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BestPal Window help
BestPal_window -
the program for searching best "linear" rna secondary structure for long sequences with a window moving along the sequence.
Output example: Program PestPal (Softberry Inc.) | Version 2.2w FoldRNA Vienna format: Length: 590 Energy: -70.1 10 20 30 40 50 60 UAUUAUCGUGUGCAGUUAAAAUUGACUUUUUAAUGCGGCUCCAUUUUUGGGUCGGUGUUU ............................................................ 70 80 90 100 110 120 ACUAUUUGAUCAAGGGCUUAAAUAUUUUUGUCUUAAUACGAAAAAACGCACAGAUUUGGU ............................................................ 130 140 150 160 170 180 AAAGGCUUAACUUAAAAUUUCAGCGCCCAAUCACCCCCUUCAGAGUUGCCACACGUUGUU ............................................................ 190 200 210 220 230 240 ACACUAAGUUAUCGAAACGAACAGCUGAUUUUUGUUUUGUAAUAUUUGAGGUUGGUUUUU ............................................................ 250 260 270 280 290 300 GUUGGCUGAAAUAUUAUUACAUUAAAUUAGAUAUGGACCUUUUACUUCAAAGCGUUUGAC ............................................................ 310 320 330 340 350 360 AAGUUGAACAUCAAACGGAAAUCUAUUAUAGCCCCAAUUGGCGAGACCAUCAAAUAAUCA ..............................(((....((((.(((((((((......((( 370 380 390 400 410 420 UUGGAAAACAACCUGAGAUGAGUUUUCCAGACAAGGCGGAGCGCAAAAAGUGCUGGAACA (((.....)))..))))))).)))))))))....)))....................... 430 440 450 460 470 480 ACCGGGACGAGUAUUGGAAAUGUCUCGAGGAGCACGCCCCAAAGCACAGUUCUACCAGUG ............................................................ 490 500 510 520 530 540 GGGAAAAGGUACCAACCCCCUGCCAGAGUCUUCGCAAAUCAUUUGAGCAAUCCUGCCCUG ............................................................ 550 560 570 580 590 GUCAAUGGGUAAAGCACUUCGACCGCAAGCGUACUUAUGACCAGUUUAAG .................................................. FoldRNA GCG format: Length: 590 Energy: -70.1 1 U 0 2 0 1 2 A 1 3 0 2 3 U 2 4 0 3 4 U 3 5 0 4 5 A 4 6 0 5 6 U 5 7 0 6 7 C 6 8 0 7 8 G 7 9 0 8 9 U 8 10 0 9 10 G 9 11 0 10 11 U 10 12 0 11 12 G 11 13 0 12 13 C 12 14 0 13 14 A 13 15 0 14 15 G 14 16 0 15 16 U 15 17 0 16 17 U 16 18 0 17 18 A 17 19 0 18 19 A 18 20 0 19 20 A 19 21 0 20 21 A 20 22 0 21 22 U 21 23 0 22 23 U 22 24 0 23 24 G 23 25 0 24 25 A 24 26 0 25 26 C 25 27 0 26 27 U 26 28 0 27 28 U 27 29 0 28 29 U 28 30 0 29 30 U 29 31 0 30 31 U 30 32 0 31 32 A 31 33 0 32 33 A 32 34 0 33 34 U 33 35 0 34 35 G 34 36 0 35 36 C 35 37 0 36 37 G 36 38 0 37 38 G 37 39 0 38 39 C 38 40 0 39 40 U 39 41 0 40 ... |
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