RNAhub
CWC15_YDR163W_1kb-b6e0dadc (CWC15_YDR163W_1kb)
The raw output files for each step of the pipeline can be found here.
Input: sequence:
>CWC15 YDR163W SGDID:S000002570, Chromosome IV:781423..781950+/- 1kb TGCTTCGACCTCCGCAACATCATCAATATCTTCCCATTCATCGTTGTCGTCGTATTCATC TTCGTTAGTGTTATCAATATTGTTTTTAGGACTAACGCTCTGTGTAATCAAATGTGTCAA ATAGAAAGGTCGAGCCTTATTCTCCACCTCGTTCTCACCATCTTCCGGCTGTATATAAGA GACAAACTCCTCCGGTACCAACCCTGTTTTTGATCCTGACTCATTTTCTGCTACTAGCCA ACCTTGCCCATGCTTGTAACTGATAAATACGATGTCACCCTCAGCCAATCTCAATTCATT ATCATTTTCGGGTTCGAAATCGTAGAGGGCAACAGCACGTTGGTTAACTATGTAGTCGTC TGGTAGTGTTATACTTTGTCTTTTATTGTATGTGTCTTCTCCATTTGAAGAATCTGAAAC CATTTCATCCTCCTCATTGTCTCCATCAAAATAACCATAATGGAGAGGATTCGAATCTGC GTACGCATAATCTTTGATTGATATATAACCTATTGTGGTTGTTTCTGTATCTTCCATTGT GTCACTATTTCCTGCCTGCACTGCCTCCACCTCTCTCCCGTTCTGTAATACTGCCTCATT GAGAACACCTATAGTTTTTTTGAGACCAGATTTCAAAATATTGGTATCTTTTTGTGTGGT CGTTTCCATCGTTGCCATCGTAGATTCAATAAATATGTCAGTGGAAGTTAAAGTAAGGTA AAGTTGAGAAAAATACTTAAAATTTGTTAGTATCTATCACGTTTTATTGGTAGCTGTTAT TATGTGTGATTGAGCGTGTTGTTACTGTGCACTGTGTTGCATTGTCCATTACAAGCTACT TCTGAAGTGAATTCTCCATTTCTCGCAACTGGAAAAATAAGTTGGTGTGACTAAAAATAA TAGTCTATCTCTTCACGAAAAGGAAATAGGAATGACAAAGCTCCAAAAGGCTCCATAAAG AACTTGCTCAGAGGCTGGCATTTGAAAGGGCTACAAGACCATGACCACATCACACAGACC ACAGTTAGAAGCAAGAAGCGGTGCAAAAGCGGCCGCTTATACACCAACAGGCATCGAGCA TGCCAGATTACTACCAGGACATACAACATTAAAATACAGGAAATTTAAAGAGGAGGAAAA TCTTAGAGCAAACTGTGCGCAAGAAGATAGGAGCAACGATAAATCTTTAGAGGAGGCAGT AATGAACGAAGAGAAACAGGATGTTGTGGGGAGTGGGAACCTCCAAGAAACCCGCAGTGA GAAAGACCAAAAAGACTCGTTGCAAGAGCTGCTGGTTACTCAAAAAAATAAAGTGGAAGA TAAAGCAGAGCTTGAAGGAAATGAACAATTAAAGGGAGGAAATTCGTCTAGGCGATCGTG GAGAAAGGGCACGGCGTTTGGACGCCATDatabase: fungi
PDB hits:
No hits were detected to the PDB database!
Rfam hits:
No hits were detected to the Rfam database!
R-scape on nhmmer alignment:
The final nhmmer alignment can be found here.
Alignments from each iteration: iteration 1, iteration 2, iteration 3.List of covarying basepairs (#42)
| In given structure | Left Position | Right Position | Score | E-value | p-value | Substitutions | Power |
|---|---|---|---|---|---|---|---|
| ~ | 1790 | 2286 | 503.25718 | 0.00179036 | 5.89301e-08 | 47 | 0.85 |
| ~ | 1790 | 1791 | 458.88630 | 0.00892263 | 2.93691e-07 | 100 | 0.97 |
| ~ | 1790 | 2353 | 443.17583 | 0.0157233 | 5.17538e-07 | 42 | 0.83 |
| ~ | 1826 | 2343 | 645.65145 | 1.01111e-05 | 3.3281e-10 | 23 | 0.64 |
| ~ | 1828 | 1830 | 552.70947 | 0.000297696 | 9.79875e-09 | 222 | 1.00 |
| ~ | 1828 | 2251 | 512.81159 | 0.00126656 | 4.16893e-08 | 221 | 1.00 |
| ~ | 1830 | 2251 | 680.83220 | 2.80678e-06 | 9.2386e-11 | 27 | 0.70 |
| ~ | 1830 | 2252 | 549.54694 | 0.000334389 | 1.10065e-08 | 207 | 1.00 |
| ~ | 1830 | 2354 | 520.65476 | 0.000952815 | 3.13622e-08 | 80 | 0.93 |
| ~ | 1830 | 2326 | 471.32771 | 0.00569025 | 1.87296e-07 | 31 | 0.75 |
| ~ | 1830 | 2376 | 437.41161 | 0.0193448 | 6.3674e-07 | 24 | 0.66 |
| ~ | 1842 | 1844 | 466.03854 | 0.00689163 | 2.2684e-07 | 420 | 1.00 |
| ~ | 1914 | 1918 | 496.25343 | 0.00230706 | 7.59377e-08 | 145 | 1.00 |
| ~ | 1918 | 2179 | 417.35313 | 0.0398112 | 1.3104e-06 | 224 | 1.00 |
| ~ | 1918 | 2173 | 416.74109 | 0.0407525 | 1.34138e-06 | 333 | 1.00 |
| ~ | 2173 | 2181 | 534.43578 | 0.000578566 | 1.90437e-08 | 268 | 1.00 |
| ~ | 2251 | 2252 | 687.78180 | 2.17822e-06 | 7.16967e-11 | 206 | 1.00 |
| ~ | 2251 | 2354 | 478.21964 | 0.00443378 | 1.45939e-07 | 79 | 0.93 |
| ~ | 2251 | 2376 | 430.29047 | 0.0250279 | 8.238e-07 | 23 | 0.64 |
| ~ | 2251 | 2326 | 419.52965 | 0.0368494 | 1.21291e-06 | 30 | 0.74 |
| ~ | 2252 | 2354 | 458.99423 | 0.00889047 | 2.92632e-07 | 259 | 1.00 |
| ~ | 2252 | 2376 | 425.68444 | 0.0295353 | 9.72165e-07 | 203 | 1.00 |
| ~ | 2252 | 2326 | 419.33190 | 0.0371154 | 1.22167e-06 | 210 | 1.00 |
| ~ | 2266 | 2275 | 1107.58403 | 4.64158e-13 | 1.52779e-17 | 89 | 0.95 |
| ~ | 2286 | 2353 | 558.29319 | 0.000243335 | 8.00944e-09 | 39 | 0.81 |
| ~ | 2286 | 2315 | 499.72532 | 0.00203607 | 6.70178e-08 | 70 | 0.91 |
| ~ | 2287 | 2288 | 871.44994 | 2.65177e-09 | 8.72838e-14 | 168 | 1.00 |
| ~ | 2288 | 2289 | 454.44914 | 0.0104778 | 3.4488e-07 | 85 | 0.94 |
| ~ | 2296 | 2298 | 721.76152 | 6.29805e-07 | 2.07302e-11 | 222 | 1.00 |
| ~ | 2298 | 2367 | 416.66641 | 0.0408258 | 1.34379e-06 | 27 | 0.70 |
| ~ | 2307 | 2308 | 919.60553 | 4.54334e-10 | 1.49546e-14 | 204 | 1.00 |
| ~ | 2313 | 2315 | 502.45981 | 0.00184301 | 6.06631e-08 | 98 | 0.97 |
| ~ | 2315 | 2353 | 547.44670 | 0.000360891 | 1.18788e-08 | 65 | 0.90 |
| ~ | 2326 | 2354 | 413.48090 | 0.045802 | 1.50759e-06 | 83 | 0.94 |
| ~ | 2330 | 2331 | 605.04536 | 4.44431e-05 | 1.46286e-09 | 44 | 0.84 |
| ~ | 2354 | 2376 | 445.32090 | 0.0145503 | 4.78927e-07 | 76 | 0.93 |
| ~ | 2358 | 2359 | 543.96791 | 0.000409059 | 1.34643e-08 | 200 | 1.00 |
| ~ | 2369 | 2371 | 496.01777 | 0.00232805 | 7.66284e-08 | 443 | 1.00 |
| ~ | 2376 | 2382 | 558.27559 | 0.000243335 | 8.00944e-09 | 58 | 0.89 |
| ~ | 2503 | 2521 | 597.19949 | 5.91401e-05 | 1.94661e-09 | 54 | 0.88 |
| ~ | 2560 | 2585 | 411.07239 | 0.0499266 | 1.64335e-06 | 324 | 1.00 |
| ~ | 2584 | 2585 | 507.62597 | 0.00152927 | 5.03363e-08 | 194 | 1.00 |
BPAIRS expected to covary 39.5 +/- 1.7 BPAIRS observed to covary 42 BPAIRS observed to covary possibly coding 38/42 (0.90%)
Alignment statistics:
Alignment number: 1 Alignment name: CWC15 Format: Stockholm Number of sequences: 1380 Alignment length: 9674 Total # residues: 397816 Smallest: 81 Largest: 1860 Average length: 288.3 Average identity: 48%
R-scape on infernal alignment:
The Infernal alignment can be found here.
List of covarying basepairs (#118)
| In given structure | Left Position | Right Position | Score | E-value | p-value | Substitutions | Power |
|---|---|---|---|---|---|---|---|
| * | 15 | 102 | 223.61873 | 0.00616169 | 1.84421e-07 | 135 | 1.00 |
| * | 108 | 1917 | 228.25762 | 0.00445998 | 1.33488e-07 | 91 | 0.96 |
| * | 110 | 611 | 255.44498 | 0.000675423 | 2.02156e-08 | 224 | 1.00 |
| 110 | 1053 | 204.98376 | 0.022519 | 6.74e-07 | 226 | 1.00 | |
| 611 | 1053 | 354.21092 | 6.99403e-07 | 2.09333e-11 | 32 | 0.76 | |
| 611 | 1196 | 291.87533 | 5.35338e-05 | 1.60228e-09 | 211 | 1.00 | |
| 611 | 1924 | 276.37973 | 0.00015734 | 4.70923e-09 | 95 | 0.96 | |
| 611 | 1782 | 231.73093 | 0.00350899 | 1.05025e-07 | 38 | 0.81 | |
| ~ | 617 | 734 | 256.99169 | 0.000606411 | 1.81501e-08 | 129 | 1.00 |
| ~ | 621 | 4024 | 236.98337 | 0.00243603 | 7.29109e-08 | 33 | 0.77 |
| ~ | 621 | 4049 | 196.20836 | 0.0413558 | 1.23779e-06 | 44 | 0.84 |
| ~ | 621 | 734 | 195.90382 | 0.0422266 | 1.26385e-06 | 146 | 1.00 |
| * | 622 | 734 | 502.89397 | 2.24651e-11 | 6.72385e-16 | 438 | 1.00 |
| ~ | 623 | 734 | 197.60205 | 0.0375234 | 1.12309e-06 | 128 | 1.00 |
| 734 | 2128 | 237.08335 | 0.00241915 | 7.24058e-08 | 150 | 1.00 | |
| ~ | 738 | 741 | 227.54421 | 0.00469865 | 1.40632e-07 | 310 | 1.00 |
| ~ | 741 | 742 | 309.71990 | 1.54654e-05 | 4.62884e-10 | 113 | 0.99 |
| ~ | 745 | 754 | 202.59091 | 0.026605 | 7.96295e-07 | 202 | 1.00 |
| ~ | 747 | 753 | 327.11551 | 4.60927e-06 | 1.37957e-10 | 135 | 1.00 |
| ~ | 747 | 751 | 310.53443 | 1.46282e-05 | 4.37827e-10 | 85 | 0.94 |
| ~ | 747 | 1009 | 196.49084 | 0.0406438 | 1.21648e-06 | 133 | 1.00 |
| ~ | 753 | 1009 | 336.25703 | 2.43866e-06 | 7.29896e-11 | 190 | 1.00 |
| ~ | 753 | 754 | 282.31907 | 0.000104019 | 3.11332e-09 | 251 | 1.00 |
| ~ | 753 | 1005 | 222.08077 | 0.00686256 | 2.05398e-07 | 329 | 1.00 |
| ~ | 1015 | 1528 | 295.28766 | 4.22587e-05 | 1.26481e-09 | 31 | 0.75 |
| ~ | 1015 | 1436 | 226.29027 | 0.00512515 | 1.53397e-07 | 255 | 1.00 |
| ~ | 1022 | 1034 | 219.28981 | 0.00833681 | 2.49523e-07 | 12 | 0.39 |
| ~ | 1022 | 1029 | 212.46238 | 0.013373 | 4.00258e-07 | 128 | 1.00 |
| ~ | 1022 | 1028 | 202.98832 | 0.0258759 | 7.74471e-07 | 10 | 0.32 |
| ~ | 1025 | 1028 | 225.55108 | 0.00538068 | 1.61045e-07 | 2 | 0.00 |
| ~ | 1025 | 1029 | 214.37497 | 0.0117189 | 3.50751e-07 | 120 | 1.00 |
| ~ | 1025 | 2595 | 205.60793 | 0.0215247 | 6.44239e-07 | 5 | 0.11 |
| ~ | 1026 | 1053 | 254.05150 | 0.000741898 | 2.22052e-08 | 29 | 0.73 |
| ~ | 1026 | 1035 | 209.94080 | 0.0159655 | 4.77851e-07 | 14 | 0.45 |
| ~ | 1028 | 1029 | 213.62827 | 0.0123459 | 3.69516e-07 | 120 | 1.00 |
| ~ | 1028 | 2595 | 205.14810 | 0.0222856 | 6.67012e-07 | 5 | 0.11 |
| ~ | 1029 | 2595 | 196.66874 | 0.0400831 | 1.1997e-06 | 123 | 1.00 |
| ~ | 1030 | 1035 | 230.98815 | 0.00369679 | 1.10646e-07 | 4 | 0.07 |
| ~ | 1035 | 1042 | 264.31336 | 0.000363741 | 1.08869e-08 | 203 | 1.00 |
| ~ | 1035 | 1053 | 209.67309 | 0.0162453 | 4.86225e-07 | 19 | 0.57 |
| ~ | 1043 | 1053 | 224.59740 | 0.00576798 | 1.72637e-07 | 37 | 0.80 |
| ~ | 1052 | 1053 | 210.37106 | 0.015474 | 4.63141e-07 | 32 | 0.76 |
| * | 1053 | 1196 | 509.46404 | 1.41898e-11 | 4.24703e-16 | 213 | 1.00 |
| 1053 | 1924 | 252.05787 | 0.00085259 | 2.55183e-08 | 97 | 0.97 | |
| 1053 | 1782 | 222.25334 | 0.00676783 | 2.02563e-07 | 40 | 0.82 | |
| 1196 | 1924 | 248.68640 | 0.00107997 | 3.23237e-08 | 276 | 1.00 | |
| 1196 | 1782 | 240.69689 | 0.00188352 | 5.63742e-08 | 219 | 1.00 | |
| 1196 | 2583 | 209.02923 | 0.0169958 | 5.08688e-07 | 255 | 1.00 | |
| ~ | 1202 | 1530 | 207.38999 | 0.0190604 | 5.70482e-07 | 28 | 0.72 |
| * | 1209 | 1315 | 641.44378 | 1.4536e-15 | 4.35067e-20 | 101 | 0.97 |
| 1315 | 1772 | 269.84790 | 0.000248129 | 7.42658e-09 | 106 | 0.98 | |
| 1315 | 1671 | 224.26547 | 0.00588951 | 1.76275e-07 | 105 | 0.98 | |
| ~ | 1318 | 1923 | 330.95847 | 3.52614e-06 | 1.05538e-10 | 61 | 0.89 |
| ~ | 1318 | 1772 | 267.66857 | 0.000288148 | 8.62433e-09 | 84 | 0.94 |
| * | 1319 | 1427 | 529.41568 | 3.53858e-12 | 1.05911e-16 | 194 | 1.00 |
| 1319 | 1536 | 212.11766 | 0.0137022 | 4.10112e-07 | 246 | 1.00 | |
| 1427 | 1428 | 291.55280 | 5.46626e-05 | 1.63607e-09 | 121 | 1.00 | |
| 1427 | 1536 | 197.70890 | 0.0372637 | 1.11531e-06 | 164 | 1.00 | |
| ~ | 1428 | 1530 | 199.54827 | 0.0328839 | 9.84223e-07 | 74 | 0.92 |
| * | 1436 | 1528 | 410.28274 | 1.41491e-08 | 4.23487e-13 | 246 | 1.00 |
| 1528 | 2131 | 209.50597 | 0.0164155 | 4.91319e-07 | 36 | 0.79 | |
| ~ | 1530 | 1531 | 223.33355 | 0.00629151 | 1.88307e-07 | 21 | 0.61 |
| ~ | 1531 | 1533 | 221.17582 | 0.00730553 | 2.18656e-07 | 26 | 0.69 |
| * | 1536 | 1666 | 435.98790 | 2.36537e-09 | 7.07963e-14 | 231 | 1.00 |
| * | 1671 | 1772 | 477.60581 | 1.30271e-10 | 3.89906e-15 | 113 | 0.99 |
| 1772 | 1923 | 260.02310 | 0.000490521 | 1.46814e-08 | 91 | 0.96 | |
| ~ | 1780 | 1783 | 207.55322 | 0.0187973 | 5.62609e-07 | 15 | 0.47 |
| * | 1785 | 1914 | 325.46377 | 5.16997e-06 | 1.54739e-10 | 60 | 0.89 |
| ~ | 1915 | 1919 | 291.22564 | 5.60098e-05 | 1.67639e-09 | 425 | 1.00 |
| 1917 | 1919 | 430.89445 | 3.37335e-09 | 1.00965e-13 | 245 | 1.00 | |
| ~ | 1919 | 1923 | 494.44660 | 4.04545e-11 | 1.21081e-15 | 251 | 1.00 |
| ~ | 1919 | 1925 | 277.56064 | 0.000144742 | 4.33215e-09 | 496 | 1.00 |
| ~ | 1919 | 1922 | 220.59789 | 0.00761661 | 2.27967e-07 | 550 | 1.00 |
| ~ | 1919 | 1921 | 216.52166 | 0.0100925 | 3.02072e-07 | 227 | 1.00 |
| ~ | 1919 | 1920 | 194.07350 | 0.0480166 | 1.43715e-06 | 221 | 1.00 |
| ~ | 1923 | 2131 | 268.90615 | 0.000264156 | 7.90627e-09 | 59 | 0.89 |
| ~ | 1924 | 2274 | 266.82091 | 0.000305694 | 9.14951e-09 | 103 | 0.98 |
| ~ | 1924 | 2583 | 197.90795 | 0.0367496 | 1.09992e-06 | 139 | 1.00 |
| * | 1926 | 2123 | 427.57974 | 4.24435e-09 | 1.27034e-13 | 231 | 1.00 |
| ~ | 2125 | 2132 | 343.07762 | 1.51939e-06 | 4.54758e-11 | 7 | 0.20 |
| ~ | 2126 | 2132 | 340.76390 | 1.78308e-06 | 5.33681e-11 | 8 | 0.24 |
| ~ | 2126 | 2587 | 236.01157 | 0.00260234 | 7.78887e-08 | 5 | 0.11 |
| ~ | 2126 | 2131 | 231.32407 | 0.00360793 | 1.07986e-07 | 27 | 0.70 |
| ~ | 2126 | 2128 | 225.52116 | 0.00539942 | 1.61606e-07 | 24 | 0.66 |
| ~ | 2126 | 2129 | 210.10314 | 0.0157452 | 4.71257e-07 | 30 | 0.74 |
| ~ | 2126 | 2271 | 206.54017 | 0.0202199 | 6.05188e-07 | 9 | 0.28 |
| ~ | 2127 | 2128 | 215.36303 | 0.0109322 | 3.27204e-07 | 227 | 1.00 |
| ~ | 2128 | 2132 | 318.65925 | 8.29755e-06 | 2.48348e-10 | 28 | 0.72 |
| ~ | 2128 | 2129 | 267.76453 | 0.000286151 | 8.56456e-09 | 50 | 0.86 |
| ~ | 2128 | 2133 | 223.38547 | 0.00626969 | 1.87653e-07 | 342 | 1.00 |
| ~ | 2128 | 2131 | 218.24833 | 0.00896792 | 2.68412e-07 | 47 | 0.85 |
| ~ | 2128 | 2130 | 212.10798 | 0.0137022 | 4.10112e-07 | 217 | 1.00 |
| ~ | 2129 | 2132 | 214.22656 | 0.0118417 | 3.54426e-07 | 34 | 0.78 |
| ~ | 2130 | 2132 | 278.08599 | 0.000139795 | 4.18409e-09 | 201 | 1.00 |
| ~ | 2131 | 2132 | 266.79277 | 0.000306759 | 9.18138e-09 | 31 | 0.75 |
| ~ | 2131 | 2271 | 197.79627 | 0.0371345 | 1.11145e-06 | 32 | 0.76 |
| ~ | 2131 | 2587 | 196.53416 | 0.0405029 | 1.21226e-06 | 28 | 0.72 |
| ~ | 2132 | 2271 | 344.98030 | 1.33123e-06 | 3.98442e-11 | 13 | 0.42 |
| ~ | 2132 | 2269 | 270.28117 | 0.000240484 | 7.19776e-09 | 163 | 1.00 |
| ~ | 2132 | 2133 | 268.20151 | 0.000277334 | 8.30068e-09 | 326 | 1.00 |
| ~ | 2132 | 2587 | 231.40861 | 0.00358294 | 1.07238e-07 | 9 | 0.28 |
| ~ | 2132 | 2274 | 225.22475 | 0.00551319 | 1.65011e-07 | 29 | 0.73 |
| ~ | 2132 | 2270 | 220.83847 | 0.00748542 | 2.24041e-07 | 363 | 1.00 |
| * | 2133 | 2269 | 306.04302 | 2.00054e-05 | 5.98768e-10 | 477 | 1.00 |
| 2269 | 2271 | 199.92690 | 0.0319827 | 9.57251e-07 | 164 | 1.00 | |
| * | 2271 | 2587 | 407.61583 | 1.70148e-08 | 5.09258e-13 | 10 | 0.32 |
| 2271 | 2274 | 383.02358 | 9.42643e-08 | 2.82136e-12 | 30 | 0.74 | |
| 2271 | 2272 | 246.51261 | 0.0012541 | 3.75355e-08 | 12 | 0.39 | |
| 2272 | 2274 | 235.67341 | 0.00266644 | 7.98071e-08 | 28 | 0.72 | |
| 2272 | 2587 | 230.28878 | 0.00388111 | 1.16163e-07 | 8 | 0.24 | |
| * | 2272 | 2586 | 203.32353 | 0.0252542 | 7.55866e-07 | 8 | 0.24 |
| * | 2274 | 2583 | 464.16036 | 3.32235e-10 | 9.94389e-15 | 82 | 0.94 |
| 2274 | 2587 | 322.67674 | 6.2819e-06 | 1.88019e-10 | 26 | 0.69 | |
| 2274 | 4023 | 255.50154 | 0.000670743 | 2.00755e-08 | 192 | 1.00 | |
| 2586 | 2587 | 207.94480 | 0.0183457 | 5.49092e-07 | 6 | 0.16 | |
| * | 2593 | 4019 | 475.38059 | 1.52359e-10 | 4.56014e-15 | 49 | 0.86 |
| ~ | 4043 | 4046 | 195.82738 | 0.0425209 | 1.27266e-06 | 200 | 1.00 |
| ~ | 4051 | 4052 | 202.22246 | 0.0272598 | 8.15894e-07 | 93 | 0.96 |
BPAIRS expected to covary 107.2 +/- 3.1 BPAIRS observed to covary 118 BPAIRS observed to covary possibly coding 112/118 (0.95%)
Job log: