stmv.conf
author Sam Bleckley <stm31415@gmail.com>
Sat Dec 03 22:20:10 2011 -0600 (5 months ago)
changeset 18 2d6f320c14a9
parent 10 3b583ecdce15
permissions -rw-r--r--
More fixes.
     1 # STMV;
     2 
     3 # Sequence info
     4 SEQ =  "AGUAAACUUACCAAUCAAAAGACCUAACCAACAGGACUGUCGUGGUCAUUUAUGCUGUUGGGGGACAUAGGGGGAAAACAUAUUGCCUUCUUCUACAAGAGGCCUUCAGUCGCCAUAAUUACUUGGCGCCCAAUUUUGGGUUUCAGUUGCUGUUUCCAGCUAUGGGGAGAGGUAAGGUUAAACCAAACCGUAAAUCGACGGGUGACAAUUCGAAUGUUGUUACUAUGAUUAGAGCUGGAAGCUAUCCUAAGGUCAAUCCGACUCCAACGUGGGUCAGAGCCAUACCUUUCGAAGUGUCAGUUCAAUCUGGUAUUGCUUUUAAAGUACCGGUCGGGUCACUAUUUUCGGCAAAUUUCCGGACAGAUUCCUUUACAAGCGUCACAGUGAUGAGUGUCCGUGCUUGGACCCAGUUAACACCGCCAGUAAAUGAGUACAGUUUUGUGAGGCUGAAGCCAUUGUUCAAGACUGGUGACUCUACUGAGGAGUUCGAAGGGCGUGCAUCAAACAUCAACACACGAGCUUCUGUAGGGUACAGGAUUCCAACUAAUUUGCGUCAGAAUACUGUGGCAGCCGACAAUGUAUGCGAAGUAAGAAGCAACUGUCGACAAGUCGCCUUGGUUAUUUCGUGUUGUUUUAACUGAACCUCGACAUAAGCCUUUUGGAUCGAAGGUUAAACGAUCCGCUCCUCGCUUGAGCUUGAGGCGGCGUAUCUCUUAUGUCAACAGAGACACUUUGGUCUAUGGUUGUAUAACAAUAGAUAGACUCCCGUUUGCAAGAUUAGGGUUAACAGAUCUUGCCGUUAGUCUGGUUAGCGCGUAACCGGCCUUGAUUUAUGGAAUAGAUCCAUUGUCCAAUGGCUUUGCCAAUGGAACGCCGACGUGGCUGUAUAAUACGUCGUUGACAAGUACGAAAUCUUGUUAGUGUUUUUCCCUCCACUUAAAUCGAAGGGUUUUGUUUUGGUCUUCCCGAACGCAUACGUUAGUGUGACUACCGUUGUUCGAAACAAGUAAAACAGGAAGGGGGUUCGAAUCCCUCCCUAACCGCGGGUAAGCGGCCCA"
     5 MODS = ".........................MM........M......M....M...M.M.......MM.M.....MMM.MM.....MM..........MMMM..........MM.......M...MM.....M...MM......M....M................M.....M......M.........MMM...MM.....MM.......MM....MM.M...........M...............M.M.........M................................................................MMM........M.............................M.M.......M.MM.....M.M...M..M..................M...MM.M.....M..MMM.....M..........M.....MM..M.......MM.................M........MM........M..MMM.M.MMM.M.MM...............MMM.......MM............M....M...............................................................................M......M.M.MM.........M...MM....MMM..M.....................................M...MMMMM....MMM................M.M.....M..............................M..............M..M.......................M...M...MM.M.M.................M...MM....MM....M.......M.MM.MM................M..MMMM....MMM.MMMMM........M...MMM...M................................................................................................................."
     6 
     7 WINDOW = 30 
     8 
     9 # helix info 
    10 LENGTH = 9
    11 TERMINAL_MISMATCHES = 3
    12 ASYMMETRY = 0
    13 MISMATCHES = 3
    14 BETWEEN_HELICES = [0, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
    15 HELICES = 30