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
Mail:
Rfam scan:
No hits were detected to the Rfam database!
R-scape on nhmmer alignment:
There is statistically significant covariation because of possible protein coding (pc) sequence
The alignment contains 1380 sequences with an average pairwise identity of 50.65%.
The secondary structure proposed contains 47 base pairs with 42 base pairs observed to covary, indicating covariation support for some of the bases in the proposed structure.
BPAIRS 47 avg substitutions per BP 131.7 BPAIRS expected to covary 39.5 +/- 1.7 BPAIRS observed to covary 42 BPAIRS observed to covary possibly coding 28/42 (66.67%)
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 |
* Base pair in the structure ~ Both residues unpaired in the structure, or no structure is present ' ' At least one residue is involved in other pairing in the structure
Alignment statistics:
None
R-scape on infernal alignment:
The alignment contains 1380 sequences with an average pairwise identity of 60.69%.
The secondary structure proposed contains 129 base pairs with 118 base pairs observed to covary, indicating covariation support for some of the bases in the proposed structure.
BPAIRS 129 avg substitutions per BP 140.5 BPAIRS expected to covary 106.2 +/- 3.1 BPAIRS observed to covary 118 BPAIRS observed to covary possibly coding 78/118 (66.10%)
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 |
* Base pair in the structure ~ Both residues unpaired in the structure, or no structure is present ' ' At least one residue is involved in other pairing in the structure
Job log: