938820447e-08	217 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.732 Multilign(20): 0.652 Sensitivity PPfold(20): 0.627 Multilign(20): 0.590 Positive Predictive Value PPfold(20): 0.855 Multilign(20): 0.722 Number of pairs reference - predicted secondary structure: 217 Wilcoxon single-rank test P-value: 3.56938820447e-08	223 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.704 Multilign(20): 0.651 Sensitivity CentroidHomfold‑LAST: 0.553 Multilign(20): 0.590 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	223 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.721 Multilign(20): 0.651 Sensitivity CentroidAlifold(20): 0.567 Multilign(20): 0.590 Positive Predictive Value CentroidAlifold(20): 0.916 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.678 Multilign(20): 0.658 Sensitivity MXScarna(seed): 0.572 Multilign(20): 0.594 Positive Predictive Value MXScarna(seed): 0.806 Multilign(20): 0.731 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	223 IPknot vs Multilign(20) Matthews Correlation Coefficient IPknot: 0.657 Multilign(20): 0.651 Sensitivity IPknot: 0.588 Multilign(20): 0.590 Positive Predictive Value IPknot: 0.735 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 5.62644058675e-08	223 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.664 Multilign(20): 0.651 Sensitivity RNAalifold(20): 0.534 Multilign(20): 0.590 Positive Predictive Value RNAalifold(20): 0.827 Multilign(20): 0.721 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 Multilign(20): 0.653 Sensitivity TurboFold(seed): 0.739 Multilign(20): 0.477 Positive Predictive Value TurboFold(seed): 0.774 Multilign(20): 0.894 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0		+ Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.651 MXScarna(20): 0.645 Sensitivity Multilign(20): 0.590 MXScarna(20): 0.573 Positive Predictive Value Multilign(20): 0.721 MXScarna(20): 0.729 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.651 CentroidFold: 0.625 Sensitivity Multilign(20): 0.590 CentroidFold: 0.560 Positive Predictive Value Multilign(20): 0.721 CentroidFold: 0.699 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.651 Contrafold: 0.610 Sensitivity Multilign(20): 0.590 Contrafold: 0.588 Positive Predictive Value Multilign(20): 0.721 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(seed) vs Multilign(20) Matthews Correlation Coefficient PPfold(seed): N/A Multilign(20): N/A Sensitivity PPfold(seed): N/A Multilign(20): N/A Positive Predictive Value PPfold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.651 Sfold: 0.584 Sensitivity Multilign(20): 0.590 Sfold: 0.521 Positive Predictive Value Multilign(20): 0.721 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.651 MaxExpect: 0.594 Sensitivity Multilign(20): 0.590 MaxExpect: 0.571 Positive Predictive Value Multilign(20): 0.721 MaxExpect: 0.619 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.651 ProbKnot: 0.593 Sensitivity Multilign(20): 0.590 ProbKnot: 0.574 Positive Predictive Value Multilign(20): 0.721 ProbKnot: 0.613 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(20): N/A Sensitivity RNASampler(seed): N/A Multilign(20): N/A Positive Predictive Value RNASampler(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.651 Fold: 0.564 Sensitivity Multilign(20): 0.590 Fold: 0.557 Positive Predictive Value Multilign(20): 0.721 Fold: 0.573 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.619 RNASampler(20): 0.554 Sensitivity Multilign(20): 0.560 RNASampler(20): 0.404 Positive Predictive Value Multilign(20): 0.685 RNASampler(20): 0.762 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.660 Murlet(20): 0.565 Sensitivity Multilign(20): 0.602 Murlet(20): 0.432 Positive Predictive Value Multilign(20): 0.724 Murlet(20): 0.740 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.651 UNAFold: 0.551 Sensitivity Multilign(20): 0.590 UNAFold: 0.539 Positive Predictive Value Multilign(20): 0.721 UNAFold: 0.564 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.651 PknotsRG: 0.525 Sensitivity Multilign(20): 0.590 PknotsRG: 0.517 Positive Predictive Value Multilign(20): 0.721 PknotsRG: 0.534 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.651 RNAfold: 0.545 Sensitivity Multilign(20): 0.590 RNAfold: 0.537 Positive Predictive Value Multilign(20): 0.721 RNAfold: 0.554 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): N/A Multilign(20): N/A Sensitivity Multilign(seed): N/A Multilign(20): N/A Positive Predictive Value Multilign(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.653 Afold: 0.557 Sensitivity Multilign(20): 0.589 Afold: 0.544 Positive Predictive Value Multilign(20): 0.726 Afold: 0.571 Number of pairs reference - predicted secondary structure: 172 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.651 RNAsubopt: 0.528 Sensitivity Multilign(20): 0.590 RNAsubopt: 0.528 Positive Predictive Value Multilign(20): 0.721 RNAsubopt: 0.530 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.658 RNAalifold(seed): 0.473 Sensitivity Multilign(20): 0.593 RNAalifold(seed): 0.272 Positive Predictive Value Multilign(20): 0.731 RNAalifold(seed): 0.825 Number of pairs reference - predicted secondary structure: 184 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.651 CMfinder(20): 0.477 Sensitivity Multilign(20): 0.590 CMfinder(20): 0.307 Positive Predictive Value Multilign(20): 0.721 CMfinder(20): 0.742 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.651 McQFold: 0.441 Sensitivity Multilign(20): 0.590 McQFold: 0.422 Positive Predictive Value Multilign(20): 0.721 McQFold: 0.462 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.651 CRWrnafold: 0.465 Sensitivity Multilign(20): 0.590 CRWrnafold: 0.457 Positive Predictive Value Multilign(20): 0.721 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.655 RNASLOpt: 0.455 Sensitivity Multilign(20): 0.595 RNASLOpt: 0.421 Positive Predictive Value Multilign(20): 0.722 RNASLOpt: 0.493 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.652 RNAshapes: 0.465 Sensitivity Multilign(20): 0.590 RNAshapes: 0.453 Positive Predictive Value Multilign(20): 0.720 RNAshapes: 0.480 Number of pairs reference - predicted secondary structure: 214 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): N/A Multilign(20): N/A Sensitivity Murlet(seed): N/A Multilign(20): N/A Positive Predictive Value Murlet(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.651 RSpredict(20): 0.393 Sensitivity Multilign(20): 0.590 RSpredict(20): 0.263 Positive Predictive Value Multilign(20): 0.721 RSpredict(20): 0.591 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.651 Carnac(20): 0.363 Sensitivity Multilign(20): 0.590 Carnac(20): 0.153 Positive Predictive Value Multilign(20): 0.721 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.651 RNAwolf: 0.367 Sensitivity Multilign(20): 0.590 RNAwolf: 0.377 Positive Predictive Value Multilign(20): 0.721 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.658 RSpredict(seed): 0.182 Sensitivity Multilign(20): 0.594 RSpredict(seed): 0.067 Positive Predictive Value Multilign(20): 0.731 RSpredict(seed): 0.495 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.650 Vsfold4: 0.359 Sensitivity Multilign(20): 0.589 Vsfold4: 0.326 Positive Predictive Value Multilign(20): 0.719 Vsfold4: 0.399 Number of pairs reference - predicted secondary structure: 219 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.651 Vsfold5: 0.342 Sensitivity Multilign(20): 0.590 Vsfold5: 0.316 Positive Predictive Value Multilign(20): 0.720 Vsfold5: 0.373 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.639 NanoFolder: 0.151 Sensitivity Multilign(20): 0.581 NanoFolder: 0.175 Positive Predictive Value Multilign(20): 0.703 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.725 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.653 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.807 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.660 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.597 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.732 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 170 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: N/A Multilign(20): N/A Sensitivity HotKnots: N/A Multilign(20): N/A Positive Predictive Value HotKnots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Multilign(20) Matthews Correlation Coefficient Pknots: N/A Multilign(20): N/A Sensitivity Pknots: N/A Multilign(20): N/A Positive Predictive Value Pknots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: N/A Multilign(20): N/A Sensitivity Cylofold: N/A Multilign(20): N/A Positive Predictive Value Cylofold: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): N/A MCFold: N/A Sensitivity Multilign(20): N/A MCFold: N/A Positive Predictive Value Multilign(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Multilign(20) Matthews Correlation Coefficient RDfolder: N/A Multilign(20): N/A Sensitivity RDfolder: N/A Multilign(20): N/A Positive Predictive Value RDfolder: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Multilign(20) Matthews Correlation Coefficient Alterna: N/A Multilign(20): N/A Sensitivity Alterna: N/A Multilign(20): N/A Positive Predictive Value Alterna: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.651 Mastr(20): 0.000 Sensitivity Multilign(20): 0.590 Mastr(20): 0.000 Positive Predictive Value Multilign(20): 0.721 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(20)	230 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 MXScarna(20): 0.647 Sensitivity PETfold_pre2.0(seed): 0.693 MXScarna(20): 0.576 Positive Predictive Value PETfold_pre2.0(seed): 0.854 MXScarna(20): 0.729 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.843 MXScarna(20): 0.654 Sensitivity ContextFold: 0.799 MXScarna(20): 0.584 Positive Predictive Value ContextFold: 0.891 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.752 MXScarna(20): 0.654 Sensitivity TurboFold(20): 0.701 MXScarna(20): 0.584 Positive Predictive Value TurboFold(20): 0.809 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 MXScarna(20): 0.679 Sensitivity CentroidAlifold(seed): 0.564 MXScarna(20): 0.599 Positive Predictive Value CentroidAlifold(seed): 0.953 MXScarna(20): 0.772 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 MXScarna(20): 0.654 Sensitivity PETfold_pre2.0(20): 0.654 MXScarna(20): 0.583 Positive Predictive Value PETfold_pre2.0(20): 0.836 MXScarna(20): 0.734 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs MXScarna(20) Matthews Correlation Coefficient PPfold(20): 0.733 MXScarna(20): 0.655 Sensitivity PPfold(20): 0.629 MXScarna(20): 0.585 Positive Predictive Value PPfold(20): 0.855 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 MXScarna(20): 0.654 Sensitivity CentroidHomfold‑LAST: 0.561 MXScarna(20): 0.584 Positive Predictive Value CentroidHomfold‑LAST: 0.898 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 MXScarna(20): 0.654 Sensitivity CentroidAlifold(20): 0.574 MXScarna(20): 0.584 Positive Predictive Value CentroidAlifold(20): 0.916 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 MXScarna(20): 0.680 Sensitivity MXScarna(seed): 0.582 MXScarna(20): 0.599 Positive Predictive Value MXScarna(seed): 0.805 MXScarna(20): 0.772 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 IPknot vs MXScarna(20) Matthews Correlation Coefficient IPknot: 0.655 MXScarna(20): 0.654 Sensitivity IPknot: 0.586 MXScarna(20): 0.584 Positive Predictive Value IPknot: 0.732 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 0.0274981398492	245 RNAalifold(20) vs MXScarna(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 MXScarna(20): 0.654 Sensitivity RNAalifold(20): 0.540 MXScarna(20): 0.584 Positive Predictive Value RNAalifold(20): 0.827 MXScarna(20): 0.735 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 MXScarna(20): 0.731 Sensitivity TurboFold(seed): 0.739 MXScarna(20): 0.727 Positive Predictive Value TurboFold(seed): 0.774 MXScarna(20): 0.736 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	223 Multilign(20) vs MXScarna(20) Matthews Correlation Coefficient Multilign(20): 0.651 MXScarna(20): 0.645 Sensitivity Multilign(20): 0.590 MXScarna(20): 0.573 Positive Predictive Value Multilign(20): 0.721 MXScarna(20): 0.729 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 4.83792096436e-08		+ MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.654 CentroidFold: 0.621 Sensitivity MXScarna(20): 0.584 CentroidFold: 0.557 Positive Predictive Value MXScarna(20): 0.735 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.654 Contrafold: 0.606 Sensitivity MXScarna(20): 0.584 Contrafold: 0.585 Positive Predictive Value MXScarna(20): 0.735 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.879 PPfold(seed): 0.847 Sensitivity MXScarna(20): 0.861 PPfold(seed): 0.782 Positive Predictive Value MXScarna(20): 0.897 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.654 Sfold: 0.584 Sensitivity MXScarna(20): 0.584 Sfold: 0.522 Positive Predictive Value MXScarna(20): 0.735 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.654 MaxExpect: 0.592 Sensitivity MXScarna(20): 0.584 MaxExpect: 0.569 Positive Predictive Value MXScarna(20): 0.735 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.654 ProbKnot: 0.590 Sensitivity MXScarna(20): 0.584 ProbKnot: 0.572 Positive Predictive Value MXScarna(20): 0.735 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(20): N/A Sensitivity RNASampler(seed): N/A MXScarna(20): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.654 Fold: 0.562 Sensitivity MXScarna(20): 0.584 Fold: 0.555 Positive Predictive Value MXScarna(20): 0.735 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.646 RNASampler(20): 0.565 Sensitivity MXScarna(20): 0.607 RNASampler(20): 0.413 Positive Predictive Value MXScarna(20): 0.690 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.646 Murlet(20): 0.573 Sensitivity MXScarna(20): 0.582 Murlet(20): 0.441 Positive Predictive Value MXScarna(20): 0.718 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.654 UNAFold: 0.547 Sensitivity MXScarna(20): 0.584 UNAFold: 0.535 Positive Predictive Value MXScarna(20): 0.735 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.654 PknotsRG: 0.525 Sensitivity MXScarna(20): 0.584 PknotsRG: 0.518 Positive Predictive Value MXScarna(20): 0.735 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.654 RNAfold: 0.544 Sensitivity MXScarna(20): 0.584 RNAfold: 0.536 Positive Predictive Value MXScarna(20): 0.735 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(20): N/A Sensitivity Multilign(seed): N/A MXScarna(20): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.665 Afold: 0.556 Sensitivity MXScarna(20): 0.584 Afold: 0.544 Positive Predictive Value MXScarna(20): 0.759 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.654 RNAsubopt: 0.530 Sensitivity MXScarna(20): 0.584 RNAsubopt: 0.529 Positive Predictive Value MXScarna(20): 0.735 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.679 RNAalifold(seed): 0.492 Sensitivity MXScarna(20): 0.599 RNAalifold(seed): 0.290 Positive Predictive Value MXScarna(20): 0.772 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.654 CMfinder(20): 0.478 Sensitivity MXScarna(20): 0.584 CMfinder(20): 0.309 Positive Predictive Value MXScarna(20): 0.735 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.654 McQFold: 0.442 Sensitivity MXScarna(20): 0.584 McQFold: 0.424 Positive Predictive Value MXScarna(20): 0.735 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.654 CRWrnafold: 0.464 Sensitivity MXScarna(20): 0.584 CRWrnafold: 0.456 Positive Predictive Value MXScarna(20): 0.735 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.651 RNASLOpt: 0.450 Sensitivity MXScarna(20): 0.582 RNASLOpt: 0.417 Positive Predictive Value MXScarna(20): 0.730 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.652 RNAshapes: 0.468 Sensitivity MXScarna(20): 0.581 RNAshapes: 0.454 Positive Predictive Value MXScarna(20): 0.732 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.879 Murlet(seed): 0.588 Sensitivity MXScarna(20): 0.861 Murlet(seed): 0.347 Positive Predictive Value MXScarna(20): 0.897 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.654 RSpredict(20): 0.418 Sensitivity MXScarna(20): 0.584 RSpredict(20): 0.285 Positive Predictive Value MXScarna(20): 0.735 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.654 Carnac(20): 0.378 Sensitivity MXScarna(20): 0.584 Carnac(20): 0.166 Positive Predictive Value MXScarna(20): 0.735 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.654 RNAwolf: 0.367 Sensitivity MXScarna(20): 0.584 RNAwolf: 0.377 Positive Predictive Value MXScarna(20): 0.735 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs MXScarna(20) Matthews Correlation Coefficient CMfinder(seed): N/A MXScarna(20): N/A Sensitivity CMfinder(seed): N/A MXScarna(20): N/A Positive Predictive Value CMfinder(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.681 RSpredict(seed): 0.197 Sensitivity MXScarna(20): 0.600 RSpredict(seed): 0.077 Positive Predictive Value MXScarna(20): 0.773 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.654 Vsfold4: 0.352 Sensitivity MXScarna(20): 0.584 Vsfold4: 0.319 Positive Predictive Value MXScarna(20): 0.734 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.652 Vsfold5: 0.333 Sensitivity MXScarna(20): 0.581 Vsfold5: 0.308 Positive Predictive Value MXScarna(20): 0.732 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.648 NanoFolder: 0.150 Sensitivity MXScarna(20): 0.577 NanoFolder: 0.173 Positive Predictive Value MXScarna(20): 0.728 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.802 Carnac(seed): 0.000 Sensitivity MXScarna(20): 0.779 Carnac(seed): 0.000 Positive Predictive Value MXScarna(20): 0.827 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.611 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.779 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs MXScarna(20) Matthews Correlation Coefficient HotKnots: N/A MXScarna(20): N/A Sensitivity HotKnots: N/A MXScarna(20): N/A Positive Predictive Value HotKnots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs MXScarna(20) Matthews Correlation Coefficient Pknots: N/A MXScarna(20): N/A Sensitivity Pknots: N/A MXScarna(20): N/A Positive Predictive Value Pknots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs MXScarna(20) Matthews Correlation Coefficient Cylofold: N/A MXScarna(20): N/A Sensitivity Cylofold: N/A MXScarna(20): N/A Positive Predictive Value Cylofold: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): N/A MCFold: N/A Sensitivity MXScarna(20): N/A MCFold: N/A Positive Predictive Value MXScarna(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs MXScarna(20) Matthews Correlation Coefficient RDfolder: N/A MXScarna(20): N/A Sensitivity RDfolder: N/A MXScarna(20): N/A Positive Predictive Value RDfolder: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs MXScarna(20) Matthews Correlation Coefficient Alterna: N/A MXScarna(20): N/A Sensitivity Alterna: N/A MXScarna(20): N/A Positive Predictive Value Alterna: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.654 Mastr(20): 0.000 Sensitivity MXScarna(20): 0.584 Mastr(20): 0.000 Positive Predictive Value MXScarna(20): 0.735 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidFold	643 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 CentroidFold: 0.587 Sensitivity PETfold_pre2.0(seed): 0.612 CentroidFold: 0.536 Positive Predictive Value PETfold_pre2.0(seed): 0.803 CentroidFold: 0.645 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.720 CentroidFold: 0.583 Sensitivity ContextFold: 0.687 CentroidFold: 0.533 Positive Predictive Value ContextFold: 0.756 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.752 CentroidFold: 0.621 Sensitivity TurboFold(20): 0.701 CentroidFold: 0.557 Positive Predictive Value TurboFold(20): 0.809 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 CentroidFold: 0.633 Sensitivity CentroidAlifold(seed): 0.556 CentroidFold: 0.580 Positive Predictive Value CentroidAlifold(seed): 0.906 CentroidFold: 0.692 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CentroidFold: 0.621 Sensitivity PETfold_pre2.0(20): 0.654 CentroidFold: 0.556 Positive Predictive Value PETfold_pre2.0(20): 0.836 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.733 CentroidFold: 0.620 Sensitivity PPfold(20): 0.629 CentroidFold: 0.556 Positive Predictive Value PPfold(20): 0.855 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 CentroidFold: 0.589 Sensitivity CentroidHomfold‑LAST: 0.491 CentroidFold: 0.540 Positive Predictive Value CentroidHomfold‑LAST: 0.862 CentroidFold: 0.644 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CentroidFold: 0.621 Sensitivity CentroidAlifold(20): 0.574 CentroidFold: 0.557 Positive Predictive Value CentroidAlifold(20): 0.916 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.637 CentroidFold: 0.633 Sensitivity MXScarna(seed): 0.535 CentroidFold: 0.580 Positive Predictive Value MXScarna(seed): 0.759 CentroidFold: 0.693 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.85233844192e-08	818 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.612 CentroidFold: 0.583 Sensitivity IPknot: 0.561 CentroidFold: 0.533 Positive Predictive Value IPknot: 0.667 CentroidFold: 0.638 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.668 CentroidFold: 0.621 Sensitivity RNAalifold(20): 0.540 CentroidFold: 0.557 Positive Predictive Value RNAalifold(20): 0.827 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.787 CentroidFold: 0.684 Sensitivity TurboFold(seed): 0.760 CentroidFold: 0.654 Positive Predictive Value TurboFold(seed): 0.815 CentroidFold: 0.717 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.05041766982e-08	223 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.651 CentroidFold: 0.625 Sensitivity Multilign(20): 0.590 CentroidFold: 0.560 Positive Predictive Value Multilign(20): 0.721 CentroidFold: 0.699 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.654 CentroidFold: 0.621 Sensitivity MXScarna(20): 0.584 CentroidFold: 0.557 Positive Predictive Value MXScarna(20): 0.735 CentroidFold: 0.694 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.583 Contrafold: 0.567 Sensitivity CentroidFold: 0.533 Contrafold: 0.558 Positive Predictive Value CentroidFold: 0.638 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): 0.716 CentroidFold: 0.655 Sensitivity PPfold(seed): 0.652 CentroidFold: 0.634 Positive Predictive Value PPfold(seed): 0.787 CentroidFold: 0.679 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.583 Sfold: 0.538 Sensitivity CentroidFold: 0.533 Sfold: 0.491 Positive Predictive Value CentroidFold: 0.638 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.583 MaxExpect: 0.536 Sensitivity CentroidFold: 0.533 MaxExpect: 0.527 Positive Predictive Value CentroidFold: 0.638 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.583 ProbKnot: 0.534 Sensitivity CentroidFold: 0.533 ProbKnot: 0.534 Positive Predictive Value CentroidFold: 0.638 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): 0.779 CentroidFold: 0.719 Sensitivity RNASampler(seed): 0.659 CentroidFold: 0.665 Positive Predictive Value RNASampler(seed): 0.921 CentroidFold: 0.778 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.583 Fold: 0.511 Sensitivity CentroidFold: 0.533 Fold: 0.517 Positive Predictive Value CentroidFold: 0.638 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.565 CentroidFold: 0.564 Sensitivity RNASampler(20): 0.413 CentroidFold: 0.513 Positive Predictive Value RNASampler(20): 0.772 CentroidFold: 0.623 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.85073699061	+ CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.607 Murlet(20): 0.573 Sensitivity CentroidFold: 0.544 Murlet(20): 0.441 Positive Predictive Value CentroidFold: 0.680 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.583 UNAFold: 0.501 Sensitivity CentroidFold: 0.533 UNAFold: 0.501 Positive Predictive Value CentroidFold: 0.638 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.583 PknotsRG: 0.499 Sensitivity CentroidFold: 0.533 PknotsRG: 0.504 Positive Predictive Value CentroidFold: 0.638 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.583 RNAfold: 0.499 Sensitivity CentroidFold: 0.533 RNAfold: 0.504 Positive Predictive Value CentroidFold: 0.638 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.734 CentroidFold: 0.629 Sensitivity Multilign(seed): 0.733 CentroidFold: 0.630 Positive Predictive Value Multilign(seed): 0.737 CentroidFold: 0.629 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.604 Afold: 0.516 Sensitivity CentroidFold: 0.554 Afold: 0.517 Positive Predictive Value CentroidFold: 0.659 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.589 RNAsubopt: 0.501 Sensitivity CentroidFold: 0.540 RNAsubopt: 0.510 Positive Predictive Value CentroidFold: 0.644 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.633 RNAalifold(seed): 0.541 Sensitivity CentroidFold: 0.579 RNAalifold(seed): 0.344 Positive Predictive Value CentroidFold: 0.692 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.621 CMfinder(20): 0.478 Sensitivity CentroidFold: 0.557 CMfinder(20): 0.309 Positive Predictive Value CentroidFold: 0.694 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.583 McQFold: 0.443 Sensitivity CentroidFold: 0.533 McQFold: 0.435 Positive Predictive Value CentroidFold: 0.638 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.583 CRWrnafold: 0.432 Sensitivity CentroidFold: 0.533 CRWrnafold: 0.438 Positive Predictive Value CentroidFold: 0.638 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.588 RNASLOpt: 0.442 Sensitivity CentroidFold: 0.538 RNASLOpt: 0.419 Positive Predictive Value CentroidFold: 0.643 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.587 RNAshapes: 0.438 Sensitivity CentroidFold: 0.538 RNAshapes: 0.434 Positive Predictive Value CentroidFold: 0.643 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.678 Murlet(seed): 0.569 Sensitivity CentroidFold: 0.649 Murlet(seed): 0.383 Positive Predictive Value CentroidFold: 0.709 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.621 RSpredict(20): 0.418 Sensitivity CentroidFold: 0.557 RSpredict(20): 0.285 Positive Predictive Value CentroidFold: 0.694 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.621 Carnac(20): 0.378 Sensitivity CentroidFold: 0.557 Carnac(20): 0.166 Positive Predictive Value CentroidFold: 0.694 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.583 RNAwolf: 0.339 Sensitivity CentroidFold: 0.533 RNAwolf: 0.355 Positive Predictive Value CentroidFold: 0.638 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.692 CMfinder(seed): 0.454 Sensitivity CentroidFold: 0.651 CMfinder(seed): 0.271 Positive Predictive Value CentroidFold: 0.738 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.633 RSpredict(seed): 0.214 Sensitivity CentroidFold: 0.579 RSpredict(seed): 0.089 Positive Predictive Value CentroidFold: 0.692 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.586 Vsfold4: 0.306 Sensitivity CentroidFold: 0.537 Vsfold4: 0.282 Positive Predictive Value CentroidFold: 0.641 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.586 Vsfold5: 0.300 Sensitivity CentroidFold: 0.537 Vsfold5: 0.286 Positive Predictive Value CentroidFold: 0.641 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.609 NanoFolder: 0.166 Sensitivity CentroidFold: 0.555 NanoFolder: 0.197 Positive Predictive Value CentroidFold: 0.670 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.609 Carnac(seed): 0.150 Sensitivity CentroidFold: 0.579 Carnac(seed): 0.028 Positive Predictive Value CentroidFold: 0.642 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.632 Mastr(seed): 0.073 Sensitivity CentroidFold: 0.581 Mastr(seed): 0.006 Positive Predictive Value CentroidFold: 0.689 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.678 HotKnots: 0.640 Sensitivity CentroidFold: 0.564 HotKnots: 0.615 Positive Predictive Value CentroidFold: 0.815 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: N/A CentroidFold: N/A Sensitivity Pknots: N/A CentroidFold: N/A Positive Predictive Value Pknots: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.626 Cylofold: 0.271 Sensitivity CentroidFold: 0.584 Cylofold: 0.241 Positive Predictive Value CentroidFold: 0.672 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: N/A MCFold: N/A Sensitivity CentroidFold: N/A MCFold: N/A Positive Predictive Value CentroidFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CentroidFold Matthews Correlation Coefficient RDfolder: N/A CentroidFold: N/A Sensitivity RDfolder: N/A CentroidFold: N/A Positive Predictive Value RDfolder: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CentroidFold Matthews Correlation Coefficient Alterna: N/A CentroidFold: N/A Sensitivity Alterna: N/A CentroidFold: N/A Positive Predictive Value Alterna: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.621 Mastr(20): 0.000 Sensitivity CentroidFold: 0.557 Mastr(20): 0.000 Positive Predictive Value CentroidFold: 0.694 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
Contrafold	643 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 Contrafold: 0.571 Sensitivity PETfold_pre2.0(seed): 0.612 Contrafold: 0.559 Positive Predictive Value PETfold_pre2.0(seed): 0.803 Contrafold: 0.584 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.720 Contrafold: 0.567 Sensitivity ContextFold: 0.687 Contrafold: 0.558 Positive Predictive Value ContextFold: 0.756 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.752 Contrafold: 0.606 Sensitivity TurboFold(20): 0.701 Contrafold: 0.585 Positive Predictive Value TurboFold(20): 0.809 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Contrafold: 0.620 Sensitivity CentroidAlifold(seed): 0.556 Contrafold: 0.605 Positive Predictive Value CentroidAlifold(seed): 0.906 Contrafold: 0.637 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Contrafold: 0.606 Sensitivity PETfold_pre2.0(20): 0.654 Contrafold: 0.584 Positive Predictive Value PETfold_pre2.0(20): 0.836 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.733 Contrafold: 0.606 Sensitivity PPfold(20): 0.629 Contrafold: 0.584 Positive Predictive Value PPfold(20): 0.855 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 Contrafold: 0.574 Sensitivity CentroidHomfold‑LAST: 0.491 Contrafold: 0.564 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Contrafold: 0.585 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Contrafold: 0.606 Sensitivity CentroidAlifold(20): 0.574 Contrafold: 0.585 Positive Predictive Value CentroidAlifold(20): 0.916 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.637 Contrafold: 0.620 Sensitivity MXScarna(seed): 0.535 Contrafold: 0.605 Positive Predictive Value MXScarna(seed): 0.759 Contrafold: 0.637 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.612 Contrafold: 0.567 Sensitivity IPknot: 0.561 Contrafold: 0.558 Positive Predictive Value IPknot: 0.667 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.668 Contrafold: 0.606 Sensitivity RNAalifold(20): 0.540 Contrafold: 0.585 Positive Predictive Value RNAalifold(20): 0.827 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.787 Contrafold: 0.678 Sensitivity TurboFold(seed): 0.760 Contrafold: 0.684 Positive Predictive Value TurboFold(seed): 0.815 Contrafold: 0.672 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.59578924681e-08	223 Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.651 Contrafold: 0.610 Sensitivity Multilign(20): 0.590 Contrafold: 0.588 Positive Predictive Value Multilign(20): 0.721 Contrafold: 0.634 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.654 Contrafold: 0.606 Sensitivity MXScarna(20): 0.584 Contrafold: 0.585 Positive Predictive Value MXScarna(20): 0.735 Contrafold: 0.630 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.583 Contrafold: 0.567 Sensitivity CentroidFold: 0.533 Contrafold: 0.558 Positive Predictive Value CentroidFold: 0.638 Contrafold: 0.577 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08		- PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): 0.716 Contrafold: 0.654 Sensitivity PPfold(seed): 0.652 Contrafold: 0.661 Positive Predictive Value PPfold(seed): 0.787 Contrafold: 0.648 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.567 Sfold: 0.538 Sensitivity Contrafold: 0.558 Sfold: 0.491 Positive Predictive Value Contrafold: 0.577 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.567 MaxExpect: 0.536 Sensitivity Contrafold: 0.558 MaxExpect: 0.527 Positive Predictive Value Contrafold: 0.577 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.567 ProbKnot: 0.534 Sensitivity Contrafold: 0.558 ProbKnot: 0.534 Positive Predictive Value Contrafold: 0.577 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.779 Contrafold: 0.706 Sensitivity RNASampler(seed): 0.659 Contrafold: 0.703 Positive Predictive Value RNASampler(seed): 0.921 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.4651262096e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.567 Fold: 0.511 Sensitivity Contrafold: 0.558 Fold: 0.517 Positive Predictive Value Contrafold: 0.577 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.565 Contrafold: 0.546 Sensitivity RNASampler(20): 0.413 Contrafold: 0.536 Positive Predictive Value RNASampler(20): 0.772 Contrafold: 0.559 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(20) Matthews Correlation Coefficient Contrafold: 0.592 Murlet(20): 0.573 Sensitivity Contrafold: 0.571 Murlet(20): 0.441 Positive Predictive Value Contrafold: 0.615 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.567 UNAFold: 0.501 Sensitivity Contrafold: 0.558 UNAFold: 0.501 Positive Predictive Value Contrafold: 0.577 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.567 PknotsRG: 0.499 Sensitivity Contrafold: 0.558 PknotsRG: 0.504 Positive Predictive Value Contrafold: 0.577 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.567 RNAfold: 0.499 Sensitivity Contrafold: 0.558 RNAfold: 0.504 Positive Predictive Value Contrafold: 0.577 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs Contrafold Matthews Correlation Coefficient Multilign(seed): 0.734 Contrafold: 0.619 Sensitivity Multilign(seed): 0.733 Contrafold: 0.643 Positive Predictive Value Multilign(seed): 0.737 Contrafold: 0.596 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.60917593777e-09	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.590 Afold: 0.516 Sensitivity Contrafold: 0.580 Afold: 0.517 Positive Predictive Value Contrafold: 0.602 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.574 RNAsubopt: 0.501 Sensitivity Contrafold: 0.564 RNAsubopt: 0.510 Positive Predictive Value Contrafold: 0.585 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.619 RNAalifold(seed): 0.541 Sensitivity Contrafold: 0.604 RNAalifold(seed): 0.344 Positive Predictive Value Contrafold: 0.636 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.606 CMfinder(20): 0.478 Sensitivity Contrafold: 0.585 CMfinder(20): 0.309 Positive Predictive Value Contrafold: 0.630 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.567 McQFold: 0.443 Sensitivity Contrafold: 0.558 McQFold: 0.435 Positive Predictive Value Contrafold: 0.577 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.567 CRWrnafold: 0.432 Sensitivity Contrafold: 0.558 CRWrnafold: 0.438 Positive Predictive Value Contrafold: 0.577 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.572 RNASLOpt: 0.442 Sensitivity Contrafold: 0.563 RNASLOpt: 0.419 Positive Predictive Value Contrafold: 0.584 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.572 RNAshapes: 0.438 Sensitivity Contrafold: 0.561 RNAshapes: 0.434 Positive Predictive Value Contrafold: 0.584 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.668 Murlet(seed): 0.569 Sensitivity Contrafold: 0.670 Murlet(seed): 0.383 Positive Predictive Value Contrafold: 0.668 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.606 RSpredict(20): 0.418 Sensitivity Contrafold: 0.585 RSpredict(20): 0.285 Positive Predictive Value Contrafold: 0.630 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.606 Carnac(20): 0.378 Sensitivity Contrafold: 0.585 Carnac(20): 0.166 Positive Predictive Value Contrafold: 0.630 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.567 RNAwolf: 0.339 Sensitivity Contrafold: 0.558 RNAwolf: 0.355 Positive Predictive Value Contrafold: 0.577 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.677 CMfinder(seed): 0.454 Sensitivity Contrafold: 0.673 CMfinder(seed): 0.271 Positive Predictive Value Contrafold: 0.683 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.620 RSpredict(seed): 0.214 Sensitivity Contrafold: 0.604 RSpredict(seed): 0.089 Positive Predictive Value Contrafold: 0.637 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.570 Vsfold4: 0.306 Sensitivity Contrafold: 0.560 Vsfold4: 0.282 Positive Predictive Value Contrafold: 0.582 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.570 Vsfold5: 0.300 Sensitivity Contrafold: 0.560 Vsfold5: 0.286 Positive Predictive Value Contrafold: 0.582 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.590 NanoFolder: 0.166 Sensitivity Contrafold: 0.577 NanoFolder: 0.197 Positive Predictive Value Contrafold: 0.604 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.599 Carnac(seed): 0.150 Sensitivity Contrafold: 0.601 Carnac(seed): 0.028 Positive Predictive Value Contrafold: 0.599 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.619 Mastr(seed): 0.073 Sensitivity Contrafold: 0.605 Mastr(seed): 0.006 Positive Predictive Value Contrafold: 0.635 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.707 HotKnots: 0.640 Sensitivity Contrafold: 0.641 HotKnots: 0.615 Positive Predictive Value Contrafold: 0.781 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs Contrafold Matthews Correlation Coefficient Pknots: N/A Contrafold: N/A Sensitivity Pknots: N/A Contrafold: N/A Positive Predictive Value Pknots: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.616 Cylofold: 0.271 Sensitivity Contrafold: 0.591 Cylofold: 0.241 Positive Predictive Value Contrafold: 0.643 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: N/A MCFold: N/A Sensitivity Contrafold: N/A MCFold: N/A Positive Predictive Value Contrafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Contrafold Matthews Correlation Coefficient RDfolder: N/A Contrafold: N/A Sensitivity RDfolder: N/A Contrafold: N/A Positive Predictive Value RDfolder: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: N/A Alterna: N/A Sensitivity Contrafold: N/A Alterna: N/A Positive Predictive Value Contrafold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.606 Mastr(20): 0.000 Sensitivity Contrafold: 0.585 Mastr(20): 0.000 Positive Predictive Value Contrafold: 0.630 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(seed)	23 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.740 PPfold(seed): 0.716 Sensitivity PETfold_pre2.0(seed): 0.706 PPfold(seed): 0.652 Positive Predictive Value PETfold_pre2.0(seed): 0.776 PPfold(seed): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.728 PPfold(seed): 0.716 Sensitivity ContextFold: 0.712 PPfold(seed): 0.652 Positive Predictive Value ContextFold: 0.745 PPfold(seed): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 1.41743914454e-05	1 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.882 PPfold(seed): 0.847 Sensitivity TurboFold(20): 0.842 PPfold(seed): 0.782 Positive Predictive Value TurboFold(20): 0.924 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	23 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.731 PPfold(seed): 0.716 Sensitivity CentroidAlifold(seed): 0.667 PPfold(seed): 0.652 Positive Predictive Value CentroidAlifold(seed): 0.802 PPfold(seed): 0.787 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	1 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.919 PPfold(seed): 0.847 Sensitivity PETfold_pre2.0(20): 0.901 PPfold(seed): 0.782 Positive Predictive Value PETfold_pre2.0(20): 0.938 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.886 PPfold(seed): 0.847 Sensitivity PPfold(20): 0.842 PPfold(seed): 0.782 Positive Predictive Value PPfold(20): 0.934 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	22 PPfold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PPfold(seed): 0.735 CentroidHomfold‑LAST: 0.723 Sensitivity PPfold(seed): 0.691 CentroidHomfold‑LAST: 0.641 Positive Predictive Value PPfold(seed): 0.783 CentroidHomfold‑LAST: 0.817 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 6.02521692575e-08	1 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.908 PPfold(seed): 0.847 Sensitivity CentroidAlifold(20): 0.871 PPfold(seed): 0.782 Positive Predictive Value CentroidAlifold(20): 0.946 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	23 PPfold(seed) vs MXScarna(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 MXScarna(seed): 0.699 Sensitivity PPfold(seed): 0.652 MXScarna(seed): 0.671 Positive Predictive Value PPfold(seed): 0.787 MXScarna(seed): 0.730 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	23 PPfold(seed) vs IPknot Matthews Correlation Coefficient PPfold(seed): 0.716 IPknot: 0.688 Sensitivity PPfold(seed): 0.652 IPknot: 0.673 Positive Predictive Value PPfold(seed): 0.787 IPknot: 0.705 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 7.95107997107e-08	1 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.886 PPfold(seed): 0.847 Sensitivity RNAalifold(20): 0.832 PPfold(seed): 0.782 Positive Predictive Value RNAalifold(20): 0.944 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	16 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.793 PPfold(seed): 0.740 Sensitivity TurboFold(seed): 0.766 PPfold(seed): 0.659 Positive Predictive Value TurboFold(seed): 0.821 PPfold(seed): 0.833 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 2.52609899389e-08	0 PPfold(seed) vs Multilign(20) Matthews Correlation Coefficient PPfold(seed): N/A Multilign(20): N/A Sensitivity PPfold(seed): N/A Multilign(20): N/A Positive Predictive Value PPfold(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.879 PPfold(seed): 0.847 Sensitivity MXScarna(20): 0.861 PPfold(seed): 0.782 Positive Predictive Value MXScarna(20): 0.897 PPfold(seed): 0.919 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	23 PPfold(seed) vs CentroidFold Matthews Correlation Coefficient PPfold(seed): 0.716 CentroidFold: 0.655 Sensitivity PPfold(seed): 0.652 CentroidFold: 0.634 Positive Predictive Value PPfold(seed): 0.787 CentroidFold: 0.679 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 PPfold(seed) vs Contrafold Matthews Correlation Coefficient PPfold(seed): 0.716 Contrafold: 0.654 Sensitivity PPfold(seed): 0.652 Contrafold: 0.661 Positive Predictive Value PPfold(seed): 0.787 Contrafold: 0.648 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08		+ PPfold(seed) vs Sfold Matthews Correlation Coefficient PPfold(seed): 0.716 Sfold: 0.668 Sensitivity PPfold(seed): 0.652 Sfold: 0.642 Positive Predictive Value PPfold(seed): 0.787 Sfold: 0.696 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PPfold(seed) vs MaxExpect Matthews Correlation Coefficient PPfold(seed): 0.716 MaxExpect: 0.631 Sensitivity PPfold(seed): 0.652 MaxExpect: 0.641 Positive Predictive Value PPfold(seed): 0.787 MaxExpect: 0.624 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PPfold(seed) vs ProbKnot Matthews Correlation Coefficient PPfold(seed): 0.716 ProbKnot: 0.639 Sensitivity PPfold(seed): 0.652 ProbKnot: 0.658 Positive Predictive Value PPfold(seed): 0.787 ProbKnot: 0.622 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	? PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.941 RNASampler(seed): 0.811 Sensitivity PPfold(seed): 0.889 RNASampler(seed): 0.687 Positive Predictive Value PPfold(seed): 0.996 RNASampler(seed): 0.959 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs Fold Matthews Correlation Coefficient PPfold(seed): 0.716 Fold: 0.618 Sensitivity PPfold(seed): 0.652 Fold: 0.633 Positive Predictive Value PPfold(seed): 0.787 Fold: 0.605 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	? PPfold(seed) vs RNASampler(20) Matthews Correlation Coefficient PPfold(seed): 0.847 RNASampler(20): 0.780 Sensitivity PPfold(seed): 0.782 RNASampler(20): 0.663 Positive Predictive Value PPfold(seed): 0.919 RNASampler(20): 0.918 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Murlet(20) Matthews Correlation Coefficient PPfold(seed): 0.847 Murlet(20): 0.782 Sensitivity PPfold(seed): 0.782 Murlet(20): 0.683 Positive Predictive Value PPfold(seed): 0.919 Murlet(20): 0.896 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs UNAFold Matthews Correlation Coefficient PPfold(seed): 0.716 UNAFold: 0.636 Sensitivity PPfold(seed): 0.652 UNAFold: 0.643 Positive Predictive Value PPfold(seed): 0.787 UNAFold: 0.630 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(seed) vs PknotsRG Matthews Correlation Coefficient PPfold(seed): 0.716 PknotsRG: 0.642 Sensitivity PPfold(seed): 0.652 PknotsRG: 0.655 Positive Predictive Value PPfold(seed): 0.787 PknotsRG: 0.631 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PPfold(seed) vs RNAfold Matthews Correlation Coefficient PPfold(seed): 0.716 RNAfold: 0.667 Sensitivity PPfold(seed): 0.652 RNAfold: 0.677 Positive Predictive Value PPfold(seed): 0.787 RNAfold: 0.657 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	? PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.792 Multilign(seed): 0.759 Sensitivity PPfold(seed): 0.748 Multilign(seed): 0.752 Positive Predictive Value PPfold(seed): 0.840 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.756 Afold: 0.627 Sensitivity PPfold(seed): 0.714 Afold: 0.639 Positive Predictive Value PPfold(seed): 0.802 Afold: 0.616 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	+ PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): 0.735 RNAsubopt: 0.641 Sensitivity PPfold(seed): 0.691 RNAsubopt: 0.658 Positive Predictive Value PPfold(seed): 0.783 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 RNAalifold(seed): 0.698 Sensitivity PPfold(seed): 0.652 RNAalifold(seed): 0.574 Positive Predictive Value PPfold(seed): 0.787 RNAalifold(seed): 0.850 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): 0.847 CMfinder(20): 0.524 Sensitivity PPfold(seed): 0.782 CMfinder(20): 0.376 Positive Predictive Value PPfold(seed): 0.919 CMfinder(20): 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs McQFold Matthews Correlation Coefficient PPfold(seed): 0.716 McQFold: 0.465 Sensitivity PPfold(seed): 0.652 McQFold: 0.458 Positive Predictive Value PPfold(seed): 0.787 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.716 CRWrnafold: 0.499 Sensitivity PPfold(seed): 0.652 CRWrnafold: 0.509 Positive Predictive Value PPfold(seed): 0.787 CRWrnafold: 0.491 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.735 RNASLOpt: 0.489 Sensitivity PPfold(seed): 0.691 RNASLOpt: 0.475 Positive Predictive Value PPfold(seed): 0.783 RNASLOpt: 0.505 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): 0.726 RNAshapes: 0.593 Sensitivity PPfold(seed): 0.682 RNAshapes: 0.602 Positive Predictive Value PPfold(seed): 0.773 RNAshapes: 0.586 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.784 Murlet(seed): 0.615 Sensitivity PPfold(seed): 0.736 Murlet(seed): 0.448 Positive Predictive Value PPfold(seed): 0.837 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	? PPfold(seed) vs RSpredict(20) Matthews Correlation Coefficient PPfold(seed): 0.847 RSpredict(20): 0.789 Sensitivity PPfold(seed): 0.782 RSpredict(20): 0.703 Positive Predictive Value PPfold(seed): 0.919 RSpredict(20): 0.888 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PPfold(seed) vs Carnac(20) Matthews Correlation Coefficient PPfold(seed): 0.847 Carnac(20): 0.429 Sensitivity PPfold(seed): 0.782 Carnac(20): 0.218 Positive Predictive Value PPfold(seed): 0.919 Carnac(20): 0.846 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.716 RNAwolf: 0.389 Sensitivity PPfold(seed): 0.652 RNAwolf: 0.408 Positive Predictive Value PPfold(seed): 0.787 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	? PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.941 CMfinder(seed): 0.558 Sensitivity PPfold(seed): 0.889 CMfinder(seed): 0.422 Positive Predictive Value PPfold(seed): 0.996 CMfinder(seed): 0.740 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 RSpredict(seed): 0.407 Sensitivity PPfold(seed): 0.652 RSpredict(seed): 0.288 Positive Predictive Value PPfold(seed): 0.787 RSpredict(seed): 0.579 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.735 Vsfold4: 0.197 Sensitivity PPfold(seed): 0.691 Vsfold4: 0.182 Positive Predictive Value PPfold(seed): 0.783 Vsfold4: 0.215 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	+ PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.735 Vsfold5: 0.192 Sensitivity PPfold(seed): 0.691 Vsfold5: 0.185 Positive Predictive Value PPfold(seed): 0.783 Vsfold5: 0.201 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	? PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.950 NanoFolder: -0.003 Sensitivity PPfold(seed): 0.902 NanoFolder: 0.000 Positive Predictive Value PPfold(seed): 1.000 NanoFolder: 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 Carnac(seed): 0.373 Sensitivity PPfold(seed): 0.652 Carnac(seed): 0.160 Positive Predictive Value PPfold(seed): 0.787 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 Mastr(seed): 0.337 Sensitivity PPfold(seed): 0.652 Mastr(seed): 0.127 Positive Predictive Value PPfold(seed): 0.787 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	? HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: N/A PPfold(seed): N/A Sensitivity HotKnots: N/A PPfold(seed): N/A Positive Predictive Value HotKnots: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Pknots Matthews Correlation Coefficient PPfold(seed): N/A Pknots: N/A Sensitivity PPfold(seed): N/A Pknots: N/A Positive Predictive Value PPfold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: N/A PPfold(seed): N/A Sensitivity Cylofold: N/A PPfold(seed): N/A Positive Predictive Value Cylofold: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs MCFold Matthews Correlation Coefficient PPfold(seed): N/A MCFold: N/A Sensitivity PPfold(seed): N/A MCFold: N/A Positive Predictive Value PPfold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: N/A PPfold(seed): N/A Sensitivity RDfolder: N/A PPfold(seed): N/A Positive Predictive Value RDfolder: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Alterna Matthews Correlation Coefficient PPfold(seed): N/A Alterna: N/A Sensitivity PPfold(seed): N/A Alterna: N/A Positive Predictive Value PPfold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PPfold(seed) vs Mastr(20) Matthews Correlation Coefficient PPfold(seed): 0.847 Mastr(20): 0.000 Sensitivity PPfold(seed): 0.782 Mastr(20): 0.000 Positive Predictive Value PPfold(seed): 0.919 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0
Sfold	643 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 Sfold: 0.542 Sensitivity PETfold_pre2.0(seed): 0.612 Sfold: 0.492 Positive Predictive Value PETfold_pre2.0(seed): 0.803 Sfold: 0.597 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.720 Sfold: 0.538 Sensitivity ContextFold: 0.687 Sfold: 0.491 Positive Predictive Value ContextFold: 0.756 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.752 Sfold: 0.584 Sensitivity TurboFold(20): 0.701 Sfold: 0.522 Positive Predictive Value TurboFold(20): 0.809 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Sfold: 0.612 Sensitivity CentroidAlifold(seed): 0.556 Sfold: 0.558 Positive Predictive Value CentroidAlifold(seed): 0.906 Sfold: 0.673 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Sfold: 0.583 Sensitivity PETfold_pre2.0(20): 0.654 Sfold: 0.521 Positive Predictive Value PETfold_pre2.0(20): 0.836 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.733 Sfold: 0.583 Sensitivity PPfold(20): 0.629 Sfold: 0.521 Positive Predictive Value PPfold(20): 0.855 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 Sfold: 0.546 Sensitivity CentroidHomfold‑LAST: 0.491 Sfold: 0.498 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Sfold: 0.600 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Sfold: 0.584 Sensitivity CentroidAlifold(20): 0.574 Sfold: 0.522 Positive Predictive Value CentroidAlifold(20): 0.916 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.637 Sfold: 0.612 Sensitivity MXScarna(seed): 0.535 Sfold: 0.558 Positive Predictive Value MXScarna(seed): 0.759 Sfold: 0.673 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.612 Sfold: 0.538 Sensitivity IPknot: 0.561 Sfold: 0.491 Positive Predictive Value IPknot: 0.667 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.668 Sfold: 0.584 Sensitivity RNAalifold(20): 0.540 Sfold: 0.522 Positive Predictive Value RNAalifold(20): 0.827 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.787 Sfold: 0.671 Sensitivity TurboFold(seed): 0.760 Sfold: 0.644 Positive Predictive Value TurboFold(seed): 0.815 Sfold: 0.701 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	223 Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.651 Sfold: 0.584 Sensitivity Multilign(20): 0.590 Sfold: 0.521 Positive Predictive Value Multilign(20): 0.721 Sfold: 0.655 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.654 Sfold: 0.584 Sensitivity MXScarna(20): 0.584 Sfold: 0.522 Positive Predictive Value MXScarna(20): 0.735 Sfold: 0.654 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.583 Sfold: 0.538 Sensitivity CentroidFold: 0.533 Sfold: 0.491 Positive Predictive Value CentroidFold: 0.638 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.567 Sfold: 0.538 Sensitivity Contrafold: 0.558 Sfold: 0.491 Positive Predictive Value Contrafold: 0.577 Sfold: 0.589 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs Sfold Matthews Correlation Coefficient PPfold(seed): 0.716 Sfold: 0.668 Sensitivity PPfold(seed): 0.652 Sfold: 0.642 Positive Predictive Value PPfold(seed): 0.787 Sfold: 0.696 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08		+ Sfold vs MaxExpect Matthews Correlation Coefficient Sfold: 0.538 MaxExpect: 0.536 Sensitivity Sfold: 0.491 MaxExpect: 0.527 Positive Predictive Value Sfold: 0.589 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.90487810335e-05	+ Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.538 ProbKnot: 0.534 Sensitivity Sfold: 0.491 ProbKnot: 0.534 Positive Predictive Value Sfold: 0.589 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.779 Sfold: 0.689 Sensitivity RNASampler(seed): 0.659 Sfold: 0.644 Positive Predictive Value RNASampler(seed): 0.921 Sfold: 0.738 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.538 Fold: 0.511 Sensitivity Sfold: 0.491 Fold: 0.517 Positive Predictive Value Sfold: 0.589 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.565 Sfold: 0.523 Sensitivity RNASampler(20): 0.413 Sfold: 0.471 Positive Predictive Value RNASampler(20): 0.772 Sfold: 0.582 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.573 Sfold: 0.570 Sensitivity Murlet(20): 0.441 Sfold: 0.506 Positive Predictive Value Murlet(20): 0.746 Sfold: 0.644 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 0.554240997957	+ Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.538 UNAFold: 0.501 Sensitivity Sfold: 0.491 UNAFold: 0.501 Positive Predictive Value Sfold: 0.589 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.538 PknotsRG: 0.499 Sensitivity Sfold: 0.491 PknotsRG: 0.504 Positive Predictive Value Sfold: 0.589 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.538 RNAfold: 0.499 Sensitivity Sfold: 0.491 RNAfold: 0.504 Positive Predictive Value Sfold: 0.589 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.734 Sfold: 0.612 Sensitivity Multilign(seed): 0.733 Sfold: 0.603 Positive Predictive Value Multilign(seed): 0.737 Sfold: 0.623 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.42028829171e-09	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.571 Afold: 0.516 Sensitivity Sfold: 0.523 Afold: 0.517 Positive Predictive Value Sfold: 0.625 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.546 RNAsubopt: 0.501 Sensitivity Sfold: 0.498 RNAsubopt: 0.510 Positive Predictive Value Sfold: 0.600 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.612 RNAalifold(seed): 0.541 Sensitivity Sfold: 0.557 RNAalifold(seed): 0.344 Positive Predictive Value Sfold: 0.673 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.584 CMfinder(20): 0.478 Sensitivity Sfold: 0.522 CMfinder(20): 0.309 Positive Predictive Value Sfold: 0.654 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.538 McQFold: 0.443 Sensitivity Sfold: 0.491 McQFold: 0.435 Positive Predictive Value Sfold: 0.589 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.538 CRWrnafold: 0.432 Sensitivity Sfold: 0.491 CRWrnafold: 0.438 Positive Predictive Value Sfold: 0.589 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.546 RNASLOpt: 0.442 Sensitivity Sfold: 0.499 RNASLOpt: 0.419 Positive Predictive Value Sfold: 0.600 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.545 RNAshapes: 0.438 Sensitivity Sfold: 0.497 RNAshapes: 0.434 Positive Predictive Value Sfold: 0.600 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.660 Murlet(seed): 0.569 Sensitivity Sfold: 0.624 Murlet(seed): 0.383 Positive Predictive Value Sfold: 0.700 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.584 RSpredict(20): 0.418 Sensitivity Sfold: 0.522 RSpredict(20): 0.285 Positive Predictive Value Sfold: 0.654 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.584 Carnac(20): 0.378 Sensitivity Sfold: 0.522 Carnac(20): 0.166 Positive Predictive Value Sfold: 0.654 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.538 RNAwolf: 0.339 Sensitivity Sfold: 0.491 RNAwolf: 0.355 Positive Predictive Value Sfold: 0.589 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.677 CMfinder(seed): 0.454 Sensitivity Sfold: 0.626 CMfinder(seed): 0.271 Positive Predictive Value Sfold: 0.733 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.612 RSpredict(seed): 0.214 Sensitivity Sfold: 0.558 RSpredict(seed): 0.089 Positive Predictive Value Sfold: 0.673 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.544 Vsfold4: 0.306 Sensitivity Sfold: 0.496 Vsfold4: 0.282 Positive Predictive Value Sfold: 0.598 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.544 Vsfold5: 0.300 Sensitivity Sfold: 0.496 Vsfold5: 0.286 Positive Predictive Value Sfold: 0.598 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.572 NanoFolder: 0.166 Sensitivity Sfold: 0.517 NanoFolder: 0.197 Positive Predictive Value Sfold: 0.635 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.613 Carnac(seed): 0.150 Sensitivity Sfold: 0.572 Carnac(seed): 0.028 Positive Predictive Value Sfold: 0.657 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.611 Mastr(seed): 0.073 Sensitivity Sfold: 0.559 Mastr(seed): 0.006 Positive Predictive Value Sfold: 0.670 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: 0.640 Sfold: 0.555 Sensitivity HotKnots: 0.615 Sfold: 0.487 Positive Predictive Value HotKnots: 0.667 Sfold: 0.633 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs Sfold Matthews Correlation Coefficient Pknots: N/A Sfold: N/A Sensitivity Pknots: N/A Sfold: N/A Positive Predictive Value Pknots: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.657 Cylofold: 0.271 Sensitivity Sfold: 0.562 Cylofold: 0.241 Positive Predictive Value Sfold: 0.770 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Sfold vs MCFold Matthews Correlation Coefficient Sfold: N/A MCFold: N/A Sensitivity Sfold: N/A MCFold: N/A Positive Predictive Value Sfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: N/A Sfold: N/A Sensitivity RDfolder: N/A Sfold: N/A Positive Predictive Value RDfolder: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Sfold Matthews Correlation Coefficient Alterna: N/A Sfold: N/A Sensitivity Alterna: N/A Sfold: N/A Positive Predictive Value Alterna: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.584 Mastr(20): 0.000 Sensitivity Sfold: 0.522 Mastr(20): 0.000 Positive Predictive Value Sfold: 0.654 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
MaxExpect	643 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 MaxExpect: 0.543 Sensitivity PETfold_pre2.0(seed): 0.612 MaxExpect: 0.531 Positive Predictive Value PETfold_pre2.0(seed): 0.803 MaxExpect: 0.557 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.720 MaxExpect: 0.536 Sensitivity ContextFold: 0.687 MaxExpect: 0.527 Positive Predictive Value ContextFold: 0.756 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.752 MaxExpect: 0.592 Sensitivity TurboFold(20): 0.701 MaxExpect: 0.569 Positive Predictive Value TurboFold(20): 0.809 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 MaxExpect: 0.598 Sensitivity CentroidAlifold(seed): 0.556 MaxExpect: 0.581 Positive Predictive Value CentroidAlifold(seed): 0.906 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 MaxExpect: 0.591 Sensitivity PETfold_pre2.0(20): 0.654 MaxExpect: 0.568 Positive Predictive Value PETfold_pre2.0(20): 0.836 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.733 MaxExpect: 0.590 Sensitivity PPfold(20): 0.629 MaxExpect: 0.567 Positive Predictive Value PPfold(20): 0.855 MaxExpect: 0.615 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 MaxExpect: 0.544 Sensitivity CentroidHomfold‑LAST: 0.491 MaxExpect: 0.533 Positive Predictive Value CentroidHomfold‑LAST: 0.862 MaxExpect: 0.556 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.725 MaxExpect: 0.592 Sensitivity CentroidAlifold(20): 0.574 MaxExpect: 0.569 Positive Predictive Value CentroidAlifold(20): 0.916 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.637 MaxExpect: 0.598 Sensitivity MXScarna(seed): 0.535 MaxExpect: 0.581 Positive Predictive Value MXScarna(seed): 0.759 MaxExpect: 0.616 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.612 MaxExpect: 0.536 Sensitivity IPknot: 0.561 MaxExpect: 0.527 Positive Predictive Value IPknot: 0.667 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.668 MaxExpect: 0.592 Sensitivity RNAalifold(20): 0.540 MaxExpect: 0.569 Positive Predictive Value RNAalifold(20): 0.827 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.787 MaxExpect: 0.641 Sensitivity TurboFold(seed): 0.760 MaxExpect: 0.652 Positive Predictive Value TurboFold(seed): 0.815 MaxExpect: 0.631 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.13260312532e-08	223 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.651 MaxExpect: 0.594 Sensitivity Multilign(20): 0.590 MaxExpect: 0.571 Positive Predictive Value Multilign(20): 0.721 MaxExpect: 0.619 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.654 MaxExpect: 0.592 Sensitivity MXScarna(20): 0.584 MaxExpect: 0.569 Positive Predictive Value MXScarna(20): 0.735 MaxExpect: 0.617 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.583 MaxExpect: 0.536 Sensitivity CentroidFold: 0.533 MaxExpect: 0.527 Positive Predictive Value CentroidFold: 0.638 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.567 MaxExpect: 0.536 Sensitivity Contrafold: 0.558 MaxExpect: 0.527 Positive Predictive Value Contrafold: 0.577 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs MaxExpect Matthews Correlation Coefficient PPfold(seed): 0.716 MaxExpect: 0.631 Sensitivity PPfold(seed): 0.652 MaxExpect: 0.641 Positive Predictive Value PPfold(seed): 0.787 MaxExpect: 0.624 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	818 Sfold vs MaxExpect Matthews Correlation Coefficient Sfold: 0.538 MaxExpect: 0.536 Sensitivity Sfold: 0.491 MaxExpect: 0.527 Positive Predictive Value Sfold: 0.589 MaxExpect: 0.546 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.90487810335e-05		+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.536 ProbKnot: 0.534 Sensitivity MaxExpect: 0.527 ProbKnot: 0.534 Positive Predictive Value MaxExpect: 0.546 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.779 MaxExpect: 0.637 Sensitivity RNASampler(seed): 0.659 MaxExpect: 0.654 Positive Predictive Value RNASampler(seed): 0.921 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 8.44035332136e-09	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.536 Fold: 0.511 Sensitivity MaxExpect: 0.527 Fold: 0.517 Positive Predictive Value MaxExpect: 0.546 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.565 MaxExpect: 0.526 Sensitivity RNASampler(20): 0.413 MaxExpect: 0.518 Positive Predictive Value RNASampler(20): 0.772 MaxExpect: 0.536 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.580 Murlet(20): 0.573 Sensitivity MaxExpect: 0.559 Murlet(20): 0.441 Positive Predictive Value MaxExpect: 0.604 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 7.5939721025e-08	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.536 UNAFold: 0.501 Sensitivity MaxExpect: 0.527 UNAFold: 0.501 Positive Predictive Value MaxExpect: 0.546 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.536 PknotsRG: 0.499 Sensitivity MaxExpect: 0.527 PknotsRG: 0.504 Positive Predictive Value MaxExpect: 0.546 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.536 RNAfold: 0.499 Sensitivity MaxExpect: 0.527 RNAfold: 0.504 Positive Predictive Value MaxExpect: 0.546 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.734 MaxExpect: 0.571 Sensitivity Multilign(seed): 0.733 MaxExpect: 0.596 Positive Predictive Value Multilign(seed): 0.737 MaxExpect: 0.548 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.38194587311e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.559 Afold: 0.516 Sensitivity MaxExpect: 0.550 Afold: 0.517 Positive Predictive Value MaxExpect: 0.570 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.544 RNAsubopt: 0.501 Sensitivity MaxExpect: 0.533 RNAsubopt: 0.510 Positive Predictive Value MaxExpect: 0.556 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAalifold(seed) Matthews Correlation Coefficient MaxExpect: 0.597 RNAalifold(seed): 0.541 Sensitivity MaxExpect: 0.581 RNAalifold(seed): 0.344 Positive Predictive Value MaxExpect: 0.616 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.592 CMfinder(20): 0.478 Sensitivity MaxExpect: 0.569 CMfinder(20): 0.309 Positive Predictive Value MaxExpect: 0.617 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.536 McQFold: 0.443 Sensitivity MaxExpect: 0.527 McQFold: 0.435 Positive Predictive Value MaxExpect: 0.546 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.536 CRWrnafold: 0.432 Sensitivity MaxExpect: 0.527 CRWrnafold: 0.438 Positive Predictive Value MaxExpect: 0.546 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.546 RNASLOpt: 0.442 Sensitivity MaxExpect: 0.535 RNASLOpt: 0.419 Positive Predictive Value MaxExpect: 0.558 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.545 RNAshapes: 0.438 Sensitivity MaxExpect: 0.533 RNAshapes: 0.434 Positive Predictive Value MaxExpect: 0.558 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.611 Murlet(seed): 0.569 Sensitivity MaxExpect: 0.612 Murlet(seed): 0.383 Positive Predictive Value MaxExpect: 0.611 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.592 RSpredict(20): 0.418 Sensitivity MaxExpect: 0.569 RSpredict(20): 0.285 Positive Predictive Value MaxExpect: 0.617 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.592 Carnac(20): 0.378 Sensitivity MaxExpect: 0.569 Carnac(20): 0.166 Positive Predictive Value MaxExpect: 0.617 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.536 RNAwolf: 0.339 Sensitivity MaxExpect: 0.527 RNAwolf: 0.355 Positive Predictive Value MaxExpect: 0.546 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.596 CMfinder(seed): 0.454 Sensitivity MaxExpect: 0.592 CMfinder(seed): 0.271 Positive Predictive Value MaxExpect: 0.601 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.598 RSpredict(seed): 0.214 Sensitivity MaxExpect: 0.582 RSpredict(seed): 0.089 Positive Predictive Value MaxExpect: 0.617 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.542 Vsfold4: 0.306 Sensitivity MaxExpect: 0.532 Vsfold4: 0.282 Positive Predictive Value MaxExpect: 0.555 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.544 Vsfold5: 0.300 Sensitivity MaxExpect: 0.533 Vsfold5: 0.286 Positive Predictive Value MaxExpect: 0.556 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.569 NanoFolder: 0.166 Sensitivity MaxExpect: 0.554 NanoFolder: 0.197 Positive Predictive Value MaxExpect: 0.586 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.563 Carnac(seed): 0.150 Sensitivity MaxExpect: 0.562 Carnac(seed): 0.028 Positive Predictive Value MaxExpect: 0.565 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.597 Mastr(seed): 0.073 Sensitivity MaxExpect: 0.582 Mastr(seed): 0.006 Positive Predictive Value MaxExpect: 0.614 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.640 MaxExpect: 0.438 Sensitivity HotKnots: 0.615 MaxExpect: 0.487 Positive Predictive Value HotKnots: 0.667 MaxExpect: 0.396 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: N/A Pknots: N/A Sensitivity MaxExpect: N/A Pknots: N/A Positive Predictive Value MaxExpect: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.631 Cylofold: 0.271 Sensitivity MaxExpect: 0.620 Cylofold: 0.241 Positive Predictive Value MaxExpect: 0.644 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: N/A MCFold: N/A Sensitivity MaxExpect: N/A MCFold: N/A Positive Predictive Value MaxExpect: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: N/A RDfolder: N/A Sensitivity MaxExpect: N/A RDfolder: N/A Positive Predictive Value MaxExpect: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: N/A Alterna: N/A Sensitivity MaxExpect: N/A Alterna: N/A Positive Predictive Value MaxExpect: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.592 Mastr(20): 0.000 Sensitivity MaxExpect: 0.569 Mastr(20): 0.000 Positive Predictive Value MaxExpect: 0.617 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	643 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 ProbKnot: 0.541 Sensitivity PETfold_pre2.0(seed): 0.612 ProbKnot: 0.537 Positive Predictive Value PETfold_pre2.0(seed): 0.803 ProbKnot: 0.547 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.720 ProbKnot: 0.534 Sensitivity ContextFold: 0.687 ProbKnot: 0.534 Positive Predictive Value ContextFold: 0.756 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.752 ProbKnot: 0.590 Sensitivity TurboFold(20): 0.701 ProbKnot: 0.572 Positive Predictive Value TurboFold(20): 0.809 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 ProbKnot: 0.597 Sensitivity CentroidAlifold(seed): 0.556 ProbKnot: 0.585 Positive Predictive Value CentroidAlifold(seed): 0.906 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 ProbKnot: 0.589 Sensitivity PETfold_pre2.0(20): 0.654 ProbKnot: 0.571 Positive Predictive Value PETfold_pre2.0(20): 0.836 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.733 ProbKnot: 0.588 Sensitivity PPfold(20): 0.629 ProbKnot: 0.570 Positive Predictive Value PPfold(20): 0.855 ProbKnot: 0.608 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 ProbKnot: 0.542 Sensitivity CentroidHomfold‑LAST: 0.491 ProbKnot: 0.539 Positive Predictive Value CentroidHomfold‑LAST: 0.862 ProbKnot: 0.547 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.725 ProbKnot: 0.590 Sensitivity CentroidAlifold(20): 0.574 ProbKnot: 0.572 Positive Predictive Value CentroidAlifold(20): 0.916 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.637 ProbKnot: 0.597 Sensitivity MXScarna(seed): 0.535 ProbKnot: 0.585 Positive Predictive Value MXScarna(seed): 0.759 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.612 ProbKnot: 0.534 Sensitivity IPknot: 0.561 ProbKnot: 0.534 Positive Predictive Value IPknot: 0.667 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.668 ProbKnot: 0.590 Sensitivity RNAalifold(20): 0.540 ProbKnot: 0.572 Positive Predictive Value RNAalifold(20): 0.827 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.787 ProbKnot: 0.651 Sensitivity TurboFold(seed): 0.760 ProbKnot: 0.668 Positive Predictive Value TurboFold(seed): 0.815 ProbKnot: 0.635 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.66062906821e-08	223 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.651 ProbKnot: 0.593 Sensitivity Multilign(20): 0.590 ProbKnot: 0.574 Positive Predictive Value Multilign(20): 0.721 ProbKnot: 0.613 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.654 ProbKnot: 0.590 Sensitivity MXScarna(20): 0.584 ProbKnot: 0.572 Positive Predictive Value MXScarna(20): 0.735 ProbKnot: 0.610 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.583 ProbKnot: 0.534 Sensitivity CentroidFold: 0.533 ProbKnot: 0.534 Positive Predictive Value CentroidFold: 0.638 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.567 ProbKnot: 0.534 Sensitivity Contrafold: 0.558 ProbKnot: 0.534 Positive Predictive Value Contrafold: 0.577 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs ProbKnot Matthews Correlation Coefficient PPfold(seed): 0.716 ProbKnot: 0.639 Sensitivity PPfold(seed): 0.652 ProbKnot: 0.658 Positive Predictive Value PPfold(seed): 0.787 ProbKnot: 0.622 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	818 Sfold vs ProbKnot Matthews Correlation Coefficient Sfold: 0.538 ProbKnot: 0.534 Sensitivity Sfold: 0.491 ProbKnot: 0.534 Positive Predictive Value Sfold: 0.589 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.536 ProbKnot: 0.534 Sensitivity MaxExpect: 0.527 ProbKnot: 0.534 Positive Predictive Value MaxExpect: 0.546 ProbKnot: 0.535 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.779 ProbKnot: 0.644 Sensitivity RNASampler(seed): 0.659 ProbKnot: 0.668 Positive Predictive Value RNASampler(seed): 0.921 ProbKnot: 0.623 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.22210847902e-08	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.534 Fold: 0.511 Sensitivity ProbKnot: 0.534 Fold: 0.517 Positive Predictive Value ProbKnot: 0.535 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.565 ProbKnot: 0.524 Sensitivity RNASampler(20): 0.413 ProbKnot: 0.524 Positive Predictive Value RNASampler(20): 0.772 ProbKnot: 0.524 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.578 Murlet(20): 0.573 Sensitivity ProbKnot: 0.562 Murlet(20): 0.441 Positive Predictive Value ProbKnot: 0.596 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 9.94962292175e-07	+ ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.534 UNAFold: 0.501 Sensitivity ProbKnot: 0.534 UNAFold: 0.501 Positive Predictive Value ProbKnot: 0.535 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.534 PknotsRG: 0.499 Sensitivity ProbKnot: 0.534 PknotsRG: 0.504 Positive Predictive Value ProbKnot: 0.535 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.534 RNAfold: 0.499 Sensitivity ProbKnot: 0.534 RNAfold: 0.504 Positive Predictive Value ProbKnot: 0.535 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.734 ProbKnot: 0.583 Sensitivity Multilign(seed): 0.733 ProbKnot: 0.609 Positive Predictive Value Multilign(seed): 0.737 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.76570236188e-09	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.556 Afold: 0.516 Sensitivity ProbKnot: 0.555 Afold: 0.517 Positive Predictive Value ProbKnot: 0.559 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.542 RNAsubopt: 0.501 Sensitivity ProbKnot: 0.539 RNAsubopt: 0.510 Positive Predictive Value ProbKnot: 0.547 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.596 RNAalifold(seed): 0.541 Sensitivity ProbKnot: 0.585 RNAalifold(seed): 0.344 Positive Predictive Value ProbKnot: 0.610 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.590 CMfinder(20): 0.478 Sensitivity ProbKnot: 0.572 CMfinder(20): 0.309 Positive Predictive Value ProbKnot: 0.610 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.534 McQFold: 0.443 Sensitivity ProbKnot: 0.534 McQFold: 0.435 Positive Predictive Value ProbKnot: 0.535 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.534 CRWrnafold: 0.432 Sensitivity ProbKnot: 0.534 CRWrnafold: 0.438 Positive Predictive Value ProbKnot: 0.535 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.544 RNASLOpt: 0.442 Sensitivity ProbKnot: 0.541 RNASLOpt: 0.419 Positive Predictive Value ProbKnot: 0.549 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.543 RNAshapes: 0.438 Sensitivity ProbKnot: 0.539 RNAshapes: 0.434 Positive Predictive Value ProbKnot: 0.548 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.619 Murlet(seed): 0.569 Sensitivity ProbKnot: 0.624 Murlet(seed): 0.383 Positive Predictive Value ProbKnot: 0.614 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.590 RSpredict(20): 0.418 Sensitivity ProbKnot: 0.572 RSpredict(20): 0.285 Positive Predictive Value ProbKnot: 0.610 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.590 Carnac(20): 0.378 Sensitivity ProbKnot: 0.572 Carnac(20): 0.166 Positive Predictive Value ProbKnot: 0.610 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.534 RNAwolf: 0.339 Sensitivity ProbKnot: 0.534 RNAwolf: 0.355 Positive Predictive Value ProbKnot: 0.535 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.600 CMfinder(seed): 0.454 Sensitivity ProbKnot: 0.599 CMfinder(seed): 0.271 Positive Predictive Value ProbKnot: 0.602 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.597 RSpredict(seed): 0.214 Sensitivity ProbKnot: 0.585 RSpredict(seed): 0.089 Positive Predictive Value ProbKnot: 0.611 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.541 Vsfold4: 0.306 Sensitivity ProbKnot: 0.538 Vsfold4: 0.282 Positive Predictive Value ProbKnot: 0.546 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.542 Vsfold5: 0.300 Sensitivity ProbKnot: 0.539 Vsfold5: 0.286 Positive Predictive Value ProbKnot: 0.547 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.567 NanoFolder: 0.166 Sensitivity ProbKnot: 0.560 NanoFolder: 0.197 Positive Predictive Value ProbKnot: 0.576 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.561 Carnac(seed): 0.150 Sensitivity ProbKnot: 0.565 Carnac(seed): 0.028 Positive Predictive Value ProbKnot: 0.558 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.596 Mastr(seed): 0.073 Sensitivity ProbKnot: 0.586 Mastr(seed): 0.006 Positive Predictive Value ProbKnot: 0.607 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.640 ProbKnot: 0.429 Sensitivity HotKnots: 0.615 ProbKnot: 0.487 Positive Predictive Value HotKnots: 0.667 ProbKnot: 0.380 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: N/A Pknots: N/A Sensitivity ProbKnot: N/A Pknots: N/A Positive Predictive Value ProbKnot: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.634 Cylofold: 0.271 Sensitivity ProbKnot: 0.620 Cylofold: 0.241 Positive Predictive Value ProbKnot: 0.649 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: N/A MCFold: N/A Sensitivity ProbKnot: N/A MCFold: N/A Positive Predictive Value ProbKnot: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs ProbKnot Matthews Correlation Coefficient RDfolder: N/A ProbKnot: N/A Sensitivity RDfolder: N/A ProbKnot: N/A Positive Predictive Value RDfolder: N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: N/A Alterna: N/A Sensitivity ProbKnot: N/A Alterna: N/A Positive Predictive Value ProbKnot: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.590 Mastr(20): 0.000 Sensitivity ProbKnot: 0.572 Mastr(20): 0.000 Positive Predictive Value ProbKnot: 0.610 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(seed)	12 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.955 RNASampler(seed): 0.779 Sensitivity PETfold_pre2.0(seed): 0.915 RNASampler(seed): 0.659 Positive Predictive Value PETfold_pre2.0(seed): 0.997 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 6.70002765408e-09	12 RNASampler(seed) vs ContextFold Matthews Correlation Coefficient RNASampler(seed): 0.779 ContextFold: 0.694 Sensitivity RNASampler(seed): 0.659 ContextFold: 0.680 Positive Predictive Value RNASampler(seed): 0.921 ContextFold: 0.709 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	0 RNASampler(seed) vs TurboFold(20) Matthews Correlation Coefficient RNASampler(seed): N/A TurboFold(20): N/A Sensitivity RNASampler(seed): N/A TurboFold(20): N/A Positive Predictive Value RNASampler(seed): N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	12 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.946 RNASampler(seed): 0.779 Sensitivity CentroidAlifold(seed): 0.900 RNASampler(seed): 0.659 Positive Predictive Value CentroidAlifold(seed): 0.995 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.98760236454e-08	0 RNASampler(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient RNASampler(seed): N/A PETfold_pre2.0(20): N/A Sensitivity RNASampler(seed): N/A PETfold_pre2.0(20): N/A Positive Predictive Value RNASampler(seed): N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs PPfold(20) Matthews Correlation Coefficient RNASampler(seed): N/A PPfold(20): N/A Sensitivity RNASampler(seed): N/A PPfold(20): N/A Positive Predictive Value RNASampler(seed): N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	12 CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.807 RNASampler(seed): 0.779 Sensitivity CentroidHomfold‑LAST: 0.729 RNASampler(seed): 0.659 Positive Predictive Value CentroidHomfold‑LAST: 0.894 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.69265863073e-08	0 RNASampler(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A CentroidAlifold(20): N/A Sensitivity RNASampler(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value RNASampler(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	12 MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.813 RNASampler(seed): 0.779 Sensitivity MXScarna(seed): 0.782 RNASampler(seed): 0.659 Positive Predictive Value MXScarna(seed): 0.845 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.08252958266e-08	12 RNASampler(seed) vs IPknot Matthews Correlation Coefficient RNASampler(seed): 0.779 IPknot: 0.757 Sensitivity RNASampler(seed): 0.659 IPknot: 0.738 Positive Predictive Value RNASampler(seed): 0.921 IPknot: 0.778 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 3.51046461328e-06	0 RNASampler(seed) vs RNAalifold(20) Matthews Correlation Coefficient RNASampler(seed): N/A RNAalifold(20): N/A Sensitivity RNASampler(seed): N/A RNAalifold(20): N/A Positive Predictive Value RNASampler(seed): N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	9 TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.900 RNASampler(seed): 0.811 Sensitivity TurboFold(seed): 0.862 RNASampler(seed): 0.687 Positive Predictive Value TurboFold(seed): 0.939 RNASampler(seed): 0.959 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs Multilign(20) Matthews Correlation Coefficient RNASampler(seed): N/A Multilign(20): N/A Sensitivity RNASampler(seed): N/A Multilign(20): N/A Positive Predictive Value RNASampler(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs MXScarna(20) Matthews Correlation Coefficient RNASampler(seed): N/A MXScarna(20): N/A Sensitivity RNASampler(seed): N/A MXScarna(20): N/A Positive Predictive Value RNASampler(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	12 RNASampler(seed) vs CentroidFold Matthews Correlation Coefficient RNASampler(seed): 0.779 CentroidFold: 0.719 Sensitivity RNASampler(seed): 0.659 CentroidFold: 0.665 Positive Predictive Value RNASampler(seed): 0.921 CentroidFold: 0.778 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.00627773251e-08	12 RNASampler(seed) vs Contrafold Matthews Correlation Coefficient RNASampler(seed): 0.779 Contrafold: 0.706 Sensitivity RNASampler(seed): 0.659 Contrafold: 0.703 Positive Predictive Value RNASampler(seed): 0.921 Contrafold: 0.709 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.4651262096e-08	9 PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.941 RNASampler(seed): 0.811 Sensitivity PPfold(seed): 0.889 RNASampler(seed): 0.687 Positive Predictive Value PPfold(seed): 0.996 RNASampler(seed): 0.959 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	12 RNASampler(seed) vs Sfold Matthews Correlation Coefficient RNASampler(seed): 0.779 Sfold: 0.689 Sensitivity RNASampler(seed): 0.659 Sfold: 0.644 Positive Predictive Value RNASampler(seed): 0.921 Sfold: 0.738 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.82627677697e-08	12 RNASampler(seed) vs MaxExpect Matthews Correlation Coefficient RNASampler(seed): 0.779 MaxExpect: 0.637 Sensitivity RNASampler(seed): 0.659 MaxExpect: 0.654 Positive Predictive Value RNASampler(seed): 0.921 MaxExpect: 0.622 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 8.44035332136e-09	12 RNASampler(seed) vs ProbKnot Matthews Correlation Coefficient RNASampler(seed): 0.779 ProbKnot: 0.644 Sensitivity RNASampler(seed): 0.659 ProbKnot: 0.668 Positive Predictive Value RNASampler(seed): 0.921 ProbKnot: 0.623 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.22210847902e-08		+ RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.779 Fold: 0.631 Sensitivity RNASampler(seed): 0.659 Fold: 0.648 Positive Predictive Value RNASampler(seed): 0.921 Fold: 0.614 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.47941000302e-08	? RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): N/A RNASampler(seed): N/A Sensitivity RNASampler(20): N/A RNASampler(seed): N/A Positive Predictive Value RNASampler(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(20): N/A Sensitivity RNASampler(seed): N/A Murlet(20): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.779 UNAFold: 0.645 Sensitivity RNASampler(seed): 0.659 UNAFold: 0.657 Positive Predictive Value RNASampler(seed): 0.921 UNAFold: 0.634 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ RNASampler(seed) vs PknotsRG Matthews Correlation Coefficient RNASampler(seed): 0.779 PknotsRG: 0.638 Sensitivity RNASampler(seed): 0.659 PknotsRG: 0.653 Positive Predictive Value RNASampler(seed): 0.921 PknotsRG: 0.624 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.39551335374e-08	+ RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.779 RNAfold: 0.711 Sensitivity RNASampler(seed): 0.659 RNAfold: 0.721 Positive Predictive Value RNASampler(seed): 0.921 RNAfold: 0.701 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.42300079339e-08	? Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.879 RNASampler(seed): 0.807 Sensitivity Multilign(seed): 0.851 RNASampler(seed): 0.679 Positive Predictive Value Multilign(seed): 0.908 RNASampler(seed): 0.959 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.773 Afold: 0.629 Sensitivity RNASampler(seed): 0.652 Afold: 0.638 Positive Predictive Value RNASampler(seed): 0.917 Afold: 0.621 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.9460272886e-09	+ RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.779 RNAsubopt: 0.643 Sensitivity RNASampler(seed): 0.659 RNAsubopt: 0.657 Positive Predictive Value RNASampler(seed): 0.921 RNAsubopt: 0.631 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.1413769576e-08	- RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.902 RNASampler(seed): 0.779 Sensitivity RNAalifold(seed): 0.818 RNASampler(seed): 0.659 Positive Predictive Value RNAalifold(seed): 0.995 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.64481516727e-08	? 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 McQFold Matthews Correlation Coefficient RNASampler(seed): 0.779 McQFold: 0.446 Sensitivity RNASampler(seed): 0.659 McQFold: 0.452 Positive Predictive Value RNASampler(seed): 0.921 McQFold: 0.442 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.779 CRWrnafold: 0.474 Sensitivity RNASampler(seed): 0.659 CRWrnafold: 0.499 Positive Predictive Value RNASampler(seed): 0.921 CRWrnafold: 0.452 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.10198558684e-08	+ RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.779 RNASLOpt: 0.568 Sensitivity RNASampler(seed): 0.659 RNASLOpt: 0.569 Positive Predictive Value RNASampler(seed): 0.921 RNASLOpt: 0.568 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.38194587311e-08	+ RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.780 RNAshapes: 0.548 Sensitivity RNASampler(seed): 0.659 RNAshapes: 0.567 Positive Predictive Value RNASampler(seed): 0.923 RNAshapes: 0.530 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.779 Murlet(seed): 0.765 Sensitivity RNASampler(seed): 0.659 Murlet(seed): 0.595 Positive Predictive Value RNASampler(seed): 0.921 Murlet(seed): 0.985 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	? RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): N/A RNASampler(seed): N/A Sensitivity RSpredict(20): N/A RNASampler(seed): N/A Positive Predictive Value RSpredict(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(20): N/A Sensitivity RNASampler(seed): N/A Carnac(20): N/A Positive Predictive Value RNASampler(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.779 RNAwolf: 0.287 Sensitivity RNASampler(seed): 0.659 RNAwolf: 0.307 Positive Predictive Value RNASampler(seed): 0.921 RNAwolf: 0.270 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.42300079339e-08	+ RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.779 CMfinder(seed): 0.534 Sensitivity RNASampler(seed): 0.659 CMfinder(seed): 0.390 Positive Predictive Value RNASampler(seed): 0.921 CMfinder(seed): 0.732 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	- RSpredict(seed) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(seed): 0.816 RNASampler(seed): 0.779 Sensitivity RSpredict(seed): 0.714 RNASampler(seed): 0.659 Positive Predictive Value RSpredict(seed): 0.934 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.30295446166e-08	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.779 Vsfold4: 0.215 Sensitivity RNASampler(seed): 0.659 Vsfold4: 0.210 Positive Predictive Value RNASampler(seed): 0.921 Vsfold4: 0.223 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.18011954625e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.779 Vsfold5: 0.290 Sensitivity RNASampler(seed): 0.659 Vsfold5: 0.303 Positive Predictive Value RNASampler(seed): 0.921 Vsfold5: 0.280 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 5.11462970451e-09	? RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.698 NanoFolder: 0.075 Sensitivity RNASampler(seed): 0.600 NanoFolder: 0.113 Positive Predictive Value RNASampler(seed): 0.814 NanoFolder: 0.054 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): 0.779 Carnac(seed): 0.659 Sensitivity RNASampler(seed): 0.659 Carnac(seed): 0.481 Positive Predictive Value RNASampler(seed): 0.921 Carnac(seed): 0.902 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.45805449719e-08	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.779 Mastr(seed): 0.564 Sensitivity RNASampler(seed): 0.659 Mastr(seed): 0.356 Positive Predictive Value RNASampler(seed): 0.921 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.04409141234e-08	? HotKnots vs RNASampler(seed) Matthews Correlation Coefficient HotKnots: 0.640 RNASampler(seed): 0.523 Sensitivity HotKnots: 0.615 RNASampler(seed): 0.436 Positive Predictive Value HotKnots: 0.667 RNASampler(seed): 0.630 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): N/A Pknots: N/A Sensitivity RNASampler(seed): N/A Pknots: N/A Positive Predictive Value RNASampler(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): N/A Cylofold: N/A Sensitivity RNASampler(seed): N/A Cylofold: N/A Positive Predictive Value RNASampler(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): N/A MCFold: N/A Sensitivity RNASampler(seed): N/A MCFold: N/A Positive Predictive Value RNASampler(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): N/A RDfolder: N/A Sensitivity RNASampler(seed): N/A RDfolder: N/A Positive Predictive Value RNASampler(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): N/A Alterna: N/A Sensitivity RNASampler(seed): N/A Alterna: N/A Positive Predictive Value RNASampler(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): N/A RNASampler(seed): N/A Sensitivity Mastr(20): N/A RNASampler(seed): N/A Positive Predictive Value Mastr(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Fold	643 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 Fold: 0.520 Sensitivity PETfold_pre2.0(seed): 0.612 Fold: 0.522 Positive Predictive Value PETfold_pre2.0(seed): 0.803 Fold: 0.519 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.720 Fold: 0.511 Sensitivity ContextFold: 0.687 Fold: 0.517 Positive Predictive Value ContextFold: 0.756 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.752 Fold: 0.562 Sensitivity TurboFold(20): 0.701 Fold: 0.555 Positive Predictive Value TurboFold(20): 0.809 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 Fold: 0.573 Sensitivity CentroidAlifold(seed): 0.556 Fold: 0.570 Positive Predictive Value CentroidAlifold(seed): 0.906 Fold: 0.577 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Fold: 0.561 Sensitivity PETfold_pre2.0(20): 0.654 Fold: 0.553 Positive Predictive Value PETfold_pre2.0(20): 0.836 Fold: 0.570 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.733 Fold: 0.562 Sensitivity PPfold(20): 0.629 Fold: 0.554 Positive Predictive Value PPfold(20): 0.855 Fold: 0.571 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 Fold: 0.521 Sensitivity CentroidHomfold‑LAST: 0.491 Fold: 0.525 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Fold: 0.519 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Fold: 0.562 Sensitivity CentroidAlifold(20): 0.574 Fold: 0.555 Positive Predictive Value CentroidAlifold(20): 0.916 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.637 Fold: 0.573 Sensitivity MXScarna(seed): 0.535 Fold: 0.570 Positive Predictive Value MXScarna(seed): 0.759 Fold: 0.577 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.612 Fold: 0.511 Sensitivity IPknot: 0.561 Fold: 0.517 Positive Predictive Value IPknot: 0.667 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.668 Fold: 0.562 Sensitivity RNAalifold(20): 0.540 Fold: 0.555 Positive Predictive Value RNAalifold(20): 0.827 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.787 Fold: 0.643 Sensitivity TurboFold(seed): 0.760 Fold: 0.658 Positive Predictive Value TurboFold(seed): 0.815 Fold: 0.630 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.41358941668e-08	223 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.651 Fold: 0.564 Sensitivity Multilign(20): 0.590 Fold: 0.557 Positive Predictive Value Multilign(20): 0.721 Fold: 0.573 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.654 Fold: 0.562 Sensitivity MXScarna(20): 0.584 Fold: 0.555 Positive Predictive Value MXScarna(20): 0.735 Fold: 0.571 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.583 Fold: 0.511 Sensitivity CentroidFold: 0.533 Fold: 0.517 Positive Predictive Value CentroidFold: 0.638 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.567 Fold: 0.511 Sensitivity Contrafold: 0.558 Fold: 0.517 Positive Predictive Value Contrafold: 0.577 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs Fold Matthews Correlation Coefficient PPfold(seed): 0.716 Fold: 0.618 Sensitivity PPfold(seed): 0.652 Fold: 0.633 Positive Predictive Value PPfold(seed): 0.787 Fold: 0.605 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	818 Sfold vs Fold Matthews Correlation Coefficient Sfold: 0.538 Fold: 0.511 Sensitivity Sfold: 0.491 Fold: 0.517 Positive Predictive Value Sfold: 0.589 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.536 Fold: 0.511 Sensitivity MaxExpect: 0.527 Fold: 0.517 Positive Predictive Value MaxExpect: 0.546 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.534 Fold: 0.511 Sensitivity ProbKnot: 0.534 Fold: 0.517 Positive Predictive Value ProbKnot: 0.535 Fold: 0.506 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs Fold Matthews Correlation Coefficient RNASampler(seed): 0.779 Fold: 0.631 Sensitivity RNASampler(seed): 0.659 Fold: 0.648 Positive Predictive Value RNASampler(seed): 0.921 Fold: 0.614 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.47941000302e-08		- RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.565 Fold: 0.524 Sensitivity RNASampler(20): 0.413 Fold: 0.528 Positive Predictive Value RNASampler(20): 0.772 Fold: 0.523 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.573 Fold: 0.556 Sensitivity Murlet(20): 0.441 Fold: 0.550 Positive Predictive Value Murlet(20): 0.746 Fold: 0.563 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.511 UNAFold: 0.501 Sensitivity Fold: 0.517 UNAFold: 0.501 Positive Predictive Value Fold: 0.506 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.511 PknotsRG: 0.499 Sensitivity Fold: 0.517 PknotsRG: 0.504 Positive Predictive Value Fold: 0.506 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.511 RNAfold: 0.499 Sensitivity Fold: 0.517 RNAfold: 0.504 Positive Predictive Value Fold: 0.506 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.734 Fold: 0.584 Sensitivity Multilign(seed): 0.733 Fold: 0.611 Positive Predictive Value Multilign(seed): 0.737 Fold: 0.560 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.36849473644e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.533 Afold: 0.516 Sensitivity Fold: 0.537 Afold: 0.517 Positive Predictive Value Fold: 0.529 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.521 RNAsubopt: 0.501 Sensitivity Fold: 0.525 RNAsubopt: 0.510 Positive Predictive Value Fold: 0.519 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.572 RNAalifold(seed): 0.541 Sensitivity Fold: 0.569 RNAalifold(seed): 0.344 Positive Predictive Value Fold: 0.577 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.562 CMfinder(20): 0.478 Sensitivity Fold: 0.555 CMfinder(20): 0.309 Positive Predictive Value Fold: 0.571 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.511 McQFold: 0.443 Sensitivity Fold: 0.517 McQFold: 0.435 Positive Predictive Value Fold: 0.506 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.511 CRWrnafold: 0.432 Sensitivity Fold: 0.517 CRWrnafold: 0.438 Positive Predictive Value Fold: 0.506 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.523 RNASLOpt: 0.442 Sensitivity Fold: 0.527 RNASLOpt: 0.419 Positive Predictive Value Fold: 0.521 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.522 RNAshapes: 0.438 Sensitivity Fold: 0.525 RNAshapes: 0.434 Positive Predictive Value Fold: 0.520 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.598 Murlet(seed): 0.569 Sensitivity Fold: 0.608 Murlet(seed): 0.383 Positive Predictive Value Fold: 0.590 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.562 RSpredict(20): 0.418 Sensitivity Fold: 0.555 RSpredict(20): 0.285 Positive Predictive Value Fold: 0.571 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.562 Carnac(20): 0.378 Sensitivity Fold: 0.555 Carnac(20): 0.166 Positive Predictive Value Fold: 0.571 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.511 RNAwolf: 0.339 Sensitivity Fold: 0.517 RNAwolf: 0.355 Positive Predictive Value Fold: 0.506 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.594 CMfinder(seed): 0.454 Sensitivity Fold: 0.604 CMfinder(seed): 0.271 Positive Predictive Value Fold: 0.586 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.573 RSpredict(seed): 0.214 Sensitivity Fold: 0.570 RSpredict(seed): 0.089 Positive Predictive Value Fold: 0.577 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.520 Vsfold4: 0.306 Sensitivity Fold: 0.524 Vsfold4: 0.282 Positive Predictive Value Fold: 0.518 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.521 Vsfold5: 0.300 Sensitivity Fold: 0.525 Vsfold5: 0.286 Positive Predictive Value Fold: 0.519 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.534 NanoFolder: 0.166 Sensitivity Fold: 0.535 NanoFolder: 0.197 Positive Predictive Value Fold: 0.536 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.557 Carnac(seed): 0.150 Sensitivity Fold: 0.566 Carnac(seed): 0.028 Positive Predictive Value Fold: 0.549 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.572 Mastr(seed): 0.073 Sensitivity Fold: 0.570 Mastr(seed): 0.006 Positive Predictive Value Fold: 0.576 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.640 Fold: 0.468 Sensitivity HotKnots: 0.615 Fold: 0.487 Positive Predictive Value HotKnots: 0.667 Fold: 0.452 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Fold vs Pknots Matthews Correlation Coefficient Fold: N/A Pknots: N/A Sensitivity Fold: N/A Pknots: N/A Positive Predictive Value Fold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.597 Cylofold: 0.271 Sensitivity Fold: 0.591 Cylofold: 0.241 Positive Predictive Value Fold: 0.604 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Fold vs MCFold Matthews Correlation Coefficient Fold: N/A MCFold: N/A Sensitivity Fold: N/A MCFold: N/A Positive Predictive Value Fold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs RDfolder Matthews Correlation Coefficient Fold: N/A RDfolder: N/A Sensitivity Fold: N/A RDfolder: N/A Positive Predictive Value Fold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Fold vs Alterna Matthews Correlation Coefficient Fold: N/A Alterna: N/A Sensitivity Fold: N/A Alterna: N/A Positive Predictive Value Fold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.562 Mastr(20): 0.000 Sensitivity Fold: 0.555 Mastr(20): 0.000 Positive Predictive Value Fold: 0.571 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(20)	66 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.756 RNASampler(20): 0.594 Sensitivity PETfold_pre2.0(seed): 0.682 RNASampler(20): 0.461 Positive Predictive Value PETfold_pre2.0(seed): 0.840 RNASampler(20): 0.766 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.790 RNASampler(20): 0.565 Sensitivity ContextFold: 0.750 RNASampler(20): 0.413 Positive Predictive Value ContextFold: 0.832 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.734 RNASampler(20): 0.565 Sensitivity TurboFold(20): 0.691 RNASampler(20): 0.413 Positive Predictive Value TurboFold(20): 0.781 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.769 RNASampler(20): 0.578 Sensitivity CentroidAlifold(seed): 0.615 RNASampler(20): 0.384 Positive Predictive Value CentroidAlifold(seed): 0.961 RNASampler(20): 0.871 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	76 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.700 RNASampler(20): 0.566 Sensitivity PETfold_pre2.0(20): 0.610 RNASampler(20): 0.417 Positive Predictive Value PETfold_pre2.0(20): 0.805 RNASampler(20): 0.771 Number of pairs reference - predicted secondary structure: 76 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.689 RNASampler(20): 0.565 Sensitivity PPfold(20): 0.567 RNASampler(20): 0.413 Positive Predictive Value PPfold(20): 0.838 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.717 RNASampler(20): 0.565 Sensitivity CentroidHomfold‑LAST: 0.582 RNASampler(20): 0.413 Positive Predictive Value CentroidHomfold‑LAST: 0.885 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.719 RNASampler(20): 0.565 Sensitivity CentroidAlifold(20): 0.588 RNASampler(20): 0.413 Positive Predictive Value CentroidAlifold(20): 0.880 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.778 RNASampler(20): 0.578 Sensitivity MXScarna(seed): 0.721 RNASampler(20): 0.384 Positive Predictive Value MXScarna(seed): 0.841 RNASampler(20): 0.871 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.631 RNASampler(20): 0.565 Sensitivity IPknot: 0.577 RNASampler(20): 0.413 Positive Predictive Value IPknot: 0.690 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.661 RNASampler(20): 0.565 Sensitivity RNAalifold(20): 0.546 RNASampler(20): 0.413 Positive Predictive Value RNAalifold(20): 0.802 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(seed) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 RNASampler(20): 0.282 Sensitivity TurboFold(seed): 0.739 RNASampler(20): 0.080 Positive Predictive Value TurboFold(seed): 0.774 RNASampler(20): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	66 Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.619 RNASampler(20): 0.554 Sensitivity Multilign(20): 0.560 RNASampler(20): 0.404 Positive Predictive Value Multilign(20): 0.685 RNASampler(20): 0.762 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.646 RNASampler(20): 0.565 Sensitivity MXScarna(20): 0.607 RNASampler(20): 0.413 Positive Predictive Value MXScarna(20): 0.690 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.565 CentroidFold: 0.564 Sensitivity RNASampler(20): 0.413 CentroidFold: 0.513 Positive Predictive Value RNASampler(20): 0.772 CentroidFold: 0.623 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.85073699061	78 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.565 Contrafold: 0.546 Sensitivity RNASampler(20): 0.413 Contrafold: 0.536 Positive Predictive Value RNASampler(20): 0.772 Contrafold: 0.559 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PPfold(seed) vs RNASampler(20) Matthews Correlation Coefficient PPfold(seed): 0.847 RNASampler(20): 0.780 Sensitivity PPfold(seed): 0.782 RNASampler(20): 0.663 Positive Predictive Value PPfold(seed): 0.919 RNASampler(20): 0.918 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	78 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.565 Sfold: 0.523 Sensitivity RNASampler(20): 0.413 Sfold: 0.471 Positive Predictive Value RNASampler(20): 0.772 Sfold: 0.582 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.565 MaxExpect: 0.526 Sensitivity RNASampler(20): 0.413 MaxExpect: 0.518 Positive Predictive Value RNASampler(20): 0.772 MaxExpect: 0.536 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.565 ProbKnot: 0.524 Sensitivity RNASampler(20): 0.413 ProbKnot: 0.524 Positive Predictive Value RNASampler(20): 0.772 ProbKnot: 0.524 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): N/A RNASampler(seed): N/A Sensitivity RNASampler(20): N/A RNASampler(seed): N/A Positive Predictive Value RNASampler(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	78 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.565 Fold: 0.524 Sensitivity RNASampler(20): 0.413 Fold: 0.528 Positive Predictive Value RNASampler(20): 0.772 Fold: 0.523 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.623 RNASampler(20): 0.584 Sensitivity Murlet(20): 0.515 RNASampler(20): 0.443 Positive Predictive Value Murlet(20): 0.755 RNASampler(20): 0.771 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.565 UNAFold: 0.481 Sensitivity RNASampler(20): 0.413 UNAFold: 0.479 Positive Predictive Value RNASampler(20): 0.772 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.565 PknotsRG: 0.478 Sensitivity RNASampler(20): 0.413 PknotsRG: 0.483 Positive Predictive Value RNASampler(20): 0.772 PknotsRG: 0.474 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.565 RNAfold: 0.497 Sensitivity RNASampler(20): 0.413 RNAfold: 0.502 Positive Predictive Value RNASampler(20): 0.772 RNAfold: 0.494 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): N/A Multilign(seed): N/A Sensitivity RNASampler(20): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	- Afold vs RNASampler(20) Matthews Correlation Coefficient Afold: 0.570 RNASampler(20): 0.537 Sensitivity Afold: 0.570 RNASampler(20): 0.354 Positive Predictive Value Afold: 0.571 RNASampler(20): 0.818 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.565 RNAsubopt: 0.461 Sensitivity RNASampler(20): 0.413 RNAsubopt: 0.471 Positive Predictive Value RNASampler(20): 0.772 RNAsubopt: 0.454 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.639 RNASampler(20): 0.578 Sensitivity RNAalifold(seed): 0.436 RNASampler(20): 0.384 Positive Predictive Value RNAalifold(seed): 0.937 RNASampler(20): 0.871 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.565 CMfinder(20): 0.413 Sensitivity RNASampler(20): 0.413 CMfinder(20): 0.258 Positive Predictive Value RNASampler(20): 0.772 CMfinder(20): 0.663 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.565 McQFold: 0.388 Sensitivity RNASampler(20): 0.413 McQFold: 0.377 Positive Predictive Value RNASampler(20): 0.772 McQFold: 0.401 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.565 CRWrnafold: 0.425 Sensitivity RNASampler(20): 0.413 CRWrnafold: 0.427 Positive Predictive Value RNASampler(20): 0.772 CRWrnafold: 0.424 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.565 RNASLOpt: 0.393 Sensitivity RNASampler(20): 0.413 RNASLOpt: 0.372 Positive Predictive Value RNASampler(20): 0.772 RNASLOpt: 0.417 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.565 RNAshapes: 0.412 Sensitivity RNASampler(20): 0.413 RNAshapes: 0.410 Positive Predictive Value RNASampler(20): 0.775 RNAshapes: 0.416 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.780 Murlet(seed): 0.588 Sensitivity RNASampler(20): 0.663 Murlet(seed): 0.347 Positive Predictive Value RNASampler(20): 0.918 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	- RSpredict(20) vs RNASampler(20) Matthews Correlation Coefficient RSpredict(20): 0.588 RNASampler(20): 0.565 Sensitivity RSpredict(20): 0.517 RNASampler(20): 0.413 Positive Predictive Value RSpredict(20): 0.670 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.565 Carnac(20): 0.467 Sensitivity RNASampler(20): 0.413 Carnac(20): 0.256 Positive Predictive Value RNASampler(20): 0.772 Carnac(20): 0.852 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.565 RNAwolf: 0.325 Sensitivity RNASampler(20): 0.413 RNAwolf: 0.340 Positive Predictive Value RNASampler(20): 0.772 RNAwolf: 0.313 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.578 RSpredict(seed): 0.465 Sensitivity RNASampler(20): 0.384 RSpredict(seed): 0.322 Positive Predictive Value RNASampler(20): 0.871 RSpredict(seed): 0.674 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.565 Vsfold4: 0.195 Sensitivity RNASampler(20): 0.413 Vsfold4: 0.181 Positive Predictive Value RNASampler(20): 0.772 Vsfold4: 0.213 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.565 Vsfold5: 0.188 Sensitivity RNASampler(20): 0.413 Vsfold5: 0.178 Positive Predictive Value RNASampler(20): 0.772 Vsfold5: 0.201 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.602 NanoFolder: 0.121 Sensitivity RNASampler(20): 0.450 NanoFolder: 0.148 Positive Predictive Value RNASampler(20): 0.805 NanoFolder: 0.102 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	? RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.506 Carnac(seed): 0.000 Sensitivity RNASampler(20): 0.297 Carnac(seed): 0.000 Positive Predictive Value RNASampler(20): 0.865 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.578 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.384 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.871 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): N/A HotKnots: N/A Sensitivity RNASampler(20): N/A HotKnots: N/A Positive Predictive Value RNASampler(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): N/A Pknots: N/A Sensitivity RNASampler(20): N/A Pknots: N/A Positive Predictive Value RNASampler(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): N/A Cylofold: N/A Sensitivity RNASampler(20): N/A Cylofold: N/A Positive Predictive Value RNASampler(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): N/A MCFold: N/A Sensitivity RNASampler(20): N/A MCFold: N/A Positive Predictive Value RNASampler(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): N/A RDfolder: N/A Sensitivity RNASampler(20): N/A RDfolder: N/A Positive Predictive Value RNASampler(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): N/A Alterna: N/A Sensitivity RNASampler(20): N/A Alterna: N/A Positive Predictive Value RNASampler(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.565 Mastr(20): 0.000 Sensitivity RNASampler(20): 0.413 Mastr(20): 0.000 Positive Predictive Value RNASampler(20): 0.772 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(20)	171 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.770 Murlet(20): 0.574 Sensitivity PETfold_pre2.0(seed): 0.697 Murlet(20): 0.444 Positive Predictive Value PETfold_pre2.0(seed): 0.852 Murlet(20): 0.744 Number of pairs reference - predicted secondary structure: 171 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.829 Murlet(20): 0.573 Sensitivity ContextFold: 0.784 Murlet(20): 0.441 Positive Predictive Value ContextFold: 0.878 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.747 Murlet(20): 0.573 Sensitivity TurboFold(20): 0.695 Murlet(20): 0.441 Positive Predictive Value TurboFold(20): 0.804 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.750 Murlet(20): 0.568 Sensitivity CentroidAlifold(seed): 0.590 Murlet(20): 0.427 Positive Predictive Value CentroidAlifold(seed): 0.954 Murlet(20): 0.758 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.738 Murlet(20): 0.573 Sensitivity PETfold_pre2.0(20): 0.660 Murlet(20): 0.441 Positive Predictive Value PETfold_pre2.0(20): 0.827 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	174 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.735 Murlet(20): 0.576 Sensitivity PPfold(20): 0.637 Murlet(20): 0.445 Positive Predictive Value PPfold(20): 0.849 Murlet(20): 0.749 Number of pairs reference - predicted secondary structure: 174 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.713 Murlet(20): 0.573 Sensitivity CentroidHomfold‑LAST: 0.569 Murlet(20): 0.441 Positive Predictive Value CentroidHomfold‑LAST: 0.893 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.732 Murlet(20): 0.573 Sensitivity CentroidAlifold(20): 0.591 Murlet(20): 0.441 Positive Predictive Value CentroidAlifold(20): 0.908 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.696 Murlet(20): 0.568 Sensitivity MXScarna(seed): 0.600 Murlet(20): 0.427 Positive Predictive Value MXScarna(seed): 0.807 Murlet(20): 0.758 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.649 Murlet(20): 0.573 Sensitivity IPknot: 0.580 Murlet(20): 0.441 Positive Predictive Value IPknot: 0.728 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.679 Murlet(20): 0.573 Sensitivity RNAalifold(20): 0.560 Murlet(20): 0.441 Positive Predictive Value RNAalifold(20): 0.823 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): N/A Murlet(20): N/A Sensitivity TurboFold(seed): N/A Murlet(20): N/A Positive Predictive Value TurboFold(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	155 Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.660 Murlet(20): 0.565 Sensitivity Multilign(20): 0.602 Murlet(20): 0.432 Positive Predictive Value Multilign(20): 0.724 Murlet(20): 0.740 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.646 Murlet(20): 0.573 Sensitivity MXScarna(20): 0.582 Murlet(20): 0.441 Positive Predictive Value MXScarna(20): 0.718 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 CentroidFold vs Murlet(20) Matthews Correlation Coefficient CentroidFold: 0.607 Murlet(20): 0.573 Sensitivity CentroidFold: 0.544 Murlet(20): 0.441 Positive Predictive Value CentroidFold: 0.680 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Contrafold vs Murlet(20) Matthews Correlation Coefficient Contrafold: 0.592 Murlet(20): 0.573 Sensitivity Contrafold: 0.571 Murlet(20): 0.441 Positive Predictive Value Contrafold: 0.615 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PPfold(seed) vs Murlet(20) Matthews Correlation Coefficient PPfold(seed): 0.847 Murlet(20): 0.782 Sensitivity PPfold(seed): 0.782 Murlet(20): 0.683 Positive Predictive Value PPfold(seed): 0.919 Murlet(20): 0.896 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	176 Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.573 Sfold: 0.570 Sensitivity Murlet(20): 0.441 Sfold: 0.506 Positive Predictive Value Murlet(20): 0.746 Sfold: 0.644 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 0.554240997957	176 MaxExpect vs Murlet(20) Matthews Correlation Coefficient MaxExpect: 0.580 Murlet(20): 0.573 Sensitivity MaxExpect: 0.559 Murlet(20): 0.441 Positive Predictive Value MaxExpect: 0.604 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 7.5939721025e-08	176 ProbKnot vs Murlet(20) Matthews Correlation Coefficient ProbKnot: 0.578 Murlet(20): 0.573 Sensitivity ProbKnot: 0.562 Murlet(20): 0.441 Positive Predictive Value ProbKnot: 0.596 Murlet(20): 0.746 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 9.94962292175e-07	0 RNASampler(seed) vs Murlet(20) Matthews Correlation Coefficient RNASampler(seed): N/A Murlet(20): N/A Sensitivity RNASampler(seed): N/A Murlet(20): N/A Positive Predictive Value RNASampler(seed): N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	176 Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.573 Fold: 0.556 Sensitivity Murlet(20): 0.441 Fold: 0.550 Positive Predictive Value Murlet(20): 0.746 Fold: 0.563 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 Murlet(20) vs RNASampler(20) Matthews Correlation Coefficient Murlet(20): 0.623 RNASampler(20): 0.584 Sensitivity Murlet(20): 0.515 RNASampler(20): 0.443 Positive Predictive Value Murlet(20): 0.755 RNASampler(20): 0.771 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.573 UNAFold: 0.532 Sensitivity Murlet(20): 0.441 UNAFold: 0.522 Positive Predictive Value Murlet(20): 0.746 UNAFold: 0.543 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.573 PknotsRG: 0.513 Sensitivity Murlet(20): 0.441 PknotsRG: 0.507 Positive Predictive Value Murlet(20): 0.746 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.573 RNAfold: 0.532 Sensitivity Murlet(20): 0.441 RNAfold: 0.526 Positive Predictive Value Murlet(20): 0.746 RNAfold: 0.540 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): N/A Multilign(seed): N/A Sensitivity Murlet(20): N/A Multilign(seed): N/A Positive Predictive Value Murlet(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	= Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.550 Afold: 0.546 Sensitivity Murlet(20): 0.410 Afold: 0.535 Positive Predictive Value Murlet(20): 0.739 Afold: 0.559 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 0.0106540216989	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.573 RNAsubopt: 0.518 Sensitivity Murlet(20): 0.441 RNAsubopt: 0.518 Positive Predictive Value Murlet(20): 0.746 RNAsubopt: 0.519 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.568 RNAalifold(seed): 0.515 Sensitivity Murlet(20): 0.427 RNAalifold(seed): 0.314 Positive Predictive Value Murlet(20): 0.758 RNAalifold(seed): 0.844 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.573 CMfinder(20): 0.467 Sensitivity Murlet(20): 0.441 CMfinder(20): 0.302 Positive Predictive Value Murlet(20): 0.746 CMfinder(20): 0.724 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.573 McQFold: 0.427 Sensitivity Murlet(20): 0.441 McQFold: 0.411 Positive Predictive Value Murlet(20): 0.746 McQFold: 0.446 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.573 CRWrnafold: 0.440 Sensitivity Murlet(20): 0.441 CRWrnafold: 0.434 Positive Predictive Value Murlet(20): 0.746 CRWrnafold: 0.449 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.581 RNASLOpt: 0.425 Sensitivity Murlet(20): 0.452 RNASLOpt: 0.395 Positive Predictive Value Murlet(20): 0.750 RNASLOpt: 0.460 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.579 RNAshapes: 0.446 Sensitivity Murlet(20): 0.446 RNAshapes: 0.434 Positive Predictive Value Murlet(20): 0.752 RNAshapes: 0.459 Number of pairs reference - predicted secondary structure: 170 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.782 Murlet(seed): 0.588 Sensitivity Murlet(20): 0.683 Murlet(seed): 0.347 Positive Predictive Value Murlet(20): 0.896 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.573 RSpredict(20): 0.451 Sensitivity Murlet(20): 0.441 RSpredict(20): 0.324 Positive Predictive Value Murlet(20): 0.746 RSpredict(20): 0.629 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.573 Carnac(20): 0.413 Sensitivity Murlet(20): 0.441 Carnac(20): 0.197 Positive Predictive Value Murlet(20): 0.746 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.573 RNAwolf: 0.354 Sensitivity Murlet(20): 0.441 RNAwolf: 0.366 Positive Predictive Value Murlet(20): 0.746 RNAwolf: 0.345 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(20): N/A CMfinder(seed): N/A Sensitivity Murlet(20): N/A CMfinder(seed): N/A Positive Predictive Value Murlet(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.568 RSpredict(seed): 0.204 Sensitivity Murlet(20): 0.427 RSpredict(seed): 0.081 Positive Predictive Value Murlet(20): 0.758 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.577 Vsfold4: 0.337 Sensitivity Murlet(20): 0.445 Vsfold4: 0.306 Positive Predictive Value Murlet(20): 0.748 Vsfold4: 0.374 Number of pairs reference - predicted secondary structure: 172 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.578 Vsfold5: 0.316 Sensitivity Murlet(20): 0.447 Vsfold5: 0.293 Positive Predictive Value Murlet(20): 0.750 Vsfold5: 0.343 Number of pairs reference - predicted secondary structure: 170 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.551 NanoFolder: 0.150 Sensitivity Murlet(20): 0.416 NanoFolder: 0.174 Positive Predictive Value Murlet(20): 0.730 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.618 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.496 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.771 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.84540901819e-09	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.575 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.435 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.762 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Murlet(20) Matthews Correlation Coefficient HotKnots: N/A Murlet(20): N/A Sensitivity HotKnots: N/A Murlet(20): N/A Positive Predictive Value HotKnots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Murlet(20) Matthews Correlation Coefficient Pknots: N/A Murlet(20): N/A Sensitivity Pknots: N/A Murlet(20): N/A Positive Predictive Value Pknots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: N/A Murlet(20): N/A Sensitivity Cylofold: N/A Murlet(20): N/A Positive Predictive Value Cylofold: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): N/A MCFold: N/A Sensitivity Murlet(20): N/A MCFold: N/A Positive Predictive Value Murlet(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Murlet(20) Matthews Correlation Coefficient RDfolder: N/A Murlet(20): N/A Sensitivity RDfolder: N/A Murlet(20): N/A Positive Predictive Value RDfolder: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): N/A Alterna: N/A Sensitivity Murlet(20): N/A Alterna: N/A Positive Predictive Value Murlet(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.573 Mastr(20): 0.000 Sensitivity Murlet(20): 0.441 Mastr(20): 0.000 Positive Predictive Value Murlet(20): 0.746 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08
UNAFold	643 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 UNAFold: 0.506 Sensitivity PETfold_pre2.0(seed): 0.612 UNAFold: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.803 UNAFold: 0.511 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.720 UNAFold: 0.501 Sensitivity ContextFold: 0.687 UNAFold: 0.501 Positive Predictive Value ContextFold: 0.756 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.752 UNAFold: 0.547 Sensitivity TurboFold(20): 0.701 UNAFold: 0.535 Positive Predictive Value TurboFold(20): 0.809 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 UNAFold: 0.576 Sensitivity CentroidAlifold(seed): 0.556 UNAFold: 0.566 Positive Predictive Value CentroidAlifold(seed): 0.906 UNAFold: 0.588 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 UNAFold: 0.546 Sensitivity PETfold_pre2.0(20): 0.654 UNAFold: 0.534 Positive Predictive Value PETfold_pre2.0(20): 0.836 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.733 UNAFold: 0.547 Sensitivity PPfold(20): 0.629 UNAFold: 0.535 Positive Predictive Value PPfold(20): 0.855 UNAFold: 0.561 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 UNAFold: 0.510 Sensitivity CentroidHomfold‑LAST: 0.491 UNAFold: 0.507 Positive Predictive Value CentroidHomfold‑LAST: 0.862 UNAFold: 0.514 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 UNAFold: 0.547 Sensitivity CentroidAlifold(20): 0.574 UNAFold: 0.535 Positive Predictive Value CentroidAlifold(20): 0.916 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.637 UNAFold: 0.576 Sensitivity MXScarna(seed): 0.535 UNAFold: 0.566 Positive Predictive Value MXScarna(seed): 0.759 UNAFold: 0.588 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.612 UNAFold: 0.501 Sensitivity IPknot: 0.561 UNAFold: 0.501 Positive Predictive Value IPknot: 0.667 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.668 UNAFold: 0.547 Sensitivity RNAalifold(20): 0.540 UNAFold: 0.535 Positive Predictive Value RNAalifold(20): 0.827 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.787 UNAFold: 0.651 Sensitivity TurboFold(seed): 0.760 UNAFold: 0.659 Positive Predictive Value TurboFold(seed): 0.815 UNAFold: 0.644 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.07760058607e-08	223 Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.651 UNAFold: 0.551 Sensitivity Multilign(20): 0.590 UNAFold: 0.539 Positive Predictive Value Multilign(20): 0.721 UNAFold: 0.564 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.654 UNAFold: 0.547 Sensitivity MXScarna(20): 0.584 UNAFold: 0.535 Positive Predictive Value MXScarna(20): 0.735 UNAFold: 0.560 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.583 UNAFold: 0.501 Sensitivity CentroidFold: 0.533 UNAFold: 0.501 Positive Predictive Value CentroidFold: 0.638 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.567 UNAFold: 0.501 Sensitivity Contrafold: 0.558 UNAFold: 0.501 Positive Predictive Value Contrafold: 0.577 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs UNAFold Matthews Correlation Coefficient PPfold(seed): 0.716 UNAFold: 0.636 Sensitivity PPfold(seed): 0.652 UNAFold: 0.643 Positive Predictive Value PPfold(seed): 0.787 UNAFold: 0.630 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	818 Sfold vs UNAFold Matthews Correlation Coefficient Sfold: 0.538 UNAFold: 0.501 Sensitivity Sfold: 0.491 UNAFold: 0.501 Positive Predictive Value Sfold: 0.589 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.536 UNAFold: 0.501 Sensitivity MaxExpect: 0.527 UNAFold: 0.501 Positive Predictive Value MaxExpect: 0.546 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.534 UNAFold: 0.501 Sensitivity ProbKnot: 0.534 UNAFold: 0.501 Positive Predictive Value ProbKnot: 0.535 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs UNAFold Matthews Correlation Coefficient RNASampler(seed): 0.779 UNAFold: 0.645 Sensitivity RNASampler(seed): 0.659 UNAFold: 0.657 Positive Predictive Value RNASampler(seed): 0.921 UNAFold: 0.634 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.04409141234e-08	818 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.511 UNAFold: 0.501 Sensitivity Fold: 0.517 UNAFold: 0.501 Positive Predictive Value Fold: 0.506 UNAFold: 0.503 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.565 UNAFold: 0.481 Sensitivity RNASampler(20): 0.413 UNAFold: 0.479 Positive Predictive Value RNASampler(20): 0.772 UNAFold: 0.484 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.573 UNAFold: 0.532 Sensitivity Murlet(20): 0.441 UNAFold: 0.522 Positive Predictive Value Murlet(20): 0.746 UNAFold: 0.543 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.501 PknotsRG: 0.499 Sensitivity UNAFold: 0.501 PknotsRG: 0.504 Positive Predictive Value UNAFold: 0.503 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.501 RNAfold: 0.499 Sensitivity UNAFold: 0.501 RNAfold: 0.504 Positive Predictive Value UNAFold: 0.503 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.734 UNAFold: 0.565 Sensitivity Multilign(seed): 0.733 UNAFold: 0.588 Positive Predictive Value Multilign(seed): 0.737 UNAFold: 0.543 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.534 Afold: 0.516 Sensitivity UNAFold: 0.532 Afold: 0.517 Positive Predictive Value UNAFold: 0.537 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.510 RNAsubopt: 0.501 Sensitivity UNAFold: 0.507 RNAsubopt: 0.510 Positive Predictive Value UNAFold: 0.514 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.576 RNAalifold(seed): 0.541 Sensitivity UNAFold: 0.566 RNAalifold(seed): 0.344 Positive Predictive Value UNAFold: 0.588 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.547 CMfinder(20): 0.478 Sensitivity UNAFold: 0.535 CMfinder(20): 0.309 Positive Predictive Value UNAFold: 0.560 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.501 McQFold: 0.443 Sensitivity UNAFold: 0.501 McQFold: 0.435 Positive Predictive Value UNAFold: 0.503 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.501 CRWrnafold: 0.432 Sensitivity UNAFold: 0.501 CRWrnafold: 0.438 Positive Predictive Value UNAFold: 0.503 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.509 RNASLOpt: 0.442 Sensitivity UNAFold: 0.506 RNASLOpt: 0.419 Positive Predictive Value UNAFold: 0.514 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.509 RNAshapes: 0.438 Sensitivity UNAFold: 0.506 RNAshapes: 0.434 Positive Predictive Value UNAFold: 0.514 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.622 Murlet(seed): 0.569 Sensitivity UNAFold: 0.626 Murlet(seed): 0.383 Positive Predictive Value UNAFold: 0.620 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.547 RSpredict(20): 0.418 Sensitivity UNAFold: 0.535 RSpredict(20): 0.285 Positive Predictive Value UNAFold: 0.560 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.547 Carnac(20): 0.378 Sensitivity UNAFold: 0.535 Carnac(20): 0.166 Positive Predictive Value UNAFold: 0.560 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.501 RNAwolf: 0.339 Sensitivity UNAFold: 0.501 RNAwolf: 0.355 Positive Predictive Value UNAFold: 0.503 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.619 CMfinder(seed): 0.454 Sensitivity UNAFold: 0.617 CMfinder(seed): 0.271 Positive Predictive Value UNAFold: 0.623 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.576 RSpredict(seed): 0.214 Sensitivity UNAFold: 0.566 RSpredict(seed): 0.089 Positive Predictive Value UNAFold: 0.588 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.508 Vsfold4: 0.306 Sensitivity UNAFold: 0.505 Vsfold4: 0.282 Positive Predictive Value UNAFold: 0.512 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.508 Vsfold5: 0.300 Sensitivity UNAFold: 0.505 Vsfold5: 0.286 Positive Predictive Value UNAFold: 0.512 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.533 NanoFolder: 0.166 Sensitivity UNAFold: 0.527 NanoFolder: 0.197 Positive Predictive Value UNAFold: 0.540 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.576 Carnac(seed): 0.150 Sensitivity UNAFold: 0.576 Carnac(seed): 0.028 Positive Predictive Value UNAFold: 0.577 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.576 Mastr(seed): 0.073 Sensitivity UNAFold: 0.567 Mastr(seed): 0.006 Positive Predictive Value UNAFold: 0.586 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.667 HotKnots: 0.640 Sensitivity UNAFold: 0.641 HotKnots: 0.615 Positive Predictive Value UNAFold: 0.694 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: N/A Pknots: N/A Sensitivity UNAFold: N/A Pknots: N/A Positive Predictive Value UNAFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.443 Cylofold: 0.271 Sensitivity UNAFold: 0.431 Cylofold: 0.241 Positive Predictive Value UNAFold: 0.457 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: N/A MCFold: N/A Sensitivity UNAFold: N/A MCFold: N/A Positive Predictive Value UNAFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: N/A RDfolder: N/A Sensitivity UNAFold: N/A RDfolder: N/A Positive Predictive Value UNAFold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: N/A Alterna: N/A Sensitivity UNAFold: N/A Alterna: N/A Positive Predictive Value UNAFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.547 Mastr(20): 0.000 Sensitivity UNAFold: 0.535 Mastr(20): 0.000 Positive Predictive Value UNAFold: 0.560 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	643 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 PknotsRG: 0.503 Sensitivity PETfold_pre2.0(seed): 0.612 PknotsRG: 0.504 Positive Predictive Value PETfold_pre2.0(seed): 0.803 PknotsRG: 0.503 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.720 PknotsRG: 0.499 Sensitivity ContextFold: 0.687 PknotsRG: 0.504 Positive Predictive Value ContextFold: 0.756 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.752 PknotsRG: 0.525 Sensitivity TurboFold(20): 0.701 PknotsRG: 0.518 Positive Predictive Value TurboFold(20): 0.809 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 PknotsRG: 0.560 Sensitivity CentroidAlifold(seed): 0.556 PknotsRG: 0.554 Positive Predictive Value CentroidAlifold(seed): 0.906 PknotsRG: 0.567 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 PknotsRG: 0.525 Sensitivity PETfold_pre2.0(20): 0.654 PknotsRG: 0.517 Positive Predictive Value PETfold_pre2.0(20): 0.836 PknotsRG: 0.534 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.733 PknotsRG: 0.524 Sensitivity PPfold(20): 0.629 PknotsRG: 0.517 Positive Predictive Value PPfold(20): 0.855 PknotsRG: 0.534 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 PknotsRG: 0.506 Sensitivity CentroidHomfold‑LAST: 0.491 PknotsRG: 0.509 Positive Predictive Value CentroidHomfold‑LAST: 0.862 PknotsRG: 0.506 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.725 PknotsRG: 0.525 Sensitivity CentroidAlifold(20): 0.574 PknotsRG: 0.518 Positive Predictive Value CentroidAlifold(20): 0.916 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.637 PknotsRG: 0.559 Sensitivity MXScarna(seed): 0.535 PknotsRG: 0.554 Positive Predictive Value MXScarna(seed): 0.759 PknotsRG: 0.566 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.612 PknotsRG: 0.499 Sensitivity IPknot: 0.561 PknotsRG: 0.504 Positive Predictive Value IPknot: 0.667 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.668 PknotsRG: 0.525 Sensitivity RNAalifold(20): 0.540 PknotsRG: 0.518 Positive Predictive Value RNAalifold(20): 0.827 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs PknotsRG Matthews Correlation Coefficient TurboFold(seed): 0.787 PknotsRG: 0.605 Sensitivity TurboFold(seed): 0.760 PknotsRG: 0.616 Positive Predictive Value TurboFold(seed): 0.815 PknotsRG: 0.594 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.10499527239e-08	223 Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.651 PknotsRG: 0.525 Sensitivity Multilign(20): 0.590 PknotsRG: 0.517 Positive Predictive Value Multilign(20): 0.721 PknotsRG: 0.534 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.654 PknotsRG: 0.525 Sensitivity MXScarna(20): 0.584 PknotsRG: 0.518 Positive Predictive Value MXScarna(20): 0.735 PknotsRG: 0.535 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.583 PknotsRG: 0.499 Sensitivity CentroidFold: 0.533 PknotsRG: 0.504 Positive Predictive Value CentroidFold: 0.638 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.567 PknotsRG: 0.499 Sensitivity Contrafold: 0.558 PknotsRG: 0.504 Positive Predictive Value Contrafold: 0.577 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs PknotsRG Matthews Correlation Coefficient PPfold(seed): 0.716 PknotsRG: 0.642 Sensitivity PPfold(seed): 0.652 PknotsRG: 0.655 Positive Predictive Value PPfold(seed): 0.787 PknotsRG: 0.631 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	818 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.538 PknotsRG: 0.499 Sensitivity Sfold: 0.491 PknotsRG: 0.504 Positive Predictive Value Sfold: 0.589 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.536 PknotsRG: 0.499 Sensitivity MaxExpect: 0.527 PknotsRG: 0.504 Positive Predictive Value MaxExpect: 0.546 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.534 PknotsRG: 0.499 Sensitivity ProbKnot: 0.534 PknotsRG: 0.504 Positive Predictive Value ProbKnot: 0.535 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs PknotsRG Matthews Correlation Coefficient RNASampler(seed): 0.779 PknotsRG: 0.638 Sensitivity RNASampler(seed): 0.659 PknotsRG: 0.653 Positive Predictive Value RNASampler(seed): 0.921 PknotsRG: 0.624 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.39551335374e-08	818 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.511 PknotsRG: 0.499 Sensitivity Fold: 0.517 PknotsRG: 0.504 Positive Predictive Value Fold: 0.506 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.565 PknotsRG: 0.478 Sensitivity RNASampler(20): 0.413 PknotsRG: 0.483 Positive Predictive Value RNASampler(20): 0.772 PknotsRG: 0.474 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.573 PknotsRG: 0.513 Sensitivity Murlet(20): 0.441 PknotsRG: 0.507 Positive Predictive Value Murlet(20): 0.746 PknotsRG: 0.521 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.501 PknotsRG: 0.499 Sensitivity UNAFold: 0.501 PknotsRG: 0.504 Positive Predictive Value UNAFold: 0.503 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08		= RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.499 PknotsRG: 0.499 Sensitivity RNAfold: 0.504 PknotsRG: 0.504 Positive Predictive Value RNAfold: 0.495 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 0.288298117014	- Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.734 PknotsRG: 0.558 Sensitivity Multilign(seed): 0.733 PknotsRG: 0.582 Positive Predictive Value Multilign(seed): 0.737 PknotsRG: 0.536 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.57547243792e-09	+ PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.523 Afold: 0.516 Sensitivity PknotsRG: 0.526 Afold: 0.517 Positive Predictive Value PknotsRG: 0.522 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.506 RNAsubopt: 0.501 Sensitivity PknotsRG: 0.509 RNAsubopt: 0.510 Positive Predictive Value PknotsRG: 0.506 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.559 RNAalifold(seed): 0.541 Sensitivity PknotsRG: 0.554 RNAalifold(seed): 0.344 Positive Predictive Value PknotsRG: 0.566 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.525 CMfinder(20): 0.478 Sensitivity PknotsRG: 0.518 CMfinder(20): 0.309 Positive Predictive Value PknotsRG: 0.535 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.499 McQFold: 0.443 Sensitivity PknotsRG: 0.504 McQFold: 0.435 Positive Predictive Value PknotsRG: 0.495 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.499 CRWrnafold: 0.432 Sensitivity PknotsRG: 0.504 CRWrnafold: 0.438 Positive Predictive Value PknotsRG: 0.495 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.504 RNASLOpt: 0.442 Sensitivity PknotsRG: 0.506 RNASLOpt: 0.419 Positive Predictive Value PknotsRG: 0.503 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.505 RNAshapes: 0.438 Sensitivity PknotsRG: 0.507 RNAshapes: 0.434 Positive Predictive Value PknotsRG: 0.505 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.607 Murlet(seed): 0.569 Sensitivity PknotsRG: 0.614 Murlet(seed): 0.383 Positive Predictive Value PknotsRG: 0.601 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.525 RSpredict(20): 0.418 Sensitivity PknotsRG: 0.518 RSpredict(20): 0.285 Positive Predictive Value PknotsRG: 0.535 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.525 Carnac(20): 0.378 Sensitivity PknotsRG: 0.518 Carnac(20): 0.166 Positive Predictive Value PknotsRG: 0.535 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.499 RNAwolf: 0.339 Sensitivity PknotsRG: 0.504 RNAwolf: 0.355 Positive Predictive Value PknotsRG: 0.495 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.606 CMfinder(seed): 0.454 Sensitivity PknotsRG: 0.611 CMfinder(seed): 0.271 Positive Predictive Value PknotsRG: 0.602 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.560 RSpredict(seed): 0.214 Sensitivity PknotsRG: 0.554 RSpredict(seed): 0.089 Positive Predictive Value PknotsRG: 0.567 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.504 Vsfold4: 0.306 Sensitivity PknotsRG: 0.507 Vsfold4: 0.282 Positive Predictive Value PknotsRG: 0.504 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.504 Vsfold5: 0.300 Sensitivity PknotsRG: 0.506 Vsfold5: 0.286 Positive Predictive Value PknotsRG: 0.504 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.518 NanoFolder: 0.166 Sensitivity PknotsRG: 0.518 NanoFolder: 0.197 Positive Predictive Value PknotsRG: 0.520 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.568 Carnac(seed): 0.150 Sensitivity PknotsRG: 0.574 Carnac(seed): 0.028 Positive Predictive Value PknotsRG: 0.563 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.559 Mastr(seed): 0.073 Sensitivity PknotsRG: 0.555 Mastr(seed): 0.006 Positive Predictive Value PknotsRG: 0.564 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.640 PknotsRG: 0.631 Sensitivity HotKnots: 0.615 PknotsRG: 0.615 Positive Predictive Value HotKnots: 0.667 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: N/A Pknots: N/A Sensitivity PknotsRG: N/A Pknots: N/A Positive Predictive Value PknotsRG: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.437 Cylofold: 0.271 Sensitivity PknotsRG: 0.438 Cylofold: 0.241 Positive Predictive Value PknotsRG: 0.438 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: N/A MCFold: N/A Sensitivity PknotsRG: N/A MCFold: N/A Positive Predictive Value PknotsRG: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: N/A RDfolder: N/A Sensitivity PknotsRG: N/A RDfolder: N/A Positive Predictive Value PknotsRG: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: N/A Alterna: N/A Sensitivity PknotsRG: N/A Alterna: N/A Positive Predictive Value PknotsRG: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.525 Mastr(20): 0.000 Sensitivity PknotsRG: 0.518 Mastr(20): 0.000 Positive Predictive Value PknotsRG: 0.535 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	643 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 RNAfold: 0.507 Sensitivity PETfold_pre2.0(seed): 0.612 RNAfold: 0.508 Positive Predictive Value PETfold_pre2.0(seed): 0.803 RNAfold: 0.507 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.720 RNAfold: 0.499 Sensitivity ContextFold: 0.687 RNAfold: 0.504 Positive Predictive Value ContextFold: 0.756 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.752 RNAfold: 0.544 Sensitivity TurboFold(20): 0.701 RNAfold: 0.536 Positive Predictive Value TurboFold(20): 0.809 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNAfold: 0.569 Sensitivity CentroidAlifold(seed): 0.556 RNAfold: 0.563 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAfold: 0.577 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAfold: 0.543 Sensitivity PETfold_pre2.0(20): 0.654 RNAfold: 0.534 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAfold: 0.552 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.733 RNAfold: 0.544 Sensitivity PPfold(20): 0.629 RNAfold: 0.537 Positive Predictive Value PPfold(20): 0.855 RNAfold: 0.554 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 RNAfold: 0.510 Sensitivity CentroidHomfold‑LAST: 0.491 RNAfold: 0.512 Positive Predictive Value CentroidHomfold‑LAST: 0.862 RNAfold: 0.509 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAfold: 0.544 Sensitivity CentroidAlifold(20): 0.574 RNAfold: 0.536 Positive Predictive Value CentroidAlifold(20): 0.916 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.637 RNAfold: 0.569 Sensitivity MXScarna(seed): 0.535 RNAfold: 0.563 Positive Predictive Value MXScarna(seed): 0.759 RNAfold: 0.577 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.612 RNAfold: 0.499 Sensitivity IPknot: 0.561 RNAfold: 0.504 Positive Predictive Value IPknot: 0.667 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAfold: 0.544 Sensitivity RNAalifold(20): 0.540 RNAfold: 0.536 Positive Predictive Value RNAalifold(20): 0.827 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.787 RNAfold: 0.671 Sensitivity TurboFold(seed): 0.760 RNAfold: 0.682 Positive Predictive Value TurboFold(seed): 0.815 RNAfold: 0.662 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.64318034126e-08	223 Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.651 RNAfold: 0.545 Sensitivity Multilign(20): 0.590 RNAfold: 0.537 Positive Predictive Value Multilign(20): 0.721 RNAfold: 0.554 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.654 RNAfold: 0.544 Sensitivity MXScarna(20): 0.584 RNAfold: 0.536 Positive Predictive Value MXScarna(20): 0.735 RNAfold: 0.553 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.583 RNAfold: 0.499 Sensitivity CentroidFold: 0.533 RNAfold: 0.504 Positive Predictive Value CentroidFold: 0.638 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.567 RNAfold: 0.499 Sensitivity Contrafold: 0.558 RNAfold: 0.504 Positive Predictive Value Contrafold: 0.577 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs RNAfold Matthews Correlation Coefficient PPfold(seed): 0.716 RNAfold: 0.667 Sensitivity PPfold(seed): 0.652 RNAfold: 0.677 Positive Predictive Value PPfold(seed): 0.787 RNAfold: 0.657 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.23657817852e-08	818 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.538 RNAfold: 0.499 Sensitivity Sfold: 0.491 RNAfold: 0.504 Positive Predictive Value Sfold: 0.589 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.536 RNAfold: 0.499 Sensitivity MaxExpect: 0.527 RNAfold: 0.504 Positive Predictive Value MaxExpect: 0.546 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.534 RNAfold: 0.499 Sensitivity ProbKnot: 0.534 RNAfold: 0.504 Positive Predictive Value ProbKnot: 0.535 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs RNAfold Matthews Correlation Coefficient RNASampler(seed): 0.779 RNAfold: 0.711 Sensitivity RNASampler(seed): 0.659 RNAfold: 0.721 Positive Predictive Value RNASampler(seed): 0.921 RNAfold: 0.701 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.42300079339e-08	818 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.511 RNAfold: 0.499 Sensitivity Fold: 0.517 RNAfold: 0.504 Positive Predictive Value Fold: 0.506 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.565 RNAfold: 0.497 Sensitivity RNASampler(20): 0.413 RNAfold: 0.502 Positive Predictive Value RNASampler(20): 0.772 RNAfold: 0.494 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.573 RNAfold: 0.532 Sensitivity Murlet(20): 0.441 RNAfold: 0.526 Positive Predictive Value Murlet(20): 0.746 RNAfold: 0.540 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.501 RNAfold: 0.499 Sensitivity UNAFold: 0.501 RNAfold: 0.504 Positive Predictive Value UNAFold: 0.503 RNAfold: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 RNAfold vs PknotsRG Matthews Correlation Coefficient RNAfold: 0.499 PknotsRG: 0.499 Sensitivity RNAfold: 0.504 PknotsRG: 0.504 Positive Predictive Value RNAfold: 0.495 PknotsRG: 0.495 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 0.288298117014		- Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.734 RNAfold: 0.631 Sensitivity Multilign(seed): 0.733 RNAfold: 0.657 Positive Predictive Value Multilign(seed): 0.737 RNAfold: 0.608 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.91686328089e-09	+ RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.526 Afold: 0.516 Sensitivity RNAfold: 0.529 Afold: 0.517 Positive Predictive Value RNAfold: 0.525 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.510 RNAsubopt: 0.501 Sensitivity RNAfold: 0.512 RNAsubopt: 0.510 Positive Predictive Value RNAfold: 0.509 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.569 RNAalifold(seed): 0.541 Sensitivity RNAfold: 0.562 RNAalifold(seed): 0.344 Positive Predictive Value RNAfold: 0.576 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.544 CMfinder(20): 0.478 Sensitivity RNAfold: 0.536 CMfinder(20): 0.309 Positive Predictive Value RNAfold: 0.553 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.499 McQFold: 0.443 Sensitivity RNAfold: 0.504 McQFold: 0.435 Positive Predictive Value RNAfold: 0.495 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.499 CRWrnafold: 0.432 Sensitivity RNAfold: 0.504 CRWrnafold: 0.438 Positive Predictive Value RNAfold: 0.495 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.510 RNASLOpt: 0.442 Sensitivity RNAfold: 0.512 RNASLOpt: 0.419 Positive Predictive Value RNAfold: 0.510 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.510 RNAshapes: 0.438 Sensitivity RNAfold: 0.511 RNAshapes: 0.434 Positive Predictive Value RNAfold: 0.510 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.631 Murlet(seed): 0.569 Sensitivity RNAfold: 0.637 Murlet(seed): 0.383 Positive Predictive Value RNAfold: 0.627 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.544 RSpredict(20): 0.418 Sensitivity RNAfold: 0.536 RSpredict(20): 0.285 Positive Predictive Value RNAfold: 0.553 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Carnac(20) Matthews Correlation Coefficient RNAfold: 0.544 Carnac(20): 0.378 Sensitivity RNAfold: 0.536 Carnac(20): 0.166 Positive Predictive Value RNAfold: 0.553 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.499 RNAwolf: 0.339 Sensitivity RNAfold: 0.504 RNAwolf: 0.355 Positive Predictive Value RNAfold: 0.495 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.607 CMfinder(seed): 0.454 Sensitivity RNAfold: 0.610 CMfinder(seed): 0.271 Positive Predictive Value RNAfold: 0.605 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.569 RSpredict(seed): 0.214 Sensitivity RNAfold: 0.563 RSpredict(seed): 0.089 Positive Predictive Value RNAfold: 0.577 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.508 Vsfold4: 0.306 Sensitivity RNAfold: 0.510 Vsfold4: 0.282 Positive Predictive Value RNAfold: 0.508 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.508 Vsfold5: 0.300 Sensitivity RNAfold: 0.510 Vsfold5: 0.286 Positive Predictive Value RNAfold: 0.508 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.531 NanoFolder: 0.166 Sensitivity RNAfold: 0.529 NanoFolder: 0.197 Positive Predictive Value RNAfold: 0.534 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.569 Carnac(seed): 0.150 Sensitivity RNAfold: 0.574 Carnac(seed): 0.028 Positive Predictive Value RNAfold: 0.566 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.569 Mastr(seed): 0.073 Sensitivity RNAfold: 0.564 Mastr(seed): 0.006 Positive Predictive Value RNAfold: 0.575 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.640 RNAfold: 0.640 Sensitivity HotKnots: 0.615 RNAfold: 0.615 Positive Predictive Value HotKnots: 0.667 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNAfold Matthews Correlation Coefficient Pknots: N/A RNAfold: N/A Sensitivity Pknots: N/A RNAfold: N/A Positive Predictive Value Pknots: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.446 Cylofold: 0.271 Sensitivity RNAfold: 0.431 Cylofold: 0.241 Positive Predictive Value RNAfold: 0.465 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: N/A MCFold: N/A Sensitivity RNAfold: N/A MCFold: N/A Positive Predictive Value RNAfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: N/A RNAfold: N/A Sensitivity RDfolder: N/A RNAfold: N/A Positive Predictive Value RDfolder: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAfold Matthews Correlation Coefficient Alterna: N/A RNAfold: N/A Sensitivity Alterna: N/A RNAfold: N/A Positive Predictive Value Alterna: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.544 Mastr(20): 0.000 Sensitivity RNAfold: 0.536 Mastr(20): 0.000 Positive Predictive Value RNAfold: 0.553 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(seed)	9 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.806 Multilign(seed): 0.759 Sensitivity PETfold_pre2.0(seed): 0.781 Multilign(seed): 0.752 Positive Predictive Value PETfold_pre2.0(seed): 0.832 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs ContextFold Matthews Correlation Coefficient Multilign(seed): 0.734 ContextFold: 0.624 Sensitivity Multilign(seed): 0.733 ContextFold: 0.618 Positive Predictive Value Multilign(seed): 0.737 ContextFold: 0.631 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.30295446166e-08	0 TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): N/A Multilign(seed): N/A Sensitivity TurboFold(20): N/A Multilign(seed): N/A Positive Predictive Value TurboFold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	9 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.806 Multilign(seed): 0.759 Sensitivity CentroidAlifold(seed): 0.767 Multilign(seed): 0.752 Positive Predictive Value CentroidAlifold(seed): 0.848 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Multilign(seed): N/A Sensitivity PETfold_pre2.0(20): N/A Multilign(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): N/A Multilign(seed): N/A Sensitivity PPfold(20): N/A Multilign(seed): N/A Positive Predictive Value PPfold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 Multilign(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient Multilign(seed): 0.734 CentroidHomfold‑LAST: 0.710 Sensitivity Multilign(seed): 0.733 CentroidHomfold‑LAST: 0.608 Positive Predictive Value Multilign(seed): 0.737 CentroidHomfold‑LAST: 0.831 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.50834591464e-08	0 Multilign(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient Multilign(seed): N/A CentroidAlifold(20): N/A Sensitivity Multilign(seed): N/A CentroidAlifold(20): N/A Positive Predictive Value Multilign(seed): N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	9 Multilign(seed) vs MXScarna(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 MXScarna(seed): 0.729 Sensitivity Multilign(seed): 0.752 MXScarna(seed): 0.703 Positive Predictive Value Multilign(seed): 0.767 MXScarna(seed): 0.756 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs IPknot Matthews Correlation Coefficient Multilign(seed): 0.734 IPknot: 0.660 Sensitivity Multilign(seed): 0.733 IPknot: 0.664 Positive Predictive Value Multilign(seed): 0.737 IPknot: 0.656 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.34341160367e-09	0 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): N/A Multilign(seed): N/A Sensitivity RNAalifold(20): N/A Multilign(seed): N/A Positive Predictive Value RNAalifold(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	9 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.782 Multilign(seed): 0.759 Sensitivity TurboFold(seed): 0.767 Multilign(seed): 0.752 Positive Predictive Value TurboFold(seed): 0.799 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 Multilign(seed) vs Multilign(20) Matthews Correlation Coefficient Multilign(seed): N/A Multilign(20): N/A Sensitivity Multilign(seed): N/A Multilign(20): N/A Positive Predictive Value Multilign(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs MXScarna(20) Matthews Correlation Coefficient Multilign(seed): N/A MXScarna(20): N/A Sensitivity Multilign(seed): N/A MXScarna(20): N/A Positive Predictive Value Multilign(seed): N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 Multilign(seed) vs CentroidFold Matthews Correlation Coefficient Multilign(seed): 0.734 CentroidFold: 0.629 Sensitivity Multilign(seed): 0.733 CentroidFold: 0.630 Positive Predictive Value Multilign(seed): 0.737 CentroidFold: 0.629 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.96907987703e-08	10 Multilign(seed) vs Contrafold Matthews Correlation Coefficient Multilign(seed): 0.734 Contrafold: 0.619 Sensitivity Multilign(seed): 0.733 Contrafold: 0.643 Positive Predictive Value Multilign(seed): 0.737 Contrafold: 0.596 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.60917593777e-09	9 PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.792 Multilign(seed): 0.759 Sensitivity PPfold(seed): 0.748 Multilign(seed): 0.752 Positive Predictive Value PPfold(seed): 0.840 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.734 Sfold: 0.612 Sensitivity Multilign(seed): 0.733 Sfold: 0.603 Positive Predictive Value Multilign(seed): 0.737 Sfold: 0.623 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.42028829171e-09	10 Multilign(seed) vs MaxExpect Matthews Correlation Coefficient Multilign(seed): 0.734 MaxExpect: 0.571 Sensitivity Multilign(seed): 0.733 MaxExpect: 0.596 Positive Predictive Value Multilign(seed): 0.737 MaxExpect: 0.548 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.38194587311e-08	10 Multilign(seed) vs ProbKnot Matthews Correlation Coefficient Multilign(seed): 0.734 ProbKnot: 0.583 Sensitivity Multilign(seed): 0.733 ProbKnot: 0.609 Positive Predictive Value Multilign(seed): 0.737 ProbKnot: 0.560 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.76570236188e-09	6 Multilign(seed) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(seed): 0.879 RNASampler(seed): 0.807 Sensitivity Multilign(seed): 0.851 RNASampler(seed): 0.679 Positive Predictive Value Multilign(seed): 0.908 RNASampler(seed): 0.959 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	10 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.734 Fold: 0.584 Sensitivity Multilign(seed): 0.733 Fold: 0.611 Positive Predictive Value Multilign(seed): 0.737 Fold: 0.560 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.36849473644e-08	0 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): N/A Multilign(seed): N/A Sensitivity RNASampler(20): N/A Multilign(seed): N/A Positive Predictive Value RNASampler(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): N/A Multilign(seed): N/A Sensitivity Murlet(20): N/A Multilign(seed): N/A Positive Predictive Value Murlet(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	10 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.734 UNAFold: 0.565 Sensitivity Multilign(seed): 0.733 UNAFold: 0.588 Positive Predictive Value Multilign(seed): 0.737 UNAFold: 0.543 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.11142658008e-08	10 Multilign(seed) vs PknotsRG Matthews Correlation Coefficient Multilign(seed): 0.734 PknotsRG: 0.558 Sensitivity Multilign(seed): 0.733 PknotsRG: 0.582 Positive Predictive Value Multilign(seed): 0.737 PknotsRG: 0.536 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 3.57547243792e-09	10 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.734 RNAfold: 0.631 Sensitivity Multilign(seed): 0.733 RNAfold: 0.657 Positive Predictive Value Multilign(seed): 0.737 RNAfold: 0.608 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.91686328089e-09		? Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.770 Afold: 0.626 Sensitivity Multilign(seed): 0.761 Afold: 0.648 Positive Predictive Value Multilign(seed): 0.779 Afold: 0.605 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.734 RNAsubopt: 0.584 Sensitivity Multilign(seed): 0.733 RNAsubopt: 0.611 Positive Predictive Value Multilign(seed): 0.737 RNAsubopt: 0.559 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12262428713e-08	? RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.794 Multilign(seed): 0.759 Sensitivity RNAalifold(seed): 0.696 Multilign(seed): 0.752 Positive Predictive Value RNAalifold(seed): 0.907 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 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	+ Multilign(seed) vs McQFold Matthews Correlation Coefficient Multilign(seed): 0.734 McQFold: 0.433 Sensitivity Multilign(seed): 0.733 McQFold: 0.438 Positive Predictive Value Multilign(seed): 0.737 McQFold: 0.429 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.99051034341e-09	+ Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.734 CRWrnafold: 0.464 Sensitivity Multilign(seed): 0.733 CRWrnafold: 0.487 Positive Predictive Value Multilign(seed): 0.737 CRWrnafold: 0.444 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.27752322258e-08	+ Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.734 RNASLOpt: 0.462 Sensitivity Multilign(seed): 0.733 RNASLOpt: 0.458 Positive Predictive Value Multilign(seed): 0.737 RNASLOpt: 0.467 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.64686604905e-09	? Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.720 RNAshapes: 0.498 Sensitivity Multilign(seed): 0.722 RNAshapes: 0.526 Positive Predictive Value Multilign(seed): 0.719 RNAshapes: 0.475 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.770 Murlet(seed): 0.725 Sensitivity Multilign(seed): 0.762 Murlet(seed): 0.558 Positive Predictive Value Multilign(seed): 0.778 Murlet(seed): 0.944 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	? RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): N/A Multilign(seed): N/A Sensitivity RSpredict(20): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(20): N/A Sensitivity Multilign(seed): N/A Carnac(20): N/A Positive Predictive Value Multilign(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.734 RNAwolf: 0.346 Sensitivity Multilign(seed): 0.733 RNAwolf: 0.368 Positive Predictive Value Multilign(seed): 0.737 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.02533530638e-08	? Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.879 CMfinder(seed): 0.544 Sensitivity Multilign(seed): 0.851 CMfinder(seed): 0.410 Positive Predictive Value Multilign(seed): 0.908 CMfinder(seed): 0.724 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 RSpredict(seed): 0.626 Sensitivity Multilign(seed): 0.752 RSpredict(seed): 0.495 Positive Predictive Value Multilign(seed): 0.767 RSpredict(seed): 0.793 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.734 Vsfold4: 0.167 Sensitivity Multilign(seed): 0.733 Vsfold4: 0.160 Positive Predictive Value Multilign(seed): 0.737 Vsfold4: 0.176 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.00475527001e-08	+ Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.734 Vsfold5: 0.228 Sensitivity Multilign(seed): 0.733 Vsfold5: 0.235 Positive Predictive Value Multilign(seed): 0.737 Vsfold5: 0.225 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.10032755566e-08	? Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 1.000 NanoFolder: -0.003 Sensitivity Multilign(seed): 1.000 NanoFolder: 0.000 Positive Predictive Value Multilign(seed): 1.000 NanoFolder: 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 Carnac(seed): 0.552 Sensitivity Multilign(seed): 0.752 Carnac(seed): 0.323 Positive Predictive Value Multilign(seed): 0.767 Carnac(seed): 0.945 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 Mastr(seed): 0.491 Sensitivity Multilign(seed): 0.752 Mastr(seed): 0.274 Positive Predictive Value Multilign(seed): 0.767 Mastr(seed): 0.879 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	? HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: N/A Multilign(seed): N/A Sensitivity HotKnots: N/A Multilign(seed): N/A Positive Predictive Value HotKnots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: N/A Multilign(seed): N/A Sensitivity Pknots: N/A Multilign(seed): N/A Positive Predictive Value Pknots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: N/A Multilign(seed): N/A Sensitivity Cylofold: N/A Multilign(seed): N/A Positive Predictive Value Cylofold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): N/A MCFold: N/A Sensitivity Multilign(seed): N/A MCFold: N/A Positive Predictive Value Multilign(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: N/A Multilign(seed): N/A Sensitivity RDfolder: N/A Multilign(seed): N/A Positive Predictive Value RDfolder: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): N/A Alterna: N/A Sensitivity Multilign(seed): N/A Alterna: N/A Positive Predictive Value Multilign(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): N/A Multilign(seed): N/A Sensitivity Mastr(20): N/A Multilign(seed): N/A Positive Predictive Value Mastr(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Afold	387 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.721 Afold: 0.529 Sensitivity PETfold_pre2.0(seed): 0.632 Afold: 0.525 Positive Predictive Value PETfold_pre2.0(seed): 0.824 Afold: 0.535 Number of pairs reference - predicted secondary structure: 387 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.742 Afold: 0.516 Sensitivity ContextFold: 0.711 Afold: 0.517 Positive Predictive Value ContextFold: 0.776 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.762 Afold: 0.556 Sensitivity TurboFold(20): 0.709 Afold: 0.544 Positive Predictive Value TurboFold(20): 0.819 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	353 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.704 Afold: 0.558 Sensitivity CentroidAlifold(seed): 0.546 Afold: 0.551 Positive Predictive Value CentroidAlifold(seed): 0.909 Afold: 0.566 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	182 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.746 Afold: 0.555 Sensitivity PETfold_pre2.0(20): 0.656 Afold: 0.542 Positive Predictive Value PETfold_pre2.0(20): 0.848 Afold: 0.570 Number of pairs reference - predicted secondary structure: 182 Wilcoxon single-rank test P-value: 3.56938820447e-08	178 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.737 Afold: 0.557 Sensitivity PPfold(20): 0.632 Afold: 0.545 Positive Predictive Value PPfold(20): 0.861 Afold: 0.572 Number of pairs reference - predicted secondary structure: 178 Wilcoxon single-rank test P-value: 3.56938820447e-08	472 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.661 Afold: 0.532 Sensitivity CentroidHomfold‑LAST: 0.508 Afold: 0.529 Positive Predictive Value CentroidHomfold‑LAST: 0.863 Afold: 0.536 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.723 Afold: 0.556 Sensitivity CentroidAlifold(20): 0.566 Afold: 0.544 Positive Predictive Value CentroidAlifold(20): 0.924 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	356 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.631 Afold: 0.558 Sensitivity MXScarna(seed): 0.526 Afold: 0.551 Positive Predictive Value MXScarna(seed): 0.757 Afold: 0.567 Number of pairs reference - predicted secondary structure: 356 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.628 Afold: 0.516 Sensitivity IPknot: 0.577 Afold: 0.517 Positive Predictive Value IPknot: 0.684 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.665 Afold: 0.556 Sensitivity RNAalifold(20): 0.531 Afold: 0.544 Positive Predictive Value RNAalifold(20): 0.836 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.799 Afold: 0.632 Sensitivity TurboFold(seed): 0.774 Afold: 0.646 Positive Predictive Value TurboFold(seed): 0.826 Afold: 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	172 Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.653 Afold: 0.557 Sensitivity Multilign(20): 0.589 Afold: 0.544 Positive Predictive Value Multilign(20): 0.726 Afold: 0.571 Number of pairs reference - predicted secondary structure: 172 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.665 Afold: 0.556 Sensitivity MXScarna(20): 0.584 Afold: 0.544 Positive Predictive Value MXScarna(20): 0.759 Afold: 0.570 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.604 Afold: 0.516 Sensitivity CentroidFold: 0.554 Afold: 0.517 Positive Predictive Value CentroidFold: 0.659 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.590 Afold: 0.516 Sensitivity Contrafold: 0.580 Afold: 0.517 Positive Predictive Value Contrafold: 0.602 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PPfold(seed) vs Afold Matthews Correlation Coefficient PPfold(seed): 0.756 Afold: 0.627 Sensitivity PPfold(seed): 0.714 Afold: 0.639 Positive Predictive Value PPfold(seed): 0.802 Afold: 0.616 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	525 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.571 Afold: 0.516 Sensitivity Sfold: 0.523 Afold: 0.517 Positive Predictive Value Sfold: 0.625 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.559 Afold: 0.516 Sensitivity MaxExpect: 0.550 Afold: 0.517 Positive Predictive Value MaxExpect: 0.570 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.556 Afold: 0.516 Sensitivity ProbKnot: 0.555 Afold: 0.517 Positive Predictive Value ProbKnot: 0.559 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNASampler(seed) vs Afold Matthews Correlation Coefficient RNASampler(seed): 0.773 Afold: 0.629 Sensitivity RNASampler(seed): 0.652 Afold: 0.638 Positive Predictive Value RNASampler(seed): 0.917 Afold: 0.621 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 9.9460272886e-09	525 Fold vs Afold Matthews Correlation Coefficient Fold: 0.533 Afold: 0.516 Sensitivity Fold: 0.537 Afold: 0.517 Positive Predictive Value Fold: 0.529 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	37 Afold vs RNASampler(20) Matthews Correlation Coefficient Afold: 0.570 RNASampler(20): 0.537 Sensitivity Afold: 0.570 RNASampler(20): 0.354 Positive Predictive Value Afold: 0.571 RNASampler(20): 0.818 Number of pairs reference - predicted secondary structure: 37 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.550 Afold: 0.546 Sensitivity Murlet(20): 0.410 Afold: 0.535 Positive Predictive Value Murlet(20): 0.739 Afold: 0.559 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 0.0106540216989	525 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.534 Afold: 0.516 Sensitivity UNAFold: 0.532 Afold: 0.517 Positive Predictive Value UNAFold: 0.537 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.523 Afold: 0.516 Sensitivity PknotsRG: 0.526 Afold: 0.517 Positive Predictive Value PknotsRG: 0.522 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	525 RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.526 Afold: 0.516 Sensitivity RNAfold: 0.529 Afold: 0.517 Positive Predictive Value RNAfold: 0.525 Afold: 0.516 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	7 Multilign(seed) vs Afold Matthews Correlation Coefficient Multilign(seed): 0.770 Afold: 0.626 Sensitivity Multilign(seed): 0.761 Afold: 0.648 Positive Predictive Value Multilign(seed): 0.779 Afold: 0.605 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0		- RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.541 Afold: 0.532 Sensitivity RNAsubopt: 0.545 Afold: 0.529 Positive Predictive Value RNAsubopt: 0.537 Afold: 0.536 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.558 RNAalifold(seed): 0.533 Sensitivity Afold: 0.551 RNAalifold(seed): 0.335 Positive Predictive Value Afold: 0.566 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.556 CMfinder(20): 0.494 Sensitivity Afold: 0.544 CMfinder(20): 0.323 Positive Predictive Value Afold: 0.570 CMfinder(20): 0.757 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.516 McQFold: 0.449 Sensitivity Afold: 0.517 McQFold: 0.440 Positive Predictive Value Afold: 0.516 McQFold: 0.460 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.516 CRWrnafold: 0.451 Sensitivity Afold: 0.517 CRWrnafold: 0.455 Positive Predictive Value Afold: 0.516 CRWrnafold: 0.449 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.537 RNASLOpt: 0.456 Sensitivity Afold: 0.533 RNASLOpt: 0.429 Positive Predictive Value Afold: 0.541 RNASLOpt: 0.487 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.534 RNAshapes: 0.486 Sensitivity Afold: 0.530 RNAshapes: 0.478 Positive Predictive Value Afold: 0.539 RNAshapes: 0.495 Number of pairs reference - predicted secondary structure: 437 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.626 Murlet(seed): 0.586 Sensitivity Afold: 0.629 Murlet(seed): 0.396 Positive Predictive Value Afold: 0.625 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.556 RSpredict(20): 0.382 Sensitivity Afold: 0.544 RSpredict(20): 0.243 Positive Predictive Value Afold: 0.570 RSpredict(20): 0.603 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Carnac(20) Matthews Correlation Coefficient Afold: 0.556 Carnac(20): 0.336 Sensitivity Afold: 0.544 Carnac(20): 0.128 Positive Predictive Value Afold: 0.570 Carnac(20): 0.882 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.516 RNAwolf: 0.351 Sensitivity Afold: 0.517 RNAwolf: 0.365 Positive Predictive Value Afold: 0.516 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.629 CMfinder(seed): 0.451 Sensitivity Afold: 0.627 CMfinder(seed): 0.271 Positive Predictive Value Afold: 0.633 CMfinder(seed): 0.753 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.558 RSpredict(seed): 0.214 Sensitivity Afold: 0.551 RSpredict(seed): 0.087 Positive Predictive Value Afold: 0.567 RSpredict(seed): 0.529 Number of pairs reference - predicted secondary structure: 355 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.532 Vsfold4: 0.328 Sensitivity Afold: 0.528 Vsfold4: 0.300 Positive Predictive Value Afold: 0.537 Vsfold4: 0.361 Number of pairs reference - predicted secondary structure: 448 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.533 Vsfold5: 0.317 Sensitivity Afold: 0.530 Vsfold5: 0.299 Positive Predictive Value Afold: 0.539 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 441 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.560 NanoFolder: 0.165 Sensitivity Afold: 0.553 NanoFolder: 0.192 Positive Predictive Value Afold: 0.568 NanoFolder: 0.144 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.556 Carnac(seed): 0.158 Sensitivity Afold: 0.561 Carnac(seed): 0.030 Positive Predictive Value Afold: 0.553 Carnac(seed): 0.840 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.558 Mastr(seed): 0.081 Sensitivity Afold: 0.552 Mastr(seed): 0.007 Positive Predictive Value Afold: 0.564 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 333 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.640 Afold: 0.640 Sensitivity HotKnots: 0.615 Afold: 0.615 Positive Predictive Value HotKnots: 0.667 Afold: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs Afold Matthews Correlation Coefficient Pknots: N/A Afold: N/A Sensitivity Pknots: N/A Afold: N/A Positive Predictive Value Pknots: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.460 Cylofold: 0.271 Sensitivity Afold: 0.460 Cylofold: 0.241 Positive Predictive Value Afold: 0.463 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Afold vs MCFold Matthews Correlation Coefficient Afold: N/A MCFold: N/A Sensitivity Afold: N/A MCFold: N/A Positive Predictive Value Afold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Afold Matthews Correlation Coefficient RDfolder: N/A Afold: N/A Sensitivity RDfolder: N/A Afold: N/A Positive Predictive Value RDfolder: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Afold Matthews Correlation Coefficient Alterna: N/A Afold: N/A Sensitivity Alterna: N/A Afold: N/A Positive Predictive Value Alterna: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.556 Mastr(20): 0.000 Sensitivity Afold: 0.544 Mastr(20): 0.000 Positive Predictive Value Afold: 0.570 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAsubopt	630 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.703 RNAsubopt: 0.495 Sensitivity PETfold_pre2.0(seed): 0.618 RNAsubopt: 0.503 Positive Predictive Value PETfold_pre2.0(seed): 0.802 RNAsubopt: 0.490 Number of pairs reference - predicted secondary structure: 630 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.741 RNAsubopt: 0.501 Sensitivity ContextFold: 0.704 RNAsubopt: 0.510 Positive Predictive Value ContextFold: 0.780 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.752 RNAsubopt: 0.530 Sensitivity TurboFold(20): 0.701 RNAsubopt: 0.529 Positive Predictive Value TurboFold(20): 0.809 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	413 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.713 RNAsubopt: 0.559 Sensitivity CentroidAlifold(seed): 0.562 RNAsubopt: 0.560 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAsubopt: 0.559 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAsubopt: 0.531 Sensitivity PETfold_pre2.0(20): 0.654 RNAsubopt: 0.530 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAsubopt: 0.533 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.733 RNAsubopt: 0.530 Sensitivity PPfold(20): 0.629 RNAsubopt: 0.530 Positive Predictive Value PPfold(20): 0.855 RNAsubopt: 0.533 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 RNAsubopt: 0.501 Sensitivity CentroidHomfold‑LAST: 0.491 RNAsubopt: 0.510 Positive Predictive Value CentroidHomfold‑LAST: 0.862 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAsubopt: 0.530 Sensitivity CentroidAlifold(20): 0.574 RNAsubopt: 0.529 Positive Predictive Value CentroidAlifold(20): 0.916 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	418 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.641 RNAsubopt: 0.559 Sensitivity MXScarna(seed): 0.541 RNAsubopt: 0.560 Positive Predictive Value MXScarna(seed): 0.762 RNAsubopt: 0.560 Number of pairs reference - predicted secondary structure: 418 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.619 RNAsubopt: 0.501 Sensitivity IPknot: 0.569 RNAsubopt: 0.510 Positive Predictive Value IPknot: 0.675 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAsubopt: 0.530 Sensitivity RNAalifold(20): 0.540 RNAsubopt: 0.529 Positive Predictive Value RNAalifold(20): 0.827 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.776 RNAsubopt: 0.590 Sensitivity TurboFold(seed): 0.753 RNAsubopt: 0.604 Positive Predictive Value TurboFold(seed): 0.802 RNAsubopt: 0.578 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.41358941668e-08	223 Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.651 RNAsubopt: 0.528 Sensitivity Multilign(20): 0.590 RNAsubopt: 0.528 Positive Predictive Value Multilign(20): 0.721 RNAsubopt: 0.530 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.654 RNAsubopt: 0.530 Sensitivity MXScarna(20): 0.584 RNAsubopt: 0.529 Positive Predictive Value MXScarna(20): 0.735 RNAsubopt: 0.532 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.589 RNAsubopt: 0.501 Sensitivity CentroidFold: 0.540 RNAsubopt: 0.510 Positive Predictive Value CentroidFold: 0.644 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.574 RNAsubopt: 0.501 Sensitivity Contrafold: 0.564 RNAsubopt: 0.510 Positive Predictive Value Contrafold: 0.585 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PPfold(seed) vs RNAsubopt Matthews Correlation Coefficient PPfold(seed): 0.735 RNAsubopt: 0.641 Sensitivity PPfold(seed): 0.691 RNAsubopt: 0.658 Positive Predictive Value PPfold(seed): 0.783 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.546 RNAsubopt: 0.501 Sensitivity Sfold: 0.498 RNAsubopt: 0.510 Positive Predictive Value Sfold: 0.600 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.544 RNAsubopt: 0.501 Sensitivity MaxExpect: 0.533 RNAsubopt: 0.510 Positive Predictive Value MaxExpect: 0.556 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.542 RNAsubopt: 0.501 Sensitivity ProbKnot: 0.539 RNAsubopt: 0.510 Positive Predictive Value ProbKnot: 0.547 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.779 RNAsubopt: 0.643 Sensitivity RNASampler(seed): 0.659 RNAsubopt: 0.657 Positive Predictive Value RNASampler(seed): 0.921 RNAsubopt: 0.631 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.1413769576e-08	759 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.521 RNAsubopt: 0.501 Sensitivity Fold: 0.525 RNAsubopt: 0.510 Positive Predictive Value Fold: 0.519 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.565 RNAsubopt: 0.461 Sensitivity RNASampler(20): 0.413 RNAsubopt: 0.471 Positive Predictive Value RNASampler(20): 0.772 RNAsubopt: 0.454 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.573 RNAsubopt: 0.518 Sensitivity Murlet(20): 0.441 RNAsubopt: 0.518 Positive Predictive Value Murlet(20): 0.746 RNAsubopt: 0.519 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.510 RNAsubopt: 0.501 Sensitivity UNAFold: 0.507 RNAsubopt: 0.510 Positive Predictive Value UNAFold: 0.514 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.506 RNAsubopt: 0.501 Sensitivity PknotsRG: 0.509 RNAsubopt: 0.510 Positive Predictive Value PknotsRG: 0.506 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 RNAfold vs RNAsubopt Matthews Correlation Coefficient RNAfold: 0.510 RNAsubopt: 0.501 Sensitivity RNAfold: 0.512 RNAsubopt: 0.510 Positive Predictive Value RNAfold: 0.509 RNAsubopt: 0.495 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.734 RNAsubopt: 0.584 Sensitivity Multilign(seed): 0.733 RNAsubopt: 0.611 Positive Predictive Value Multilign(seed): 0.737 RNAsubopt: 0.559 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.12262428713e-08	472 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.541 Afold: 0.532 Sensitivity RNAsubopt: 0.545 Afold: 0.529 Positive Predictive Value RNAsubopt: 0.537 Afold: 0.536 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.558 RNAalifold(seed): 0.542 Sensitivity RNAsubopt: 0.560 RNAalifold(seed): 0.345 Positive Predictive Value RNAsubopt: 0.559 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 414 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.530 CMfinder(20): 0.478 Sensitivity RNAsubopt: 0.529 CMfinder(20): 0.309 Positive Predictive Value RNAsubopt: 0.532 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.501 McQFold: 0.452 Sensitivity RNAsubopt: 0.510 McQFold: 0.442 Positive Predictive Value RNAsubopt: 0.495 McQFold: 0.463 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.501 CRWrnafold: 0.442 Sensitivity RNAsubopt: 0.510 CRWrnafold: 0.445 Positive Predictive Value RNAsubopt: 0.495 CRWrnafold: 0.440 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.502 RNASLOpt: 0.442 Sensitivity RNAsubopt: 0.510 RNASLOpt: 0.419 Positive Predictive Value RNAsubopt: 0.496 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.501 RNAshapes: 0.438 Sensitivity RNAsubopt: 0.509 RNAshapes: 0.434 Positive Predictive Value RNAsubopt: 0.495 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.606 Murlet(seed): 0.556 Sensitivity RNAsubopt: 0.619 Murlet(seed): 0.366 Positive Predictive Value RNAsubopt: 0.595 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.530 RSpredict(20): 0.418 Sensitivity RNAsubopt: 0.529 RSpredict(20): 0.285 Positive Predictive Value RNAsubopt: 0.532 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.530 Carnac(20): 0.378 Sensitivity RNAsubopt: 0.529 Carnac(20): 0.166 Positive Predictive Value RNAsubopt: 0.532 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.501 RNAwolf: 0.349 Sensitivity RNAsubopt: 0.510 RNAwolf: 0.364 Positive Predictive Value RNAsubopt: 0.495 RNAwolf: 0.336 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.602 CMfinder(seed): 0.454 Sensitivity RNAsubopt: 0.612 CMfinder(seed): 0.271 Positive Predictive Value RNAsubopt: 0.595 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.559 RSpredict(seed): 0.212 Sensitivity RNAsubopt: 0.560 RSpredict(seed): 0.087 Positive Predictive Value RNAsubopt: 0.559 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.500 Vsfold4: 0.306 Sensitivity RNAsubopt: 0.508 Vsfold4: 0.282 Positive Predictive Value RNAsubopt: 0.493 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.500 Vsfold5: 0.300 Sensitivity RNAsubopt: 0.508 Vsfold5: 0.286 Positive Predictive Value RNAsubopt: 0.493 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.528 NanoFolder: 0.170 Sensitivity RNAsubopt: 0.533 NanoFolder: 0.201 Positive Predictive Value RNAsubopt: 0.524 NanoFolder: 0.146 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.556 Carnac(seed): 0.154 Sensitivity RNAsubopt: 0.567 Carnac(seed): 0.027 Positive Predictive Value RNAsubopt: 0.547 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.561 Mastr(seed): 0.075 Sensitivity RNAsubopt: 0.564 Mastr(seed): 0.006 Positive Predictive Value RNAsubopt: 0.560 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 394 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.640 RNAsubopt: 0.461 Sensitivity HotKnots: 0.615 RNAsubopt: 0.462 Positive Predictive Value HotKnots: 0.667 RNAsubopt: 0.462 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: N/A RNAsubopt: N/A Sensitivity Pknots: N/A RNAsubopt: N/A Positive Predictive Value Pknots: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.437 Cylofold: 0.271 Sensitivity RNAsubopt: 0.431 Cylofold: 0.241 Positive Predictive Value RNAsubopt: 0.447 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: N/A MCFold: N/A Sensitivity RNAsubopt: N/A MCFold: N/A Positive Predictive Value RNAsubopt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: N/A RNAsubopt: N/A Sensitivity RDfolder: N/A RNAsubopt: N/A Positive Predictive Value RDfolder: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAsubopt Matthews Correlation Coefficient Alterna: N/A RNAsubopt: N/A Sensitivity Alterna: N/A RNAsubopt: N/A Positive Predictive Value Alterna: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.530 Mastr(20): 0.000 Sensitivity RNAsubopt: 0.529 Mastr(20): 0.000 Positive Predictive Value RNAsubopt: 0.532 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(seed)	412 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 RNAalifold(seed): 0.541 Sensitivity PETfold_pre2.0(seed): 0.654 RNAalifold(seed): 0.345 Positive Predictive Value PETfold_pre2.0(seed): 0.834 RNAalifold(seed): 0.848 Number of pairs reference - predicted secondary structure: 412 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.802 RNAalifold(seed): 0.541 Sensitivity ContextFold: 0.765 RNAalifold(seed): 0.344 Positive Predictive Value ContextFold: 0.840 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 RNAalifold(seed): 0.492 Sensitivity TurboFold(20): 0.718 RNAalifold(seed): 0.290 Positive Predictive Value TurboFold(20): 0.828 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNAalifold(seed): 0.541 Sensitivity CentroidAlifold(seed): 0.556 RNAalifold(seed): 0.344 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	200 PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.756 RNAalifold(seed): 0.491 Sensitivity PETfold_pre2.0(20): 0.670 RNAalifold(seed): 0.289 Positive Predictive Value PETfold_pre2.0(20): 0.855 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 200 Wilcoxon single-rank test P-value: 3.56938820447e-08	196 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.748 RNAalifold(seed): 0.492 Sensitivity PPfold(20): 0.646 RNAalifold(seed): 0.290 Positive Predictive Value PPfold(20): 0.866 RNAalifold(seed): 0.837 Number of pairs reference - predicted secondary structure: 196 Wilcoxon single-rank test P-value: 3.56938820447e-08	414 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.686 RNAalifold(seed): 0.542 Sensitivity CentroidHomfold‑LAST: 0.539 RNAalifold(seed): 0.345 Positive Predictive Value CentroidHomfold‑LAST: 0.874 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 414 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.732 RNAalifold(seed): 0.492 Sensitivity CentroidAlifold(20): 0.578 RNAalifold(seed): 0.290 Positive Predictive Value CentroidAlifold(20): 0.929 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.637 RNAalifold(seed): 0.541 Sensitivity MXScarna(seed): 0.536 RNAalifold(seed): 0.344 Positive Predictive Value MXScarna(seed): 0.759 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.654 RNAalifold(seed): 0.541 Sensitivity IPknot: 0.599 RNAalifold(seed): 0.344 Positive Predictive Value IPknot: 0.715 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.676 RNAalifold(seed): 0.492 Sensitivity RNAalifold(20): 0.542 RNAalifold(seed): 0.290 Positive Predictive Value RNAalifold(20): 0.843 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 RNAalifold(seed): 0.726 Sensitivity TurboFold(seed): 0.760 RNAalifold(seed): 0.595 Positive Predictive Value TurboFold(seed): 0.815 RNAalifold(seed): 0.888 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	184 Multilign(20) vs RNAalifold(seed) Matthews Correlation Coefficient Multilign(20): 0.658 RNAalifold(seed): 0.473 Sensitivity Multilign(20): 0.593 RNAalifold(seed): 0.272 Positive Predictive Value Multilign(20): 0.731 RNAalifold(seed): 0.825 Number of pairs reference - predicted secondary structure: 184 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.679 RNAalifold(seed): 0.492 Sensitivity MXScarna(20): 0.599 RNAalifold(seed): 0.290 Positive Predictive Value MXScarna(20): 0.772 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.633 RNAalifold(seed): 0.541 Sensitivity CentroidFold: 0.579 RNAalifold(seed): 0.344 Positive Predictive Value CentroidFold: 0.692 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.619 RNAalifold(seed): 0.541 Sensitivity Contrafold: 0.604 RNAalifold(seed): 0.344 Positive Predictive Value Contrafold: 0.636 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 RNAalifold(seed): 0.698 Sensitivity PPfold(seed): 0.652 RNAalifold(seed): 0.574 Positive Predictive Value PPfold(seed): 0.787 RNAalifold(seed): 0.850 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.612 RNAalifold(seed): 0.541 Sensitivity Sfold: 0.557 RNAalifold(seed): 0.344 Positive Predictive Value Sfold: 0.673 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 MaxExpect vs RNAalifold(seed) Matthews Correlation Coefficient MaxExpect: 0.597 RNAalifold(seed): 0.541 Sensitivity MaxExpect: 0.581 RNAalifold(seed): 0.344 Positive Predictive Value MaxExpect: 0.616 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.596 RNAalifold(seed): 0.541 Sensitivity ProbKnot: 0.585 RNAalifold(seed): 0.344 Positive Predictive Value ProbKnot: 0.610 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.902 RNASampler(seed): 0.779 Sensitivity RNAalifold(seed): 0.818 RNASampler(seed): 0.659 Positive Predictive Value RNAalifold(seed): 0.995 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.64481516727e-08	427 Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.572 RNAalifold(seed): 0.541 Sensitivity Fold: 0.569 RNAalifold(seed): 0.344 Positive Predictive Value Fold: 0.577 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.639 RNASampler(20): 0.578 Sensitivity RNAalifold(seed): 0.436 RNASampler(20): 0.384 Positive Predictive Value RNAalifold(seed): 0.937 RNASampler(20): 0.871 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 Murlet(20) vs RNAalifold(seed) Matthews Correlation Coefficient Murlet(20): 0.568 RNAalifold(seed): 0.515 Sensitivity Murlet(20): 0.427 RNAalifold(seed): 0.314 Positive Predictive Value Murlet(20): 0.758 RNAalifold(seed): 0.844 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.576 RNAalifold(seed): 0.541 Sensitivity UNAFold: 0.566 RNAalifold(seed): 0.344 Positive Predictive Value UNAFold: 0.588 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.559 RNAalifold(seed): 0.541 Sensitivity PknotsRG: 0.554 RNAalifold(seed): 0.344 Positive Predictive Value PknotsRG: 0.566 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.569 RNAalifold(seed): 0.541 Sensitivity RNAfold: 0.562 RNAalifold(seed): 0.344 Positive Predictive Value RNAfold: 0.576 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.794 Multilign(seed): 0.759 Sensitivity RNAalifold(seed): 0.696 Multilign(seed): 0.752 Positive Predictive Value RNAalifold(seed): 0.907 Multilign(seed): 0.767 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	353 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.558 RNAalifold(seed): 0.533 Sensitivity Afold: 0.551 RNAalifold(seed): 0.335 Positive Predictive Value Afold: 0.566 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	414 RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.558 RNAalifold(seed): 0.542 Sensitivity RNAsubopt: 0.560 RNAalifold(seed): 0.345 Positive Predictive Value RNAsubopt: 0.559 RNAalifold(seed): 0.851 Number of pairs reference - predicted secondary structure: 414 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.497 RNAalifold(seed): 0.492 Sensitivity CMfinder(20): 0.327 RNAalifold(seed): 0.290 Positive Predictive Value CMfinder(20): 0.758 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 8.67590017402e-07	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.541 McQFold: 0.465 Sensitivity RNAalifold(seed): 0.344 McQFold: 0.448 Positive Predictive Value RNAalifold(seed): 0.851 McQFold: 0.484 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.541 CRWrnafold: 0.481 Sensitivity RNAalifold(seed): 0.344 CRWrnafold: 0.477 Positive Predictive Value RNAalifold(seed): 0.851 CRWrnafold: 0.488 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.551 RNASLOpt: 0.464 Sensitivity RNAalifold(seed): 0.355 RNASLOpt: 0.433 Positive Predictive Value RNAalifold(seed): 0.855 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 366 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.540 RNAshapes: 0.507 Sensitivity RNAalifold(seed): 0.344 RNAshapes: 0.495 Positive Predictive Value RNAalifold(seed): 0.849 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 389 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.758 Murlet(seed): 0.569 Sensitivity RNAalifold(seed): 0.635 Murlet(seed): 0.383 Positive Predictive Value RNAalifold(seed): 0.904 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.492 RSpredict(20): 0.404 Sensitivity RNAalifold(seed): 0.290 RSpredict(20): 0.260 Positive Predictive Value RNAalifold(seed): 0.836 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.492 Carnac(20): 0.361 Sensitivity RNAalifold(seed): 0.290 Carnac(20): 0.148 Positive Predictive Value RNAalifold(seed): 0.836 Carnac(20): 0.881 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.541 RNAwolf: 0.379 Sensitivity RNAalifold(seed): 0.344 RNAwolf: 0.389 Positive Predictive Value RNAalifold(seed): 0.851 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.706 CMfinder(seed): 0.454 Sensitivity RNAalifold(seed): 0.543 CMfinder(seed): 0.271 Positive Predictive Value RNAalifold(seed): 0.918 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.541 RSpredict(seed): 0.215 Sensitivity RNAalifold(seed): 0.344 RSpredict(seed): 0.090 Positive Predictive Value RNAalifold(seed): 0.851 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.543 Vsfold4: 0.336 Sensitivity RNAalifold(seed): 0.348 Vsfold4: 0.305 Positive Predictive Value RNAalifold(seed): 0.850 Vsfold4: 0.372 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.543 Vsfold5: 0.315 Sensitivity RNAalifold(seed): 0.347 Vsfold5: 0.294 Positive Predictive Value RNAalifold(seed): 0.850 Vsfold5: 0.340 Number of pairs reference - predicted secondary structure: 394 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.537 NanoFolder: 0.176 Sensitivity RNAalifold(seed): 0.335 NanoFolder: 0.203 Positive Predictive Value RNAalifold(seed): 0.861 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 Carnac(seed): 0.150 Sensitivity RNAalifold(seed): 0.482 Carnac(seed): 0.028 Positive Predictive Value RNAalifold(seed): 0.896 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.550 Mastr(seed): 0.073 Sensitivity RNAalifold(seed): 0.354 Mastr(seed): 0.006 Positive Predictive Value RNAalifold(seed): 0.855 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 400 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.877 HotKnots: 0.640 Sensitivity RNAalifold(seed): 0.769 HotKnots: 0.615 Positive Predictive Value RNAalifold(seed): 1.000 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: N/A RNAalifold(seed): N/A Sensitivity Pknots: N/A RNAalifold(seed): N/A Positive Predictive Value Pknots: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(seed): N/A Sensitivity Cylofold: N/A RNAalifold(seed): N/A Positive Predictive Value Cylofold: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): N/A MCFold: N/A Sensitivity RNAalifold(seed): N/A MCFold: N/A Positive Predictive Value RNAalifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAalifold(seed) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(seed): N/A Sensitivity RDfolder: N/A RNAalifold(seed): N/A Positive Predictive Value RDfolder: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): N/A Alterna: N/A Sensitivity RNAalifold(seed): N/A Alterna: N/A Positive Predictive Value RNAalifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.492 Mastr(20): 0.000 Sensitivity RNAalifold(seed): 0.290 Mastr(20): 0.000 Positive Predictive Value RNAalifold(seed): 0.836 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(20)	230 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 CMfinder(20): 0.482 Sensitivity PETfold_pre2.0(seed): 0.693 CMfinder(20): 0.314 Positive Predictive Value PETfold_pre2.0(seed): 0.854 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.843 CMfinder(20): 0.478 Sensitivity ContextFold: 0.799 CMfinder(20): 0.309 Positive Predictive Value ContextFold: 0.891 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.752 CMfinder(20): 0.478 Sensitivity TurboFold(20): 0.701 CMfinder(20): 0.309 Positive Predictive Value TurboFold(20): 0.809 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 CMfinder(20): 0.497 Sensitivity CentroidAlifold(seed): 0.564 CMfinder(20): 0.327 Positive Predictive Value CentroidAlifold(seed): 0.953 CMfinder(20): 0.758 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CMfinder(20): 0.479 Sensitivity PETfold_pre2.0(20): 0.654 CMfinder(20): 0.310 Positive Predictive Value PETfold_pre2.0(20): 0.836 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.733 CMfinder(20): 0.479 Sensitivity PPfold(20): 0.629 CMfinder(20): 0.310 Positive Predictive Value PPfold(20): 0.855 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 CMfinder(20): 0.478 Sensitivity CentroidHomfold‑LAST: 0.561 CMfinder(20): 0.309 Positive Predictive Value CentroidHomfold‑LAST: 0.898 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CMfinder(20): 0.478 Sensitivity CentroidAlifold(20): 0.574 CMfinder(20): 0.309 Positive Predictive Value CentroidAlifold(20): 0.916 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 CMfinder(20): 0.497 Sensitivity MXScarna(seed): 0.582 CMfinder(20): 0.327 Positive Predictive Value MXScarna(seed): 0.805 CMfinder(20): 0.758 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.655 CMfinder(20): 0.478 Sensitivity IPknot: 0.586 CMfinder(20): 0.309 Positive Predictive Value IPknot: 0.732 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 CMfinder(20): 0.478 Sensitivity RNAalifold(20): 0.540 CMfinder(20): 0.309 Positive Predictive Value RNAalifold(20): 0.827 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 CMfinder(20): 0.414 Sensitivity TurboFold(seed): 0.739 CMfinder(20): 0.261 Positive Predictive Value TurboFold(seed): 0.774 CMfinder(20): 0.657 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	223 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.651 CMfinder(20): 0.477 Sensitivity Multilign(20): 0.590 CMfinder(20): 0.307 Positive Predictive Value Multilign(20): 0.721 CMfinder(20): 0.742 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.654 CMfinder(20): 0.478 Sensitivity MXScarna(20): 0.584 CMfinder(20): 0.309 Positive Predictive Value MXScarna(20): 0.735 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidFold vs CMfinder(20) Matthews Correlation Coefficient CentroidFold: 0.621 CMfinder(20): 0.478 Sensitivity CentroidFold: 0.557 CMfinder(20): 0.309 Positive Predictive Value CentroidFold: 0.694 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 Contrafold vs CMfinder(20) Matthews Correlation Coefficient Contrafold: 0.606 CMfinder(20): 0.478 Sensitivity Contrafold: 0.585 CMfinder(20): 0.309 Positive Predictive Value Contrafold: 0.630 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PPfold(seed) vs CMfinder(20) Matthews Correlation Coefficient PPfold(seed): 0.847 CMfinder(20): 0.524 Sensitivity PPfold(seed): 0.782 CMfinder(20): 0.376 Positive Predictive Value PPfold(seed): 0.919 CMfinder(20): 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	245 Sfold vs CMfinder(20) Matthews Correlation Coefficient Sfold: 0.584 CMfinder(20): 0.478 Sensitivity Sfold: 0.522 CMfinder(20): 0.309 Positive Predictive Value Sfold: 0.654 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MaxExpect vs CMfinder(20) Matthews Correlation Coefficient MaxExpect: 0.592 CMfinder(20): 0.478 Sensitivity MaxExpect: 0.569 CMfinder(20): 0.309 Positive Predictive Value MaxExpect: 0.617 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ProbKnot vs CMfinder(20) Matthews Correlation Coefficient ProbKnot: 0.590 CMfinder(20): 0.478 Sensitivity ProbKnot: 0.572 CMfinder(20): 0.309 Positive Predictive Value ProbKnot: 0.610 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	245 Fold vs CMfinder(20) Matthews Correlation Coefficient Fold: 0.562 CMfinder(20): 0.478 Sensitivity Fold: 0.555 CMfinder(20): 0.309 Positive Predictive Value Fold: 0.571 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.565 CMfinder(20): 0.413 Sensitivity RNASampler(20): 0.413 CMfinder(20): 0.258 Positive Predictive Value RNASampler(20): 0.772 CMfinder(20): 0.663 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.573 CMfinder(20): 0.467 Sensitivity Murlet(20): 0.441 CMfinder(20): 0.302 Positive Predictive Value Murlet(20): 0.746 CMfinder(20): 0.724 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 UNAFold vs CMfinder(20) Matthews Correlation Coefficient UNAFold: 0.547 CMfinder(20): 0.478 Sensitivity UNAFold: 0.535 CMfinder(20): 0.309 Positive Predictive Value UNAFold: 0.560 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 PknotsRG vs CMfinder(20) Matthews Correlation Coefficient PknotsRG: 0.525 CMfinder(20): 0.478 Sensitivity PknotsRG: 0.518 CMfinder(20): 0.309 Positive Predictive Value PknotsRG: 0.535 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAfold vs CMfinder(20) Matthews Correlation Coefficient RNAfold: 0.544 CMfinder(20): 0.478 Sensitivity RNAfold: 0.536 CMfinder(20): 0.309 Positive Predictive Value RNAfold: 0.553 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	185 Afold vs CMfinder(20) Matthews Correlation Coefficient Afold: 0.556 CMfinder(20): 0.494 Sensitivity Afold: 0.544 CMfinder(20): 0.323 Positive Predictive Value Afold: 0.570 CMfinder(20): 0.757 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAsubopt vs CMfinder(20) Matthews Correlation Coefficient RNAsubopt: 0.530 CMfinder(20): 0.478 Sensitivity RNAsubopt: 0.529 CMfinder(20): 0.309 Positive Predictive Value RNAsubopt: 0.532 CMfinder(20): 0.741 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.497 RNAalifold(seed): 0.492 Sensitivity CMfinder(20): 0.327 RNAalifold(seed): 0.290 Positive Predictive Value CMfinder(20): 0.758 RNAalifold(seed): 0.836 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 8.67590017402e-07		+ CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.478 McQFold: 0.442 Sensitivity CMfinder(20): 0.309 McQFold: 0.424 Positive Predictive Value CMfinder(20): 0.741 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.478 CRWrnafold: 0.464 Sensitivity CMfinder(20): 0.309 CRWrnafold: 0.456 Positive Predictive Value CMfinder(20): 0.741 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.487 RNASLOpt: 0.450 Sensitivity CMfinder(20): 0.318 RNASLOpt: 0.417 Positive Predictive Value CMfinder(20): 0.746 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.486 RNAshapes: 0.468 Sensitivity CMfinder(20): 0.316 RNAshapes: 0.454 Positive Predictive Value CMfinder(20): 0.747 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): 0.588 CMfinder(20): 0.524 Sensitivity Murlet(seed): 0.347 CMfinder(20): 0.376 Positive Predictive Value Murlet(seed): 1.000 CMfinder(20): 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.478 RSpredict(20): 0.418 Sensitivity CMfinder(20): 0.309 RSpredict(20): 0.285 Positive Predictive Value CMfinder(20): 0.741 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.478 Carnac(20): 0.378 Sensitivity CMfinder(20): 0.309 Carnac(20): 0.166 Positive Predictive Value CMfinder(20): 0.741 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.478 RNAwolf: 0.367 Sensitivity CMfinder(20): 0.309 RNAwolf: 0.377 Positive Predictive Value CMfinder(20): 0.741 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.498 RSpredict(seed): 0.197 Sensitivity CMfinder(20): 0.328 RSpredict(seed): 0.077 Positive Predictive Value CMfinder(20): 0.758 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.483 Vsfold4: 0.352 Sensitivity CMfinder(20): 0.314 Vsfold4: 0.319 Positive Predictive Value CMfinder(20): 0.745 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.485 Vsfold5: 0.333 Sensitivity CMfinder(20): 0.316 Vsfold5: 0.308 Positive Predictive Value CMfinder(20): 0.747 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.476 NanoFolder: 0.150 Sensitivity CMfinder(20): 0.303 NanoFolder: 0.173 Positive Predictive Value CMfinder(20): 0.751 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.456 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.322 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.649 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.31583660336e-08	+ CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.497 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.329 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.753 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CMfinder(20) Matthews Correlation Coefficient HotKnots: N/A CMfinder(20): N/A Sensitivity HotKnots: N/A CMfinder(20): N/A Positive Predictive Value HotKnots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs CMfinder(20) Matthews Correlation Coefficient Pknots: N/A CMfinder(20): N/A Sensitivity Pknots: N/A CMfinder(20): N/A Positive Predictive Value Pknots: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? MCFold vs CMfinder(20) Matthews Correlation Coefficient MCFold: N/A CMfinder(20): N/A Sensitivity MCFold: N/A CMfinder(20): N/A Positive Predictive Value MCFold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? Alterna vs CMfinder(20) Matthews Correlation Coefficient Alterna: N/A CMfinder(20): N/A Sensitivity Alterna: N/A CMfinder(20): N/A Positive Predictive Value Alterna: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.478 Mastr(20): 0.000 Sensitivity CMfinder(20): 0.309 Mastr(20): 0.000 Positive Predictive Value CMfinder(20): 0.741 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
McQFold	643 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 McQFold: 0.448 Sensitivity PETfold_pre2.0(seed): 0.612 McQFold: 0.438 Positive Predictive Value PETfold_pre2.0(seed): 0.803 McQFold: 0.461 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.720 McQFold: 0.443 Sensitivity ContextFold: 0.687 McQFold: 0.435 Positive Predictive Value ContextFold: 0.756 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.752 McQFold: 0.442 Sensitivity TurboFold(20): 0.701 McQFold: 0.424 Positive Predictive Value TurboFold(20): 0.809 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 McQFold: 0.465 Sensitivity CentroidAlifold(seed): 0.556 McQFold: 0.449 Positive Predictive Value CentroidAlifold(seed): 0.906 McQFold: 0.484 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 McQFold: 0.442 Sensitivity PETfold_pre2.0(20): 0.654 McQFold: 0.423 Positive Predictive Value PETfold_pre2.0(20): 0.836 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.733 McQFold: 0.442 Sensitivity PPfold(20): 0.629 McQFold: 0.423 Positive Predictive Value PPfold(20): 0.855 McQFold: 0.463 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 McQFold: 0.452 Sensitivity CentroidHomfold‑LAST: 0.491 McQFold: 0.442 Positive Predictive Value CentroidHomfold‑LAST: 0.862 McQFold: 0.463 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 McQFold: 0.442 Sensitivity CentroidAlifold(20): 0.574 McQFold: 0.424 Positive Predictive Value CentroidAlifold(20): 0.916 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.637 McQFold: 0.466 Sensitivity MXScarna(seed): 0.535 McQFold: 0.450 Positive Predictive Value MXScarna(seed): 0.759 McQFold: 0.485 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.612 McQFold: 0.443 Sensitivity IPknot: 0.561 McQFold: 0.435 Positive Predictive Value IPknot: 0.667 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.668 McQFold: 0.442 Sensitivity RNAalifold(20): 0.540 McQFold: 0.424 Positive Predictive Value RNAalifold(20): 0.827 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.787 McQFold: 0.461 Sensitivity TurboFold(seed): 0.760 McQFold: 0.452 Positive Predictive Value TurboFold(seed): 0.815 McQFold: 0.471 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.8150742666e-08	223 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.651 McQFold: 0.441 Sensitivity Multilign(20): 0.590 McQFold: 0.422 Positive Predictive Value Multilign(20): 0.721 McQFold: 0.462 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.654 McQFold: 0.442 Sensitivity MXScarna(20): 0.584 McQFold: 0.424 Positive Predictive Value MXScarna(20): 0.735 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.583 McQFold: 0.443 Sensitivity CentroidFold: 0.533 McQFold: 0.435 Positive Predictive Value CentroidFold: 0.638 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.567 McQFold: 0.443 Sensitivity Contrafold: 0.558 McQFold: 0.435 Positive Predictive Value Contrafold: 0.577 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs McQFold Matthews Correlation Coefficient PPfold(seed): 0.716 McQFold: 0.465 Sensitivity PPfold(seed): 0.652 McQFold: 0.458 Positive Predictive Value PPfold(seed): 0.787 McQFold: 0.475 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	818 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.538 McQFold: 0.443 Sensitivity Sfold: 0.491 McQFold: 0.435 Positive Predictive Value Sfold: 0.589 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.536 McQFold: 0.443 Sensitivity MaxExpect: 0.527 McQFold: 0.435 Positive Predictive Value MaxExpect: 0.546 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.534 McQFold: 0.443 Sensitivity ProbKnot: 0.534 McQFold: 0.435 Positive Predictive Value ProbKnot: 0.535 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs McQFold Matthews Correlation Coefficient RNASampler(seed): 0.779 McQFold: 0.446 Sensitivity RNASampler(seed): 0.659 McQFold: 0.452 Positive Predictive Value RNASampler(seed): 0.921 McQFold: 0.442 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	818 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.511 McQFold: 0.443 Sensitivity Fold: 0.517 McQFold: 0.435 Positive Predictive Value Fold: 0.506 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.565 McQFold: 0.388 Sensitivity RNASampler(20): 0.413 McQFold: 0.377 Positive Predictive Value RNASampler(20): 0.772 McQFold: 0.401 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.573 McQFold: 0.427 Sensitivity Murlet(20): 0.441 McQFold: 0.411 Positive Predictive Value Murlet(20): 0.746 McQFold: 0.446 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.501 McQFold: 0.443 Sensitivity UNAFold: 0.501 McQFold: 0.435 Positive Predictive Value UNAFold: 0.503 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.499 McQFold: 0.443 Sensitivity PknotsRG: 0.504 McQFold: 0.435 Positive Predictive Value PknotsRG: 0.495 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.499 McQFold: 0.443 Sensitivity RNAfold: 0.504 McQFold: 0.435 Positive Predictive Value RNAfold: 0.495 McQFold: 0.452 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs McQFold Matthews Correlation Coefficient Multilign(seed): 0.734 McQFold: 0.433 Sensitivity Multilign(seed): 0.733 McQFold: 0.438 Positive Predictive Value Multilign(seed): 0.737 McQFold: 0.429 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 6.99051034341e-09	525 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.516 McQFold: 0.449 Sensitivity Afold: 0.517 McQFold: 0.440 Positive Predictive Value Afold: 0.516 McQFold: 0.460 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.501 McQFold: 0.452 Sensitivity RNAsubopt: 0.510 McQFold: 0.442 Positive Predictive Value RNAsubopt: 0.495 McQFold: 0.463 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.541 McQFold: 0.465 Sensitivity RNAalifold(seed): 0.344 McQFold: 0.448 Positive Predictive Value RNAalifold(seed): 0.851 McQFold: 0.484 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.478 McQFold: 0.442 Sensitivity CMfinder(20): 0.309 McQFold: 0.424 Positive Predictive Value CMfinder(20): 0.741 McQFold: 0.464 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.443 CRWrnafold: 0.432 Sensitivity McQFold: 0.435 CRWrnafold: 0.438 Positive Predictive Value McQFold: 0.452 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.450 RNASLOpt: 0.442 Sensitivity McQFold: 0.440 RNASLOpt: 0.419 Positive Predictive Value McQFold: 0.462 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.452 RNAshapes: 0.438 Sensitivity McQFold: 0.441 RNAshapes: 0.434 Positive Predictive Value McQFold: 0.465 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs McQFold Matthews Correlation Coefficient Murlet(seed): 0.569 McQFold: 0.461 Sensitivity Murlet(seed): 0.383 McQFold: 0.455 Positive Predictive Value Murlet(seed): 0.845 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.442 RSpredict(20): 0.418 Sensitivity McQFold: 0.424 RSpredict(20): 0.285 Positive Predictive Value McQFold: 0.464 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.442 Carnac(20): 0.378 Sensitivity McQFold: 0.424 Carnac(20): 0.166 Positive Predictive Value McQFold: 0.464 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.443 RNAwolf: 0.339 Sensitivity McQFold: 0.435 RNAwolf: 0.355 Positive Predictive Value McQFold: 0.452 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.492 CMfinder(seed): 0.454 Sensitivity McQFold: 0.484 CMfinder(seed): 0.271 Positive Predictive Value McQFold: 0.500 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.465 RSpredict(seed): 0.214 Sensitivity McQFold: 0.449 RSpredict(seed): 0.089 Positive Predictive Value McQFold: 0.484 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.451 Vsfold4: 0.306 Sensitivity McQFold: 0.441 Vsfold4: 0.282 Positive Predictive Value McQFold: 0.463 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.452 Vsfold5: 0.300 Sensitivity McQFold: 0.442 Vsfold5: 0.286 Positive Predictive Value McQFold: 0.464 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.456 NanoFolder: 0.166 Sensitivity McQFold: 0.444 NanoFolder: 0.197 Positive Predictive Value McQFold: 0.471 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.432 Carnac(seed): 0.150 Sensitivity McQFold: 0.425 Carnac(seed): 0.028 Positive Predictive Value McQFold: 0.440 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.467 Mastr(seed): 0.073 Sensitivity McQFold: 0.451 Mastr(seed): 0.006 Positive Predictive Value McQFold: 0.484 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.640 McQFold: 0.361 Sensitivity HotKnots: 0.615 McQFold: 0.385 Positive Predictive Value HotKnots: 0.667 McQFold: 0.341 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? McQFold vs Pknots Matthews Correlation Coefficient McQFold: N/A Pknots: N/A Sensitivity McQFold: N/A Pknots: N/A Positive Predictive Value McQFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.526 Cylofold: 0.271 Sensitivity McQFold: 0.489 Cylofold: 0.241 Positive Predictive Value McQFold: 0.568 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? McQFold vs MCFold Matthews Correlation Coefficient McQFold: N/A MCFold: N/A Sensitivity McQFold: N/A MCFold: N/A Positive Predictive Value McQFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs McQFold Matthews Correlation Coefficient RDfolder: N/A McQFold: N/A Sensitivity RDfolder: N/A McQFold: N/A Positive Predictive Value RDfolder: N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? McQFold vs Alterna Matthews Correlation Coefficient McQFold: N/A Alterna: N/A Sensitivity McQFold: N/A Alterna: N/A Positive Predictive Value McQFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.442 Mastr(20): 0.000 Sensitivity McQFold: 0.424 Mastr(20): 0.000 Positive Predictive Value McQFold: 0.464 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
CRWrnafold	643 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 CRWrnafold: 0.436 Sensitivity PETfold_pre2.0(seed): 0.612 CRWrnafold: 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.803 CRWrnafold: 0.436 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.720 CRWrnafold: 0.432 Sensitivity ContextFold: 0.687 CRWrnafold: 0.438 Positive Predictive Value ContextFold: 0.756 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.752 CRWrnafold: 0.464 Sensitivity TurboFold(20): 0.701 CRWrnafold: 0.456 Positive Predictive Value TurboFold(20): 0.809 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 CRWrnafold: 0.482 Sensitivity CentroidAlifold(seed): 0.556 CRWrnafold: 0.477 Positive Predictive Value CentroidAlifold(seed): 0.906 CRWrnafold: 0.488 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 CRWrnafold: 0.462 Sensitivity PETfold_pre2.0(20): 0.654 CRWrnafold: 0.454 Positive Predictive Value PETfold_pre2.0(20): 0.836 CRWrnafold: 0.472 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.733 CRWrnafold: 0.463 Sensitivity PPfold(20): 0.629 CRWrnafold: 0.455 Positive Predictive Value PPfold(20): 0.855 CRWrnafold: 0.473 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 CRWrnafold: 0.442 Sensitivity CentroidHomfold‑LAST: 0.491 CRWrnafold: 0.445 Positive Predictive Value CentroidHomfold‑LAST: 0.862 CRWrnafold: 0.440 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.725 CRWrnafold: 0.464 Sensitivity CentroidAlifold(20): 0.574 CRWrnafold: 0.456 Positive Predictive Value CentroidAlifold(20): 0.916 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.637 CRWrnafold: 0.482 Sensitivity MXScarna(seed): 0.535 CRWrnafold: 0.478 Positive Predictive Value MXScarna(seed): 0.759 CRWrnafold: 0.488 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.612 CRWrnafold: 0.432 Sensitivity IPknot: 0.561 CRWrnafold: 0.438 Positive Predictive Value IPknot: 0.667 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.668 CRWrnafold: 0.464 Sensitivity RNAalifold(20): 0.540 CRWrnafold: 0.456 Positive Predictive Value RNAalifold(20): 0.827 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.787 CRWrnafold: 0.508 Sensitivity TurboFold(seed): 0.760 CRWrnafold: 0.517 Positive Predictive Value TurboFold(seed): 0.815 CRWrnafold: 0.500 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	223 Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.651 CRWrnafold: 0.465 Sensitivity Multilign(20): 0.590 CRWrnafold: 0.457 Positive Predictive Value Multilign(20): 0.721 CRWrnafold: 0.475 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.654 CRWrnafold: 0.464 Sensitivity MXScarna(20): 0.584 CRWrnafold: 0.456 Positive Predictive Value MXScarna(20): 0.735 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.583 CRWrnafold: 0.432 Sensitivity CentroidFold: 0.533 CRWrnafold: 0.438 Positive Predictive Value CentroidFold: 0.638 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.567 CRWrnafold: 0.432 Sensitivity Contrafold: 0.558 CRWrnafold: 0.438 Positive Predictive Value Contrafold: 0.577 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs CRWrnafold Matthews Correlation Coefficient PPfold(seed): 0.716 CRWrnafold: 0.499 Sensitivity PPfold(seed): 0.652 CRWrnafold: 0.509 Positive Predictive Value PPfold(seed): 0.787 CRWrnafold: 0.491 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	818 Sfold vs CRWrnafold Matthews Correlation Coefficient Sfold: 0.538 CRWrnafold: 0.432 Sensitivity Sfold: 0.491 CRWrnafold: 0.438 Positive Predictive Value Sfold: 0.589 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.536 CRWrnafold: 0.432 Sensitivity MaxExpect: 0.527 CRWrnafold: 0.438 Positive Predictive Value MaxExpect: 0.546 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs CRWrnafold Matthews Correlation Coefficient ProbKnot: 0.534 CRWrnafold: 0.432 Sensitivity ProbKnot: 0.534 CRWrnafold: 0.438 Positive Predictive Value ProbKnot: 0.535 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.779 CRWrnafold: 0.474 Sensitivity RNASampler(seed): 0.659 CRWrnafold: 0.499 Positive Predictive Value RNASampler(seed): 0.921 CRWrnafold: 0.452 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.10198558684e-08	818 Fold vs CRWrnafold Matthews Correlation Coefficient Fold: 0.511 CRWrnafold: 0.432 Sensitivity Fold: 0.517 CRWrnafold: 0.438 Positive Predictive Value Fold: 0.506 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs CRWrnafold Matthews Correlation Coefficient RNASampler(20): 0.565 CRWrnafold: 0.425 Sensitivity RNASampler(20): 0.413 CRWrnafold: 0.427 Positive Predictive Value RNASampler(20): 0.772 CRWrnafold: 0.424 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs CRWrnafold Matthews Correlation Coefficient Murlet(20): 0.573 CRWrnafold: 0.440 Sensitivity Murlet(20): 0.441 CRWrnafold: 0.434 Positive Predictive Value Murlet(20): 0.746 CRWrnafold: 0.449 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 UNAFold vs CRWrnafold Matthews Correlation Coefficient UNAFold: 0.501 CRWrnafold: 0.432 Sensitivity UNAFold: 0.501 CRWrnafold: 0.438 Positive Predictive Value UNAFold: 0.503 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 PknotsRG vs CRWrnafold Matthews Correlation Coefficient PknotsRG: 0.499 CRWrnafold: 0.432 Sensitivity PknotsRG: 0.504 CRWrnafold: 0.438 Positive Predictive Value PknotsRG: 0.495 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 RNAfold vs CRWrnafold Matthews Correlation Coefficient RNAfold: 0.499 CRWrnafold: 0.432 Sensitivity RNAfold: 0.504 CRWrnafold: 0.438 Positive Predictive Value RNAfold: 0.495 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.734 CRWrnafold: 0.464 Sensitivity Multilign(seed): 0.733 CRWrnafold: 0.487 Positive Predictive Value Multilign(seed): 0.737 CRWrnafold: 0.444 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.27752322258e-08	525 Afold vs CRWrnafold Matthews Correlation Coefficient Afold: 0.516 CRWrnafold: 0.451 Sensitivity Afold: 0.517 CRWrnafold: 0.455 Positive Predictive Value Afold: 0.516 CRWrnafold: 0.449 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 RNAsubopt vs CRWrnafold Matthews Correlation Coefficient RNAsubopt: 0.501 CRWrnafold: 0.442 Sensitivity RNAsubopt: 0.510 CRWrnafold: 0.445 Positive Predictive Value RNAsubopt: 0.495 CRWrnafold: 0.440 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 RNAalifold(seed) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(seed): 0.541 CRWrnafold: 0.481 Sensitivity RNAalifold(seed): 0.344 CRWrnafold: 0.477 Positive Predictive Value RNAalifold(seed): 0.851 CRWrnafold: 0.488 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CMfinder(20) vs CRWrnafold Matthews Correlation Coefficient CMfinder(20): 0.478 CRWrnafold: 0.464 Sensitivity CMfinder(20): 0.309 CRWrnafold: 0.456 Positive Predictive Value CMfinder(20): 0.741 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 McQFold vs CRWrnafold Matthews Correlation Coefficient McQFold: 0.443 CRWrnafold: 0.432 Sensitivity McQFold: 0.435 CRWrnafold: 0.438 Positive Predictive Value McQFold: 0.452 CRWrnafold: 0.428 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08		= CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.443 RNASLOpt: 0.442 Sensitivity CRWrnafold: 0.445 RNASLOpt: 0.419 Positive Predictive Value CRWrnafold: 0.442 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 0.192299791283	+ CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.442 RNAshapes: 0.438 Sensitivity CRWrnafold: 0.444 RNAshapes: 0.434 Positive Predictive Value CRWrnafold: 0.442 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.85233844192e-08	- Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.569 CRWrnafold: 0.532 Sensitivity Murlet(seed): 0.383 CRWrnafold: 0.539 Positive Predictive Value Murlet(seed): 0.845 CRWrnafold: 0.527 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.464 RSpredict(20): 0.418 Sensitivity CRWrnafold: 0.456 RSpredict(20): 0.285 Positive Predictive Value CRWrnafold: 0.474 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.464 Carnac(20): 0.378 Sensitivity CRWrnafold: 0.456 Carnac(20): 0.166 Positive Predictive Value CRWrnafold: 0.474 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.432 RNAwolf: 0.339 Sensitivity CRWrnafold: 0.438 RNAwolf: 0.355 Positive Predictive Value CRWrnafold: 0.428 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.589 CMfinder(seed): 0.454 Sensitivity CRWrnafold: 0.596 CMfinder(seed): 0.271 Positive Predictive Value CRWrnafold: 0.584 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.481 RSpredict(seed): 0.214 Sensitivity CRWrnafold: 0.477 RSpredict(seed): 0.089 Positive Predictive Value CRWrnafold: 0.488 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.441 Vsfold4: 0.306 Sensitivity CRWrnafold: 0.443 Vsfold4: 0.282 Positive Predictive Value CRWrnafold: 0.440 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.441 Vsfold5: 0.300 Sensitivity CRWrnafold: 0.443 Vsfold5: 0.286 Positive Predictive Value CRWrnafold: 0.440 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.472 NanoFolder: 0.166 Sensitivity CRWrnafold: 0.472 NanoFolder: 0.197 Positive Predictive Value CRWrnafold: 0.473 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.487 Carnac(seed): 0.150 Sensitivity CRWrnafold: 0.493 Carnac(seed): 0.028 Positive Predictive Value CRWrnafold: 0.483 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.482 Mastr(seed): 0.073 Sensitivity CRWrnafold: 0.479 Mastr(seed): 0.006 Positive Predictive Value CRWrnafold: 0.487 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.640 CRWrnafold: 0.548 Sensitivity HotKnots: 0.615 CRWrnafold: 0.590 Positive Predictive Value HotKnots: 0.667 CRWrnafold: 0.511 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: N/A CRWrnafold: N/A Sensitivity Pknots: N/A CRWrnafold: N/A Positive Predictive Value Pknots: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.470 Cylofold: 0.271 Sensitivity CRWrnafold: 0.474 Cylofold: 0.241 Positive Predictive Value CRWrnafold: 0.468 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: N/A MCFold: N/A Sensitivity CRWrnafold: N/A MCFold: N/A Positive Predictive Value CRWrnafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: N/A CRWrnafold: N/A Sensitivity RDfolder: N/A CRWrnafold: N/A Positive Predictive Value RDfolder: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs CRWrnafold Matthews Correlation Coefficient Alterna: N/A CRWrnafold: N/A Sensitivity Alterna: N/A CRWrnafold: N/A Positive Predictive Value Alterna: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.464 Mastr(20): 0.000 Sensitivity CRWrnafold: 0.456 Mastr(20): 0.000 Positive Predictive Value CRWrnafold: 0.474 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASLOpt	561 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.716 RNASLOpt: 0.445 Sensitivity PETfold_pre2.0(seed): 0.635 RNASLOpt: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.808 RNASLOpt: 0.471 Number of pairs reference - predicted secondary structure: 561 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.747 RNASLOpt: 0.442 Sensitivity ContextFold: 0.711 RNASLOpt: 0.419 Positive Predictive Value ContextFold: 0.787 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.750 RNASLOpt: 0.450 Sensitivity TurboFold(20): 0.699 RNASLOpt: 0.417 Positive Predictive Value TurboFold(20): 0.805 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	365 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.728 RNASLOpt: 0.465 Sensitivity CentroidAlifold(seed): 0.581 RNASLOpt: 0.433 Positive Predictive Value CentroidAlifold(seed): 0.912 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 365 Wilcoxon single-rank test P-value: 3.56938820447e-08	224 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 RNASLOpt: 0.449 Sensitivity PETfold_pre2.0(20): 0.658 RNASLOpt: 0.415 Positive Predictive Value PETfold_pre2.0(20): 0.835 RNASLOpt: 0.487 Number of pairs reference - predicted secondary structure: 224 Wilcoxon single-rank test P-value: 3.56938820447e-08	222 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.736 RNASLOpt: 0.450 Sensitivity PPfold(20): 0.633 RNASLOpt: 0.417 Positive Predictive Value PPfold(20): 0.856 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 222 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.659 RNASLOpt: 0.442 Sensitivity CentroidHomfold‑LAST: 0.506 RNASLOpt: 0.419 Positive Predictive Value CentroidHomfold‑LAST: 0.860 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.726 RNASLOpt: 0.450 Sensitivity CentroidAlifold(20): 0.577 RNASLOpt: 0.417 Positive Predictive Value CentroidAlifold(20): 0.914 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	370 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.662 RNASLOpt: 0.465 Sensitivity MXScarna(seed): 0.567 RNASLOpt: 0.434 Positive Predictive Value MXScarna(seed): 0.775 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 370 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.621 RNASLOpt: 0.442 Sensitivity IPknot: 0.571 RNASLOpt: 0.419 Positive Predictive Value IPknot: 0.678 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.670 RNASLOpt: 0.450 Sensitivity RNAalifold(20): 0.544 RNASLOpt: 0.417 Positive Predictive Value RNAalifold(20): 0.827 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.776 RNASLOpt: 0.463 Sensitivity TurboFold(seed): 0.753 RNASLOpt: 0.454 Positive Predictive Value TurboFold(seed): 0.802 RNASLOpt: 0.473 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.78993384543e-08	209 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.655 RNASLOpt: 0.455 Sensitivity Multilign(20): 0.595 RNASLOpt: 0.421 Positive Predictive Value Multilign(20): 0.722 RNASLOpt: 0.493 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.651 RNASLOpt: 0.450 Sensitivity MXScarna(20): 0.582 RNASLOpt: 0.417 Positive Predictive Value MXScarna(20): 0.730 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.588 RNASLOpt: 0.442 Sensitivity CentroidFold: 0.538 RNASLOpt: 0.419 Positive Predictive Value CentroidFold: 0.643 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.572 RNASLOpt: 0.442 Sensitivity Contrafold: 0.563 RNASLOpt: 0.419 Positive Predictive Value Contrafold: 0.584 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PPfold(seed) vs RNASLOpt Matthews Correlation Coefficient PPfold(seed): 0.735 RNASLOpt: 0.489 Sensitivity PPfold(seed): 0.691 RNASLOpt: 0.475 Positive Predictive Value PPfold(seed): 0.783 RNASLOpt: 0.505 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.98172311752e-08	660 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.546 RNASLOpt: 0.442 Sensitivity Sfold: 0.499 RNASLOpt: 0.419 Positive Predictive Value Sfold: 0.600 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.546 RNASLOpt: 0.442 Sensitivity MaxExpect: 0.535 RNASLOpt: 0.419 Positive Predictive Value MaxExpect: 0.558 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.544 RNASLOpt: 0.442 Sensitivity ProbKnot: 0.541 RNASLOpt: 0.419 Positive Predictive Value ProbKnot: 0.549 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.779 RNASLOpt: 0.568 Sensitivity RNASampler(seed): 0.659 RNASLOpt: 0.569 Positive Predictive Value RNASampler(seed): 0.921 RNASLOpt: 0.568 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.38194587311e-08	660 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.523 RNASLOpt: 0.442 Sensitivity Fold: 0.527 RNASLOpt: 0.419 Positive Predictive Value Fold: 0.521 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.565 RNASLOpt: 0.393 Sensitivity RNASampler(20): 0.413 RNASLOpt: 0.372 Positive Predictive Value RNASampler(20): 0.772 RNASLOpt: 0.417 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.581 RNASLOpt: 0.425 Sensitivity Murlet(20): 0.452 RNASLOpt: 0.395 Positive Predictive Value Murlet(20): 0.750 RNASLOpt: 0.460 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.509 RNASLOpt: 0.442 Sensitivity UNAFold: 0.506 RNASLOpt: 0.419 Positive Predictive Value UNAFold: 0.514 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.504 RNASLOpt: 0.442 Sensitivity PknotsRG: 0.506 RNASLOpt: 0.419 Positive Predictive Value PknotsRG: 0.503 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.510 RNASLOpt: 0.442 Sensitivity RNAfold: 0.512 RNASLOpt: 0.419 Positive Predictive Value RNAfold: 0.510 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs RNASLOpt Matthews Correlation Coefficient Multilign(seed): 0.734 RNASLOpt: 0.462 Sensitivity Multilign(seed): 0.733 RNASLOpt: 0.458 Positive Predictive Value Multilign(seed): 0.737 RNASLOpt: 0.467 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 9.64686604905e-09	413 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.537 RNASLOpt: 0.456 Sensitivity Afold: 0.533 RNASLOpt: 0.429 Positive Predictive Value Afold: 0.541 RNASLOpt: 0.487 Number of pairs reference - predicted secondary structure: 413 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.502 RNASLOpt: 0.442 Sensitivity RNAsubopt: 0.510 RNASLOpt: 0.419 Positive Predictive Value RNAsubopt: 0.496 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	366 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.551 RNASLOpt: 0.464 Sensitivity RNAalifold(seed): 0.355 RNASLOpt: 0.433 Positive Predictive Value RNAalifold(seed): 0.855 RNASLOpt: 0.500 Number of pairs reference - predicted secondary structure: 366 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.487 RNASLOpt: 0.450 Sensitivity CMfinder(20): 0.318 RNASLOpt: 0.417 Positive Predictive Value CMfinder(20): 0.746 RNASLOpt: 0.488 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.450 RNASLOpt: 0.442 Sensitivity McQFold: 0.440 RNASLOpt: 0.419 Positive Predictive Value McQFold: 0.462 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.443 RNASLOpt: 0.442 Sensitivity CRWrnafold: 0.445 RNASLOpt: 0.419 Positive Predictive Value CRWrnafold: 0.442 RNASLOpt: 0.468 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 0.192299791283		+ RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.443 RNAshapes: 0.437 Sensitivity RNASLOpt: 0.420 RNAshapes: 0.434 Positive Predictive Value RNASLOpt: 0.469 RNAshapes: 0.442 Number of pairs reference - predicted secondary structure: 651 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.556 RNASLOpt: 0.479 Sensitivity Murlet(seed): 0.366 RNASLOpt: 0.466 Positive Predictive Value Murlet(seed): 0.846 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.450 RSpredict(20): 0.429 Sensitivity RNASLOpt: 0.417 RSpredict(20): 0.296 Positive Predictive Value RNASLOpt: 0.488 RSpredict(20): 0.623 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.450 Carnac(20): 0.375 Sensitivity RNASLOpt: 0.417 Carnac(20): 0.163 Positive Predictive Value RNASLOpt: 0.488 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.442 RNAwolf: 0.351 Sensitivity RNASLOpt: 0.419 RNAwolf: 0.366 Positive Predictive Value RNASLOpt: 0.468 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.485 CMfinder(seed): 0.464 Sensitivity RNASLOpt: 0.465 CMfinder(seed): 0.285 Positive Predictive Value RNASLOpt: 0.507 CMfinder(seed): 0.760 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.465 RSpredict(seed): 0.230 Sensitivity RNASLOpt: 0.434 RSpredict(seed): 0.099 Positive Predictive Value RNASLOpt: 0.500 RSpredict(seed): 0.538 Number of pairs reference - predicted secondary structure: 368 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.442 Vsfold4: 0.305 Sensitivity RNASLOpt: 0.419 Vsfold4: 0.281 Positive Predictive Value RNASLOpt: 0.468 Vsfold4: 0.333 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.442 Vsfold5: 0.299 Sensitivity RNASLOpt: 0.419 Vsfold5: 0.285 Positive Predictive Value RNASLOpt: 0.468 Vsfold5: 0.315 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.457 NanoFolder: 0.173 Sensitivity RNASLOpt: 0.428 NanoFolder: 0.204 Positive Predictive Value RNASLOpt: 0.491 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.423 Carnac(seed): 0.167 Sensitivity RNASLOpt: 0.401 Carnac(seed): 0.032 Positive Predictive Value RNASLOpt: 0.448 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.463 Mastr(seed): 0.080 Sensitivity RNASLOpt: 0.433 Mastr(seed): 0.007 Positive Predictive Value RNASLOpt: 0.497 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASLOpt vs HotKnots Matthews Correlation Coefficient RNASLOpt: 0.658 HotKnots: 0.640 Sensitivity RNASLOpt: 0.641 HotKnots: 0.615 Positive Predictive Value RNASLOpt: 0.676 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: N/A RNASLOpt: N/A Sensitivity Pknots: N/A RNASLOpt: N/A Positive Predictive Value Pknots: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.382 Cylofold: 0.271 Sensitivity RNASLOpt: 0.358 Cylofold: 0.241 Positive Predictive Value RNASLOpt: 0.412 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: N/A MCFold: N/A Sensitivity RNASLOpt: N/A MCFold: N/A Positive Predictive Value RNASLOpt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNASLOpt Matthews Correlation Coefficient RDfolder: N/A RNASLOpt: N/A Sensitivity RDfolder: N/A RNASLOpt: N/A Positive Predictive Value RDfolder: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: N/A RNASLOpt: N/A Sensitivity Alterna: N/A RNASLOpt: N/A Positive Predictive Value Alterna: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.450 Mastr(20): 0.000 Sensitivity RNASLOpt: 0.417 Mastr(20): 0.000 Positive Predictive Value RNASLOpt: 0.488 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAshapes	597 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.706 RNAshapes: 0.425 Sensitivity PETfold_pre2.0(seed): 0.622 RNAshapes: 0.421 Positive Predictive Value PETfold_pre2.0(seed): 0.801 RNAshapes: 0.430 Number of pairs reference - predicted secondary structure: 597 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.746 RNAshapes: 0.438 Sensitivity ContextFold: 0.708 RNAshapes: 0.434 Positive Predictive Value ContextFold: 0.786 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.751 RNAshapes: 0.468 Sensitivity TurboFold(20): 0.700 RNAshapes: 0.454 Positive Predictive Value TurboFold(20): 0.808 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	388 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.717 RNAshapes: 0.507 Sensitivity CentroidAlifold(seed): 0.567 RNAshapes: 0.495 Positive Predictive Value CentroidAlifold(seed): 0.908 RNAshapes: 0.521 Number of pairs reference - predicted secondary structure: 388 Wilcoxon single-rank test P-value: 3.56938820447e-08	232 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 RNAshapes: 0.467 Sensitivity PETfold_pre2.0(20): 0.656 RNAshapes: 0.453 Positive Predictive Value PETfold_pre2.0(20): 0.838 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 232 Wilcoxon single-rank test P-value: 3.56938820447e-08	229 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.736 RNAshapes: 0.467 Sensitivity PPfold(20): 0.632 RNAshapes: 0.454 Positive Predictive Value PPfold(20): 0.858 RNAshapes: 0.482 Number of pairs reference - predicted secondary structure: 229 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.654 RNAshapes: 0.438 Sensitivity CentroidHomfold‑LAST: 0.496 RNAshapes: 0.434 Positive Predictive Value CentroidHomfold‑LAST: 0.863 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAshapes: 0.468 Sensitivity CentroidAlifold(20): 0.575 RNAshapes: 0.454 Positive Predictive Value CentroidAlifold(20): 0.916 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.648 RNAshapes: 0.506 Sensitivity MXScarna(seed): 0.549 RNAshapes: 0.495 Positive Predictive Value MXScarna(seed): 0.766 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.620 RNAshapes: 0.438 Sensitivity IPknot: 0.569 RNAshapes: 0.434 Positive Predictive Value IPknot: 0.678 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.670 RNAshapes: 0.468 Sensitivity RNAalifold(20): 0.542 RNAshapes: 0.454 Positive Predictive Value RNAalifold(20): 0.830 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	16 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.772 RNAshapes: 0.593 Sensitivity TurboFold(seed): 0.750 RNAshapes: 0.603 Positive Predictive Value TurboFold(seed): 0.796 RNAshapes: 0.585 Number of pairs reference - predicted secondary structure: 16 Wilcoxon single-rank test P-value: 1.58287649515e-08	214 Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.652 RNAshapes: 0.465 Sensitivity Multilign(20): 0.590 RNAshapes: 0.453 Positive Predictive Value Multilign(20): 0.720 RNAshapes: 0.480 Number of pairs reference - predicted secondary structure: 214 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.652 RNAshapes: 0.468 Sensitivity MXScarna(20): 0.581 RNAshapes: 0.454 Positive Predictive Value MXScarna(20): 0.732 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.587 RNAshapes: 0.438 Sensitivity CentroidFold: 0.538 RNAshapes: 0.434 Positive Predictive Value CentroidFold: 0.643 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.572 RNAshapes: 0.438 Sensitivity Contrafold: 0.561 RNAshapes: 0.434 Positive Predictive Value Contrafold: 0.584 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 PPfold(seed) vs RNAshapes Matthews Correlation Coefficient PPfold(seed): 0.726 RNAshapes: 0.593 Sensitivity PPfold(seed): 0.682 RNAshapes: 0.602 Positive Predictive Value PPfold(seed): 0.773 RNAshapes: 0.586 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	706 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.545 RNAshapes: 0.438 Sensitivity Sfold: 0.497 RNAshapes: 0.434 Positive Predictive Value Sfold: 0.600 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.545 RNAshapes: 0.438 Sensitivity MaxExpect: 0.533 RNAshapes: 0.434 Positive Predictive Value MaxExpect: 0.558 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.543 RNAshapes: 0.438 Sensitivity ProbKnot: 0.539 RNAshapes: 0.434 Positive Predictive Value ProbKnot: 0.548 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 RNASampler(seed) vs RNAshapes Matthews Correlation Coefficient RNASampler(seed): 0.780 RNAshapes: 0.548 Sensitivity RNASampler(seed): 0.659 RNAshapes: 0.567 Positive Predictive Value RNASampler(seed): 0.923 RNAshapes: 0.530 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 2.06323189071e-08	706 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.522 RNAshapes: 0.438 Sensitivity Fold: 0.525 RNAshapes: 0.434 Positive Predictive Value Fold: 0.520 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.565 RNAshapes: 0.412 Sensitivity RNASampler(20): 0.413 RNAshapes: 0.410 Positive Predictive Value RNASampler(20): 0.775 RNAshapes: 0.416 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	170 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.579 RNAshapes: 0.446 Sensitivity Murlet(20): 0.446 RNAshapes: 0.434 Positive Predictive Value Murlet(20): 0.752 RNAshapes: 0.459 Number of pairs reference - predicted secondary structure: 170 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.509 RNAshapes: 0.438 Sensitivity UNAFold: 0.506 RNAshapes: 0.434 Positive Predictive Value UNAFold: 0.514 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.505 RNAshapes: 0.438 Sensitivity PknotsRG: 0.507 RNAshapes: 0.434 Positive Predictive Value PknotsRG: 0.505 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 RNAfold vs RNAshapes Matthews Correlation Coefficient RNAfold: 0.510 RNAshapes: 0.438 Sensitivity RNAfold: 0.511 RNAshapes: 0.434 Positive Predictive Value RNAfold: 0.510 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.720 RNAshapes: 0.498 Sensitivity Multilign(seed): 0.722 RNAshapes: 0.526 Positive Predictive Value Multilign(seed): 0.719 RNAshapes: 0.475 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	437 Afold vs RNAshapes Matthews Correlation Coefficient Afold: 0.534 RNAshapes: 0.486 Sensitivity Afold: 0.530 RNAshapes: 0.478 Positive Predictive Value Afold: 0.539 RNAshapes: 0.495 Number of pairs reference - predicted secondary structure: 437 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.501 RNAshapes: 0.438 Sensitivity RNAsubopt: 0.509 RNAshapes: 0.434 Positive Predictive Value RNAsubopt: 0.495 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	389 RNAalifold(seed) vs RNAshapes Matthews Correlation Coefficient RNAalifold(seed): 0.540 RNAshapes: 0.507 Sensitivity RNAalifold(seed): 0.344 RNAshapes: 0.495 Positive Predictive Value RNAalifold(seed): 0.849 RNAshapes: 0.520 Number of pairs reference - predicted secondary structure: 389 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.486 RNAshapes: 0.468 Sensitivity CMfinder(20): 0.316 RNAshapes: 0.454 Positive Predictive Value CMfinder(20): 0.747 RNAshapes: 0.483 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 McQFold vs RNAshapes Matthews Correlation Coefficient McQFold: 0.452 RNAshapes: 0.438 Sensitivity McQFold: 0.441 RNAshapes: 0.434 Positive Predictive Value McQFold: 0.465 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.442 RNAshapes: 0.438 Sensitivity CRWrnafold: 0.444 RNAshapes: 0.434 Positive Predictive Value CRWrnafold: 0.442 RNAshapes: 0.443 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.85233844192e-08	651 RNASLOpt vs RNAshapes Matthews Correlation Coefficient RNASLOpt: 0.443 RNAshapes: 0.437 Sensitivity RNASLOpt: 0.420 RNAshapes: 0.434 Positive Predictive Value RNASLOpt: 0.469 RNAshapes: 0.442 Number of pairs reference - predicted secondary structure: 651 Wilcoxon single-rank test P-value: 3.56938820447e-08		= Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): 0.544 RNAshapes: 0.542 Sensitivity Murlet(seed): 0.354 RNAshapes: 0.549 Positive Predictive Value Murlet(seed): 0.836 RNAshapes: 0.537 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.239390405605	+ RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.468 RSpredict(20): 0.425 Sensitivity RNAshapes: 0.454 RSpredict(20): 0.292 Positive Predictive Value RNAshapes: 0.483 RSpredict(20): 0.621 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.468 Carnac(20): 0.378 Sensitivity RNAshapes: 0.454 Carnac(20): 0.166 Positive Predictive Value RNAshapes: 0.483 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.438 RNAwolf: 0.352 Sensitivity RNAshapes: 0.434 RNAwolf: 0.366 Positive Predictive Value RNAshapes: 0.443 RNAwolf: 0.340 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.560 CMfinder(seed): 0.457 Sensitivity RNAshapes: 0.558 CMfinder(seed): 0.274 Positive Predictive Value RNAshapes: 0.564 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.506 RSpredict(seed): 0.216 Sensitivity RNAshapes: 0.494 RSpredict(seed): 0.089 Positive Predictive Value RNAshapes: 0.520 RSpredict(seed): 0.522 Number of pairs reference - predicted secondary structure: 391 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.436 Vsfold4: 0.308 Sensitivity RNAshapes: 0.433 Vsfold4: 0.284 Positive Predictive Value RNAshapes: 0.441 Vsfold4: 0.337 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.436 Vsfold5: 0.301 Sensitivity RNAshapes: 0.433 Vsfold5: 0.286 Positive Predictive Value RNAshapes: 0.441 Vsfold5: 0.318 Number of pairs reference - predicted secondary structure: 701 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.457 NanoFolder: 0.171 Sensitivity RNAshapes: 0.449 NanoFolder: 0.202 Positive Predictive Value RNAshapes: 0.466 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.522 Carnac(seed): 0.149 Sensitivity RNAshapes: 0.519 Carnac(seed): 0.025 Positive Predictive Value RNAshapes: 0.528 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.505 Mastr(seed): 0.067 Sensitivity RNAshapes: 0.495 Mastr(seed): 0.005 Positive Predictive Value RNAshapes: 0.518 Mastr(seed): 0.890 Number of pairs reference - predicted secondary structure: 371 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.640 RNAshapes: 0.439 Sensitivity HotKnots: 0.615 RNAshapes: 0.462 Positive Predictive Value HotKnots: 0.667 RNAshapes: 0.419 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: N/A RNAshapes: N/A Sensitivity Pknots: N/A RNAshapes: N/A Positive Predictive Value Pknots: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.455 Cylofold: 0.271 Sensitivity RNAshapes: 0.453 Cylofold: 0.241 Positive Predictive Value RNAshapes: 0.459 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: N/A MCFold: N/A Sensitivity RNAshapes: N/A MCFold: N/A Positive Predictive Value RNAshapes: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: N/A RNAshapes: N/A Sensitivity RDfolder: N/A RNAshapes: N/A Positive Predictive Value RDfolder: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAshapes Matthews Correlation Coefficient Alterna: N/A RNAshapes: N/A Sensitivity Alterna: N/A RNAshapes: N/A Positive Predictive Value Alterna: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.468 Mastr(20): 0.000 Sensitivity RNAshapes: 0.454 Mastr(20): 0.000 Positive Predictive Value RNAshapes: 0.483 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(seed)	31 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.825 Murlet(seed): 0.569 Sensitivity PETfold_pre2.0(seed): 0.790 Murlet(seed): 0.383 Positive Predictive Value PETfold_pre2.0(seed): 0.863 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.780 Murlet(seed): 0.569 Sensitivity ContextFold: 0.764 Murlet(seed): 0.383 Positive Predictive Value ContextFold: 0.798 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.882 Murlet(seed): 0.588 Sensitivity TurboFold(20): 0.842 Murlet(seed): 0.347 Positive Predictive Value TurboFold(20): 0.924 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	31 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.814 Murlet(seed): 0.569 Sensitivity CentroidAlifold(seed): 0.748 Murlet(seed): 0.383 Positive Predictive Value CentroidAlifold(seed): 0.886 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.919 Murlet(seed): 0.588 Sensitivity PETfold_pre2.0(20): 0.901 Murlet(seed): 0.347 Positive Predictive Value PETfold_pre2.0(20): 0.938 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.886 Murlet(seed): 0.588 Sensitivity PPfold(20): 0.842 Murlet(seed): 0.347 Positive Predictive Value PPfold(20): 0.934 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	29 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.725 Murlet(seed): 0.556 Sensitivity CentroidHomfold‑LAST: 0.611 Murlet(seed): 0.366 Positive Predictive Value CentroidHomfold‑LAST: 0.862 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	1 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.908 Murlet(seed): 0.588 Sensitivity CentroidAlifold(20): 0.871 Murlet(seed): 0.347 Positive Predictive Value CentroidAlifold(20): 0.946 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	31 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.742 Murlet(seed): 0.569 Sensitivity MXScarna(seed): 0.721 Murlet(seed): 0.383 Positive Predictive Value MXScarna(seed): 0.765 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.718 Murlet(seed): 0.569 Sensitivity IPknot: 0.699 Murlet(seed): 0.383 Positive Predictive Value IPknot: 0.738 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.886 Murlet(seed): 0.588 Sensitivity RNAalifold(20): 0.832 Murlet(seed): 0.347 Positive Predictive Value RNAalifold(20): 0.944 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	13 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.794 Murlet(seed): 0.703 Sensitivity TurboFold(seed): 0.773 Murlet(seed): 0.540 Positive Predictive Value TurboFold(seed): 0.815 Murlet(seed): 0.916 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.10032755566e-08	0 Murlet(seed) vs Multilign(20) Matthews Correlation Coefficient Murlet(seed): N/A Multilign(20): N/A Sensitivity Murlet(seed): N/A Multilign(20): N/A Positive Predictive Value Murlet(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.879 Murlet(seed): 0.588 Sensitivity MXScarna(20): 0.861 Murlet(seed): 0.347 Positive Predictive Value MXScarna(20): 0.897 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	31 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.678 Murlet(seed): 0.569 Sensitivity CentroidFold: 0.649 Murlet(seed): 0.383 Positive Predictive Value CentroidFold: 0.709 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.668 Murlet(seed): 0.569 Sensitivity Contrafold: 0.670 Murlet(seed): 0.383 Positive Predictive Value Contrafold: 0.668 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.784 Murlet(seed): 0.615 Sensitivity PPfold(seed): 0.736 Murlet(seed): 0.448 Positive Predictive Value PPfold(seed): 0.837 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.9966815982e-08	31 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.660 Murlet(seed): 0.569 Sensitivity Sfold: 0.624 Murlet(seed): 0.383 Positive Predictive Value Sfold: 0.700 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.611 Murlet(seed): 0.569 Sensitivity MaxExpect: 0.612 Murlet(seed): 0.383 Positive Predictive Value MaxExpect: 0.611 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.619 Murlet(seed): 0.569 Sensitivity ProbKnot: 0.624 Murlet(seed): 0.383 Positive Predictive Value ProbKnot: 0.614 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.779 Murlet(seed): 0.765 Sensitivity RNASampler(seed): 0.659 Murlet(seed): 0.595 Positive Predictive Value RNASampler(seed): 0.921 Murlet(seed): 0.985 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.31583660336e-08	31 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.598 Murlet(seed): 0.569 Sensitivity Fold: 0.608 Murlet(seed): 0.383 Positive Predictive Value Fold: 0.590 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 RNASampler(20) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(20): 0.780 Murlet(seed): 0.588 Sensitivity RNASampler(20): 0.663 Murlet(seed): 0.347 Positive Predictive Value RNASampler(20): 0.918 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.782 Murlet(seed): 0.588 Sensitivity Murlet(20): 0.683 Murlet(seed): 0.347 Positive Predictive Value Murlet(20): 0.896 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	31 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.622 Murlet(seed): 0.569 Sensitivity UNAFold: 0.626 Murlet(seed): 0.383 Positive Predictive Value UNAFold: 0.620 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.607 Murlet(seed): 0.569 Sensitivity PknotsRG: 0.614 Murlet(seed): 0.383 Positive Predictive Value PknotsRG: 0.601 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.85233844192e-08	31 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.631 Murlet(seed): 0.569 Sensitivity RNAfold: 0.637 Murlet(seed): 0.383 Positive Predictive Value RNAfold: 0.627 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	8 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.770 Murlet(seed): 0.725 Sensitivity Multilign(seed): 0.762 Murlet(seed): 0.558 Positive Predictive Value Multilign(seed): 0.778 Murlet(seed): 0.944 Number of pairs reference - predicted secondary structure: 8 Wilcoxon single-rank test P-value: 0.0	25 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.626 Murlet(seed): 0.586 Sensitivity Afold: 0.629 Murlet(seed): 0.396 Positive Predictive Value Afold: 0.625 Murlet(seed): 0.868 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	29 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.606 Murlet(seed): 0.556 Sensitivity RNAsubopt: 0.619 Murlet(seed): 0.366 Positive Predictive Value RNAsubopt: 0.595 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	31 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.758 Murlet(seed): 0.569 Sensitivity RNAalifold(seed): 0.635 Murlet(seed): 0.383 Positive Predictive Value RNAalifold(seed): 0.904 Murlet(seed): 0.845 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 Murlet(seed) vs CMfinder(20) Matthews Correlation Coefficient Murlet(seed): 0.588 CMfinder(20): 0.524 Sensitivity Murlet(seed): 0.347 CMfinder(20): 0.376 Positive Predictive Value Murlet(seed): 1.000 CMfinder(20): 0.731 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	31 Murlet(seed) vs McQFold Matthews Correlation Coefficient Murlet(seed): 0.569 McQFold: 0.461 Sensitivity Murlet(seed): 0.383 McQFold: 0.455 Positive Predictive Value Murlet(seed): 0.845 McQFold: 0.469 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Murlet(seed) vs CRWrnafold Matthews Correlation Coefficient Murlet(seed): 0.569 CRWrnafold: 0.532 Sensitivity Murlet(seed): 0.383 CRWrnafold: 0.539 Positive Predictive Value Murlet(seed): 0.845 CRWrnafold: 0.527 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Murlet(seed) vs RNASLOpt Matthews Correlation Coefficient Murlet(seed): 0.556 RNASLOpt: 0.479 Sensitivity Murlet(seed): 0.366 RNASLOpt: 0.466 Positive Predictive Value Murlet(seed): 0.846 RNASLOpt: 0.494 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.10776592382e-08	28 Murlet(seed) vs RNAshapes Matthews Correlation Coefficient Murlet(seed): 0.544 RNAshapes: 0.542 Sensitivity Murlet(seed): 0.354 RNAshapes: 0.549 Positive Predictive Value Murlet(seed): 0.836 RNAshapes: 0.537 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 0.239390405605		? RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): 0.789 Murlet(seed): 0.588 Sensitivity RSpredict(20): 0.703 Murlet(seed): 0.347 Positive Predictive Value RSpredict(20): 0.888 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Murlet(seed) vs Carnac(20) Matthews Correlation Coefficient Murlet(seed): 0.588 Carnac(20): 0.429 Sensitivity Murlet(seed): 0.347 Carnac(20): 0.218 Positive Predictive Value Murlet(seed): 1.000 Carnac(20): 0.846 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.569 RNAwolf: 0.411 Sensitivity Murlet(seed): 0.383 RNAwolf: 0.427 Positive Predictive Value Murlet(seed): 0.845 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.612 CMfinder(seed): 0.490 Sensitivity Murlet(seed): 0.408 CMfinder(seed): 0.328 Positive Predictive Value Murlet(seed): 0.920 CMfinder(seed): 0.734 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.569 RSpredict(seed): 0.536 Sensitivity Murlet(seed): 0.383 RSpredict(seed): 0.403 Positive Predictive Value Murlet(seed): 0.845 RSpredict(seed): 0.714 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.556 Vsfold4: 0.208 Sensitivity Murlet(seed): 0.366 Vsfold4: 0.196 Positive Predictive Value Murlet(seed): 0.846 Vsfold4: 0.223 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.556 Vsfold5: 0.216 Sensitivity Murlet(seed): 0.366 Vsfold5: 0.212 Positive Predictive Value Murlet(seed): 0.846 Vsfold5: 0.224 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	? Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.488 NanoFolder: 0.161 Sensitivity Murlet(seed): 0.281 NanoFolder: 0.193 Positive Predictive Value Murlet(seed): 0.848 NanoFolder: 0.138 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.569 Carnac(seed): 0.351 Sensitivity Murlet(seed): 0.383 Carnac(seed): 0.145 Positive Predictive Value Murlet(seed): 0.845 Carnac(seed): 0.848 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.569 Mastr(seed): 0.286 Sensitivity Murlet(seed): 0.383 Mastr(seed): 0.092 Positive Predictive Value Murlet(seed): 0.845 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.640 Murlet(seed): 0.000 Sensitivity HotKnots: 0.615 Murlet(seed): 0.000 Positive Predictive Value HotKnots: 0.667 Murlet(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: N/A Murlet(seed): N/A Sensitivity Pknots: N/A Murlet(seed): N/A Positive Predictive Value Pknots: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: N/A Murlet(seed): N/A Sensitivity Cylofold: N/A Murlet(seed): N/A Positive Predictive Value Cylofold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): N/A MCFold: N/A Sensitivity Murlet(seed): N/A MCFold: N/A Positive Predictive Value Murlet(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: N/A Murlet(seed): N/A Sensitivity RDfolder: N/A Murlet(seed): N/A Positive Predictive Value RDfolder: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: N/A Murlet(seed): N/A Sensitivity Alterna: N/A Murlet(seed): N/A Positive Predictive Value Alterna: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.588 Mastr(20): 0.000 Sensitivity Murlet(seed): 0.347 Mastr(20): 0.000 Positive Predictive Value Murlet(seed): 1.000 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0
RSpredict(20)	230 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 RSpredict(20): 0.402 Sensitivity PETfold_pre2.0(seed): 0.693 RSpredict(20): 0.269 Positive Predictive Value PETfold_pre2.0(seed): 0.854 RSpredict(20): 0.602 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.843 RSpredict(20): 0.418 Sensitivity ContextFold: 0.799 RSpredict(20): 0.285 Positive Predictive Value ContextFold: 0.891 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.752 RSpredict(20): 0.418 Sensitivity TurboFold(20): 0.701 RSpredict(20): 0.285 Positive Predictive Value TurboFold(20): 0.809 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 RSpredict(20): 0.404 Sensitivity CentroidAlifold(seed): 0.564 RSpredict(20): 0.260 Positive Predictive Value CentroidAlifold(seed): 0.953 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RSpredict(20): 0.416 Sensitivity PETfold_pre2.0(20): 0.654 RSpredict(20): 0.284 Positive Predictive Value PETfold_pre2.0(20): 0.836 RSpredict(20): 0.613 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.733 RSpredict(20): 0.421 Sensitivity PPfold(20): 0.629 RSpredict(20): 0.289 Positive Predictive Value PPfold(20): 0.855 RSpredict(20): 0.616 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 RSpredict(20): 0.418 Sensitivity CentroidHomfold‑LAST: 0.561 RSpredict(20): 0.285 Positive Predictive Value CentroidHomfold‑LAST: 0.898 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RSpredict(20): 0.418 Sensitivity CentroidAlifold(20): 0.574 RSpredict(20): 0.285 Positive Predictive Value CentroidAlifold(20): 0.916 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 RSpredict(20): 0.402 Sensitivity MXScarna(seed): 0.582 RSpredict(20): 0.258 Positive Predictive Value MXScarna(seed): 0.805 RSpredict(20): 0.629 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 IPknot vs RSpredict(20) Matthews Correlation Coefficient IPknot: 0.655 RSpredict(20): 0.418 Sensitivity IPknot: 0.586 RSpredict(20): 0.285 Positive Predictive Value IPknot: 0.732 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 RSpredict(20): 0.418 Sensitivity RNAalifold(20): 0.540 RSpredict(20): 0.285 Positive Predictive Value RNAalifold(20): 0.827 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 RSpredict(20): 0.617 Sensitivity TurboFold(seed): 0.739 RSpredict(20): 0.523 Positive Predictive Value TurboFold(seed): 0.774 RSpredict(20): 0.730 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	223 Multilign(20) vs RSpredict(20) Matthews Correlation Coefficient Multilign(20): 0.651 RSpredict(20): 0.393 Sensitivity Multilign(20): 0.590 RSpredict(20): 0.263 Positive Predictive Value Multilign(20): 0.721 RSpredict(20): 0.591 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.654 RSpredict(20): 0.418 Sensitivity MXScarna(20): 0.584 RSpredict(20): 0.285 Positive Predictive Value MXScarna(20): 0.735 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidFold vs RSpredict(20) Matthews Correlation Coefficient CentroidFold: 0.621 RSpredict(20): 0.418 Sensitivity CentroidFold: 0.557 RSpredict(20): 0.285 Positive Predictive Value CentroidFold: 0.694 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 Contrafold vs RSpredict(20) Matthews Correlation Coefficient Contrafold: 0.606 RSpredict(20): 0.418 Sensitivity Contrafold: 0.585 RSpredict(20): 0.285 Positive Predictive Value Contrafold: 0.630 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PPfold(seed) vs RSpredict(20) Matthews Correlation Coefficient PPfold(seed): 0.847 RSpredict(20): 0.789 Sensitivity PPfold(seed): 0.782 RSpredict(20): 0.703 Positive Predictive Value PPfold(seed): 0.919 RSpredict(20): 0.888 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	245 Sfold vs RSpredict(20) Matthews Correlation Coefficient Sfold: 0.584 RSpredict(20): 0.418 Sensitivity Sfold: 0.522 RSpredict(20): 0.285 Positive Predictive Value Sfold: 0.654 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MaxExpect vs RSpredict(20) Matthews Correlation Coefficient MaxExpect: 0.592 RSpredict(20): 0.418 Sensitivity MaxExpect: 0.569 RSpredict(20): 0.285 Positive Predictive Value MaxExpect: 0.617 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ProbKnot vs RSpredict(20) Matthews Correlation Coefficient ProbKnot: 0.590 RSpredict(20): 0.418 Sensitivity ProbKnot: 0.572 RSpredict(20): 0.285 Positive Predictive Value ProbKnot: 0.610 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): N/A RNASampler(seed): N/A Sensitivity RSpredict(20): N/A RNASampler(seed): N/A Positive Predictive Value RSpredict(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	245 Fold vs RSpredict(20) Matthews Correlation Coefficient Fold: 0.562 RSpredict(20): 0.418 Sensitivity Fold: 0.555 RSpredict(20): 0.285 Positive Predictive Value Fold: 0.571 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RSpredict(20) vs RNASampler(20) Matthews Correlation Coefficient RSpredict(20): 0.588 RNASampler(20): 0.565 Sensitivity RSpredict(20): 0.517 RNASampler(20): 0.413 Positive Predictive Value RSpredict(20): 0.670 RNASampler(20): 0.772 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs RSpredict(20) Matthews Correlation Coefficient Murlet(20): 0.573 RSpredict(20): 0.451 Sensitivity Murlet(20): 0.441 RSpredict(20): 0.324 Positive Predictive Value Murlet(20): 0.746 RSpredict(20): 0.629 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 UNAFold vs RSpredict(20) Matthews Correlation Coefficient UNAFold: 0.547 RSpredict(20): 0.418 Sensitivity UNAFold: 0.535 RSpredict(20): 0.285 Positive Predictive Value UNAFold: 0.560 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 PknotsRG vs RSpredict(20) Matthews Correlation Coefficient PknotsRG: 0.525 RSpredict(20): 0.418 Sensitivity PknotsRG: 0.518 RSpredict(20): 0.285 Positive Predictive Value PknotsRG: 0.535 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAfold vs RSpredict(20) Matthews Correlation Coefficient RNAfold: 0.544 RSpredict(20): 0.418 Sensitivity RNAfold: 0.536 RSpredict(20): 0.285 Positive Predictive Value RNAfold: 0.553 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): N/A Multilign(seed): N/A Sensitivity RSpredict(20): N/A Multilign(seed): N/A Positive Predictive Value RSpredict(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	185 Afold vs RSpredict(20) Matthews Correlation Coefficient Afold: 0.556 RSpredict(20): 0.382 Sensitivity Afold: 0.544 RSpredict(20): 0.243 Positive Predictive Value Afold: 0.570 RSpredict(20): 0.603 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAsubopt vs RSpredict(20) Matthews Correlation Coefficient RNAsubopt: 0.530 RSpredict(20): 0.418 Sensitivity RNAsubopt: 0.529 RSpredict(20): 0.285 Positive Predictive Value RNAsubopt: 0.532 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 RNAalifold(seed) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(seed): 0.492 RSpredict(20): 0.404 Sensitivity RNAalifold(seed): 0.290 RSpredict(20): 0.260 Positive Predictive Value RNAalifold(seed): 0.836 RSpredict(20): 0.631 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CMfinder(20) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(20): 0.478 RSpredict(20): 0.418 Sensitivity CMfinder(20): 0.309 RSpredict(20): 0.285 Positive Predictive Value CMfinder(20): 0.741 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 McQFold vs RSpredict(20) Matthews Correlation Coefficient McQFold: 0.442 RSpredict(20): 0.418 Sensitivity McQFold: 0.424 RSpredict(20): 0.285 Positive Predictive Value McQFold: 0.464 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CRWrnafold vs RSpredict(20) Matthews Correlation Coefficient CRWrnafold: 0.464 RSpredict(20): 0.418 Sensitivity CRWrnafold: 0.456 RSpredict(20): 0.285 Positive Predictive Value CRWrnafold: 0.474 RSpredict(20): 0.614 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 RNASLOpt vs RSpredict(20) Matthews Correlation Coefficient RNASLOpt: 0.450 RSpredict(20): 0.429 Sensitivity RNASLOpt: 0.417 RSpredict(20): 0.296 Positive Predictive Value RNASLOpt: 0.488 RSpredict(20): 0.623 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 RNAshapes vs RSpredict(20) Matthews Correlation Coefficient RNAshapes: 0.468 RSpredict(20): 0.425 Sensitivity RNAshapes: 0.454 RSpredict(20): 0.292 Positive Predictive Value RNAshapes: 0.483 RSpredict(20): 0.621 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): 0.789 Murlet(seed): 0.588 Sensitivity RSpredict(20): 0.703 Murlet(seed): 0.347 Positive Predictive Value RSpredict(20): 0.888 Murlet(seed): 1.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0		+ RSpredict(20) vs Carnac(20) Matthews Correlation Coefficient RSpredict(20): 0.418 Carnac(20): 0.378 Sensitivity RSpredict(20): 0.285 Carnac(20): 0.166 Positive Predictive Value RSpredict(20): 0.614 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.418 RNAwolf: 0.367 Sensitivity RSpredict(20): 0.285 RNAwolf: 0.377 Positive Predictive Value RSpredict(20): 0.614 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-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	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.403 RSpredict(seed): 0.197 Sensitivity RSpredict(20): 0.259 RSpredict(seed): 0.077 Positive Predictive Value RSpredict(20): 0.630 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.422 Vsfold4: 0.352 Sensitivity RSpredict(20): 0.290 Vsfold4: 0.319 Positive Predictive Value RSpredict(20): 0.618 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.424 Vsfold5: 0.333 Sensitivity RSpredict(20): 0.291 Vsfold5: 0.308 Positive Predictive Value RSpredict(20): 0.618 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.397 NanoFolder: 0.150 Sensitivity RSpredict(20): 0.265 NanoFolder: 0.173 Positive Predictive Value RSpredict(20): 0.595 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.714 Carnac(seed): 0.000 Sensitivity RSpredict(20): 0.610 Carnac(seed): 0.000 Positive Predictive Value RSpredict(20): 0.836 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.59578924681e-08	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.410 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.265 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.636 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): N/A HotKnots: N/A Sensitivity RSpredict(20): N/A HotKnots: N/A Positive Predictive Value RSpredict(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): N/A Pknots: N/A Sensitivity RSpredict(20): N/A Pknots: N/A Positive Predictive Value RSpredict(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): N/A Cylofold: N/A Sensitivity RSpredict(20): N/A Cylofold: N/A Positive Predictive Value RSpredict(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): N/A MCFold: N/A Sensitivity RSpredict(20): N/A MCFold: N/A Positive Predictive Value RSpredict(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): N/A RDfolder: N/A Sensitivity RSpredict(20): N/A RDfolder: N/A Positive Predictive Value RSpredict(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): N/A Alterna: N/A Sensitivity RSpredict(20): N/A Alterna: N/A Positive Predictive Value RSpredict(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.418 Mastr(20): 0.000 Sensitivity RSpredict(20): 0.285 Mastr(20): 0.000 Positive Predictive Value RSpredict(20): 0.614 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(20)	230 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Carnac(20): 0.386 Sensitivity PETfold_pre2.0(seed): 0.693 Carnac(20): 0.173 Positive Predictive Value PETfold_pre2.0(seed): 0.854 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.843 Carnac(20): 0.378 Sensitivity ContextFold: 0.799 Carnac(20): 0.166 Positive Predictive Value ContextFold: 0.891 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.752 Carnac(20): 0.378 Sensitivity TurboFold(20): 0.701 Carnac(20): 0.166 Positive Predictive Value TurboFold(20): 0.809 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Carnac(20): 0.361 Sensitivity CentroidAlifold(seed): 0.564 Carnac(20): 0.148 Positive Predictive Value CentroidAlifold(seed): 0.953 Carnac(20): 0.881 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Carnac(20): 0.380 Sensitivity PETfold_pre2.0(20): 0.654 Carnac(20): 0.167 Positive Predictive Value PETfold_pre2.0(20): 0.836 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.733 Carnac(20): 0.383 Sensitivity PPfold(20): 0.629 Carnac(20): 0.170 Positive Predictive Value PPfold(20): 0.855 Carnac(20): 0.864 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 Carnac(20): 0.378 Sensitivity CentroidHomfold‑LAST: 0.561 Carnac(20): 0.166 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Carnac(20): 0.378 Sensitivity CentroidAlifold(20): 0.574 Carnac(20): 0.166 Positive Predictive Value CentroidAlifold(20): 0.916 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 Carnac(20): 0.360 Sensitivity MXScarna(seed): 0.582 Carnac(20): 0.147 Positive Predictive Value MXScarna(seed): 0.805 Carnac(20): 0.880 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.655 Carnac(20): 0.378 Sensitivity IPknot: 0.586 Carnac(20): 0.166 Positive Predictive Value IPknot: 0.732 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 Carnac(20): 0.378 Sensitivity RNAalifold(20): 0.540 Carnac(20): 0.166 Positive Predictive Value RNAalifold(20): 0.827 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 Carnac(20): 0.303 Sensitivity TurboFold(seed): 0.739 Carnac(20): 0.102 Positive Predictive Value TurboFold(seed): 0.774 Carnac(20): 0.900 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	223 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.651 Carnac(20): 0.363 Sensitivity Multilign(20): 0.590 Carnac(20): 0.153 Positive Predictive Value Multilign(20): 0.721 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.654 Carnac(20): 0.378 Sensitivity MXScarna(20): 0.584 Carnac(20): 0.166 Positive Predictive Value MXScarna(20): 0.735 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.621 Carnac(20): 0.378 Sensitivity CentroidFold: 0.557 Carnac(20): 0.166 Positive Predictive Value CentroidFold: 0.694 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.606 Carnac(20): 0.378 Sensitivity Contrafold: 0.585 Carnac(20): 0.166 Positive Predictive Value Contrafold: 0.630 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PPfold(seed) vs Carnac(20) Matthews Correlation Coefficient PPfold(seed): 0.847 Carnac(20): 0.429 Sensitivity PPfold(seed): 0.782 Carnac(20): 0.218 Positive Predictive Value PPfold(seed): 0.919 Carnac(20): 0.846 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	245 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.584 Carnac(20): 0.378 Sensitivity Sfold: 0.522 Carnac(20): 0.166 Positive Predictive Value Sfold: 0.654 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.592 Carnac(20): 0.378 Sensitivity MaxExpect: 0.569 Carnac(20): 0.166 Positive Predictive Value MaxExpect: 0.617 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.590 Carnac(20): 0.378 Sensitivity ProbKnot: 0.572 Carnac(20): 0.166 Positive Predictive Value ProbKnot: 0.610 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): N/A Carnac(20): N/A Sensitivity RNASampler(seed): N/A Carnac(20): N/A Positive Predictive Value RNASampler(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	245 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.562 Carnac(20): 0.378 Sensitivity Fold: 0.555 Carnac(20): 0.166 Positive Predictive Value Fold: 0.571 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.565 Carnac(20): 0.467 Sensitivity RNASampler(20): 0.413 Carnac(20): 0.256 Positive Predictive Value RNASampler(20): 0.772 Carnac(20): 0.852 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.573 Carnac(20): 0.413 Sensitivity Murlet(20): 0.441 Carnac(20): 0.197 Positive Predictive Value Murlet(20): 0.746 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.547 Carnac(20): 0.378 Sensitivity UNAFold: 0.535 Carnac(20): 0.166 Positive Predictive Value UNAFold: 0.560 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.525 Carnac(20): 0.378 Sensitivity PknotsRG: 0.518 Carnac(20): 0.166 Positive Predictive Value PknotsRG: 0.535 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAfold vs Carnac(20) Matthews Correlation Coefficient RNAfold: 0.544 Carnac(20): 0.378 Sensitivity RNAfold: 0.536 Carnac(20): 0.166 Positive Predictive Value RNAfold: 0.553 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Multilign(seed) vs Carnac(20) Matthews Correlation Coefficient Multilign(seed): N/A Carnac(20): N/A Sensitivity Multilign(seed): N/A Carnac(20): N/A Positive Predictive Value Multilign(seed): N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	185 Afold vs Carnac(20) Matthews Correlation Coefficient Afold: 0.556 Carnac(20): 0.336 Sensitivity Afold: 0.544 Carnac(20): 0.128 Positive Predictive Value Afold: 0.570 Carnac(20): 0.882 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.530 Carnac(20): 0.378 Sensitivity RNAsubopt: 0.529 Carnac(20): 0.166 Positive Predictive Value RNAsubopt: 0.532 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.492 Carnac(20): 0.361 Sensitivity RNAalifold(seed): 0.290 Carnac(20): 0.148 Positive Predictive Value RNAalifold(seed): 0.836 Carnac(20): 0.881 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.478 Carnac(20): 0.378 Sensitivity CMfinder(20): 0.309 Carnac(20): 0.166 Positive Predictive Value CMfinder(20): 0.741 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 McQFold vs Carnac(20) Matthews Correlation Coefficient McQFold: 0.442 Carnac(20): 0.378 Sensitivity McQFold: 0.424 Carnac(20): 0.166 Positive Predictive Value McQFold: 0.464 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.464 Carnac(20): 0.378 Sensitivity CRWrnafold: 0.456 Carnac(20): 0.166 Positive Predictive Value CRWrnafold: 0.474 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 RNASLOpt vs Carnac(20) Matthews Correlation Coefficient RNASLOpt: 0.450 Carnac(20): 0.375 Sensitivity RNASLOpt: 0.417 Carnac(20): 0.163 Positive Predictive Value RNASLOpt: 0.488 Carnac(20): 0.861 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.468 Carnac(20): 0.378 Sensitivity RNAshapes: 0.454 Carnac(20): 0.166 Positive Predictive Value RNAshapes: 0.483 Carnac(20): 0.865 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 Murlet(seed) vs Carnac(20) Matthews Correlation Coefficient Murlet(seed): 0.588 Carnac(20): 0.429 Sensitivity Murlet(seed): 0.347 Carnac(20): 0.218 Positive Predictive Value Murlet(seed): 1.000 Carnac(20): 0.846 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	245 RSpredict(20) vs Carnac(20) Matthews Correlation Coefficient RSpredict(20): 0.418 Carnac(20): 0.378 Sensitivity RSpredict(20): 0.285 Carnac(20): 0.166 Positive Predictive Value RSpredict(20): 0.614 Carnac(20): 0.863 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.378 RNAwolf: 0.367 Sensitivity Carnac(20): 0.166 RNAwolf: 0.377 Positive Predictive Value Carnac(20): 0.863 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-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	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.359 RSpredict(seed): 0.197 Sensitivity Carnac(20): 0.147 RSpredict(seed): 0.077 Positive Predictive Value Carnac(20): 0.881 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.377 Vsfold4: 0.352 Sensitivity Carnac(20): 0.165 Vsfold4: 0.319 Positive Predictive Value Carnac(20): 0.865 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.378 Vsfold5: 0.333 Sensitivity Carnac(20): 0.166 Vsfold5: 0.308 Positive Predictive Value Carnac(20): 0.865 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.393 NanoFolder: 0.150 Sensitivity Carnac(20): 0.179 NanoFolder: 0.173 Positive Predictive Value Carnac(20): 0.866 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.444 Carnac(seed): 0.000 Sensitivity Carnac(20): 0.219 Carnac(seed): 0.000 Positive Predictive Value Carnac(20): 0.903 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.48055519165e-08	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.364 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.151 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.882 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: N/A Carnac(20): N/A Sensitivity HotKnots: N/A Carnac(20): N/A Positive Predictive Value HotKnots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Carnac(20) Matthews Correlation Coefficient Pknots: N/A Carnac(20): N/A Sensitivity Pknots: N/A Carnac(20): N/A Positive Predictive Value Pknots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: N/A Carnac(20): N/A Sensitivity Cylofold: N/A Carnac(20): N/A Positive Predictive Value Cylofold: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): N/A MCFold: N/A Sensitivity Carnac(20): N/A MCFold: N/A Positive Predictive Value Carnac(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Carnac(20) Matthews Correlation Coefficient RDfolder: N/A Carnac(20): N/A Sensitivity RDfolder: N/A Carnac(20): N/A Positive Predictive Value RDfolder: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Carnac(20) Matthews Correlation Coefficient Alterna: N/A Carnac(20): N/A Sensitivity Alterna: N/A Carnac(20): N/A Positive Predictive Value Alterna: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.378 Mastr(20): 0.000 Sensitivity Carnac(20): 0.166 Mastr(20): 0.000 Positive Predictive Value Carnac(20): 0.863 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAwolf	643 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.701 RNAwolf: 0.349 Sensitivity PETfold_pre2.0(seed): 0.612 RNAwolf: 0.364 Positive Predictive Value PETfold_pre2.0(seed): 0.803 RNAwolf: 0.337 Number of pairs reference - predicted secondary structure: 643 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.720 RNAwolf: 0.339 Sensitivity ContextFold: 0.687 RNAwolf: 0.355 Positive Predictive Value ContextFold: 0.756 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.752 RNAwolf: 0.367 Sensitivity TurboFold(20): 0.701 RNAwolf: 0.377 Positive Predictive Value TurboFold(20): 0.809 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RNAwolf: 0.379 Sensitivity CentroidAlifold(seed): 0.556 RNAwolf: 0.389 Positive Predictive Value CentroidAlifold(seed): 0.906 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 RNAwolf: 0.367 Sensitivity PETfold_pre2.0(20): 0.654 RNAwolf: 0.376 Positive Predictive Value PETfold_pre2.0(20): 0.836 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.733 RNAwolf: 0.369 Sensitivity PPfold(20): 0.629 RNAwolf: 0.378 Positive Predictive Value PPfold(20): 0.855 RNAwolf: 0.361 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.650 RNAwolf: 0.349 Sensitivity CentroidHomfold‑LAST: 0.491 RNAwolf: 0.364 Positive Predictive Value CentroidHomfold‑LAST: 0.862 RNAwolf: 0.336 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.725 RNAwolf: 0.367 Sensitivity CentroidAlifold(20): 0.574 RNAwolf: 0.377 Positive Predictive Value CentroidAlifold(20): 0.916 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	431 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.637 RNAwolf: 0.379 Sensitivity MXScarna(seed): 0.535 RNAwolf: 0.389 Positive Predictive Value MXScarna(seed): 0.759 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 431 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.612 RNAwolf: 0.339 Sensitivity IPknot: 0.561 RNAwolf: 0.355 Positive Predictive Value IPknot: 0.667 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.668 RNAwolf: 0.367 Sensitivity RNAalifold(20): 0.540 RNAwolf: 0.377 Positive Predictive Value RNAalifold(20): 0.827 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.787 RNAwolf: 0.369 Sensitivity TurboFold(seed): 0.760 RNAwolf: 0.385 Positive Predictive Value TurboFold(seed): 0.815 RNAwolf: 0.355 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.9966815982e-08	223 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.651 RNAwolf: 0.367 Sensitivity Multilign(20): 0.590 RNAwolf: 0.377 Positive Predictive Value Multilign(20): 0.721 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.654 RNAwolf: 0.367 Sensitivity MXScarna(20): 0.584 RNAwolf: 0.377 Positive Predictive Value MXScarna(20): 0.735 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.583 RNAwolf: 0.339 Sensitivity CentroidFold: 0.533 RNAwolf: 0.355 Positive Predictive Value CentroidFold: 0.638 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.567 RNAwolf: 0.339 Sensitivity Contrafold: 0.558 RNAwolf: 0.355 Positive Predictive Value Contrafold: 0.577 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs RNAwolf Matthews Correlation Coefficient PPfold(seed): 0.716 RNAwolf: 0.389 Sensitivity PPfold(seed): 0.652 RNAwolf: 0.408 Positive Predictive Value PPfold(seed): 0.787 RNAwolf: 0.373 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.06544643719e-08	818 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.538 RNAwolf: 0.339 Sensitivity Sfold: 0.491 RNAwolf: 0.355 Positive Predictive Value Sfold: 0.589 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.536 RNAwolf: 0.339 Sensitivity MaxExpect: 0.527 RNAwolf: 0.355 Positive Predictive Value MaxExpect: 0.546 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.534 RNAwolf: 0.339 Sensitivity ProbKnot: 0.534 RNAwolf: 0.355 Positive Predictive Value ProbKnot: 0.535 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.779 RNAwolf: 0.287 Sensitivity RNASampler(seed): 0.659 RNAwolf: 0.307 Positive Predictive Value RNASampler(seed): 0.921 RNAwolf: 0.270 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.42300079339e-08	818 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.511 RNAwolf: 0.339 Sensitivity Fold: 0.517 RNAwolf: 0.355 Positive Predictive Value Fold: 0.506 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.565 RNAwolf: 0.325 Sensitivity RNASampler(20): 0.413 RNAwolf: 0.340 Positive Predictive Value RNASampler(20): 0.772 RNAwolf: 0.313 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.573 RNAwolf: 0.354 Sensitivity Murlet(20): 0.441 RNAwolf: 0.366 Positive Predictive Value Murlet(20): 0.746 RNAwolf: 0.345 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.501 RNAwolf: 0.339 Sensitivity UNAFold: 0.501 RNAwolf: 0.355 Positive Predictive Value UNAFold: 0.503 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.499 RNAwolf: 0.339 Sensitivity PknotsRG: 0.504 RNAwolf: 0.355 Positive Predictive Value PknotsRG: 0.495 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.499 RNAwolf: 0.339 Sensitivity RNAfold: 0.504 RNAwolf: 0.355 Positive Predictive Value RNAfold: 0.495 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.734 RNAwolf: 0.346 Sensitivity Multilign(seed): 0.733 RNAwolf: 0.368 Positive Predictive Value Multilign(seed): 0.737 RNAwolf: 0.326 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.02533530638e-08	525 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.516 RNAwolf: 0.351 Sensitivity Afold: 0.517 RNAwolf: 0.365 Positive Predictive Value Afold: 0.516 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 525 Wilcoxon single-rank test P-value: 3.56938820447e-08	759 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.501 RNAwolf: 0.349 Sensitivity RNAsubopt: 0.510 RNAwolf: 0.364 Positive Predictive Value RNAsubopt: 0.495 RNAwolf: 0.336 Number of pairs reference - predicted secondary structure: 759 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.541 RNAwolf: 0.379 Sensitivity RNAalifold(seed): 0.344 RNAwolf: 0.389 Positive Predictive Value RNAalifold(seed): 0.851 RNAwolf: 0.371 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.478 RNAwolf: 0.367 Sensitivity CMfinder(20): 0.309 RNAwolf: 0.377 Positive Predictive Value CMfinder(20): 0.741 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.443 RNAwolf: 0.339 Sensitivity McQFold: 0.435 RNAwolf: 0.355 Positive Predictive Value McQFold: 0.452 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	818 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.432 RNAwolf: 0.339 Sensitivity CRWrnafold: 0.438 RNAwolf: 0.355 Positive Predictive Value CRWrnafold: 0.428 RNAwolf: 0.325 Number of pairs reference - predicted secondary structure: 818 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.442 RNAwolf: 0.351 Sensitivity RNASLOpt: 0.419 RNAwolf: 0.366 Positive Predictive Value RNASLOpt: 0.468 RNAwolf: 0.339 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	706 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.438 RNAwolf: 0.352 Sensitivity RNAshapes: 0.434 RNAwolf: 0.366 Positive Predictive Value RNAshapes: 0.443 RNAwolf: 0.340 Number of pairs reference - predicted secondary structure: 706 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.569 RNAwolf: 0.411 Sensitivity Murlet(seed): 0.383 RNAwolf: 0.427 Positive Predictive Value Murlet(seed): 0.845 RNAwolf: 0.398 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.418 RNAwolf: 0.367 Sensitivity RSpredict(20): 0.285 RNAwolf: 0.377 Positive Predictive Value RSpredict(20): 0.614 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.378 RNAwolf: 0.367 Sensitivity Carnac(20): 0.166 RNAwolf: 0.377 Positive Predictive Value Carnac(20): 0.863 RNAwolf: 0.360 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.454 RNAwolf: 0.427 Sensitivity CMfinder(seed): 0.271 RNAwolf: 0.442 Positive Predictive Value CMfinder(seed): 0.762 RNAwolf: 0.414 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.379 RSpredict(seed): 0.214 Sensitivity RNAwolf: 0.389 RSpredict(seed): 0.089 Positive Predictive Value RNAwolf: 0.371 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.350 Vsfold4: 0.306 Sensitivity RNAwolf: 0.365 Vsfold4: 0.282 Positive Predictive Value RNAwolf: 0.338 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.351 Vsfold5: 0.300 Sensitivity RNAwolf: 0.366 Vsfold5: 0.286 Positive Predictive Value RNAwolf: 0.339 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.357 NanoFolder: 0.166 Sensitivity RNAwolf: 0.369 NanoFolder: 0.197 Positive Predictive Value RNAwolf: 0.347 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.350 Carnac(seed): 0.150 Sensitivity RNAwolf: 0.364 Carnac(seed): 0.028 Positive Predictive Value RNAwolf: 0.337 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.377 Mastr(seed): 0.073 Sensitivity RNAwolf: 0.387 Mastr(seed): 0.006 Positive Predictive Value RNAwolf: 0.368 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.640 RNAwolf: 0.209 Sensitivity HotKnots: 0.615 RNAwolf: 0.231 Positive Predictive Value HotKnots: 0.667 RNAwolf: 0.191 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: N/A RNAwolf: N/A Sensitivity Pknots: N/A RNAwolf: N/A Positive Predictive Value Pknots: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RNAwolf vs Cylofold Matthews Correlation Coefficient RNAwolf: 0.339 Cylofold: 0.271 Sensitivity RNAwolf: 0.350 Cylofold: 0.241 Positive Predictive Value RNAwolf: 0.331 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: N/A MCFold: N/A Sensitivity RNAwolf: N/A MCFold: N/A Positive Predictive Value RNAwolf: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: N/A RNAwolf: N/A Sensitivity RDfolder: N/A RNAwolf: N/A Positive Predictive Value RDfolder: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: N/A RNAwolf: N/A Sensitivity Alterna: N/A RNAwolf: N/A Positive Predictive Value Alterna: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.367 Mastr(20): 0.000 Sensitivity RNAwolf: 0.377 Mastr(20): 0.000 Positive Predictive Value RNAwolf: 0.360 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(seed)	51 PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 CMfinder(seed): 0.454 Sensitivity PETfold_pre2.0(seed): 0.667 CMfinder(seed): 0.271 Positive Predictive Value PETfold_pre2.0(seed): 0.888 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.800 CMfinder(seed): 0.454 Sensitivity ContextFold: 0.774 CMfinder(seed): 0.271 Positive Predictive Value ContextFold: 0.827 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): N/A CMfinder(seed): N/A Sensitivity TurboFold(20): N/A CMfinder(seed): N/A Positive Predictive Value TurboFold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	51 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.753 CMfinder(seed): 0.454 Sensitivity CentroidAlifold(seed): 0.625 CMfinder(seed): 0.271 Positive Predictive Value CentroidAlifold(seed): 0.909 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 PETfold_pre2.0(20) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): N/A CMfinder(seed): N/A Sensitivity PETfold_pre2.0(20): N/A CMfinder(seed): N/A Positive Predictive Value PETfold_pre2.0(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(20): N/A CMfinder(seed): N/A Sensitivity PPfold(20): N/A CMfinder(seed): N/A Positive Predictive Value PPfold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	51 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.731 CMfinder(seed): 0.454 Sensitivity CentroidHomfold‑LAST: 0.587 CMfinder(seed): 0.271 Positive Predictive Value CentroidHomfold‑LAST: 0.911 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	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	51 MXScarna(seed) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(seed): 0.696 CMfinder(seed): 0.454 Sensitivity MXScarna(seed): 0.605 CMfinder(seed): 0.271 Positive Predictive Value MXScarna(seed): 0.802 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.725 CMfinder(seed): 0.454 Sensitivity IPknot: 0.696 CMfinder(seed): 0.271 Positive Predictive Value IPknot: 0.756 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNAalifold(20) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(20): N/A CMfinder(seed): N/A Sensitivity RNAalifold(20): N/A CMfinder(seed): N/A Positive Predictive Value RNAalifold(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	9 TurboFold(seed) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(seed): 0.900 CMfinder(seed): 0.558 Sensitivity TurboFold(seed): 0.862 CMfinder(seed): 0.422 Positive Predictive Value TurboFold(seed): 0.939 CMfinder(seed): 0.740 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	0 CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): N/A Multilign(20): N/A Sensitivity CMfinder(seed): N/A Multilign(20): N/A Positive Predictive Value CMfinder(seed): N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	51 CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.692 CMfinder(seed): 0.454 Sensitivity CentroidFold: 0.651 CMfinder(seed): 0.271 Positive Predictive Value CentroidFold: 0.738 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.677 CMfinder(seed): 0.454 Sensitivity Contrafold: 0.673 CMfinder(seed): 0.271 Positive Predictive Value Contrafold: 0.683 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.941 CMfinder(seed): 0.558 Sensitivity PPfold(seed): 0.889 CMfinder(seed): 0.422 Positive Predictive Value PPfold(seed): 0.996 CMfinder(seed): 0.740 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	51 Sfold vs CMfinder(seed) Matthews Correlation Coefficient Sfold: 0.677 CMfinder(seed): 0.454 Sensitivity Sfold: 0.626 CMfinder(seed): 0.271 Positive Predictive Value Sfold: 0.733 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.596 CMfinder(seed): 0.454 Sensitivity MaxExpect: 0.592 CMfinder(seed): 0.271 Positive Predictive Value MaxExpect: 0.601 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 ProbKnot vs CMfinder(seed) Matthews Correlation Coefficient ProbKnot: 0.600 CMfinder(seed): 0.454 Sensitivity ProbKnot: 0.599 CMfinder(seed): 0.271 Positive Predictive Value ProbKnot: 0.602 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(seed): 0.779 CMfinder(seed): 0.534 Sensitivity RNASampler(seed): 0.659 CMfinder(seed): 0.390 Positive Predictive Value RNASampler(seed): 0.921 CMfinder(seed): 0.732 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.32677072069e-08	51 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.594 CMfinder(seed): 0.454 Sensitivity Fold: 0.604 CMfinder(seed): 0.271 Positive Predictive Value Fold: 0.586 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 RNASampler(20) vs CMfinder(seed) Matthews Correlation Coefficient RNASampler(20): N/A CMfinder(seed): N/A Sensitivity RNASampler(20): N/A CMfinder(seed): N/A Positive Predictive Value RNASampler(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	51 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.619 CMfinder(seed): 0.454 Sensitivity UNAFold: 0.617 CMfinder(seed): 0.271 Positive Predictive Value UNAFold: 0.623 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.606 CMfinder(seed): 0.454 Sensitivity PknotsRG: 0.611 CMfinder(seed): 0.271 Positive Predictive Value PknotsRG: 0.602 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 RNAfold vs CMfinder(seed) Matthews Correlation Coefficient RNAfold: 0.607 CMfinder(seed): 0.454 Sensitivity RNAfold: 0.610 CMfinder(seed): 0.271 Positive Predictive Value RNAfold: 0.605 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 Multilign(seed) vs CMfinder(seed) Matthews Correlation Coefficient Multilign(seed): 0.879 CMfinder(seed): 0.544 Sensitivity Multilign(seed): 0.851 CMfinder(seed): 0.410 Positive Predictive Value Multilign(seed): 0.908 CMfinder(seed): 0.724 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	46 Afold vs CMfinder(seed) Matthews Correlation Coefficient Afold: 0.629 CMfinder(seed): 0.451 Sensitivity Afold: 0.627 CMfinder(seed): 0.271 Positive Predictive Value Afold: 0.633 CMfinder(seed): 0.753 Number of pairs reference - predicted secondary structure: 46 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 RNAsubopt vs CMfinder(seed) Matthews Correlation Coefficient RNAsubopt: 0.602 CMfinder(seed): 0.454 Sensitivity RNAsubopt: 0.612 CMfinder(seed): 0.271 Positive Predictive Value RNAsubopt: 0.595 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.706 CMfinder(seed): 0.454 Sensitivity RNAalifold(seed): 0.543 CMfinder(seed): 0.271 Positive Predictive Value RNAalifold(seed): 0.918 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): N/A CMfinder(20): N/A Sensitivity CMfinder(seed): N/A CMfinder(20): N/A Positive Predictive Value CMfinder(seed): N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	51 McQFold vs CMfinder(seed) Matthews Correlation Coefficient McQFold: 0.492 CMfinder(seed): 0.454 Sensitivity McQFold: 0.484 CMfinder(seed): 0.271 Positive Predictive Value McQFold: 0.500 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 CRWrnafold vs CMfinder(seed) Matthews Correlation Coefficient CRWrnafold: 0.589 CMfinder(seed): 0.454 Sensitivity CRWrnafold: 0.596 CMfinder(seed): 0.271 Positive Predictive Value CRWrnafold: 0.584 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	47 RNASLOpt vs CMfinder(seed) Matthews Correlation Coefficient RNASLOpt: 0.485 CMfinder(seed): 0.464 Sensitivity RNASLOpt: 0.465 CMfinder(seed): 0.285 Positive Predictive Value RNASLOpt: 0.507 CMfinder(seed): 0.760 Number of pairs reference - predicted secondary structure: 47 Wilcoxon single-rank test P-value: 3.56938820447e-08	48 RNAshapes vs CMfinder(seed) Matthews Correlation Coefficient RNAshapes: 0.560 CMfinder(seed): 0.457 Sensitivity RNAshapes: 0.558 CMfinder(seed): 0.274 Positive Predictive Value RNAshapes: 0.564 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 Murlet(seed) vs CMfinder(seed) Matthews Correlation Coefficient Murlet(seed): 0.612 CMfinder(seed): 0.490 Sensitivity Murlet(seed): 0.408 CMfinder(seed): 0.328 Positive Predictive Value Murlet(seed): 0.920 CMfinder(seed): 0.734 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.02343278931e-08	0 RSpredict(20) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(20): N/A CMfinder(seed): N/A Sensitivity RSpredict(20): N/A CMfinder(seed): N/A Positive Predictive Value RSpredict(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	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	51 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.454 RNAwolf: 0.427 Sensitivity CMfinder(seed): 0.271 RNAwolf: 0.442 Positive Predictive Value CMfinder(seed): 0.762 RNAwolf: 0.414 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): 0.475 CMfinder(seed): 0.454 Sensitivity RSpredict(seed): 0.307 CMfinder(seed): 0.271 Positive Predictive Value RSpredict(seed): 0.738 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 6.06606238843e-08	+ CMfinder(seed) vs Vsfold4 Matthews Correlation Coefficient CMfinder(seed): 0.456 Vsfold4: 0.271 Sensitivity CMfinder(seed): 0.275 Vsfold4: 0.251 Positive Predictive Value CMfinder(seed): 0.759 Vsfold4: 0.295 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Vsfold5 Matthews Correlation Coefficient CMfinder(seed): 0.456 Vsfold5: 0.254 Sensitivity CMfinder(seed): 0.275 Vsfold5: 0.246 Positive Predictive Value CMfinder(seed): 0.759 Vsfold5: 0.264 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.430 NanoFolder: 0.188 Sensitivity CMfinder(seed): 0.239 NanoFolder: 0.221 Positive Predictive Value CMfinder(seed): 0.775 NanoFolder: 0.162 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.50834591464e-08	+ CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.454 Carnac(seed): 0.255 Sensitivity CMfinder(seed): 0.272 Carnac(seed): 0.074 Positive Predictive Value CMfinder(seed): 0.759 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.454 Mastr(seed): 0.215 Sensitivity CMfinder(seed): 0.271 Mastr(seed): 0.052 Positive Predictive Value CMfinder(seed): 0.762 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: 0.640 CMfinder(seed): -0.001 Sensitivity HotKnots: 0.615 CMfinder(seed): 0.000 Positive Predictive Value HotKnots: 0.667 CMfinder(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs CMfinder(seed) Matthews Correlation Coefficient Pknots: N/A CMfinder(seed): N/A Sensitivity Pknots: N/A CMfinder(seed): N/A Positive Predictive Value Pknots: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs CMfinder(seed) Matthews Correlation Coefficient Cylofold: N/A CMfinder(seed): N/A Sensitivity Cylofold: N/A CMfinder(seed): N/A Positive Predictive Value Cylofold: N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? 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	? 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	? 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
RSpredict(seed)	414 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.738 RSpredict(seed): 0.194 Sensitivity PETfold_pre2.0(seed): 0.654 RSpredict(seed): 0.077 Positive Predictive Value PETfold_pre2.0(seed): 0.834 RSpredict(seed): 0.494 Number of pairs reference - predicted secondary structure: 414 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.802 RSpredict(seed): 0.214 Sensitivity ContextFold: 0.766 RSpredict(seed): 0.089 Positive Predictive Value ContextFold: 0.841 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.771 RSpredict(seed): 0.197 Sensitivity TurboFold(20): 0.718 RSpredict(seed): 0.077 Positive Predictive Value TurboFold(20): 0.828 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	426 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.709 RSpredict(seed): 0.215 Sensitivity CentroidAlifold(seed): 0.556 RSpredict(seed): 0.090 Positive Predictive Value CentroidAlifold(seed): 0.906 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 426 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.757 RSpredict(seed): 0.191 Sensitivity PETfold_pre2.0(20): 0.670 RSpredict(seed): 0.073 Positive Predictive Value PETfold_pre2.0(20): 0.855 RSpredict(seed): 0.505 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	198 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.749 RSpredict(seed): 0.201 Sensitivity PPfold(20): 0.647 RSpredict(seed): 0.079 Positive Predictive Value PPfold(20): 0.867 RSpredict(seed): 0.514 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	416 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.686 RSpredict(seed): 0.212 Sensitivity CentroidHomfold‑LAST: 0.539 RSpredict(seed): 0.087 Positive Predictive Value CentroidHomfold‑LAST: 0.874 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.733 RSpredict(seed): 0.197 Sensitivity CentroidAlifold(20): 0.578 RSpredict(seed): 0.077 Positive Predictive Value CentroidAlifold(20): 0.930 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	428 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.637 RSpredict(seed): 0.215 Sensitivity MXScarna(seed): 0.536 RSpredict(seed): 0.090 Positive Predictive Value MXScarna(seed): 0.759 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 428 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.654 RSpredict(seed): 0.214 Sensitivity IPknot: 0.599 RSpredict(seed): 0.089 Positive Predictive Value IPknot: 0.715 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.676 RSpredict(seed): 0.197 Sensitivity RNAalifold(20): 0.543 RSpredict(seed): 0.077 Positive Predictive Value RNAalifold(20): 0.844 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 RSpredict(seed): 0.510 Sensitivity TurboFold(seed): 0.760 RSpredict(seed): 0.389 Positive Predictive Value TurboFold(seed): 0.815 RSpredict(seed): 0.670 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.84041289224e-08	186 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.658 RSpredict(seed): 0.182 Sensitivity Multilign(20): 0.594 RSpredict(seed): 0.067 Positive Predictive Value Multilign(20): 0.731 RSpredict(seed): 0.495 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.681 RSpredict(seed): 0.197 Sensitivity MXScarna(20): 0.600 RSpredict(seed): 0.077 Positive Predictive Value MXScarna(20): 0.773 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.633 RSpredict(seed): 0.214 Sensitivity CentroidFold: 0.579 RSpredict(seed): 0.089 Positive Predictive Value CentroidFold: 0.692 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.620 RSpredict(seed): 0.214 Sensitivity Contrafold: 0.604 RSpredict(seed): 0.089 Positive Predictive Value Contrafold: 0.637 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 RSpredict(seed): 0.407 Sensitivity PPfold(seed): 0.652 RSpredict(seed): 0.288 Positive Predictive Value PPfold(seed): 0.787 RSpredict(seed): 0.579 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.612 RSpredict(seed): 0.214 Sensitivity Sfold: 0.558 RSpredict(seed): 0.089 Positive Predictive Value Sfold: 0.673 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.598 RSpredict(seed): 0.214 Sensitivity MaxExpect: 0.582 RSpredict(seed): 0.089 Positive Predictive Value MaxExpect: 0.617 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.597 RSpredict(seed): 0.214 Sensitivity ProbKnot: 0.585 RSpredict(seed): 0.089 Positive Predictive Value ProbKnot: 0.611 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RSpredict(seed) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(seed): 0.816 RNASampler(seed): 0.779 Sensitivity RSpredict(seed): 0.714 RNASampler(seed): 0.659 Positive Predictive Value RSpredict(seed): 0.934 RNASampler(seed): 0.921 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.30295446166e-08	429 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.573 RSpredict(seed): 0.214 Sensitivity Fold: 0.570 RSpredict(seed): 0.089 Positive Predictive Value Fold: 0.577 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.578 RSpredict(seed): 0.465 Sensitivity RNASampler(20): 0.384 RSpredict(seed): 0.322 Positive Predictive Value RNASampler(20): 0.871 RSpredict(seed): 0.674 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.568 RSpredict(seed): 0.204 Sensitivity Murlet(20): 0.427 RSpredict(seed): 0.081 Positive Predictive Value Murlet(20): 0.758 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.576 RSpredict(seed): 0.214 Sensitivity UNAFold: 0.566 RSpredict(seed): 0.089 Positive Predictive Value UNAFold: 0.588 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.560 RSpredict(seed): 0.214 Sensitivity PknotsRG: 0.554 RSpredict(seed): 0.089 Positive Predictive Value PknotsRG: 0.567 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.569 RSpredict(seed): 0.214 Sensitivity RNAfold: 0.563 RSpredict(seed): 0.089 Positive Predictive Value RNAfold: 0.577 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 RSpredict(seed): 0.626 Sensitivity Multilign(seed): 0.752 RSpredict(seed): 0.495 Positive Predictive Value Multilign(seed): 0.767 RSpredict(seed): 0.793 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	355 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.558 RSpredict(seed): 0.214 Sensitivity Afold: 0.551 RSpredict(seed): 0.087 Positive Predictive Value Afold: 0.567 RSpredict(seed): 0.529 Number of pairs reference - predicted secondary structure: 355 Wilcoxon single-rank test P-value: 3.56938820447e-08	416 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.559 RSpredict(seed): 0.212 Sensitivity RNAsubopt: 0.560 RSpredict(seed): 0.087 Positive Predictive Value RNAsubopt: 0.559 RSpredict(seed): 0.520 Number of pairs reference - predicted secondary structure: 416 Wilcoxon single-rank test P-value: 3.56938820447e-08	427 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.541 RSpredict(seed): 0.215 Sensitivity RNAalifold(seed): 0.344 RSpredict(seed): 0.090 Positive Predictive Value RNAalifold(seed): 0.851 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 427 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.498 RSpredict(seed): 0.197 Sensitivity CMfinder(20): 0.328 RSpredict(seed): 0.077 Positive Predictive Value CMfinder(20): 0.758 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.465 RSpredict(seed): 0.214 Sensitivity McQFold: 0.449 RSpredict(seed): 0.089 Positive Predictive Value McQFold: 0.484 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.481 RSpredict(seed): 0.214 Sensitivity CRWrnafold: 0.477 RSpredict(seed): 0.089 Positive Predictive Value CRWrnafold: 0.488 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	368 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.465 RSpredict(seed): 0.230 Sensitivity RNASLOpt: 0.434 RSpredict(seed): 0.099 Positive Predictive Value RNASLOpt: 0.500 RSpredict(seed): 0.538 Number of pairs reference - predicted secondary structure: 368 Wilcoxon single-rank test P-value: 3.56938820447e-08	391 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.506 RSpredict(seed): 0.216 Sensitivity RNAshapes: 0.494 RSpredict(seed): 0.089 Positive Predictive Value RNAshapes: 0.520 RSpredict(seed): 0.522 Number of pairs reference - predicted secondary structure: 391 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Murlet(seed) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(seed): 0.569 RSpredict(seed): 0.536 Sensitivity Murlet(seed): 0.383 RSpredict(seed): 0.403 Positive Predictive Value Murlet(seed): 0.845 RSpredict(seed): 0.714 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 5.23657817852e-08	205 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.403 RSpredict(seed): 0.197 Sensitivity RSpredict(20): 0.259 RSpredict(seed): 0.077 Positive Predictive Value RSpredict(20): 0.630 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.359 RSpredict(seed): 0.197 Sensitivity Carnac(20): 0.147 RSpredict(seed): 0.077 Positive Predictive Value Carnac(20): 0.881 RSpredict(seed): 0.510 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	429 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.379 RSpredict(seed): 0.214 Sensitivity RNAwolf: 0.389 RSpredict(seed): 0.089 Positive Predictive Value RNAwolf: 0.371 RSpredict(seed): 0.517 Number of pairs reference - predicted secondary structure: 429 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 RSpredict(seed) vs CMfinder(seed) Matthews Correlation Coefficient RSpredict(seed): 0.475 CMfinder(seed): 0.454 Sensitivity RSpredict(seed): 0.307 CMfinder(seed): 0.271 Positive Predictive Value RSpredict(seed): 0.738 CMfinder(seed): 0.762 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 6.06606238843e-08		- Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.336 RSpredict(seed): 0.217 Sensitivity Vsfold4: 0.305 RSpredict(seed): 0.091 Positive Predictive Value Vsfold4: 0.373 RSpredict(seed): 0.523 Number of pairs reference - predicted secondary structure: 401 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.315 RSpredict(seed): 0.218 Sensitivity Vsfold5: 0.294 RSpredict(seed): 0.091 Positive Predictive Value Vsfold5: 0.340 RSpredict(seed): 0.524 Number of pairs reference - predicted secondary structure: 396 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs NanoFolder Matthews Correlation Coefficient RSpredict(seed): 0.219 NanoFolder: 0.176 Sensitivity RSpredict(seed): 0.090 NanoFolder: 0.203 Positive Predictive Value RSpredict(seed): 0.533 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.310 Carnac(seed): 0.150 Sensitivity RSpredict(seed): 0.163 Carnac(seed): 0.028 Positive Predictive Value RSpredict(seed): 0.593 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.224 Mastr(seed): 0.073 Sensitivity RSpredict(seed): 0.096 Mastr(seed): 0.006 Positive Predictive Value RSpredict(seed): 0.526 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.640 RSpredict(seed): -0.001 Sensitivity HotKnots: 0.615 RSpredict(seed): 0.000 Positive Predictive Value HotKnots: 0.667 RSpredict(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? RSpredict(seed) vs Pknots Matthews Correlation Coefficient RSpredict(seed): N/A Pknots: N/A Sensitivity RSpredict(seed): N/A Pknots: N/A Positive Predictive Value RSpredict(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs Cylofold Matthews Correlation Coefficient RSpredict(seed): N/A Cylofold: N/A Sensitivity RSpredict(seed): N/A Cylofold: N/A Positive Predictive Value RSpredict(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): N/A MCFold: N/A Sensitivity RSpredict(seed): N/A MCFold: N/A Positive Predictive Value RSpredict(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): N/A RDfolder: N/A Sensitivity RSpredict(seed): N/A RDfolder: N/A Positive Predictive Value RSpredict(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): N/A Alterna: N/A Sensitivity RSpredict(seed): N/A Alterna: N/A Positive Predictive Value RSpredict(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ RSpredict(seed) vs Mastr(20) Matthews Correlation Coefficient RSpredict(seed): 0.197 Mastr(20): 0.000 Sensitivity RSpredict(seed): 0.077 Mastr(20): 0.000 Positive Predictive Value RSpredict(seed): 0.510 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold4	615 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.705 Vsfold4: 0.307 Sensitivity PETfold_pre2.0(seed): 0.621 Vsfold4: 0.282 Positive Predictive Value PETfold_pre2.0(seed): 0.801 Vsfold4: 0.336 Number of pairs reference - predicted secondary structure: 615 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.743 Vsfold4: 0.306 Sensitivity ContextFold: 0.706 Vsfold4: 0.282 Positive Predictive Value ContextFold: 0.782 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	240 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.751 Vsfold4: 0.352 Sensitivity TurboFold(20): 0.700 Vsfold4: 0.319 Positive Predictive Value TurboFold(20): 0.808 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	398 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.717 Vsfold4: 0.336 Sensitivity CentroidAlifold(seed): 0.568 Vsfold4: 0.304 Positive Predictive Value CentroidAlifold(seed): 0.906 Vsfold4: 0.372 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.740 Vsfold4: 0.355 Sensitivity PETfold_pre2.0(20): 0.656 Vsfold4: 0.321 Positive Predictive Value PETfold_pre2.0(20): 0.837 Vsfold4: 0.395 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.735 Vsfold4: 0.351 Sensitivity PPfold(20): 0.632 Vsfold4: 0.318 Positive Predictive Value PPfold(20): 0.856 Vsfold4: 0.390 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.655 Vsfold4: 0.306 Sensitivity CentroidHomfold‑LAST: 0.497 Vsfold4: 0.282 Positive Predictive Value CentroidHomfold‑LAST: 0.863 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	240 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Vsfold4: 0.352 Sensitivity CentroidAlifold(20): 0.575 Vsfold4: 0.319 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	403 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.649 Vsfold4: 0.337 Sensitivity MXScarna(seed): 0.550 Vsfold4: 0.305 Positive Predictive Value MXScarna(seed): 0.766 Vsfold4: 0.373 Number of pairs reference - predicted secondary structure: 403 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.619 Vsfold4: 0.306 Sensitivity IPknot: 0.568 Vsfold4: 0.282 Positive Predictive Value IPknot: 0.675 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	240 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.669 Vsfold4: 0.352 Sensitivity RNAalifold(20): 0.542 Vsfold4: 0.319 Positive Predictive Value RNAalifold(20): 0.828 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.776 Vsfold4: 0.171 Sensitivity TurboFold(seed): 0.753 Vsfold4: 0.159 Positive Predictive Value TurboFold(seed): 0.802 Vsfold4: 0.188 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.21671975982e-08	219 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.650 Vsfold4: 0.359 Sensitivity Multilign(20): 0.589 Vsfold4: 0.326 Positive Predictive Value Multilign(20): 0.719 Vsfold4: 0.399 Number of pairs reference - predicted secondary structure: 219 Wilcoxon single-rank test P-value: 3.56938820447e-08	240 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.654 Vsfold4: 0.352 Sensitivity MXScarna(20): 0.584 Vsfold4: 0.319 Positive Predictive Value MXScarna(20): 0.734 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.586 Vsfold4: 0.306 Sensitivity CentroidFold: 0.537 Vsfold4: 0.282 Positive Predictive Value CentroidFold: 0.641 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.570 Vsfold4: 0.306 Sensitivity Contrafold: 0.560 Vsfold4: 0.282 Positive Predictive Value Contrafold: 0.582 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.735 Vsfold4: 0.197 Sensitivity PPfold(seed): 0.691 Vsfold4: 0.182 Positive Predictive Value PPfold(seed): 0.783 Vsfold4: 0.215 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.06544643719e-08	730 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.544 Vsfold4: 0.306 Sensitivity Sfold: 0.496 Vsfold4: 0.282 Positive Predictive Value Sfold: 0.598 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.542 Vsfold4: 0.306 Sensitivity MaxExpect: 0.532 Vsfold4: 0.282 Positive Predictive Value MaxExpect: 0.555 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.541 Vsfold4: 0.306 Sensitivity ProbKnot: 0.538 Vsfold4: 0.282 Positive Predictive Value ProbKnot: 0.546 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.779 Vsfold4: 0.215 Sensitivity RNASampler(seed): 0.659 Vsfold4: 0.210 Positive Predictive Value RNASampler(seed): 0.921 Vsfold4: 0.223 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.18011954625e-08	730 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.520 Vsfold4: 0.306 Sensitivity Fold: 0.524 Vsfold4: 0.282 Positive Predictive Value Fold: 0.518 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.565 Vsfold4: 0.195 Sensitivity RNASampler(20): 0.413 Vsfold4: 0.181 Positive Predictive Value RNASampler(20): 0.772 Vsfold4: 0.213 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	172 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.577 Vsfold4: 0.337 Sensitivity Murlet(20): 0.445 Vsfold4: 0.306 Positive Predictive Value Murlet(20): 0.748 Vsfold4: 0.374 Number of pairs reference - predicted secondary structure: 172 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.508 Vsfold4: 0.306 Sensitivity UNAFold: 0.505 Vsfold4: 0.282 Positive Predictive Value UNAFold: 0.512 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.504 Vsfold4: 0.306 Sensitivity PknotsRG: 0.507 Vsfold4: 0.282 Positive Predictive Value PknotsRG: 0.504 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.508 Vsfold4: 0.306 Sensitivity RNAfold: 0.510 Vsfold4: 0.282 Positive Predictive Value RNAfold: 0.508 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.734 Vsfold4: 0.167 Sensitivity Multilign(seed): 0.733 Vsfold4: 0.160 Positive Predictive Value Multilign(seed): 0.737 Vsfold4: 0.176 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.00475527001e-08	448 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.532 Vsfold4: 0.328 Sensitivity Afold: 0.528 Vsfold4: 0.300 Positive Predictive Value Afold: 0.537 Vsfold4: 0.361 Number of pairs reference - predicted secondary structure: 448 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.500 Vsfold4: 0.306 Sensitivity RNAsubopt: 0.508 Vsfold4: 0.282 Positive Predictive Value RNAsubopt: 0.493 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	399 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.543 Vsfold4: 0.336 Sensitivity RNAalifold(seed): 0.348 Vsfold4: 0.305 Positive Predictive Value RNAalifold(seed): 0.850 Vsfold4: 0.372 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	240 CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.483 Vsfold4: 0.352 Sensitivity CMfinder(20): 0.314 Vsfold4: 0.319 Positive Predictive Value CMfinder(20): 0.745 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.451 Vsfold4: 0.306 Sensitivity McQFold: 0.441 Vsfold4: 0.282 Positive Predictive Value McQFold: 0.463 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.441 Vsfold4: 0.306 Sensitivity CRWrnafold: 0.443 Vsfold4: 0.282 Positive Predictive Value CRWrnafold: 0.440 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.442 Vsfold4: 0.305 Sensitivity RNASLOpt: 0.419 Vsfold4: 0.281 Positive Predictive Value RNASLOpt: 0.468 Vsfold4: 0.333 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	702 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.436 Vsfold4: 0.308 Sensitivity RNAshapes: 0.433 Vsfold4: 0.284 Positive Predictive Value RNAshapes: 0.441 Vsfold4: 0.337 Number of pairs reference - predicted secondary structure: 702 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.556 Vsfold4: 0.208 Sensitivity Murlet(seed): 0.366 Vsfold4: 0.196 Positive Predictive Value Murlet(seed): 0.846 Vsfold4: 0.223 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.19332990918e-08	240 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.422 Vsfold4: 0.352 Sensitivity RSpredict(20): 0.290 Vsfold4: 0.319 Positive Predictive Value RSpredict(20): 0.618 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	240 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.377 Vsfold4: 0.352 Sensitivity Carnac(20): 0.165 Vsfold4: 0.319 Positive Predictive Value Carnac(20): 0.865 Vsfold4: 0.391 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	730 RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.350 Vsfold4: 0.306 Sensitivity RNAwolf: 0.365 Vsfold4: 0.282 Positive Predictive Value RNAwolf: 0.338 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 730 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 CMfinder(seed) vs Vsfold4 Matthews Correlation Coefficient CMfinder(seed): 0.456 Vsfold4: 0.271 Sensitivity CMfinder(seed): 0.275 Vsfold4: 0.251 Positive Predictive Value CMfinder(seed): 0.759 Vsfold4: 0.295 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	401 Vsfold4 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold4: 0.336 RSpredict(seed): 0.217 Sensitivity Vsfold4: 0.305 RSpredict(seed): 0.091 Positive Predictive Value Vsfold4: 0.373 RSpredict(seed): 0.523 Number of pairs reference - predicted secondary structure: 401 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.307 Vsfold5: 0.300 Sensitivity Vsfold4: 0.283 Vsfold5: 0.286 Positive Predictive Value Vsfold4: 0.335 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.329 NanoFolder: 0.171 Sensitivity Vsfold4: 0.300 NanoFolder: 0.203 Positive Predictive Value Vsfold4: 0.362 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.222 Carnac(seed): 0.160 Sensitivity Vsfold4: 0.205 Carnac(seed): 0.029 Positive Predictive Value Vsfold4: 0.243 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.328 Mastr(seed): 0.076 Sensitivity Vsfold4: 0.298 Mastr(seed): 0.007 Positive Predictive Value Vsfold4: 0.363 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 381 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.640 Vsfold4: 0.221 Sensitivity HotKnots: 0.615 Vsfold4: 0.231 Positive Predictive Value HotKnots: 0.667 Vsfold4: 0.214 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: N/A Vsfold4: N/A Sensitivity Pknots: N/A Vsfold4: N/A Positive Predictive Value Pknots: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.271 Vsfold4: 0.267 Sensitivity Cylofold: 0.241 Vsfold4: 0.241 Positive Predictive Value Cylofold: 0.308 Vsfold4: 0.300 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: N/A MCFold: N/A Sensitivity Vsfold4: N/A MCFold: N/A Positive Predictive Value Vsfold4: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: N/A Vsfold4: N/A Sensitivity RDfolder: N/A Vsfold4: N/A Positive Predictive Value RDfolder: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: N/A Alterna: N/A Sensitivity Vsfold4: N/A Alterna: N/A Positive Predictive Value Vsfold4: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.352 Mastr(20): 0.000 Sensitivity Vsfold4: 0.319 Mastr(20): 0.000 Positive Predictive Value Vsfold4: 0.391 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold5	608 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.705 Vsfold5: 0.300 Sensitivity PETfold_pre2.0(seed): 0.622 Vsfold5: 0.285 Positive Predictive Value PETfold_pre2.0(seed): 0.801 Vsfold5: 0.318 Number of pairs reference - predicted secondary structure: 608 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.745 Vsfold5: 0.300 Sensitivity ContextFold: 0.707 Vsfold5: 0.286 Positive Predictive Value ContextFold: 0.785 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.751 Vsfold5: 0.333 Sensitivity TurboFold(20): 0.699 Vsfold5: 0.308 Positive Predictive Value TurboFold(20): 0.807 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	393 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.718 Vsfold5: 0.314 Sensitivity CentroidAlifold(seed): 0.569 Vsfold5: 0.293 Positive Predictive Value CentroidAlifold(seed): 0.907 Vsfold5: 0.339 Number of pairs reference - predicted secondary structure: 393 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.741 Vsfold5: 0.336 Sensitivity PETfold_pre2.0(20): 0.657 Vsfold5: 0.311 Positive Predictive Value PETfold_pre2.0(20): 0.837 Vsfold5: 0.365 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	231 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.736 Vsfold5: 0.331 Sensitivity PPfold(20): 0.632 Vsfold5: 0.306 Positive Predictive Value PPfold(20): 0.857 Vsfold5: 0.360 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.655 Vsfold5: 0.300 Sensitivity CentroidHomfold‑LAST: 0.497 Vsfold5: 0.286 Positive Predictive Value CentroidHomfold‑LAST: 0.864 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.726 Vsfold5: 0.333 Sensitivity CentroidAlifold(20): 0.575 Vsfold5: 0.308 Positive Predictive Value CentroidAlifold(20): 0.916 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	398 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.649 Vsfold5: 0.316 Sensitivity MXScarna(seed): 0.550 Vsfold5: 0.295 Positive Predictive Value MXScarna(seed): 0.766 Vsfold5: 0.341 Number of pairs reference - predicted secondary structure: 398 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.619 Vsfold5: 0.300 Sensitivity IPknot: 0.568 Vsfold5: 0.286 Positive Predictive Value IPknot: 0.676 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.670 Vsfold5: 0.333 Sensitivity RNAalifold(20): 0.542 Vsfold5: 0.308 Positive Predictive Value RNAalifold(20): 0.828 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.776 Vsfold5: 0.241 Sensitivity TurboFold(seed): 0.753 Vsfold5: 0.240 Positive Predictive Value TurboFold(seed): 0.802 Vsfold5: 0.245 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.13260312532e-08	216 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.651 Vsfold5: 0.342 Sensitivity Multilign(20): 0.590 Vsfold5: 0.316 Positive Predictive Value Multilign(20): 0.720 Vsfold5: 0.373 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.652 Vsfold5: 0.333 Sensitivity MXScarna(20): 0.581 Vsfold5: 0.308 Positive Predictive Value MXScarna(20): 0.732 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.586 Vsfold5: 0.300 Sensitivity CentroidFold: 0.537 Vsfold5: 0.286 Positive Predictive Value CentroidFold: 0.641 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.570 Vsfold5: 0.300 Sensitivity Contrafold: 0.560 Vsfold5: 0.286 Positive Predictive Value Contrafold: 0.582 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.735 Vsfold5: 0.192 Sensitivity PPfold(seed): 0.691 Vsfold5: 0.185 Positive Predictive Value PPfold(seed): 0.783 Vsfold5: 0.201 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.23657817852e-08	720 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.544 Vsfold5: 0.300 Sensitivity Sfold: 0.496 Vsfold5: 0.286 Positive Predictive Value Sfold: 0.598 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.544 Vsfold5: 0.300 Sensitivity MaxExpect: 0.533 Vsfold5: 0.286 Positive Predictive Value MaxExpect: 0.556 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.542 Vsfold5: 0.300 Sensitivity ProbKnot: 0.539 Vsfold5: 0.286 Positive Predictive Value ProbKnot: 0.547 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.779 Vsfold5: 0.290 Sensitivity RNASampler(seed): 0.659 Vsfold5: 0.303 Positive Predictive Value RNASampler(seed): 0.921 Vsfold5: 0.280 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 5.11462970451e-09	720 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.521 Vsfold5: 0.300 Sensitivity Fold: 0.525 Vsfold5: 0.286 Positive Predictive Value Fold: 0.519 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.565 Vsfold5: 0.188 Sensitivity RNASampler(20): 0.413 Vsfold5: 0.178 Positive Predictive Value RNASampler(20): 0.772 Vsfold5: 0.201 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	170 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.578 Vsfold5: 0.316 Sensitivity Murlet(20): 0.447 Vsfold5: 0.293 Positive Predictive Value Murlet(20): 0.750 Vsfold5: 0.343 Number of pairs reference - predicted secondary structure: 170 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.508 Vsfold5: 0.300 Sensitivity UNAFold: 0.505 Vsfold5: 0.286 Positive Predictive Value UNAFold: 0.512 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.504 Vsfold5: 0.300 Sensitivity PknotsRG: 0.506 Vsfold5: 0.286 Positive Predictive Value PknotsRG: 0.504 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.508 Vsfold5: 0.300 Sensitivity RNAfold: 0.510 Vsfold5: 0.286 Positive Predictive Value RNAfold: 0.508 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	10 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.734 Vsfold5: 0.228 Sensitivity Multilign(seed): 0.733 Vsfold5: 0.235 Positive Predictive Value Multilign(seed): 0.737 Vsfold5: 0.225 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 1.10032755566e-08	441 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.533 Vsfold5: 0.317 Sensitivity Afold: 0.530 Vsfold5: 0.299 Positive Predictive Value Afold: 0.539 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 441 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.500 Vsfold5: 0.300 Sensitivity RNAsubopt: 0.508 Vsfold5: 0.286 Positive Predictive Value RNAsubopt: 0.493 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	394 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.543 Vsfold5: 0.315 Sensitivity RNAalifold(seed): 0.347 Vsfold5: 0.294 Positive Predictive Value RNAalifold(seed): 0.850 Vsfold5: 0.340 Number of pairs reference - predicted secondary structure: 394 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.485 Vsfold5: 0.333 Sensitivity CMfinder(20): 0.316 Vsfold5: 0.308 Positive Predictive Value CMfinder(20): 0.747 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.452 Vsfold5: 0.300 Sensitivity McQFold: 0.442 Vsfold5: 0.286 Positive Predictive Value McQFold: 0.464 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.441 Vsfold5: 0.300 Sensitivity CRWrnafold: 0.443 Vsfold5: 0.286 Positive Predictive Value CRWrnafold: 0.440 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	660 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.442 Vsfold5: 0.299 Sensitivity RNASLOpt: 0.419 Vsfold5: 0.285 Positive Predictive Value RNASLOpt: 0.468 Vsfold5: 0.315 Number of pairs reference - predicted secondary structure: 660 Wilcoxon single-rank test P-value: 3.56938820447e-08	701 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.436 Vsfold5: 0.301 Sensitivity RNAshapes: 0.433 Vsfold5: 0.286 Positive Predictive Value RNAshapes: 0.441 Vsfold5: 0.318 Number of pairs reference - predicted secondary structure: 701 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.556 Vsfold5: 0.216 Sensitivity Murlet(seed): 0.366 Vsfold5: 0.212 Positive Predictive Value Murlet(seed): 0.846 Vsfold5: 0.224 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.23657817852e-08	237 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.424 Vsfold5: 0.333 Sensitivity RSpredict(20): 0.291 Vsfold5: 0.308 Positive Predictive Value RSpredict(20): 0.618 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.378 Vsfold5: 0.333 Sensitivity Carnac(20): 0.166 Vsfold5: 0.308 Positive Predictive Value Carnac(20): 0.865 Vsfold5: 0.362 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.351 Vsfold5: 0.300 Sensitivity RNAwolf: 0.366 Vsfold5: 0.286 Positive Predictive Value RNAwolf: 0.339 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 CMfinder(seed) vs Vsfold5 Matthews Correlation Coefficient CMfinder(seed): 0.456 Vsfold5: 0.254 Sensitivity CMfinder(seed): 0.275 Vsfold5: 0.246 Positive Predictive Value CMfinder(seed): 0.759 Vsfold5: 0.264 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	396 Vsfold5 vs RSpredict(seed) Matthews Correlation Coefficient Vsfold5: 0.315 RSpredict(seed): 0.218 Sensitivity Vsfold5: 0.294 RSpredict(seed): 0.091 Positive Predictive Value Vsfold5: 0.340 RSpredict(seed): 0.524 Number of pairs reference - predicted secondary structure: 396 Wilcoxon single-rank test P-value: 3.56938820447e-08	720 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.307 Vsfold5: 0.300 Sensitivity Vsfold4: 0.283 Vsfold5: 0.286 Positive Predictive Value Vsfold4: 0.335 Vsfold5: 0.317 Number of pairs reference - predicted secondary structure: 720 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.316 NanoFolder: 0.171 Sensitivity Vsfold5: 0.297 NanoFolder: 0.203 Positive Predictive Value Vsfold5: 0.337 NanoFolder: 0.148 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.210 Carnac(seed): 0.163 Sensitivity Vsfold5: 0.201 Carnac(seed): 0.030 Positive Predictive Value Vsfold5: 0.221 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.309 Mastr(seed): 0.077 Sensitivity Vsfold5: 0.289 Mastr(seed): 0.007 Positive Predictive Value Vsfold5: 0.332 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 376 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.640 Vsfold5: 0.232 Sensitivity HotKnots: 0.615 Vsfold5: 0.231 Positive Predictive Value HotKnots: 0.667 Vsfold5: 0.237 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs Pknots Matthews Correlation Coefficient Vsfold5: N/A Pknots: N/A Sensitivity Vsfold5: N/A Pknots: N/A Positive Predictive Value Vsfold5: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold5 vs Cylofold Matthews Correlation Coefficient Vsfold5: 0.357 Cylofold: 0.271 Sensitivity Vsfold5: 0.336 Cylofold: 0.241 Positive Predictive Value Vsfold5: 0.383 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	? Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: N/A MCFold: N/A Sensitivity Vsfold5: N/A MCFold: N/A Positive Predictive Value Vsfold5: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Vsfold5 Matthews Correlation Coefficient RDfolder: N/A Vsfold5: N/A Sensitivity RDfolder: N/A Vsfold5: N/A Positive Predictive Value RDfolder: N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: N/A Alterna: N/A Sensitivity Vsfold5: N/A Alterna: N/A Positive Predictive Value Vsfold5: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.333 Mastr(20): 0.000 Sensitivity Vsfold5: 0.308 Mastr(20): 0.000 Positive Predictive Value Vsfold5: 0.362 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08
NanoFolder	109 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.722 NanoFolder: 0.174 Sensitivity PETfold_pre2.0(seed): 0.634 NanoFolder: 0.205 Positive Predictive Value PETfold_pre2.0(seed): 0.824 NanoFolder: 0.149 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.778 NanoFolder: 0.166 Sensitivity ContextFold: 0.738 NanoFolder: 0.197 Positive Predictive Value ContextFold: 0.820 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.735 NanoFolder: 0.150 Sensitivity TurboFold(20): 0.684 NanoFolder: 0.173 Positive Predictive Value TurboFold(20): 0.791 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.721 NanoFolder: 0.176 Sensitivity CentroidAlifold(seed): 0.560 NanoFolder: 0.203 Positive Predictive Value CentroidAlifold(seed): 0.929 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.731 NanoFolder: 0.151 Sensitivity PETfold_pre2.0(20): 0.643 NanoFolder: 0.174 Positive Predictive Value PETfold_pre2.0(20): 0.831 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	55 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.722 NanoFolder: 0.152 Sensitivity PPfold(20): 0.614 NanoFolder: 0.176 Positive Predictive Value PPfold(20): 0.849 NanoFolder: 0.135 Number of pairs reference - predicted secondary structure: 55 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.660 NanoFolder: 0.170 Sensitivity CentroidHomfold‑LAST: 0.493 NanoFolder: 0.201 Positive Predictive Value CentroidHomfold‑LAST: 0.886 NanoFolder: 0.146 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.714 NanoFolder: 0.150 Sensitivity CentroidAlifold(20): 0.562 NanoFolder: 0.173 Positive Predictive Value CentroidAlifold(20): 0.908 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.646 NanoFolder: 0.176 Sensitivity MXScarna(seed): 0.540 NanoFolder: 0.203 Positive Predictive Value MXScarna(seed): 0.773 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.659 NanoFolder: 0.166 Sensitivity IPknot: 0.600 NanoFolder: 0.197 Positive Predictive Value IPknot: 0.725 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.662 NanoFolder: 0.150 Sensitivity RNAalifold(20): 0.538 NanoFolder: 0.173 Positive Predictive Value RNAalifold(20): 0.817 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	2 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.834 NanoFolder: 0.088 Sensitivity TurboFold(seed): 0.822 NanoFolder: 0.116 Positive Predictive Value TurboFold(seed): 0.848 NanoFolder: 0.070 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	51 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.639 NanoFolder: 0.151 Sensitivity Multilign(20): 0.581 NanoFolder: 0.175 Positive Predictive Value Multilign(20): 0.703 NanoFolder: 0.134 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.648 NanoFolder: 0.150 Sensitivity MXScarna(20): 0.577 NanoFolder: 0.173 Positive Predictive Value MXScarna(20): 0.728 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.609 NanoFolder: 0.166 Sensitivity CentroidFold: 0.555 NanoFolder: 0.197 Positive Predictive Value CentroidFold: 0.670 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.590 NanoFolder: 0.166 Sensitivity Contrafold: 0.577 NanoFolder: 0.197 Positive Predictive Value Contrafold: 0.604 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.950 NanoFolder: -0.003 Sensitivity PPfold(seed): 0.902 NanoFolder: 0.000 Positive Predictive Value PPfold(seed): 1.000 NanoFolder: 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	134 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.572 NanoFolder: 0.166 Sensitivity Sfold: 0.517 NanoFolder: 0.197 Positive Predictive Value Sfold: 0.635 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.569 NanoFolder: 0.166 Sensitivity MaxExpect: 0.554 NanoFolder: 0.197 Positive Predictive Value MaxExpect: 0.586 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.567 NanoFolder: 0.166 Sensitivity ProbKnot: 0.560 NanoFolder: 0.197 Positive Predictive Value ProbKnot: 0.576 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	2 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.698 NanoFolder: 0.075 Sensitivity RNASampler(seed): 0.600 NanoFolder: 0.113 Positive Predictive Value RNASampler(seed): 0.814 NanoFolder: 0.054 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	134 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.534 NanoFolder: 0.166 Sensitivity Fold: 0.535 NanoFolder: 0.197 Positive Predictive Value Fold: 0.536 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.602 NanoFolder: 0.121 Sensitivity RNASampler(20): 0.450 NanoFolder: 0.148 Positive Predictive Value RNASampler(20): 0.805 NanoFolder: 0.102 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 2.41358941668e-08	45 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.551 NanoFolder: 0.150 Sensitivity Murlet(20): 0.416 NanoFolder: 0.174 Positive Predictive Value Murlet(20): 0.730 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 45 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.533 NanoFolder: 0.166 Sensitivity UNAFold: 0.527 NanoFolder: 0.197 Positive Predictive Value UNAFold: 0.540 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.518 NanoFolder: 0.166 Sensitivity PknotsRG: 0.518 NanoFolder: 0.197 Positive Predictive Value PknotsRG: 0.520 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.531 NanoFolder: 0.166 Sensitivity RNAfold: 0.529 NanoFolder: 0.197 Positive Predictive Value RNAfold: 0.534 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 Multilign(seed) vs NanoFolder Matthews Correlation Coefficient Multilign(seed): 1.000 NanoFolder: -0.003 Sensitivity Multilign(seed): 1.000 NanoFolder: 0.000 Positive Predictive Value Multilign(seed): 1.000 NanoFolder: 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	88 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.560 NanoFolder: 0.165 Sensitivity Afold: 0.553 NanoFolder: 0.192 Positive Predictive Value Afold: 0.568 NanoFolder: 0.144 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.528 NanoFolder: 0.170 Sensitivity RNAsubopt: 0.533 NanoFolder: 0.201 Positive Predictive Value RNAsubopt: 0.524 NanoFolder: 0.146 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.537 NanoFolder: 0.176 Sensitivity RNAalifold(seed): 0.335 NanoFolder: 0.203 Positive Predictive Value RNAalifold(seed): 0.861 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.476 NanoFolder: 0.150 Sensitivity CMfinder(20): 0.303 NanoFolder: 0.173 Positive Predictive Value CMfinder(20): 0.751 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.456 NanoFolder: 0.166 Sensitivity McQFold: 0.444 NanoFolder: 0.197 Positive Predictive Value McQFold: 0.471 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.472 NanoFolder: 0.166 Sensitivity CRWrnafold: 0.472 NanoFolder: 0.197 Positive Predictive Value CRWrnafold: 0.473 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.457 NanoFolder: 0.173 Sensitivity RNASLOpt: 0.428 NanoFolder: 0.204 Positive Predictive Value RNASLOpt: 0.491 NanoFolder: 0.150 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	128 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.457 NanoFolder: 0.171 Sensitivity RNAshapes: 0.449 NanoFolder: 0.202 Positive Predictive Value RNAshapes: 0.466 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	6 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.488 NanoFolder: 0.161 Sensitivity Murlet(seed): 0.281 NanoFolder: 0.193 Positive Predictive Value Murlet(seed): 0.848 NanoFolder: 0.138 Number of pairs reference - predicted secondary structure: 6 Wilcoxon single-rank test P-value: 0.0	57 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.397 NanoFolder: 0.150 Sensitivity RSpredict(20): 0.265 NanoFolder: 0.173 Positive Predictive Value RSpredict(20): 0.595 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.393 NanoFolder: 0.150 Sensitivity Carnac(20): 0.179 NanoFolder: 0.173 Positive Predictive Value Carnac(20): 0.866 NanoFolder: 0.133 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.357 NanoFolder: 0.166 Sensitivity RNAwolf: 0.369 NanoFolder: 0.197 Positive Predictive Value RNAwolf: 0.347 NanoFolder: 0.142 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	14 CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.430 NanoFolder: 0.188 Sensitivity CMfinder(seed): 0.239 NanoFolder: 0.221 Positive Predictive Value CMfinder(seed): 0.775 NanoFolder: 0.162 Number of pairs reference - predicted secondary structure: 14 Wilcoxon single-rank test P-value: 1.50834591464e-08	78 RSpredict(seed) vs NanoFolder Matthews Correlation Coefficient RSpredict(seed): 0.219 NanoFolder: 0.176 Sensitivity RSpredict(seed): 0.090 NanoFolder: 0.203 Positive Predictive Value RSpredict(seed): 0.533 NanoFolder: 0.156 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	129 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.329 NanoFolder: 0.171 Sensitivity Vsfold4: 0.300 NanoFolder: 0.203 Positive Predictive Value Vsfold4: 0.362 NanoFolder: 0.147 Number of pairs reference - predicted secondary structure: 129 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.316 NanoFolder: 0.171 Sensitivity Vsfold5: 0.297 NanoFolder: 0.203 Positive Predictive Value Vsfold5: 0.337 NanoFolder: 0.148 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.197 Carnac(seed): 0.094 Sensitivity NanoFolder: 0.233 Carnac(seed): 0.013 Positive Predictive Value NanoFolder: 0.170 Carnac(seed): 0.677 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08	+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.175 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.203 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.155 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.640 NanoFolder: 0.158 Sensitivity HotKnots: 0.615 NanoFolder: 0.231 Positive Predictive Value HotKnots: 0.667 NanoFolder: 0.111 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs Pknots Matthews Correlation Coefficient NanoFolder: N/A Pknots: N/A Sensitivity NanoFolder: N/A Pknots: N/A Positive Predictive Value NanoFolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.378 NanoFolder: 0.076 Sensitivity Cylofold: 0.333 NanoFolder: 0.091 Positive Predictive Value Cylofold: 0.431 NanoFolder: 0.067 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: N/A MCFold: N/A Sensitivity NanoFolder: N/A MCFold: N/A Positive Predictive Value NanoFolder: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: N/A RDfolder: N/A Sensitivity NanoFolder: N/A RDfolder: N/A Positive Predictive Value NanoFolder: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? NanoFolder vs Alterna Matthews Correlation Coefficient NanoFolder: N/A Alterna: N/A Sensitivity NanoFolder: N/A Alterna: N/A Positive Predictive Value NanoFolder: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ NanoFolder vs Mastr(20) Matthews Correlation Coefficient NanoFolder: 0.150 Mastr(20): 0.000 Sensitivity NanoFolder: 0.173 Mastr(20): 0.000 Positive Predictive Value NanoFolder: 0.133 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(seed)	144 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.711 Carnac(seed): 0.151 Sensitivity PETfold_pre2.0(seed): 0.608 Carnac(seed): 0.028 Positive Predictive Value PETfold_pre2.0(seed): 0.832 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.719 Carnac(seed): 0.150 Sensitivity ContextFold: 0.697 Carnac(seed): 0.028 Positive Predictive Value ContextFold: 0.742 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.851 Carnac(seed): 0.000 Sensitivity TurboFold(20): 0.825 Carnac(seed): 0.000 Positive Predictive Value TurboFold(20): 0.878 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.67657656842e-08	145 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.708 Carnac(seed): 0.150 Sensitivity CentroidAlifold(seed): 0.578 Carnac(seed): 0.028 Positive Predictive Value CentroidAlifold(seed): 0.869 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.828 Carnac(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.767 Carnac(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.894 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.26497248087e-08	12 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.803 Carnac(seed): 0.000 Sensitivity PPfold(20): 0.725 Carnac(seed): 0.000 Positive Predictive Value PPfold(20): 0.890 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 1.80908287419e-08	132 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.669 Carnac(seed): 0.154 Sensitivity CentroidHomfold‑LAST: 0.550 Carnac(seed): 0.027 Positive Predictive Value CentroidHomfold‑LAST: 0.817 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.846 Carnac(seed): 0.000 Sensitivity CentroidAlifold(20): 0.773 Carnac(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.927 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.50834591464e-08	145 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.643 Carnac(seed): 0.150 Sensitivity MXScarna(seed): 0.553 Carnac(seed): 0.028 Positive Predictive Value MXScarna(seed): 0.749 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.625 Carnac(seed): 0.150 Sensitivity IPknot: 0.597 Carnac(seed): 0.028 Positive Predictive Value IPknot: 0.655 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.737 Carnac(seed): 0.000 Sensitivity RNAalifold(20): 0.627 Carnac(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.868 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	18 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 Carnac(seed): 0.435 Sensitivity TurboFold(seed): 0.760 Carnac(seed): 0.217 Positive Predictive Value TurboFold(seed): 0.815 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.94377603181e-08	7 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.725 Carnac(seed): 0.000 Sensitivity Multilign(20): 0.653 Carnac(seed): 0.000 Positive Predictive Value Multilign(20): 0.807 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 7 Wilcoxon single-rank test P-value: 0.0	13 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.802 Carnac(seed): 0.000 Sensitivity MXScarna(20): 0.779 Carnac(seed): 0.000 Positive Predictive Value MXScarna(20): 0.827 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	145 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.609 Carnac(seed): 0.150 Sensitivity CentroidFold: 0.579 Carnac(seed): 0.028 Positive Predictive Value CentroidFold: 0.642 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.599 Carnac(seed): 0.150 Sensitivity Contrafold: 0.601 Carnac(seed): 0.028 Positive Predictive Value Contrafold: 0.599 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 Carnac(seed): 0.373 Sensitivity PPfold(seed): 0.652 Carnac(seed): 0.160 Positive Predictive Value PPfold(seed): 0.787 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	145 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.613 Carnac(seed): 0.150 Sensitivity Sfold: 0.572 Carnac(seed): 0.028 Positive Predictive Value Sfold: 0.657 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.563 Carnac(seed): 0.150 Sensitivity MaxExpect: 0.562 Carnac(seed): 0.028 Positive Predictive Value MaxExpect: 0.565 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.561 Carnac(seed): 0.150 Sensitivity ProbKnot: 0.565 Carnac(seed): 0.028 Positive Predictive Value ProbKnot: 0.558 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.779 Carnac(seed): 0.659 Sensitivity RNASampler(seed): 0.659 Carnac(seed): 0.481 Positive Predictive Value RNASampler(seed): 0.921 Carnac(seed): 0.902 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.45805449719e-08	145 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.557 Carnac(seed): 0.150 Sensitivity Fold: 0.566 Carnac(seed): 0.028 Positive Predictive Value Fold: 0.549 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.506 Carnac(seed): 0.000 Sensitivity RNASampler(20): 0.297 Carnac(seed): 0.000 Positive Predictive Value RNASampler(20): 0.865 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	12 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.618 Carnac(seed): 0.000 Sensitivity Murlet(20): 0.496 Carnac(seed): 0.000 Positive Predictive Value Murlet(20): 0.771 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 9.84540901819e-09	145 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.576 Carnac(seed): 0.150 Sensitivity UNAFold: 0.576 Carnac(seed): 0.028 Positive Predictive Value UNAFold: 0.577 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.568 Carnac(seed): 0.150 Sensitivity PknotsRG: 0.574 Carnac(seed): 0.028 Positive Predictive Value PknotsRG: 0.563 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.569 Carnac(seed): 0.150 Sensitivity RNAfold: 0.574 Carnac(seed): 0.028 Positive Predictive Value RNAfold: 0.566 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 Multilign(seed) vs Carnac(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 Carnac(seed): 0.552 Sensitivity Multilign(seed): 0.752 Carnac(seed): 0.323 Positive Predictive Value Multilign(seed): 0.767 Carnac(seed): 0.945 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	124 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.556 Carnac(seed): 0.158 Sensitivity Afold: 0.561 Carnac(seed): 0.030 Positive Predictive Value Afold: 0.553 Carnac(seed): 0.840 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	132 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.556 Carnac(seed): 0.154 Sensitivity RNAsubopt: 0.567 Carnac(seed): 0.027 Positive Predictive Value RNAsubopt: 0.547 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 Carnac(seed): 0.150 Sensitivity RNAalifold(seed): 0.482 Carnac(seed): 0.028 Positive Predictive Value RNAalifold(seed): 0.896 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.456 Carnac(seed): 0.000 Sensitivity CMfinder(20): 0.322 Carnac(seed): 0.000 Positive Predictive Value CMfinder(20): 0.649 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.31583660336e-08	145 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.432 Carnac(seed): 0.150 Sensitivity McQFold: 0.425 Carnac(seed): 0.028 Positive Predictive Value McQFold: 0.440 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.487 Carnac(seed): 0.150 Sensitivity CRWrnafold: 0.493 Carnac(seed): 0.028 Positive Predictive Value CRWrnafold: 0.483 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.423 Carnac(seed): 0.167 Sensitivity RNASLOpt: 0.401 Carnac(seed): 0.032 Positive Predictive Value RNASLOpt: 0.448 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	118 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.522 Carnac(seed): 0.149 Sensitivity RNAshapes: 0.519 Carnac(seed): 0.025 Positive Predictive Value RNAshapes: 0.528 Carnac(seed): 0.875 Number of pairs reference - predicted secondary structure: 118 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.569 Carnac(seed): 0.351 Sensitivity Murlet(seed): 0.383 Carnac(seed): 0.145 Positive Predictive Value Murlet(seed): 0.845 Carnac(seed): 0.848 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.714 Carnac(seed): 0.000 Sensitivity RSpredict(20): 0.610 Carnac(seed): 0.000 Positive Predictive Value RSpredict(20): 0.836 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.59578924681e-08	13 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.444 Carnac(seed): 0.000 Sensitivity Carnac(20): 0.219 Carnac(seed): 0.000 Positive Predictive Value Carnac(20): 0.903 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.48055519165e-08	145 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.350 Carnac(seed): 0.150 Sensitivity RNAwolf: 0.364 Carnac(seed): 0.028 Positive Predictive Value RNAwolf: 0.337 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.454 Carnac(seed): 0.255 Sensitivity CMfinder(seed): 0.272 Carnac(seed): 0.074 Positive Predictive Value CMfinder(seed): 0.759 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.310 Carnac(seed): 0.150 Sensitivity RSpredict(seed): 0.163 Carnac(seed): 0.028 Positive Predictive Value RSpredict(seed): 0.593 Carnac(seed): 0.809 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	124 Vsfold4 vs Carnac(seed) Matthews Correlation Coefficient Vsfold4: 0.222 Carnac(seed): 0.160 Sensitivity Vsfold4: 0.205 Carnac(seed): 0.029 Positive Predictive Value Vsfold4: 0.243 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 124 Wilcoxon single-rank test P-value: 3.56938820447e-08	121 Vsfold5 vs Carnac(seed) Matthews Correlation Coefficient Vsfold5: 0.210 Carnac(seed): 0.163 Sensitivity Vsfold5: 0.201 Carnac(seed): 0.030 Positive Predictive Value Vsfold5: 0.221 Carnac(seed): 0.885 Number of pairs reference - predicted secondary structure: 121 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 NanoFolder vs Carnac(seed) Matthews Correlation Coefficient NanoFolder: 0.197 Carnac(seed): 0.094 Sensitivity NanoFolder: 0.233 Carnac(seed): 0.013 Positive Predictive Value NanoFolder: 0.170 Carnac(seed): 0.677 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 3.05041766982e-08		+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.150 Mastr(seed): 0.124 Sensitivity Carnac(seed): 0.028 Mastr(seed): 0.017 Positive Predictive Value Carnac(seed): 0.809 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	? HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.640 Carnac(seed): 0.132 Sensitivity HotKnots: 0.615 Carnac(seed): 0.077 Positive Predictive Value HotKnots: 0.667 Carnac(seed): 0.231 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: N/A Carnac(seed): N/A Sensitivity Pknots: N/A Carnac(seed): N/A Positive Predictive Value Pknots: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: N/A Carnac(seed): N/A Sensitivity Cylofold: N/A Carnac(seed): N/A Positive Predictive Value Cylofold: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Carnac(seed) vs MCFold Matthews Correlation Coefficient Carnac(seed): N/A MCFold: N/A Sensitivity Carnac(seed): N/A MCFold: N/A Positive Predictive Value Carnac(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: N/A Carnac(seed): N/A Sensitivity RDfolder: N/A Carnac(seed): N/A Positive Predictive Value RDfolder: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: N/A Carnac(seed): N/A Sensitivity Alterna: N/A Carnac(seed): N/A Positive Predictive Value Alterna: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	= Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0
Mastr(seed)	392 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.739 Mastr(seed): 0.074 Sensitivity PETfold_pre2.0(seed): 0.656 Mastr(seed): 0.006 Positive Predictive Value PETfold_pre2.0(seed): 0.834 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 392 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.796 Mastr(seed): 0.073 Sensitivity ContextFold: 0.761 Mastr(seed): 0.006 Positive Predictive Value ContextFold: 0.833 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	189 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.772 Mastr(seed): 0.000 Sensitivity TurboFold(20): 0.721 Mastr(seed): 0.000 Positive Predictive Value TurboFold(20): 0.828 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	399 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.712 Mastr(seed): 0.074 Sensitivity CentroidAlifold(seed): 0.560 Mastr(seed): 0.006 Positive Predictive Value CentroidAlifold(seed): 0.905 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 399 Wilcoxon single-rank test P-value: 3.56938820447e-08	186 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.759 Mastr(seed): 0.000 Sensitivity PETfold_pre2.0(20): 0.674 Mastr(seed): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.855 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 186 Wilcoxon single-rank test P-value: 3.56938820447e-08	183 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.750 Mastr(seed): 0.000 Sensitivity PPfold(20): 0.649 Mastr(seed): 0.000 Positive Predictive Value PPfold(20): 0.868 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 183 Wilcoxon single-rank test P-value: 3.56938820447e-08	394 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.687 Mastr(seed): 0.075 Sensitivity CentroidHomfold‑LAST: 0.543 Mastr(seed): 0.006 Positive Predictive Value CentroidHomfold‑LAST: 0.871 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 394 Wilcoxon single-rank test P-value: 3.56938820447e-08	189 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.736 Mastr(seed): 0.000 Sensitivity CentroidAlifold(20): 0.583 Mastr(seed): 0.000 Positive Predictive Value CentroidAlifold(20): 0.930 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	404 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.641 Mastr(seed): 0.073 Sensitivity MXScarna(seed): 0.541 Mastr(seed): 0.006 Positive Predictive Value MXScarna(seed): 0.760 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 404 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.653 Mastr(seed): 0.073 Sensitivity IPknot: 0.600 Mastr(seed): 0.006 Positive Predictive Value IPknot: 0.711 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	189 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.677 Mastr(seed): 0.000 Sensitivity RNAalifold(20): 0.545 Mastr(seed): 0.000 Positive Predictive Value RNAalifold(20): 0.843 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.787 Mastr(seed): 0.393 Sensitivity TurboFold(seed): 0.760 Mastr(seed): 0.173 Positive Predictive Value TurboFold(seed): 0.815 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 3.16042554876e-08	170 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.660 Mastr(seed): 0.000 Sensitivity Multilign(20): 0.597 Mastr(seed): 0.000 Positive Predictive Value Multilign(20): 0.732 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 170 Wilcoxon single-rank test P-value: 3.56938820447e-08	189 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.689 Mastr(seed): 0.000 Sensitivity MXScarna(20): 0.611 Mastr(seed): 0.000 Positive Predictive Value MXScarna(20): 0.779 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.632 Mastr(seed): 0.073 Sensitivity CentroidFold: 0.581 Mastr(seed): 0.006 Positive Predictive Value CentroidFold: 0.689 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.619 Mastr(seed): 0.073 Sensitivity Contrafold: 0.605 Mastr(seed): 0.006 Positive Predictive Value Contrafold: 0.635 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.716 Mastr(seed): 0.337 Sensitivity PPfold(seed): 0.652 Mastr(seed): 0.127 Positive Predictive Value PPfold(seed): 0.787 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	407 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.611 Mastr(seed): 0.073 Sensitivity Sfold: 0.559 Mastr(seed): 0.006 Positive Predictive Value Sfold: 0.670 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.597 Mastr(seed): 0.073 Sensitivity MaxExpect: 0.582 Mastr(seed): 0.006 Positive Predictive Value MaxExpect: 0.614 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.596 Mastr(seed): 0.073 Sensitivity ProbKnot: 0.586 Mastr(seed): 0.006 Positive Predictive Value ProbKnot: 0.607 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	12 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.779 Mastr(seed): 0.564 Sensitivity RNASampler(seed): 0.659 Mastr(seed): 0.356 Positive Predictive Value RNASampler(seed): 0.921 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 2.04409141234e-08	407 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.572 Mastr(seed): 0.073 Sensitivity Fold: 0.570 Mastr(seed): 0.006 Positive Predictive Value Fold: 0.576 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	41 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.578 Mastr(seed): 0.000 Sensitivity RNASampler(20): 0.384 Mastr(seed): 0.000 Positive Predictive Value RNASampler(20): 0.871 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 41 Wilcoxon single-rank test P-value: 3.56938820447e-08	127 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.575 Mastr(seed): 0.000 Sensitivity Murlet(20): 0.435 Mastr(seed): 0.000 Positive Predictive Value Murlet(20): 0.762 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 127 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.576 Mastr(seed): 0.073 Sensitivity UNAFold: 0.567 Mastr(seed): 0.006 Positive Predictive Value UNAFold: 0.586 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.559 Mastr(seed): 0.073 Sensitivity PknotsRG: 0.555 Mastr(seed): 0.006 Positive Predictive Value PknotsRG: 0.564 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.569 Mastr(seed): 0.073 Sensitivity RNAfold: 0.564 Mastr(seed): 0.006 Positive Predictive Value RNAfold: 0.575 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 Multilign(seed) vs Mastr(seed) Matthews Correlation Coefficient Multilign(seed): 0.759 Mastr(seed): 0.491 Sensitivity Multilign(seed): 0.752 Mastr(seed): 0.274 Positive Predictive Value Multilign(seed): 0.767 Mastr(seed): 0.879 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	333 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.558 Mastr(seed): 0.081 Sensitivity Afold: 0.552 Mastr(seed): 0.007 Positive Predictive Value Afold: 0.564 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 333 Wilcoxon single-rank test P-value: 3.56938820447e-08	394 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.561 Mastr(seed): 0.075 Sensitivity RNAsubopt: 0.564 Mastr(seed): 0.006 Positive Predictive Value RNAsubopt: 0.560 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 394 Wilcoxon single-rank test P-value: 3.56938820447e-08	400 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.550 Mastr(seed): 0.073 Sensitivity RNAalifold(seed): 0.354 Mastr(seed): 0.006 Positive Predictive Value RNAalifold(seed): 0.855 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 400 Wilcoxon single-rank test P-value: 3.56938820447e-08	189 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.497 Mastr(seed): 0.000 Sensitivity CMfinder(20): 0.329 Mastr(seed): 0.000 Positive Predictive Value CMfinder(20): 0.753 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.467 Mastr(seed): 0.073 Sensitivity McQFold: 0.451 Mastr(seed): 0.006 Positive Predictive Value McQFold: 0.484 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.482 Mastr(seed): 0.073 Sensitivity CRWrnafold: 0.479 Mastr(seed): 0.006 Positive Predictive Value CRWrnafold: 0.487 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	353 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.463 Mastr(seed): 0.080 Sensitivity RNASLOpt: 0.433 Mastr(seed): 0.007 Positive Predictive Value RNASLOpt: 0.497 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 353 Wilcoxon single-rank test P-value: 3.56938820447e-08	371 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.505 Mastr(seed): 0.067 Sensitivity RNAshapes: 0.495 Mastr(seed): 0.005 Positive Predictive Value RNAshapes: 0.518 Mastr(seed): 0.890 Number of pairs reference - predicted secondary structure: 371 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.569 Mastr(seed): 0.286 Sensitivity Murlet(seed): 0.383 Mastr(seed): 0.092 Positive Predictive Value Murlet(seed): 0.845 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	189 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.410 Mastr(seed): 0.000 Sensitivity RSpredict(20): 0.265 Mastr(seed): 0.000 Positive Predictive Value RSpredict(20): 0.636 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	189 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.364 Mastr(seed): 0.000 Sensitivity Carnac(20): 0.151 Mastr(seed): 0.000 Positive Predictive Value Carnac(20): 0.882 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.377 Mastr(seed): 0.073 Sensitivity RNAwolf: 0.387 Mastr(seed): 0.006 Positive Predictive Value RNAwolf: 0.368 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	51 CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.454 Mastr(seed): 0.215 Sensitivity CMfinder(seed): 0.271 Mastr(seed): 0.052 Positive Predictive Value CMfinder(seed): 0.762 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 51 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.224 Mastr(seed): 0.073 Sensitivity RSpredict(seed): 0.096 Mastr(seed): 0.006 Positive Predictive Value RSpredict(seed): 0.526 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	381 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.328 Mastr(seed): 0.076 Sensitivity Vsfold4: 0.298 Mastr(seed): 0.007 Positive Predictive Value Vsfold4: 0.363 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 381 Wilcoxon single-rank test P-value: 3.56938820447e-08	376 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.309 Mastr(seed): 0.077 Sensitivity Vsfold5: 0.289 Mastr(seed): 0.007 Positive Predictive Value Vsfold5: 0.332 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 376 Wilcoxon single-rank test P-value: 3.56938820447e-08	77 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.175 Mastr(seed): 0.000 Sensitivity NanoFolder: 0.203 Mastr(seed): 0.000 Positive Predictive Value NanoFolder: 0.155 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 77 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.150 Mastr(seed): 0.124 Sensitivity Carnac(seed): 0.028 Mastr(seed): 0.017 Positive Predictive Value Carnac(seed): 0.809 Mastr(seed): 0.895 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08		? HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.640 Mastr(seed): 0.000 Sensitivity HotKnots: 0.615 Mastr(seed): 0.000 Positive Predictive Value HotKnots: 0.667 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	? Mastr(seed) vs Pknots Matthews Correlation Coefficient Mastr(seed): N/A Pknots: N/A Sensitivity Mastr(seed): N/A Pknots: N/A Positive Predictive Value Mastr(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: N/A Mastr(seed): N/A Sensitivity Cylofold: N/A Mastr(seed): N/A Positive Predictive Value Cylofold: N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): N/A MCFold: N/A Sensitivity Mastr(seed): N/A MCFold: N/A Positive Predictive Value Mastr(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs RDfolder Matthews Correlation Coefficient Mastr(seed): N/A RDfolder: N/A Sensitivity Mastr(seed): N/A RDfolder: N/A Positive Predictive Value Mastr(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(seed) vs Alterna Matthews Correlation Coefficient Mastr(seed): N/A Alterna: N/A Sensitivity Mastr(seed): N/A Alterna: N/A Positive Predictive Value Mastr(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	+ Mastr(seed) vs Mastr(20) Matthews Correlation Coefficient Mastr(seed): 0.000 Mastr(20): 0.000 Sensitivity Mastr(seed): 0.000 Mastr(20): 0.000 Positive Predictive Value Mastr(seed): 0.000 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 1.14021447951e-07
HotKnots	1 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.891 HotKnots: 0.640 Sensitivity PETfold_pre2.0(seed): 0.795 HotKnots: 0.615 Positive Predictive Value PETfold_pre2.0(seed): 1.000 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs ContextFold Matthews Correlation Coefficient HotKnots: 0.640 ContextFold: 0.576 Sensitivity HotKnots: 0.615 ContextFold: 0.538 Positive Predictive Value HotKnots: 0.667 ContextFold: 0.618 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 HotKnots vs TurboFold(20) Matthews Correlation Coefficient HotKnots: N/A TurboFold(20): N/A Sensitivity HotKnots: N/A TurboFold(20): N/A Positive Predictive Value HotKnots: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.906 HotKnots: 0.640 Sensitivity CentroidAlifold(seed): 0.821 HotKnots: 0.615 Positive Predictive Value CentroidAlifold(seed): 1.000 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 HotKnots vs PETfold_pre2.0(20) Matthews Correlation Coefficient HotKnots: N/A PETfold_pre2.0(20): N/A Sensitivity HotKnots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value HotKnots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs PPfold(20) Matthews Correlation Coefficient HotKnots: N/A PPfold(20): N/A Sensitivity HotKnots: N/A PPfold(20): N/A Positive Predictive Value HotKnots: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 HotKnots vs CentroidHomfold‑LAST Matthews Correlation Coefficient HotKnots: 0.640 CentroidHomfold‑LAST: 0.232 Sensitivity HotKnots: 0.615 CentroidHomfold‑LAST: 0.154 Positive Predictive Value HotKnots: 0.667 CentroidHomfold‑LAST: 0.353 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 HotKnots vs CentroidAlifold(20) Matthews Correlation Coefficient HotKnots: N/A CentroidAlifold(20): N/A Sensitivity HotKnots: N/A CentroidAlifold(20): N/A Positive Predictive Value HotKnots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 HotKnots vs MXScarna(seed) Matthews Correlation Coefficient HotKnots: 0.640 MXScarna(seed): 0.203 Sensitivity HotKnots: 0.615 MXScarna(seed): 0.179 Positive Predictive Value HotKnots: 0.667 MXScarna(seed): 0.233 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs IPknot Matthews Correlation Coefficient HotKnots: 0.640 IPknot: 0.597 Sensitivity HotKnots: 0.615 IPknot: 0.590 Positive Predictive Value HotKnots: 0.667 IPknot: 0.605 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 HotKnots vs RNAalifold(20) Matthews Correlation Coefficient HotKnots: N/A RNAalifold(20): N/A Sensitivity HotKnots: N/A RNAalifold(20): N/A Positive Predictive Value HotKnots: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): N/A HotKnots: N/A Sensitivity TurboFold(seed): N/A HotKnots: N/A Positive Predictive Value TurboFold(seed): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Multilign(20) Matthews Correlation Coefficient HotKnots: N/A Multilign(20): N/A Sensitivity HotKnots: N/A Multilign(20): N/A Positive Predictive Value HotKnots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs MXScarna(20) Matthews Correlation Coefficient HotKnots: N/A MXScarna(20): N/A Sensitivity HotKnots: N/A MXScarna(20): N/A Positive Predictive Value HotKnots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.678 HotKnots: 0.640 Sensitivity CentroidFold: 0.564 HotKnots: 0.615 Positive Predictive Value CentroidFold: 0.815 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.707 HotKnots: 0.640 Sensitivity Contrafold: 0.641 HotKnots: 0.615 Positive Predictive Value Contrafold: 0.781 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: N/A PPfold(seed): N/A Sensitivity HotKnots: N/A PPfold(seed): N/A Positive Predictive Value HotKnots: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 HotKnots vs Sfold Matthews Correlation Coefficient HotKnots: 0.640 Sfold: 0.555 Sensitivity HotKnots: 0.615 Sfold: 0.487 Positive Predictive Value HotKnots: 0.667 Sfold: 0.633 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs MaxExpect Matthews Correlation Coefficient HotKnots: 0.640 MaxExpect: 0.438 Sensitivity HotKnots: 0.615 MaxExpect: 0.487 Positive Predictive Value HotKnots: 0.667 MaxExpect: 0.396 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs ProbKnot Matthews Correlation Coefficient HotKnots: 0.640 ProbKnot: 0.429 Sensitivity HotKnots: 0.615 ProbKnot: 0.487 Positive Predictive Value HotKnots: 0.667 ProbKnot: 0.380 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs RNASampler(seed) Matthews Correlation Coefficient HotKnots: 0.640 RNASampler(seed): 0.523 Sensitivity HotKnots: 0.615 RNASampler(seed): 0.436 Positive Predictive Value HotKnots: 0.667 RNASampler(seed): 0.630 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs Fold Matthews Correlation Coefficient HotKnots: 0.640 Fold: 0.468 Sensitivity HotKnots: 0.615 Fold: 0.487 Positive Predictive Value HotKnots: 0.667 Fold: 0.452 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): N/A HotKnots: N/A Sensitivity RNASampler(20): N/A HotKnots: N/A Positive Predictive Value RNASampler(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Murlet(20) Matthews Correlation Coefficient HotKnots: N/A Murlet(20): N/A Sensitivity HotKnots: N/A Murlet(20): N/A Positive Predictive Value HotKnots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.667 HotKnots: 0.640 Sensitivity UNAFold: 0.641 HotKnots: 0.615 Positive Predictive Value UNAFold: 0.694 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs PknotsRG Matthews Correlation Coefficient HotKnots: 0.640 PknotsRG: 0.631 Sensitivity HotKnots: 0.615 PknotsRG: 0.615 Positive Predictive Value HotKnots: 0.667 PknotsRG: 0.649 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.640 RNAfold: 0.640 Sensitivity HotKnots: 0.615 RNAfold: 0.615 Positive Predictive Value HotKnots: 0.667 RNAfold: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: N/A Multilign(seed): N/A Sensitivity HotKnots: N/A Multilign(seed): N/A Positive Predictive Value HotKnots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.640 Afold: 0.640 Sensitivity HotKnots: 0.615 Afold: 0.615 Positive Predictive Value HotKnots: 0.667 Afold: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs RNAsubopt Matthews Correlation Coefficient HotKnots: 0.640 RNAsubopt: 0.461 Sensitivity HotKnots: 0.615 RNAsubopt: 0.462 Positive Predictive Value HotKnots: 0.667 RNAsubopt: 0.462 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 RNAalifold(seed) vs HotKnots Matthews Correlation Coefficient RNAalifold(seed): 0.877 HotKnots: 0.640 Sensitivity RNAalifold(seed): 0.769 HotKnots: 0.615 Positive Predictive Value RNAalifold(seed): 1.000 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	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	1 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.640 McQFold: 0.361 Sensitivity HotKnots: 0.615 McQFold: 0.385 Positive Predictive Value HotKnots: 0.667 McQFold: 0.341 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs CRWrnafold Matthews Correlation Coefficient HotKnots: 0.640 CRWrnafold: 0.548 Sensitivity HotKnots: 0.615 CRWrnafold: 0.590 Positive Predictive Value HotKnots: 0.667 CRWrnafold: 0.511 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 RNASLOpt vs HotKnots Matthews Correlation Coefficient RNASLOpt: 0.658 HotKnots: 0.640 Sensitivity RNASLOpt: 0.641 HotKnots: 0.615 Positive Predictive Value RNASLOpt: 0.676 HotKnots: 0.667 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs RNAshapes Matthews Correlation Coefficient HotKnots: 0.640 RNAshapes: 0.439 Sensitivity HotKnots: 0.615 RNAshapes: 0.462 Positive Predictive Value HotKnots: 0.667 RNAshapes: 0.419 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.640 Murlet(seed): 0.000 Sensitivity HotKnots: 0.615 Murlet(seed): 0.000 Positive Predictive Value HotKnots: 0.667 Murlet(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): N/A HotKnots: N/A Sensitivity RSpredict(20): N/A HotKnots: N/A Positive Predictive Value RSpredict(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: N/A Carnac(20): N/A Sensitivity HotKnots: N/A Carnac(20): N/A Positive Predictive Value HotKnots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	1 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.640 RNAwolf: 0.209 Sensitivity HotKnots: 0.615 RNAwolf: 0.231 Positive Predictive Value HotKnots: 0.667 RNAwolf: 0.191 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs CMfinder(seed) Matthews Correlation Coefficient HotKnots: 0.640 CMfinder(seed): -0.001 Sensitivity HotKnots: 0.615 CMfinder(seed): 0.000 Positive Predictive Value HotKnots: 0.667 CMfinder(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.640 RSpredict(seed): -0.001 Sensitivity HotKnots: 0.615 RSpredict(seed): 0.000 Positive Predictive Value HotKnots: 0.667 RSpredict(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.640 Vsfold4: 0.221 Sensitivity HotKnots: 0.615 Vsfold4: 0.231 Positive Predictive Value HotKnots: 0.667 Vsfold4: 0.214 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.640 Vsfold5: 0.232 Sensitivity HotKnots: 0.615 Vsfold5: 0.231 Positive Predictive Value HotKnots: 0.667 Vsfold5: 0.237 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.640 NanoFolder: 0.158 Sensitivity HotKnots: 0.615 NanoFolder: 0.231 Positive Predictive Value HotKnots: 0.667 NanoFolder: 0.111 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.640 Carnac(seed): 0.132 Sensitivity HotKnots: 0.615 Carnac(seed): 0.077 Positive Predictive Value HotKnots: 0.667 Carnac(seed): 0.231 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	1 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.640 Mastr(seed): 0.000 Sensitivity HotKnots: 0.615 Mastr(seed): 0.000 Positive Predictive Value HotKnots: 0.667 Mastr(seed): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0		? HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: N/A Pknots: N/A Sensitivity HotKnots: N/A Pknots: N/A Positive Predictive Value HotKnots: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: N/A HotKnots: N/A Sensitivity Cylofold: N/A HotKnots: N/A Positive Predictive Value Cylofold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: N/A MCFold: N/A Sensitivity HotKnots: N/A MCFold: N/A Positive Predictive Value HotKnots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: N/A RDfolder: N/A Sensitivity HotKnots: N/A RDfolder: N/A Positive Predictive Value HotKnots: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: N/A Alterna: N/A Sensitivity HotKnots: N/A Alterna: N/A Positive Predictive Value HotKnots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): N/A HotKnots: N/A Sensitivity Mastr(20): N/A HotKnots: N/A Positive Predictive Value Mastr(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Pknots	0 Pknots vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(seed): N/A Sensitivity Pknots: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: N/A Pknots: N/A Sensitivity ContextFold: N/A Pknots: N/A Positive Predictive Value ContextFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): N/A Pknots: N/A Sensitivity TurboFold(20): N/A Pknots: N/A Positive Predictive Value TurboFold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): N/A Pknots: N/A Sensitivity CentroidAlifold(seed): N/A Pknots: N/A Positive Predictive Value CentroidAlifold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs PETfold_pre2.0(20) Matthews Correlation Coefficient Pknots: N/A PETfold_pre2.0(20): N/A Sensitivity Pknots: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Pknots: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): N/A Pknots: N/A Sensitivity PPfold(20): N/A Pknots: N/A Positive Predictive Value PPfold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CentroidHomfold‑LAST Matthews Correlation Coefficient Pknots: N/A CentroidHomfold‑LAST: N/A Sensitivity Pknots: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Pknots: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CentroidAlifold(20) Matthews Correlation Coefficient Pknots: N/A CentroidAlifold(20): N/A Sensitivity Pknots: N/A CentroidAlifold(20): N/A Positive Predictive Value Pknots: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs MXScarna(seed) Matthews Correlation Coefficient Pknots: N/A MXScarna(seed): N/A Sensitivity Pknots: N/A MXScarna(seed): N/A Positive Predictive Value Pknots: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs IPknot Matthews Correlation Coefficient Pknots: N/A IPknot: N/A Sensitivity Pknots: N/A IPknot: N/A Positive Predictive Value Pknots: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): N/A Pknots: N/A Sensitivity RNAalifold(20): N/A Pknots: N/A Positive Predictive Value RNAalifold(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): N/A Pknots: N/A Sensitivity TurboFold(seed): N/A Pknots: N/A Positive Predictive Value TurboFold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Multilign(20) Matthews Correlation Coefficient Pknots: N/A Multilign(20): N/A Sensitivity Pknots: N/A Multilign(20): N/A Positive Predictive Value Pknots: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs MXScarna(20) Matthews Correlation Coefficient Pknots: N/A MXScarna(20): N/A Sensitivity Pknots: N/A MXScarna(20): N/A Positive Predictive Value Pknots: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CentroidFold Matthews Correlation Coefficient Pknots: N/A CentroidFold: N/A Sensitivity Pknots: N/A CentroidFold: N/A Positive Predictive Value Pknots: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Contrafold Matthews Correlation Coefficient Pknots: N/A Contrafold: N/A Sensitivity Pknots: N/A Contrafold: N/A Positive Predictive Value Pknots: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Pknots Matthews Correlation Coefficient PPfold(seed): N/A Pknots: N/A Sensitivity PPfold(seed): N/A Pknots: N/A Positive Predictive Value PPfold(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Sfold Matthews Correlation Coefficient Pknots: N/A Sfold: N/A Sensitivity Pknots: N/A Sfold: N/A Positive Predictive Value Pknots: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: N/A Pknots: N/A Sensitivity MaxExpect: N/A Pknots: N/A Positive Predictive Value MaxExpect: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: N/A Pknots: N/A Sensitivity ProbKnot: N/A Pknots: N/A Positive Predictive Value ProbKnot: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): N/A Pknots: N/A Sensitivity RNASampler(seed): N/A Pknots: N/A Positive Predictive Value RNASampler(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs Pknots Matthews Correlation Coefficient Fold: N/A Pknots: N/A Sensitivity Fold: N/A Pknots: N/A Positive Predictive Value Fold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): N/A Pknots: N/A Sensitivity RNASampler(20): N/A Pknots: N/A Positive Predictive Value RNASampler(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Murlet(20) Matthews Correlation Coefficient Pknots: N/A Murlet(20): N/A Sensitivity Pknots: N/A Murlet(20): N/A Positive Predictive Value Pknots: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs Pknots Matthews Correlation Coefficient UNAFold: N/A Pknots: N/A Sensitivity UNAFold: N/A Pknots: N/A Positive Predictive Value UNAFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs Pknots Matthews Correlation Coefficient PknotsRG: N/A Pknots: N/A Sensitivity PknotsRG: N/A Pknots: N/A Positive Predictive Value PknotsRG: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAfold Matthews Correlation Coefficient Pknots: N/A RNAfold: N/A Sensitivity Pknots: N/A RNAfold: N/A Positive Predictive Value Pknots: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: N/A Multilign(seed): N/A Sensitivity Pknots: N/A Multilign(seed): N/A Positive Predictive Value Pknots: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Afold Matthews Correlation Coefficient Pknots: N/A Afold: N/A Sensitivity Pknots: N/A Afold: N/A Positive Predictive Value Pknots: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAsubopt Matthews Correlation Coefficient Pknots: N/A RNAsubopt: N/A Sensitivity Pknots: N/A RNAsubopt: N/A Positive Predictive Value Pknots: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAalifold(seed) Matthews Correlation Coefficient Pknots: N/A RNAalifold(seed): N/A Sensitivity Pknots: N/A RNAalifold(seed): N/A Positive Predictive Value Pknots: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs 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 McQFold vs Pknots Matthews Correlation Coefficient McQFold: N/A Pknots: N/A Sensitivity McQFold: N/A Pknots: N/A Positive Predictive Value McQFold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs CRWrnafold Matthews Correlation Coefficient Pknots: N/A CRWrnafold: N/A Sensitivity Pknots: N/A CRWrnafold: N/A Positive Predictive Value Pknots: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNASLOpt Matthews Correlation Coefficient Pknots: N/A RNASLOpt: N/A Sensitivity Pknots: N/A RNASLOpt: N/A Positive Predictive Value Pknots: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: N/A RNAshapes: N/A Sensitivity Pknots: N/A RNAshapes: N/A Positive Predictive Value Pknots: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Murlet(seed) Matthews Correlation Coefficient Pknots: N/A Murlet(seed): N/A Sensitivity Pknots: N/A Murlet(seed): N/A Positive Predictive Value Pknots: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): N/A Pknots: N/A Sensitivity RSpredict(20): N/A Pknots: N/A Positive Predictive Value RSpredict(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Carnac(20) Matthews Correlation Coefficient Pknots: N/A Carnac(20): N/A Sensitivity Pknots: N/A Carnac(20): N/A Positive Predictive Value Pknots: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: N/A RNAwolf: N/A Sensitivity Pknots: N/A RNAwolf: N/A Positive Predictive Value Pknots: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 RSpredict(seed) vs Pknots Matthews Correlation Coefficient RSpredict(seed): N/A Pknots: N/A Sensitivity RSpredict(seed): N/A Pknots: N/A Positive Predictive Value RSpredict(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: N/A Vsfold4: N/A Sensitivity Pknots: N/A Vsfold4: N/A Positive Predictive Value Pknots: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs Pknots Matthews Correlation Coefficient Vsfold5: N/A Pknots: N/A Sensitivity Vsfold5: N/A Pknots: N/A Positive Predictive Value Vsfold5: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs Pknots Matthews Correlation Coefficient NanoFolder: N/A Pknots: N/A Sensitivity NanoFolder: N/A Pknots: N/A Positive Predictive Value NanoFolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Carnac(seed) Matthews Correlation Coefficient Pknots: N/A Carnac(seed): N/A Sensitivity Pknots: N/A Carnac(seed): N/A Positive Predictive Value Pknots: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs Pknots Matthews Correlation Coefficient Mastr(seed): N/A Pknots: N/A Sensitivity Mastr(seed): N/A Pknots: N/A Positive Predictive Value Mastr(seed): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Pknots Matthews Correlation Coefficient HotKnots: N/A Pknots: N/A Sensitivity HotKnots: N/A Pknots: N/A Positive Predictive Value HotKnots: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: N/A Pknots: N/A Sensitivity Cylofold: N/A Pknots: N/A Positive Predictive Value Cylofold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs MCFold Matthews Correlation Coefficient Pknots: N/A MCFold: N/A Sensitivity Pknots: N/A MCFold: N/A Positive Predictive Value Pknots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? RDfolder vs Pknots Matthews Correlation Coefficient RDfolder: N/A Pknots: N/A Sensitivity RDfolder: N/A Pknots: N/A Positive Predictive Value RDfolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Pknots vs Alterna Matthews Correlation Coefficient Pknots: N/A Alterna: N/A Sensitivity Pknots: N/A Alterna: N/A Positive Predictive Value Pknots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): N/A Pknots: N/A Sensitivity Mastr(20): N/A Pknots: N/A Positive Predictive Value Mastr(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Cylofold	0 Cylofold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(seed): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Cylofold: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.944 Cylofold: 0.271 Sensitivity ContextFold: 0.905 Cylofold: 0.241 Positive Predictive Value ContextFold: 0.984 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs TurboFold(20) Matthews Correlation Coefficient Cylofold: N/A TurboFold(20): N/A Sensitivity Cylofold: N/A TurboFold(20): N/A Positive Predictive Value Cylofold: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): N/A Cylofold: N/A Sensitivity CentroidAlifold(seed): N/A Cylofold: N/A Positive Predictive Value CentroidAlifold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs PETfold_pre2.0(20) Matthews Correlation Coefficient Cylofold: N/A PETfold_pre2.0(20): N/A Sensitivity Cylofold: N/A PETfold_pre2.0(20): N/A Positive Predictive Value Cylofold: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs PPfold(20) Matthews Correlation Coefficient Cylofold: N/A PPfold(20): N/A Sensitivity Cylofold: N/A PPfold(20): N/A Positive Predictive Value Cylofold: N/A PPfold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.703 Cylofold: 0.271 Sensitivity CentroidHomfold‑LAST: 0.613 Cylofold: 0.241 Positive Predictive Value CentroidHomfold‑LAST: 0.808 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs CentroidAlifold(20) Matthews Correlation Coefficient Cylofold: N/A CentroidAlifold(20): N/A Sensitivity Cylofold: N/A CentroidAlifold(20): N/A Positive Predictive Value Cylofold: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs MXScarna(seed) Matthews Correlation Coefficient Cylofold: N/A MXScarna(seed): N/A Sensitivity Cylofold: N/A MXScarna(seed): N/A Positive Predictive Value Cylofold: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.648 Cylofold: 0.271 Sensitivity IPknot: 0.584 Cylofold: 0.241 Positive Predictive Value IPknot: 0.721 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs RNAalifold(20) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(20): N/A Sensitivity Cylofold: N/A RNAalifold(20): N/A Positive Predictive Value Cylofold: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): N/A Cylofold: N/A Sensitivity TurboFold(seed): N/A Cylofold: N/A Positive Predictive Value TurboFold(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Multilign(20) Matthews Correlation Coefficient Cylofold: N/A Multilign(20): N/A Sensitivity Cylofold: N/A Multilign(20): N/A Positive Predictive Value Cylofold: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs MXScarna(20) Matthews Correlation Coefficient Cylofold: N/A MXScarna(20): N/A Sensitivity Cylofold: N/A MXScarna(20): N/A Positive Predictive Value Cylofold: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.626 Cylofold: 0.271 Sensitivity CentroidFold: 0.584 Cylofold: 0.241 Positive Predictive Value CentroidFold: 0.672 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.616 Cylofold: 0.271 Sensitivity Contrafold: 0.591 Cylofold: 0.241 Positive Predictive Value Contrafold: 0.643 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: N/A PPfold(seed): N/A Sensitivity Cylofold: N/A PPfold(seed): N/A Positive Predictive Value Cylofold: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.657 Cylofold: 0.271 Sensitivity Sfold: 0.562 Cylofold: 0.241 Positive Predictive Value Sfold: 0.770 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.631 Cylofold: 0.271 Sensitivity MaxExpect: 0.620 Cylofold: 0.241 Positive Predictive Value MaxExpect: 0.644 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.634 Cylofold: 0.271 Sensitivity ProbKnot: 0.620 Cylofold: 0.241 Positive Predictive Value ProbKnot: 0.649 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): N/A Cylofold: N/A Sensitivity RNASampler(seed): N/A Cylofold: N/A Positive Predictive Value RNASampler(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.597 Cylofold: 0.271 Sensitivity Fold: 0.591 Cylofold: 0.241 Positive Predictive Value Fold: 0.604 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): N/A Cylofold: N/A Sensitivity RNASampler(20): N/A Cylofold: N/A Positive Predictive Value RNASampler(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Murlet(20) Matthews Correlation Coefficient Cylofold: N/A Murlet(20): N/A Sensitivity Cylofold: N/A Murlet(20): N/A Positive Predictive Value Cylofold: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.443 Cylofold: 0.271 Sensitivity UNAFold: 0.431 Cylofold: 0.241 Positive Predictive Value UNAFold: 0.457 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.437 Cylofold: 0.271 Sensitivity PknotsRG: 0.438 Cylofold: 0.241 Positive Predictive Value PknotsRG: 0.438 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.446 Cylofold: 0.271 Sensitivity RNAfold: 0.431 Cylofold: 0.241 Positive Predictive Value RNAfold: 0.465 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: N/A Multilign(seed): N/A Sensitivity Cylofold: N/A Multilign(seed): N/A Positive Predictive Value Cylofold: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.460 Cylofold: 0.271 Sensitivity Afold: 0.460 Cylofold: 0.241 Positive Predictive Value Afold: 0.463 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.437 Cylofold: 0.271 Sensitivity RNAsubopt: 0.431 Cylofold: 0.241 Positive Predictive Value RNAsubopt: 0.447 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs RNAalifold(seed) Matthews Correlation Coefficient Cylofold: N/A RNAalifold(seed): N/A Sensitivity Cylofold: N/A RNAalifold(seed): N/A Positive Predictive Value Cylofold: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs CMfinder(20) Matthews Correlation Coefficient Cylofold: N/A CMfinder(20): N/A Sensitivity Cylofold: N/A CMfinder(20): N/A Positive Predictive Value Cylofold: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.526 Cylofold: 0.271 Sensitivity McQFold: 0.489 Cylofold: 0.241 Positive Predictive Value McQFold: 0.568 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.470 Cylofold: 0.271 Sensitivity CRWrnafold: 0.474 Cylofold: 0.241 Positive Predictive Value CRWrnafold: 0.468 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.382 Cylofold: 0.271 Sensitivity RNASLOpt: 0.358 Cylofold: 0.241 Positive Predictive Value RNASLOpt: 0.412 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.455 Cylofold: 0.271 Sensitivity RNAshapes: 0.453 Cylofold: 0.241 Positive Predictive Value RNAshapes: 0.459 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: N/A Murlet(seed): N/A Sensitivity Cylofold: N/A Murlet(seed): N/A Positive Predictive Value Cylofold: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): N/A Cylofold: N/A Sensitivity RSpredict(20): N/A Cylofold: N/A Positive Predictive Value RSpredict(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Carnac(20) Matthews Correlation Coefficient Cylofold: N/A Carnac(20): N/A Sensitivity Cylofold: N/A Carnac(20): N/A Positive Predictive Value Cylofold: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 RNAwolf vs Cylofold Matthews Correlation Coefficient RNAwolf: 0.339 Cylofold: 0.271 Sensitivity RNAwolf: 0.350 Cylofold: 0.241 Positive Predictive Value RNAwolf: 0.331 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	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 RSpredict(seed) vs Cylofold Matthews Correlation Coefficient RSpredict(seed): N/A Cylofold: N/A Sensitivity RSpredict(seed): N/A Cylofold: N/A Positive Predictive Value RSpredict(seed): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	2 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.271 Vsfold4: 0.267 Sensitivity Cylofold: 0.241 Vsfold4: 0.241 Positive Predictive Value Cylofold: 0.308 Vsfold4: 0.300 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	2 Vsfold5 vs Cylofold Matthews Correlation Coefficient Vsfold5: 0.357 Cylofold: 0.271 Sensitivity Vsfold5: 0.336 Cylofold: 0.241 Positive Predictive Value Vsfold5: 0.383 Cylofold: 0.308 Number of pairs reference - predicted secondary structure: 2 Wilcoxon single-rank test P-value: 0.0	1 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.378 NanoFolder: 0.076 Sensitivity Cylofold: 0.333 NanoFolder: 0.091 Positive Predictive Value Cylofold: 0.431 NanoFolder: 0.067 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	0 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: N/A Carnac(seed): N/A Sensitivity Cylofold: N/A Carnac(seed): N/A Positive Predictive Value Cylofold: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: N/A Mastr(seed): N/A Sensitivity Cylofold: N/A Mastr(seed): N/A Positive Predictive Value Cylofold: N/A Mastr(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs HotKnots Matthews Correlation Coefficient Cylofold: N/A HotKnots: N/A Sensitivity Cylofold: N/A HotKnots: N/A Positive Predictive Value Cylofold: N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: N/A Pknots: N/A Sensitivity Cylofold: N/A Pknots: N/A Positive Predictive Value Cylofold: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: N/A MCFold: N/A Sensitivity Cylofold: N/A MCFold: N/A Positive Predictive Value Cylofold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: N/A RDfolder: N/A Sensitivity Cylofold: N/A RDfolder: N/A Positive Predictive Value Cylofold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: N/A Alterna: N/A Sensitivity Cylofold: N/A Alterna: N/A Positive Predictive Value Cylofold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): N/A Cylofold: N/A Sensitivity Mastr(20): N/A Cylofold: N/A Positive Predictive Value Mastr(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
MCFold	0 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): N/A MCFold: N/A Sensitivity PETfold_pre2.0(seed): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: N/A MCFold: N/A Sensitivity ContextFold: N/A MCFold: N/A Positive Predictive Value ContextFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): N/A MCFold: N/A Sensitivity TurboFold(20): N/A MCFold: N/A Positive Predictive Value TurboFold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): N/A MCFold: N/A Sensitivity CentroidAlifold(seed): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): N/A MCFold: N/A Sensitivity PETfold_pre2.0(20): N/A MCFold: N/A Positive Predictive Value PETfold_pre2.0(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): N/A MCFold: N/A Sensitivity PPfold(20): N/A MCFold: N/A Positive Predictive Value PPfold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: N/A MCFold: N/A Sensitivity CentroidHomfold‑LAST: N/A MCFold: N/A Positive Predictive Value CentroidHomfold‑LAST: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): N/A MCFold: N/A Sensitivity CentroidAlifold(20): N/A MCFold: N/A Positive Predictive Value CentroidAlifold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): N/A MCFold: N/A Sensitivity MXScarna(seed): N/A MCFold: N/A Positive Predictive Value MXScarna(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MCFold vs IPknot Matthews Correlation Coefficient MCFold: N/A IPknot: N/A Sensitivity MCFold: N/A IPknot: N/A Positive Predictive Value MCFold: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): N/A MCFold: N/A Sensitivity RNAalifold(20): N/A MCFold: N/A Positive Predictive Value RNAalifold(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): N/A MCFold: N/A Sensitivity TurboFold(seed): N/A MCFold: N/A Positive Predictive Value TurboFold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): N/A MCFold: N/A Sensitivity Multilign(20): N/A MCFold: N/A Positive Predictive Value Multilign(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): N/A MCFold: N/A Sensitivity MXScarna(20): N/A MCFold: N/A Positive Predictive Value MXScarna(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: N/A MCFold: N/A Sensitivity CentroidFold: N/A MCFold: N/A Positive Predictive Value CentroidFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: N/A MCFold: N/A Sensitivity Contrafold: N/A MCFold: N/A Positive Predictive Value Contrafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs MCFold Matthews Correlation Coefficient PPfold(seed): N/A MCFold: N/A Sensitivity PPfold(seed): N/A MCFold: N/A Positive Predictive Value PPfold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Sfold vs MCFold Matthews Correlation Coefficient Sfold: N/A MCFold: N/A Sensitivity Sfold: N/A MCFold: N/A Positive Predictive Value Sfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: N/A MCFold: N/A Sensitivity MaxExpect: N/A MCFold: N/A Positive Predictive Value MaxExpect: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: N/A MCFold: N/A Sensitivity ProbKnot: N/A MCFold: N/A Positive Predictive Value ProbKnot: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): N/A MCFold: N/A Sensitivity RNASampler(seed): N/A MCFold: N/A Positive Predictive Value RNASampler(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs MCFold Matthews Correlation Coefficient Fold: N/A MCFold: N/A Sensitivity Fold: N/A MCFold: N/A Positive Predictive Value Fold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): N/A MCFold: N/A Sensitivity RNASampler(20): N/A MCFold: N/A Positive Predictive Value RNASampler(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): N/A MCFold: N/A Sensitivity Murlet(20): N/A MCFold: N/A Positive Predictive Value Murlet(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: N/A MCFold: N/A Sensitivity UNAFold: N/A MCFold: N/A Positive Predictive Value UNAFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: N/A MCFold: N/A Sensitivity PknotsRG: N/A MCFold: N/A Positive Predictive Value PknotsRG: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: N/A MCFold: N/A Sensitivity RNAfold: N/A MCFold: N/A Positive Predictive Value RNAfold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): N/A MCFold: N/A Sensitivity Multilign(seed): N/A MCFold: N/A Positive Predictive Value Multilign(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Afold vs MCFold Matthews Correlation Coefficient Afold: N/A MCFold: N/A Sensitivity Afold: N/A MCFold: N/A Positive Predictive Value Afold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: N/A MCFold: N/A Sensitivity RNAsubopt: N/A MCFold: N/A Positive Predictive Value RNAsubopt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): N/A MCFold: N/A Sensitivity RNAalifold(seed): N/A MCFold: N/A Positive Predictive Value RNAalifold(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 McQFold vs MCFold Matthews Correlation Coefficient McQFold: N/A MCFold: N/A Sensitivity McQFold: N/A MCFold: N/A Positive Predictive Value McQFold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: N/A MCFold: N/A Sensitivity CRWrnafold: N/A MCFold: N/A Positive Predictive Value CRWrnafold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: N/A MCFold: N/A Sensitivity RNASLOpt: N/A MCFold: N/A Positive Predictive Value RNASLOpt: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: N/A MCFold: N/A Sensitivity RNAshapes: N/A MCFold: N/A Positive Predictive Value RNAshapes: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): N/A MCFold: N/A Sensitivity Murlet(seed): N/A MCFold: N/A Positive Predictive Value Murlet(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): N/A MCFold: N/A Sensitivity RSpredict(20): N/A MCFold: N/A Positive Predictive Value RSpredict(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): N/A MCFold: N/A Sensitivity Carnac(20): N/A MCFold: N/A Positive Predictive Value Carnac(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: N/A MCFold: N/A Sensitivity RNAwolf: N/A MCFold: N/A Positive Predictive Value RNAwolf: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): N/A MCFold: N/A Sensitivity CMfinder(seed): N/A MCFold: N/A Positive Predictive Value CMfinder(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(seed) vs MCFold Matthews Correlation Coefficient RSpredict(seed): N/A MCFold: N/A Sensitivity RSpredict(seed): N/A MCFold: N/A Positive Predictive Value RSpredict(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: N/A MCFold: N/A Sensitivity Vsfold4: N/A MCFold: N/A Positive Predictive Value Vsfold4: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: N/A MCFold: N/A Sensitivity Vsfold5: N/A MCFold: N/A Positive Predictive Value Vsfold5: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs MCFold Matthews Correlation Coefficient NanoFolder: N/A MCFold: N/A Sensitivity NanoFolder: N/A MCFold: N/A Positive Predictive Value NanoFolder: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Carnac(seed) vs MCFold Matthews Correlation Coefficient Carnac(seed): N/A MCFold: N/A Sensitivity Carnac(seed): N/A MCFold: N/A Positive Predictive Value Carnac(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs MCFold Matthews Correlation Coefficient Mastr(seed): N/A MCFold: N/A Sensitivity Mastr(seed): N/A MCFold: N/A Positive Predictive Value Mastr(seed): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: N/A MCFold: N/A Sensitivity HotKnots: N/A MCFold: N/A Positive Predictive Value HotKnots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs MCFold Matthews Correlation Coefficient Pknots: N/A MCFold: N/A Sensitivity Pknots: N/A MCFold: N/A Positive Predictive Value Pknots: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: N/A MCFold: N/A Sensitivity Cylofold: N/A MCFold: N/A Positive Predictive Value Cylofold: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: N/A MCFold: N/A Sensitivity RDfolder: N/A MCFold: N/A Positive Predictive Value RDfolder: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Alterna vs MCFold Matthews Correlation Coefficient Alterna: N/A MCFold: N/A Sensitivity Alterna: N/A MCFold: N/A Positive Predictive Value Alterna: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): N/A MCFold: N/A Sensitivity Mastr(20): N/A MCFold: N/A Positive Predictive Value Mastr(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
RDfolder	0 RDfolder vs PETfold_pre2.0(seed) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(seed): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value RDfolder: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs ContextFold Matthews Correlation Coefficient RDfolder: N/A ContextFold: N/A Sensitivity RDfolder: N/A ContextFold: N/A Positive Predictive Value RDfolder: N/A ContextFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs TurboFold(20) Matthews Correlation Coefficient RDfolder: N/A TurboFold(20): N/A Sensitivity RDfolder: N/A TurboFold(20): N/A Positive Predictive Value RDfolder: N/A TurboFold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): N/A RDfolder: N/A Sensitivity CentroidAlifold(seed): N/A RDfolder: N/A Positive Predictive Value CentroidAlifold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PETfold_pre2.0(20) Matthews Correlation Coefficient RDfolder: N/A PETfold_pre2.0(20): N/A Sensitivity RDfolder: N/A PETfold_pre2.0(20): N/A Positive Predictive Value RDfolder: N/A PETfold_pre2.0(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): N/A RDfolder: N/A Sensitivity PPfold(20): N/A RDfolder: N/A Positive Predictive Value PPfold(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CentroidHomfold‑LAST Matthews Correlation Coefficient RDfolder: N/A CentroidHomfold‑LAST: N/A Sensitivity RDfolder: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value RDfolder: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CentroidAlifold(20) Matthews Correlation Coefficient RDfolder: N/A CentroidAlifold(20): N/A Sensitivity RDfolder: N/A CentroidAlifold(20): N/A Positive Predictive Value RDfolder: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs MXScarna(seed) Matthews Correlation Coefficient RDfolder: N/A MXScarna(seed): N/A Sensitivity RDfolder: N/A MXScarna(seed): N/A Positive Predictive Value RDfolder: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs IPknot Matthews Correlation Coefficient RDfolder: N/A IPknot: N/A Sensitivity RDfolder: N/A IPknot: N/A Positive Predictive Value RDfolder: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAalifold(20) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(20): N/A Sensitivity RDfolder: N/A RNAalifold(20): N/A Positive Predictive Value RDfolder: N/A RNAalifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): N/A RDfolder: N/A Sensitivity TurboFold(seed): N/A RDfolder: N/A Positive Predictive Value TurboFold(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Multilign(20) Matthews Correlation Coefficient RDfolder: N/A Multilign(20): N/A Sensitivity RDfolder: N/A Multilign(20): N/A Positive Predictive Value RDfolder: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs MXScarna(20) Matthews Correlation Coefficient RDfolder: N/A MXScarna(20): N/A Sensitivity RDfolder: N/A MXScarna(20): N/A Positive Predictive Value RDfolder: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CentroidFold Matthews Correlation Coefficient RDfolder: N/A CentroidFold: N/A Sensitivity RDfolder: N/A CentroidFold: N/A Positive Predictive Value RDfolder: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Contrafold Matthews Correlation Coefficient RDfolder: N/A Contrafold: N/A Sensitivity RDfolder: N/A Contrafold: N/A Positive Predictive Value RDfolder: N/A Contrafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: N/A PPfold(seed): N/A Sensitivity RDfolder: N/A PPfold(seed): N/A Positive Predictive Value RDfolder: N/A PPfold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Sfold Matthews Correlation Coefficient RDfolder: N/A Sfold: N/A Sensitivity RDfolder: N/A Sfold: N/A Positive Predictive Value RDfolder: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: N/A RDfolder: N/A Sensitivity MaxExpect: N/A RDfolder: N/A Positive Predictive Value MaxExpect: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs ProbKnot Matthews Correlation Coefficient RDfolder: N/A ProbKnot: N/A Sensitivity RDfolder: N/A ProbKnot: N/A Positive Predictive Value RDfolder: N/A ProbKnot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): N/A RDfolder: N/A Sensitivity RNASampler(seed): N/A RDfolder: N/A Positive Predictive Value RNASampler(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs RDfolder Matthews Correlation Coefficient Fold: N/A RDfolder: N/A Sensitivity Fold: N/A RDfolder: N/A Positive Predictive Value Fold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): N/A RDfolder: N/A Sensitivity RNASampler(20): N/A RDfolder: N/A Positive Predictive Value RNASampler(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Murlet(20) Matthews Correlation Coefficient RDfolder: N/A Murlet(20): N/A Sensitivity RDfolder: N/A Murlet(20): N/A Positive Predictive Value RDfolder: N/A Murlet(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: N/A RDfolder: N/A Sensitivity UNAFold: N/A RDfolder: N/A Positive Predictive Value UNAFold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: N/A RDfolder: N/A Sensitivity PknotsRG: N/A RDfolder: N/A Positive Predictive Value PknotsRG: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAfold Matthews Correlation Coefficient RDfolder: N/A RNAfold: N/A Sensitivity RDfolder: N/A RNAfold: N/A Positive Predictive Value RDfolder: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Multilign(seed) Matthews Correlation Coefficient RDfolder: N/A Multilign(seed): N/A Sensitivity RDfolder: N/A Multilign(seed): N/A Positive Predictive Value RDfolder: N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Afold Matthews Correlation Coefficient RDfolder: N/A Afold: N/A Sensitivity RDfolder: N/A Afold: N/A Positive Predictive Value RDfolder: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAsubopt Matthews Correlation Coefficient RDfolder: N/A RNAsubopt: N/A Sensitivity RDfolder: N/A RNAsubopt: N/A Positive Predictive Value RDfolder: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAalifold(seed) Matthews Correlation Coefficient RDfolder: N/A RNAalifold(seed): N/A Sensitivity RDfolder: N/A RNAalifold(seed): N/A Positive Predictive Value RDfolder: N/A RNAalifold(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CMfinder(20) Matthews Correlation Coefficient RDfolder: N/A CMfinder(20): N/A Sensitivity RDfolder: N/A CMfinder(20): N/A Positive Predictive Value RDfolder: N/A CMfinder(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs McQFold Matthews Correlation Coefficient RDfolder: N/A McQFold: N/A Sensitivity RDfolder: N/A McQFold: N/A Positive Predictive Value RDfolder: N/A McQFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs CRWrnafold Matthews Correlation Coefficient RDfolder: N/A CRWrnafold: N/A Sensitivity RDfolder: N/A CRWrnafold: N/A Positive Predictive Value RDfolder: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNASLOpt Matthews Correlation Coefficient RDfolder: N/A RNASLOpt: N/A Sensitivity RDfolder: N/A RNASLOpt: N/A Positive Predictive Value RDfolder: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAshapes Matthews Correlation Coefficient RDfolder: N/A RNAshapes: N/A Sensitivity RDfolder: N/A RNAshapes: N/A Positive Predictive Value RDfolder: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Murlet(seed) Matthews Correlation Coefficient RDfolder: N/A Murlet(seed): N/A Sensitivity RDfolder: N/A Murlet(seed): N/A Positive Predictive Value RDfolder: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): N/A RDfolder: N/A Sensitivity RSpredict(20): N/A RDfolder: N/A Positive Predictive Value RSpredict(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Carnac(20) Matthews Correlation Coefficient RDfolder: N/A Carnac(20): N/A Sensitivity RDfolder: N/A Carnac(20): N/A Positive Predictive Value RDfolder: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs RNAwolf Matthews Correlation Coefficient RDfolder: N/A RNAwolf: N/A Sensitivity RDfolder: N/A RNAwolf: N/A Positive Predictive Value RDfolder: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs 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 RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): N/A RDfolder: N/A Sensitivity RSpredict(seed): N/A RDfolder: N/A Positive Predictive Value RSpredict(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Vsfold4 Matthews Correlation Coefficient RDfolder: N/A Vsfold4: N/A Sensitivity RDfolder: N/A Vsfold4: N/A Positive Predictive Value RDfolder: N/A Vsfold4: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Vsfold5 Matthews Correlation Coefficient RDfolder: N/A Vsfold5: N/A Sensitivity RDfolder: N/A Vsfold5: N/A Positive Predictive Value RDfolder: N/A Vsfold5: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs RDfolder Matthews Correlation Coefficient NanoFolder: N/A RDfolder: N/A Sensitivity NanoFolder: N/A RDfolder: N/A Positive Predictive Value NanoFolder: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Carnac(seed) Matthews Correlation Coefficient RDfolder: N/A Carnac(seed): N/A Sensitivity RDfolder: N/A Carnac(seed): N/A Positive Predictive Value RDfolder: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs RDfolder Matthews Correlation Coefficient Mastr(seed): N/A RDfolder: N/A Sensitivity Mastr(seed): N/A RDfolder: N/A Positive Predictive Value Mastr(seed): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: N/A RDfolder: N/A Sensitivity HotKnots: N/A RDfolder: N/A Positive Predictive Value HotKnots: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Pknots Matthews Correlation Coefficient RDfolder: N/A Pknots: N/A Sensitivity RDfolder: N/A Pknots: N/A Positive Predictive Value RDfolder: N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: N/A RDfolder: N/A Sensitivity Cylofold: N/A RDfolder: N/A Positive Predictive Value Cylofold: N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: N/A MCFold: N/A Sensitivity RDfolder: N/A MCFold: N/A Positive Predictive Value RDfolder: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: N/A Alterna: N/A Sensitivity RDfolder: N/A Alterna: N/A Positive Predictive Value RDfolder: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	? Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): N/A RDfolder: N/A Sensitivity Mastr(20): N/A RDfolder: N/A Positive Predictive Value Mastr(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Alterna	0 Alterna vs PETfold_pre2.0(seed) Matthews Correlation Coefficient Alterna: N/A PETfold_pre2.0(seed): N/A Sensitivity Alterna: N/A PETfold_pre2.0(seed): N/A Positive Predictive Value Alterna: N/A PETfold_pre2.0(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: N/A Alterna: N/A Sensitivity ContextFold: N/A Alterna: N/A Positive Predictive Value ContextFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): N/A Alterna: N/A Sensitivity TurboFold(20): N/A Alterna: N/A Positive Predictive Value TurboFold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): N/A Alterna: N/A Sensitivity CentroidAlifold(seed): N/A Alterna: N/A Positive Predictive Value CentroidAlifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): N/A Alterna: N/A Sensitivity PETfold_pre2.0(20): N/A Alterna: N/A Positive Predictive Value PETfold_pre2.0(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): N/A Alterna: N/A Sensitivity PPfold(20): N/A Alterna: N/A Positive Predictive Value PPfold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CentroidHomfold‑LAST Matthews Correlation Coefficient Alterna: N/A CentroidHomfold‑LAST: N/A Sensitivity Alterna: N/A CentroidHomfold‑LAST: N/A Positive Predictive Value Alterna: N/A CentroidHomfold‑LAST: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CentroidAlifold(20) Matthews Correlation Coefficient Alterna: N/A CentroidAlifold(20): N/A Sensitivity Alterna: N/A CentroidAlifold(20): N/A Positive Predictive Value Alterna: N/A CentroidAlifold(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs MXScarna(seed) Matthews Correlation Coefficient Alterna: N/A MXScarna(seed): N/A Sensitivity Alterna: N/A MXScarna(seed): N/A Positive Predictive Value Alterna: N/A MXScarna(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs IPknot Matthews Correlation Coefficient Alterna: N/A IPknot: N/A Sensitivity Alterna: N/A IPknot: N/A Positive Predictive Value Alterna: N/A IPknot: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): N/A Alterna: N/A Sensitivity RNAalifold(20): N/A Alterna: N/A Positive Predictive Value RNAalifold(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): N/A Alterna: N/A Sensitivity TurboFold(seed): N/A Alterna: N/A Positive Predictive Value TurboFold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Multilign(20) Matthews Correlation Coefficient Alterna: N/A Multilign(20): N/A Sensitivity Alterna: N/A Multilign(20): N/A Positive Predictive Value Alterna: N/A Multilign(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs MXScarna(20) Matthews Correlation Coefficient Alterna: N/A MXScarna(20): N/A Sensitivity Alterna: N/A MXScarna(20): N/A Positive Predictive Value Alterna: N/A MXScarna(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CentroidFold Matthews Correlation Coefficient Alterna: N/A CentroidFold: N/A Sensitivity Alterna: N/A CentroidFold: N/A Positive Predictive Value Alterna: N/A CentroidFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: N/A Alterna: N/A Sensitivity Contrafold: N/A Alterna: N/A Positive Predictive Value Contrafold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PPfold(seed) vs Alterna Matthews Correlation Coefficient PPfold(seed): N/A Alterna: N/A Sensitivity PPfold(seed): N/A Alterna: N/A Positive Predictive Value PPfold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Sfold Matthews Correlation Coefficient Alterna: N/A Sfold: N/A Sensitivity Alterna: N/A Sfold: N/A Positive Predictive Value Alterna: N/A Sfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: N/A Alterna: N/A Sensitivity MaxExpect: N/A Alterna: N/A Positive Predictive Value MaxExpect: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: N/A Alterna: N/A Sensitivity ProbKnot: N/A Alterna: N/A Positive Predictive Value ProbKnot: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): N/A Alterna: N/A Sensitivity RNASampler(seed): N/A Alterna: N/A Positive Predictive Value RNASampler(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Fold vs Alterna Matthews Correlation Coefficient Fold: N/A Alterna: N/A Sensitivity Fold: N/A Alterna: N/A Positive Predictive Value Fold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): N/A Alterna: N/A Sensitivity RNASampler(20): N/A Alterna: N/A Positive Predictive Value RNASampler(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): N/A Alterna: N/A Sensitivity Murlet(20): N/A Alterna: N/A Positive Predictive Value Murlet(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: N/A Alterna: N/A Sensitivity UNAFold: N/A Alterna: N/A Positive Predictive Value UNAFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: N/A Alterna: N/A Sensitivity PknotsRG: N/A Alterna: N/A Positive Predictive Value PknotsRG: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAfold Matthews Correlation Coefficient Alterna: N/A RNAfold: N/A Sensitivity Alterna: N/A RNAfold: N/A Positive Predictive Value Alterna: N/A RNAfold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): N/A Alterna: N/A Sensitivity Multilign(seed): N/A Alterna: N/A Positive Predictive Value Multilign(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Afold Matthews Correlation Coefficient Alterna: N/A Afold: N/A Sensitivity Alterna: N/A Afold: N/A Positive Predictive Value Alterna: N/A Afold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAsubopt Matthews Correlation Coefficient Alterna: N/A RNAsubopt: N/A Sensitivity Alterna: N/A RNAsubopt: N/A Positive Predictive Value Alterna: N/A RNAsubopt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): N/A Alterna: N/A Sensitivity RNAalifold(seed): N/A Alterna: N/A Positive Predictive Value RNAalifold(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs 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 McQFold vs Alterna Matthews Correlation Coefficient McQFold: N/A Alterna: N/A Sensitivity McQFold: N/A Alterna: N/A Positive Predictive Value McQFold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs CRWrnafold Matthews Correlation Coefficient Alterna: N/A CRWrnafold: N/A Sensitivity Alterna: N/A CRWrnafold: N/A Positive Predictive Value Alterna: N/A CRWrnafold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNASLOpt Matthews Correlation Coefficient Alterna: N/A RNASLOpt: N/A Sensitivity Alterna: N/A RNASLOpt: N/A Positive Predictive Value Alterna: N/A RNASLOpt: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAshapes Matthews Correlation Coefficient Alterna: N/A RNAshapes: N/A Sensitivity Alterna: N/A RNAshapes: N/A Positive Predictive Value Alterna: N/A RNAshapes: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: N/A Murlet(seed): N/A Sensitivity Alterna: N/A Murlet(seed): N/A Positive Predictive Value Alterna: N/A Murlet(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): N/A Alterna: N/A Sensitivity RSpredict(20): N/A Alterna: N/A Positive Predictive Value RSpredict(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Carnac(20) Matthews Correlation Coefficient Alterna: N/A Carnac(20): N/A Sensitivity Alterna: N/A Carnac(20): N/A Positive Predictive Value Alterna: N/A Carnac(20): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: N/A RNAwolf: N/A Sensitivity Alterna: N/A RNAwolf: N/A Positive Predictive Value Alterna: N/A RNAwolf: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 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 RSpredict(seed) vs Alterna Matthews Correlation Coefficient RSpredict(seed): N/A Alterna: N/A Sensitivity RSpredict(seed): N/A Alterna: N/A Positive Predictive Value RSpredict(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: N/A Alterna: N/A Sensitivity Vsfold4: N/A Alterna: N/A Positive Predictive Value Vsfold4: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: N/A Alterna: N/A Sensitivity Vsfold5: N/A Alterna: N/A Positive Predictive Value Vsfold5: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 NanoFolder vs Alterna Matthews Correlation Coefficient NanoFolder: N/A Alterna: N/A Sensitivity NanoFolder: N/A Alterna: N/A Positive Predictive Value NanoFolder: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: N/A Carnac(seed): N/A Sensitivity Alterna: N/A Carnac(seed): N/A Positive Predictive Value Alterna: N/A Carnac(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(seed) vs Alterna Matthews Correlation Coefficient Mastr(seed): N/A Alterna: N/A Sensitivity Mastr(seed): N/A Alterna: N/A Positive Predictive Value Mastr(seed): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: N/A Alterna: N/A Sensitivity HotKnots: N/A Alterna: N/A Positive Predictive Value HotKnots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Pknots vs Alterna Matthews Correlation Coefficient Pknots: N/A Alterna: N/A Sensitivity Pknots: N/A Alterna: N/A Positive Predictive Value Pknots: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: N/A Alterna: N/A Sensitivity Cylofold: N/A Alterna: N/A Positive Predictive Value Cylofold: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Alterna vs MCFold Matthews Correlation Coefficient Alterna: N/A MCFold: N/A Sensitivity Alterna: N/A MCFold: N/A Positive Predictive Value Alterna: N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 RDfolder vs Alterna Matthews Correlation Coefficient RDfolder: N/A Alterna: N/A Sensitivity RDfolder: N/A Alterna: N/A Positive Predictive Value RDfolder: N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A		? Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): N/A Alterna: N/A Sensitivity Mastr(20): N/A Alterna: N/A Positive Predictive Value Mastr(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A
Mastr(20)	230 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(seed): 0.693 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(seed): 0.854 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.843 Mastr(20): 0.000 Sensitivity ContextFold: 0.799 Mastr(20): 0.000 Positive Predictive Value ContextFold: 0.891 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.752 Mastr(20): 0.000 Sensitivity TurboFold(20): 0.701 Mastr(20): 0.000 Positive Predictive Value TurboFold(20): 0.809 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.733 Mastr(20): 0.000 Sensitivity CentroidAlifold(seed): 0.564 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(seed): 0.953 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	242 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.739 Mastr(20): 0.000 Sensitivity PETfold_pre2.0(20): 0.654 Mastr(20): 0.000 Positive Predictive Value PETfold_pre2.0(20): 0.836 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 242 Wilcoxon single-rank test P-value: 3.56938820447e-08	238 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.733 Mastr(20): 0.000 Sensitivity PPfold(20): 0.629 Mastr(20): 0.000 Positive Predictive Value PPfold(20): 0.855 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 238 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.710 Mastr(20): 0.000 Sensitivity CentroidHomfold‑LAST: 0.561 Mastr(20): 0.000 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.725 Mastr(20): 0.000 Sensitivity CentroidAlifold(20): 0.574 Mastr(20): 0.000 Positive Predictive Value CentroidAlifold(20): 0.916 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.684 Mastr(20): 0.000 Sensitivity MXScarna(seed): 0.582 Mastr(20): 0.000 Positive Predictive Value MXScarna(seed): 0.805 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.655 Mastr(20): 0.000 Sensitivity IPknot: 0.586 Mastr(20): 0.000 Positive Predictive Value IPknot: 0.732 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.668 Mastr(20): 0.000 Sensitivity RNAalifold(20): 0.540 Mastr(20): 0.000 Positive Predictive Value RNAalifold(20): 0.827 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.755 Mastr(20): 0.000 Sensitivity TurboFold(seed): 0.739 Mastr(20): 0.000 Positive Predictive Value TurboFold(seed): 0.774 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	223 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.651 Mastr(20): 0.000 Sensitivity Multilign(20): 0.590 Mastr(20): 0.000 Positive Predictive Value Multilign(20): 0.721 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 223 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.654 Mastr(20): 0.000 Sensitivity MXScarna(20): 0.584 Mastr(20): 0.000 Positive Predictive Value MXScarna(20): 0.735 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.621 Mastr(20): 0.000 Sensitivity CentroidFold: 0.557 Mastr(20): 0.000 Positive Predictive Value CentroidFold: 0.694 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.606 Mastr(20): 0.000 Sensitivity Contrafold: 0.585 Mastr(20): 0.000 Positive Predictive Value Contrafold: 0.630 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 PPfold(seed) vs Mastr(20) Matthews Correlation Coefficient PPfold(seed): 0.847 Mastr(20): 0.000 Sensitivity PPfold(seed): 0.782 Mastr(20): 0.000 Positive Predictive Value PPfold(seed): 0.919 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	245 Sfold vs Mastr(20) Matthews Correlation Coefficient Sfold: 0.584 Mastr(20): 0.000 Sensitivity Sfold: 0.522 Mastr(20): 0.000 Positive Predictive Value Sfold: 0.654 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.592 Mastr(20): 0.000 Sensitivity MaxExpect: 0.569 Mastr(20): 0.000 Positive Predictive Value MaxExpect: 0.617 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 ProbKnot vs Mastr(20) Matthews Correlation Coefficient ProbKnot: 0.590 Mastr(20): 0.000 Sensitivity ProbKnot: 0.572 Mastr(20): 0.000 Positive Predictive Value ProbKnot: 0.610 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): N/A RNASampler(seed): N/A Sensitivity Mastr(20): N/A RNASampler(seed): N/A Positive Predictive Value Mastr(20): N/A RNASampler(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	245 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.562 Mastr(20): 0.000 Sensitivity Fold: 0.555 Mastr(20): 0.000 Positive Predictive Value Fold: 0.571 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.565 Mastr(20): 0.000 Sensitivity RNASampler(20): 0.413 Mastr(20): 0.000 Positive Predictive Value RNASampler(20): 0.772 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	176 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.573 Mastr(20): 0.000 Sensitivity Murlet(20): 0.441 Mastr(20): 0.000 Positive Predictive Value Murlet(20): 0.746 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 176 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 UNAFold vs Mastr(20) Matthews Correlation Coefficient UNAFold: 0.547 Mastr(20): 0.000 Sensitivity UNAFold: 0.535 Mastr(20): 0.000 Positive Predictive Value UNAFold: 0.560 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 PknotsRG vs Mastr(20) Matthews Correlation Coefficient PknotsRG: 0.525 Mastr(20): 0.000 Sensitivity PknotsRG: 0.518 Mastr(20): 0.000 Positive Predictive Value PknotsRG: 0.535 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAfold vs Mastr(20) Matthews Correlation Coefficient RNAfold: 0.544 Mastr(20): 0.000 Sensitivity RNAfold: 0.536 Mastr(20): 0.000 Positive Predictive Value RNAfold: 0.553 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): N/A Multilign(seed): N/A Sensitivity Mastr(20): N/A Multilign(seed): N/A Positive Predictive Value Mastr(20): N/A Multilign(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	185 Afold vs Mastr(20) Matthews Correlation Coefficient Afold: 0.556 Mastr(20): 0.000 Sensitivity Afold: 0.544 Mastr(20): 0.000 Positive Predictive Value Afold: 0.570 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAsubopt vs Mastr(20) Matthews Correlation Coefficient RNAsubopt: 0.530 Mastr(20): 0.000 Sensitivity RNAsubopt: 0.529 Mastr(20): 0.000 Positive Predictive Value RNAsubopt: 0.532 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	203 RNAalifold(seed) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(seed): 0.492 Mastr(20): 0.000 Sensitivity RNAalifold(seed): 0.290 Mastr(20): 0.000 Positive Predictive Value RNAalifold(seed): 0.836 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 203 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.478 Mastr(20): 0.000 Sensitivity CMfinder(20): 0.309 Mastr(20): 0.000 Positive Predictive Value CMfinder(20): 0.741 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 McQFold vs Mastr(20) Matthews Correlation Coefficient McQFold: 0.442 Mastr(20): 0.000 Sensitivity McQFold: 0.424 Mastr(20): 0.000 Positive Predictive Value McQFold: 0.464 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.464 Mastr(20): 0.000 Sensitivity CRWrnafold: 0.456 Mastr(20): 0.000 Positive Predictive Value CRWrnafold: 0.474 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	227 RNASLOpt vs Mastr(20) Matthews Correlation Coefficient RNASLOpt: 0.450 Mastr(20): 0.000 Sensitivity RNASLOpt: 0.417 Mastr(20): 0.000 Positive Predictive Value RNASLOpt: 0.488 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 227 Wilcoxon single-rank test P-value: 3.56938820447e-08	235 RNAshapes vs Mastr(20) Matthews Correlation Coefficient RNAshapes: 0.468 Mastr(20): 0.000 Sensitivity RNAshapes: 0.454 Mastr(20): 0.000 Positive Predictive Value RNAshapes: 0.483 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 235 Wilcoxon single-rank test P-value: 3.56938820447e-08	1 Murlet(seed) vs Mastr(20) Matthews Correlation Coefficient Murlet(seed): 0.588 Mastr(20): 0.000 Sensitivity Murlet(seed): 0.347 Mastr(20): 0.000 Positive Predictive Value Murlet(seed): 1.000 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 1 Wilcoxon single-rank test P-value: 0.0	245 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.418 Mastr(20): 0.000 Sensitivity RSpredict(20): 0.285 Mastr(20): 0.000 Positive Predictive Value RSpredict(20): 0.614 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 Carnac(20) vs Mastr(20) Matthews Correlation Coefficient Carnac(20): 0.378 Mastr(20): 0.000 Sensitivity Carnac(20): 0.166 Mastr(20): 0.000 Positive Predictive Value Carnac(20): 0.863 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	245 RNAwolf vs Mastr(20) Matthews Correlation Coefficient RNAwolf: 0.367 Mastr(20): 0.000 Sensitivity RNAwolf: 0.377 Mastr(20): 0.000 Positive Predictive Value RNAwolf: 0.360 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 245 Wilcoxon single-rank test P-value: 3.56938820447e-08	0 Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): N/A CMfinder(seed): N/A Sensitivity Mastr(20): N/A CMfinder(seed): N/A Positive Predictive Value Mastr(20): N/A CMfinder(seed): N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	205 RSpredict(seed) vs Mastr(20) Matthews Correlation Coefficient RSpredict(seed): 0.197 Mastr(20): 0.000 Sensitivity RSpredict(seed): 0.077 Mastr(20): 0.000 Positive Predictive Value RSpredict(seed): 0.510 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	240 Vsfold4 vs Mastr(20) Matthews Correlation Coefficient Vsfold4: 0.352 Mastr(20): 0.000 Sensitivity Vsfold4: 0.319 Mastr(20): 0.000 Positive Predictive Value Vsfold4: 0.391 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 240 Wilcoxon single-rank test P-value: 3.56938820447e-08	237 Vsfold5 vs Mastr(20) Matthews Correlation Coefficient Vsfold5: 0.333 Mastr(20): 0.000 Sensitivity Vsfold5: 0.308 Mastr(20): 0.000 Positive Predictive Value Vsfold5: 0.362 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 237 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 NanoFolder vs Mastr(20) Matthews Correlation Coefficient NanoFolder: 0.150 Mastr(20): 0.000 Sensitivity NanoFolder: 0.173 Mastr(20): 0.000 Positive Predictive Value NanoFolder: 0.133 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.000 Carnac(seed): 0.000 Sensitivity Mastr(20): 0.000 Carnac(seed): 0.000 Positive Predictive Value Mastr(20): 0.000 Carnac(seed): 0.000 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0	189 Mastr(seed) vs Mastr(20) Matthews Correlation Coefficient Mastr(seed): 0.000 Mastr(20): 0.000 Sensitivity Mastr(seed): 0.000 Mastr(20): 0.000 Positive Predictive Value Mastr(seed): 0.000 Mastr(20): 0.000 Number of pairs reference - predicted secondary structure: 189 Wilcoxon single-rank test P-value: 1.14021447951e-07	0 Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): N/A HotKnots: N/A Sensitivity Mastr(20): N/A HotKnots: N/A Positive Predictive Value Mastr(20): N/A HotKnots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): N/A Pknots: N/A Sensitivity Mastr(20): N/A Pknots: N/A Positive Predictive Value Mastr(20): N/A Pknots: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): N/A Cylofold: N/A Sensitivity Mastr(20): N/A Cylofold: N/A Positive Predictive Value Mastr(20): N/A Cylofold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): N/A MCFold: N/A Sensitivity Mastr(20): N/A MCFold: N/A Positive Predictive Value Mastr(20): N/A MCFold: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): N/A RDfolder: N/A Sensitivity Mastr(20): N/A RDfolder: N/A Positive Predictive Value Mastr(20): N/A RDfolder: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A	0 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): N/A Alterna: N/A Sensitivity Mastr(20): N/A Alterna: N/A Positive Predictive Value Mastr(20): N/A Alterna: N/A Number of pairs reference - predicted secondary structure: 0 Wilcoxon single-rank test P-value: N/A

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).