motif.py

#!/usr/bin/env python
# encoding: utf-8
"""
msat/motif.py

Part of 454_msatcommander.

Created by Brant Faircloth on 2009-03-29.
Copyright (c) 2009 Brant Faircloth. All rights reserved.
"""
mononucleotide=(1,'A','C')
dinucleotide=(2,'AC','AG','AT','CG')
trinucleotide=(3,'AAC','AAG','AAT','ACC','ACG','ACT','AGC','AGG','ATC','CCG')
tetranucleotide=(4,'AAAC','AAAG','AAAT','AACC','AACG','AACT','AAGC','AAGG','AAGT','ACAG','ACAT','ACCC','ACCG','ACCT','ACGC','ACGT','ACTC','ACTG','AGAT','AATC','AATG','AATT','ACGG','AGCC','AGCG','AGGC','AGGG','ATCC','ATCG','ATGC','CCCG','CCGG')
pentanucleotide=(5,'AAAAC','AAAAG','AAAAT','AAACC','AAACG','AAACT','AAAGC','AAAGG','AAAGT','AAATC','AAATG','AAATT','AACAC','AACAG','AACAT','AACCC','AACCG','AACCT','AACGC','AACGG','AACGT','AACTC','AACTG','AACTT','AAGAC','AAGAG','AAGAT','AAGCC','AAGCG','AAGCT','AAGGC','AAGGG','AAGGT','AAGTC','AAGTG','AATAC','AATAG','AATAT','AATCC','AATCG','AATCT','AATGC','AATGG','AATGT','AATTC','ACACC','ACACG','ACACT','ACAGC','ACAGG','ACAGT','ACATC','ACATG','ACCAG','ACCAT','ACCCC','ACCCG','ACCCT','ACCGC','ACCGG','ACCGT','ACCTC','ACCTG','ACGAG','ACGAT','ACGCC','ACGCG','ACGCT','ACGGC','ACGGG','ACGTC','ACTAG','ACTAT','ACTCC','ACTCG','ACTCT','ACTGC','ACTGG','AGAGC','AGAGG','AGATC','AGATG','AGCAT','AGCCC','AGCCG','AGCCT','AGCGC','AGCGG','AGCTC','AGGAT','AGGCC','AGGCG','AGGGC','AGGGG','ATATC','ATCCC','ATCCG','ATCGC','ATGCC','CCCCG','CCCGG','CCGCG')
hexanucleotide=(6,'AAAAAC','AAAAAG','AAAAAT','AAAACC','AAAACG','AAAACT','AAAAGC','AAAAGG','AAAAGT','AAAATC','AAAATG','AAAATT','AAACAC','AAACAG','AAACAT','AAACCC','AAACCG','AAACCT','AAACGC','AAACGG','AAACGT','AAACTC','AAACTG','AAACTT','AAAGAC','AAAGAG','AAAGAT','AAAGCC','AAAGCG','AAAGCT','AAAGGC','AAAGGG','AAAGGT','AAAGTC','AAAGTG','AAAGTT','AAATAC','AAATAG','AAATAT','AAATCC','AAATCG','AAATCT','AAATGC','AAATGG','AAATGT','AAATTC','AAATTG','AAATTT','AACAAG','AACAAT','AACACC','AACACG','AACACT','AACAGC','AACAGG','AACAGT','AACATC','AACATG','AACATT','AACCAC','AACCAG','AACCAT','AACCCC','AACCCG','AACCCT','AACCGC','AACCGG','AACCGT','AACCTC','AACCTG','AACCTT','AACGAC','AACGAG','AACGAT','AACGCC','AACGCG','AACGCT','AACGGC','AACGGG','AACGGT','AACGTC','AACGTG','AACGTT','AACTAC','AACTAG','AACTAT','AACTCC','AACTCG','AACTCT','AACTGC','AACTGG','AACTGT','AACTTC','AACTTG','AAGAAT','AAGACC','AAGACG','AAGACT','AAGAGC','AAGAGG','AAGAGT','AAGATC','AAGATG','AAGATT','AAGCAC','AAGCAG','AAGCAT','AAGCCC','AAGCCG','AAGCCT','AAGCGC','AAGCGG','AAGCGT','AAGCTC','AAGCTG','AAGCTT','AAGGAC','AAGGAG','AAGGAT','AAGGCC','AAGGCG','AAGGCT','AAGGGC','AAGGGG','AAGGGT','AAGGTC','AAGGTG','AAGTAC','AAGTAG','AAGTAT','AAGTCC','AAGTCG','AAGTCT','AAGTGC','AAGTGG','AAGTGT','AATACC','AATACG','AATACT','AATAGC','AATAGG','AATAGT','AATATC','AATATG','AATATT','AATCAC','AATCAG','AATCAT','AATCCC','AATCCG','AATCCT','AATCGC','AATCGG','AATCGT','AATCTC','AATCTG','AATGAC','AATGAG','AATGAT','AATGCC','AATGCG','AATGCT','AATGGC','AATGGG','AATGGT','AATGTC','AATGTG','AATTAC','AATTAG','AATTAT','AATTCC','AATTCG','AATTGC','ACACAG','ACACAT','ACACCC','ACACCG','ACACCT','ACACGC','ACACGG','ACACGT','ACACTC','ACACTG','ACAGAG','ACAGAT','ACAGCC','ACAGCG','ACAGCT','ACAGGC','ACAGGG','ACAGGT','ACAGTC','ACAGTG','ACATAG','ACATAT','ACATCC','ACATCG','ACATCT','ACATGC','ACATGG','ACATGT','ACCACG','ACCACT','ACCAGC','ACCAGG','ACCAGT','ACCATC','ACCATG','ACCCAG','ACCCAT','ACCCCC','ACCCCG','ACCCCT','ACCCGC','ACCCGG','ACCCGT','ACCCTC','ACCCTG','ACCGAG','ACCGAT','ACCGCC','ACCGCG','ACCGCT','ACCGGC','ACCGGG','ACCGGT','ACCGTC','ACCGTG','ACCTAG','ACCTAT','ACCTCC','ACCTCG','ACCTCT','ACCTGC','ACCTGG','ACGACT','ACGAGC','ACGAGG','ACGAGT','ACGATC','ACGATG','ACGCAG','ACGCAT','ACGCCC','ACGCCG','ACGCCT','ACGCGC','ACGCGG','ACGCGT','ACGCTC','ACGCTG','ACGGAG','ACGGAT','ACGGCC','ACGGCG','ACGGCT','ACGGGC','ACGGGG','ACGTAG','ACGTAT','ACGTCC','ACGTCG','ACGTGC','ACTAGC','ACTAGG','ACTAGT','ACTATC','ACTATG','ACTCAG','ACTCAT','ACTCCC','ACTCCG','ACTCCT','ACTCGC','ACTCGG','ACTCTC','ACTCTG','ACTGAG','ACTGAT','ACTGCC','ACTGCG','ACTGCT','ACTGGC','ACTGGG','AGAGAT','AGAGCC','AGAGCG','AGAGCT','AGAGGC','AGAGGG','AGATAT','AGATCC','AGATCG','AGATCT','AGATGC','AGATGG','AGCAGG','AGCATC','AGCATG','AGCCAT','AGCCCC','AGCCCG','AGCCCT','AGCCGC','AGCCGG','AGCCTC','AGCCTG','AGCGAT','AGCGCC','AGCGCG','AGCGCT','AGCGGC','AGCGGG','AGCTAT','AGCTCC','AGCTCG','AGCTGC','AGGATC','AGGATG','AGGCAT','AGGCCC','AGGCCG','AGGCCT','AGGCGC','AGGCGG','AGGGAT','AGGGCC','AGGGCG','AGGGGC','AGGGGG','ATATCC','ATATCG','ATATGC','ATCATG','ATCCCC','ATCCCG','ATCCGC','ATCCGG','ATCGCC','ATCGCG','ATCGGC','ATGCCC','ATGCGC','ATGGCC','CCCCCG','CCCCGG','CCCGCG','CCCGGG','CCGCGG','CCGGCG')