Table A1.
Summary of boundary predictions from multiple sequence alignments with RNAbound and Dotu et al. The base pair probabilities were calculated with PETfold.
| Window | Family (n) | RNAbound | Dotu et al. | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Left | Right | Left | Right | ||||||
| Median | std | Median | std | Median | std | Median | std | ||
| 100 | Single hairpin structures | ||||||||
| miRNA (244) | 4.0 | 12.50 | 1.0 | 14.34 | 1.0 | 16.85 | 0.0 | 14.30 | |
| cisreg (28) | 5.0 | 10.23 | −2.0 | 14.83 | −8.5 | 14.58 | −15.5 | 18.21 | |
| snoRNA (6) | 1.5 | 10.57 | −6.0 | 15.80 | −18.0 | 15.20 | −17.5 | 18.86 | |
| all (279) | 4.0 | 12.47 | 0.0 | 14.39 | 1.0 | 16.67 | −1.0 | 14.93 | |
| Branched structures | |||||||||
| tRNA (185) | −5.0 | 11.07 | −9.0 | 12.38 | 0.0 | 21.19 | −2.0 | 11.17 | |
| cisreg (2) | 7.5 | 3.54 | 7.5 | 3.54 | 5.0 | 0.0 | 7.5 | 2.12 | |
| ribozyme (2) | −8.0 | 15.56 | −10.5 | 2.12 | −25.0 | 35.36 | −8.0 | 7.07 | |
| snRNA (1) | −33.0 | 0.00 | −12.0 | 0.00 | −33.0 | 0.00 | −13.0 | 0.00 | |
| all (190) | −5.0 | 11.07 | −9.0 | 12.41 | 0.0 | 21.23 | −2.0 | 11.16 | |
| 150 | Single hairpin structures | ||||||||
| miRNA (642) | 11.0 | 27.29 | 9.0 | 26.62 | −1.0 | 33.91 | −1.5 | 29.71 | |
| cisreg (36) | 9.0 | 18.35 | 7.0 | 21.42 | −5.0 | 21.14 | −8.5 | 24.76 | |
| snoRNA (24) | 5.5 | 19.48 | −1.5 | 16.01 | 7.0 | 15.46 | 3.0 | 21.32 | |
| all (709) | 9.0 | 26.61 | 8.0 | 26.04 | −1.0 | 32.86 | −2.0 | 29.17 | |
| Branched structures | |||||||||
| tRNA (166) | −6.0 | 18.34 | −9.0 | 20.09 | 0.0 | 22.96 | −2.0 | 14.53 | |
| cisreg (6) | −4.5 | 24.70 | 3.0 | 39.39 | −4.5 | 50.49 | 1.0 | 40.18 | |
| snoRNA (13) | 0.0 | 21.45 | −12.0 | 36.90 | −14.0 | 32.78 | −82.0 | 44.22 | |
| ribozyme (3) | −51.0 | 32.97 | −14.0 | 15.39 | −50.0 | 33.26 | −13.0 | 15.28 | |
| snRNA (3) | −17.0 | 15.01 | −50.0 | 33.60 | −80.0 | 32.75 | −13.0 | 9.02 | |
| all (190) | −6.0 | 19.23 | −9.5 | 23.24 | 0.0 | 26.23 | −3.0 | 21.68 | |
| 200 | Single hairpin structures | ||||||||
| miRNA (661) | 30.0 | 43.96 | 33.0 | 39.94 | −2.0 | 49.87 | 1.0 | 45.70 | |
| cisreg (37) | 33.0 | 31.60 | 29.0 | 41.10 | −5.0 | 29.04 | −16.0 | 34.79 | |
| snoRNA (20) | 12.0 | 34.34 | 5.0 | 44.38 | 7.0 | 28.95 | 3.0 | 33.36 | |
| all (727) | 29.0 | 43.47 | 32.0 | 40.06 | −1.0 | 45.58 | 0.0 | 45.27 | |
| Branched structures | |||||||||
| tRNA (127) | −6.0 | 30.38 | −9.0 | 34.29 | 0.0 | 29.02 | −3.0 | 19.67 | |
| cisreg (9) | 23.0 | 32.20 | 26.0 | 61.57 | 16.0 | 35.36 | 26 | 75.80 | |
| snoRNA (61) | −7.0 | 36.62 | −69.0 | 44.87 | −18.0 | 36.99 | −86.0 | 39.29 | |
| ribozyme (2) | −35.0 | 49.50 | −14.5 | 31.82 | −31.5 | 44.55 | −18.0 | 21.21 | |
| snRNA (6) | −22.0 | 38.90 | −48.5 | 29.95 | −86.0 | 44.46 | −12.0 | 32.94 | |
| all (206) | −6.0 | 34.85 | −11.5 | 43.77 | −14.0 | 35.76 | −9.0 | 40.63 | |