pattern clusters.py

genome = 'AGGATTGGCAGTACTGCTGCGTGAACACGCGATGCGTTTCGGGTAACGACTTCCACCCGCTTAAAGATAACAAAAATGTCTAATAAACAATCGGTTGTATGAAATTATGCCAGTCTAGCCCAAGAGCATTACATCTGGTTCCATAAATACGGTCGGCTTGTCGCCAGCGGCTTAGTCGCGGATTAGCGTAGTCCGAGGTTACCCTTTCCCTCCCACTCGAACGGACGATTGTGCCTACATCTTGGTCTGCTTACCAATTCCATACGCAGCCATGCCTAATTCAGCTCTGTAGGCTATGGTCACCACGTAGGAACTATTCGACTGTACCCACAAGCGCGTGATTCGGATATTAAACTCAGGAGGTCACTTGGCGTTCATGGATACCACACAGAGCTATTTATGGATATTAAAACCCAGAATACGATACAGGATGTAATTGACCCATACTGCTTATGAAAAATGTGCCTCTGAGCTCATCGACGATAGTTTATGTACTCGGTTTCTGGGTTATGCTGCGGTCCGTAATCCATCTCCGCCGCGGGAGCCTAACTCCCTCCACTAGGAAGTGACCATACGAGTGTGCGGGTTGGGTCACCATAAGGCGCTGGTCAACTGATGAGTCAGACCTGGACGCGGTACCTCTCTAGTTCTCCTTTGCGTGCCCGGTTGAAGATCACGATGTGTTCGTCCCAGGAAACGGCGGCTGGCTGGCTCGGGTAACTAACCCTCAGAGCTCACAGAGGGGTGCTACGCACGGAAGATATAACCTGTGACTTATACGTCAACTCTACTGTATGCTTCGTCCGGCCTCACTGTATTGACCAGCACGTTGCATGGGAAACATGAGGACACAGCGTGACAGACTTTCATAGGCGCCGCCTCTGAGGGGCGCGCCCGGTAGTACCACTAAGCGCCCTCGAAAGCTGTTCTGGACGCCTGGTTCGGGGCGTATTAGGGATTGAATAGGGTAATGCCTGCAAGACTGGCATAGGCTCGAGTTTTTCTTCAGATTAACATCCTTAGACAAAGTAAGGTAAATGTTACGCGTTAGGCTATGCAACGTCCCACAATTAAATGTCCACGTCGAATTGTGGCTCGTGATGTGTACTTCAATCAGGGTAGATAGTCGTAGCCAAGTTGTAGAGCATCACCAACTGTTACCACCAACTGTTACCATAACAACGCCAACTGTTACCGTCGATCCAACTGTTACCGGATGTTCTTAGGACCCGTCGCCAACTGTTACCGTTCCAACTGTTACCTTACCACTAATTGGTTAGCTCCAACTGTTACCTATGGACCAACTGTTACCGCCAACTGTTACCCGCCGCCAACTGTTACCGGAGAAACACCTAACTTCTGGAGAAACACCTCCCCAACTCCAACTGTTACCCTGGTGGAGAAACACCCCGGGTCTTGGAGAAACACCAACTGTTACCTCCAACTGTTACCACGAGGGAACAACCTCCAGCAACCTTGACTGCCACTTACCAACTGTTACCTAATTGTTCCAACCCAACTGTTACCAACCCAACTGTTACCGCTGAATGCCCAACTGTTACCCACTGCCAACCCCAACTGTTACCTAACCCCCAACTGTTACCTTACCGAGAAACACCCTTTCATGGAGAAACACCCACGTAAGGGTGCTGCATCTGCCAACCCAACTGTTACCAACTGTTACCCAACTGTTACCAACACCCACCCCGCCCAACTGTTACCTGCATCTGGAGAAACACCATGTACTGTGGTGTTCTGGAGAAACACCTGATGGAGAAACACTGGTGGAGAAACACCCCCTGGAGAAACACCGGCGGTTGTGTGGAGAAACACCCCTGGAGAAACACCTGCTGCATCTGTGCTGCATCTGAATTGCTGCATCTGTGGAGAAACACCGCATCTGACTGTGCTGCATCTGAAAAAGCTCTGTAGCCCCACTAATTGTCGATGCTGCATCTGAGATTTGTGAGCGCGAGGCGTGCTGCATCTGAGGTGTTGTTCGCTATCTAGTTTGAGCTGATTCGCTGCTGCATCTTGCTGCATCTGATGGATAATGCTGCTGCATCTGATCTTGCTGCATCTGATTGGTTCCTGATGATGCTGCATGCTGCATCTGACTGAGACTTATAGGTGGTCCCCAGTACCATTTAGAATAAAATCGGAACTCCCGCTGCGGCACTGTTCGTCTGGTTTCACAGTATCCGATAGCGCCTCACATAGATCCTATAATAGTATCCTACCCCTTTGGAGCTCTTTGAGGCTATGACCACGTTAATTCCTGAGCATACATCAATCAACGATGACGTACTGATCCGGGACAGGCATATTCTCGGTGATCCGGGACAGTATGTGGCGATCCGGGACGATCCGGGACAGTCCCATGCAGCTGGTAATCCAGTCGTGCTGACCGATCCGGGACAGCCGGGACAGGCAGATTGTCGGATAGGATCCGGGACAGCGGGACAGGCTATGGGCTTCCCGATCCGGGACAGAATGGTGCGCGGATCCGGGACAGTCGAGACTCCGCCGGGGTAGATCCGGGACAGCAGATGTAGGGCCGTAGGAGCTCTGGTACAAGATCCGGGACAGCGATCCGGGACAGGTACACCACCGCTGAGTTGGACCGGATGCCTCGATCCGGATCCGGGACAGTCGGCGGATGCTCACTGTCCTTAGCTTGTTCATGCAGATCCGGGACAGGGGATCCGGGACAGTTAAAGCAACGTTCCCTAATTGGTGGCAAGCAACGTTCCAAAGCAACGTTCCGACAGCGAAGCAACGTTCCCGGGACAGCAAGCAACGTTCCACAGGACAGCGAAGCAAGCAACGTTCCAACGTTCCAAGCAACGAAGCAACGTTCCAAGACGCCGATCCGGAAGCAACGTTCCCTTAAGTGAAGCAACGTTCCATATCTGCCGCGCGCCGCTCAATAATAAGCAACGTTCCTAGGACGTTGCATAGGTACGAGTAGCCTCGAGCTCAGGAATAAGTGAGCAACGCAAAAAGCAACGTTCCTGTAAACTATAGAAAGCAACGTTCCTTCCTATCTCTCTTGAGGAAGCAACGTTCCAGCAACGTTCCCGTTCCATATGGTTTTCCCCTTGTAAAGCAACGTTCCTCCTTCCGAAAAACACGACGATCTTATGAAGCAACGTTCCCGCTAAATACGTAAGCAACGTTCCAAGCAACGTTCCGGAAGCAACGTACTTGGCAGGACACGTTCCTTCCAGACTTGGCAGGACAACGTTCCGAAAAGCAACGTTCCTGGCCCGTATCCGCGCCAAGTAACTTGGCAGGACTCTAGTACATCCGCGCCAAGTCGCGCCAAGTCCAATCCGCGCACACTTGGCAGGACTTGGCAGGACGCCAAGTTAGGAAAACTTCCTGGTACTTGGCAGGACATTCCCTACCGTATACTTGGCAGGACACGACCAAGTAATATAACTTGGCAGGACACTGGCAGGACCTTGGCAGGACGTCGCCAAGTACTTGGCAGGACAGGACCCCCTCTAGGACGAGCTTGTCTCCAACTTGGCAACTTGGCAGGACAGTAGTCCCTCCCCTCTCCGCACTTGGCAGGACCGCGCCAAGTCCATTTCCGCGCCAAGTACTCCGCGCCAAGACTTGGCAGGACCAGGACCCTTGGCAGGACAGACTTGGCAGGACTTGGCAGGACTTGGCAGGACGCGTTGCCTTAGCTGCGATCTCCGCGCCAAGTGCTAGGACACTTGGCAGGACAAGTTATTGAACTGCAACTTGGCAACTTGGCAGGACTTGGCAGGACTTGGCAGGACCGCGCCAAGTTCAAGTAGGTTCCGTCCGCGTCCGCGCCAAGTAAGTGCTGACCACATCACACTGTTTTCCCTCTAGGACGTTTATGGCCACCCTCTAGGACGGCAGCCCTCTAGGACGGCGTTAGTTTATATTCCGCACGTTAGCGGTTACCCCTCTAGGACGAGGACCCCCTCTAGGACGGGACCCCTCTAGGACGGGACGATCCCTCTAGGACGATCCCCTCCCCCGTAGTAGGCGGTAGTAGGCGTCCGTAGTAGGCGTAGCTCCGTACCGTAGTAGGCGGTAGGCGGTATCTGCCCGTAGTAGGCGCGTACCGTAGTAGGCGGTCTTGTCTGGCTTACTCGGGTGCCCGTTCCCGTAGTAGGCGAGGCGACCACTTATATTGCCGTAGTAGGCGACCGTAGTAGGCGACTGAATATGGCCGACTTCGCCTGTTCTGTTCCATGCTCCGTAGTAGGCGCCGATCACGCGCGAGGACGTTCGACTTGTCACCGTAGTAGGCGTCCAACGACCGTAGTCCGTAGTAGGCGCGTACCAAAGCCGTAGTAGCCGTAGTAGGCGCCCCCTAATTGCTAACTGCTACTATCGATTGCCCGTAGTAGGCGCCATTGGACCTGCAAAAATTGTGATACGCCACCGTCCGTAGTAGGCGTAGGCGCGAGACTGTGGGAACCGTAGTAGGCGGTAGTAGGCGGGCGCAACGTAAACCTCGCCTTGACGAGAGTAAAGCTGCAACCGTAGTAGGCGAGGCGGCAGCCGAGCCGTCCGTACGTTAGACTTGCAGCTAGCTTGGTACTAACAGTGTTGATAATCTCCGCCAAGCAACGTTTCACATAGGGGCTGGGGTCAAAAGTTAAAACCCGCGCGAATTTCTCGCACCATGTTTGGCGCGGGTACTGTCCTAAGGTAGTCGGTGGGCTCACGAACTCGGTCCCGTCCTGCTTCGAGGGCTTGTATCCAACATTCCGGAAGCTTGACTCTAGGACTGCCATCCGATAGCGGACTCTAACATAACTGTTTTAAACTTGCGACTCGACCTAGCACGAGACGTCGGCCAGTGATGCTCACACCTACAGTTGCATCCCCCGATCAGAACGGGCGTTTTGTCATGGTCTCGAATATGGCAATAATACCGCGACTACGTGGTCCCGCTAAGTATTCAATTACTAGGTCAGTCATGCGGTATCCCGATAATTCTGACTACGCTTTTAAGGCGCGTGCGAATTAGCCTCTAGGGCTCCTATTCATCTAGACAAAATTAGTCTCGTGCCGCGTCGAAGTACACTCCAGCCGGGTTTTCCACACGACGGATATCCGAGATCCTTAGAAGCCGGGTTCTGTCGATTGTTAAATACTTCGCAAGGGAAGGTTGTCGCGTCGAATACCTCTATCAGGATTGTTGCTCACTATAGTCCGGAAAAGGGATAGTCCGGAAACAAAACTTAGTTAGCAAGACCAATAGTCCGGAAACTTCAAACAGGTAAGATAGTCCGGAAAGAATAGTCCGGAAAGTCCGGAAAGTAGTATTGTCATTTAGGATAGTCCGGAAAAAAAAATGGGACATAGTCCGGAAAATAGTCCGGAAAGGAAAGACAGTACCTCAGCCCACCCAGCAACCGGATTGGTCAGGAGATAGTCCGATAGTCCGGAATAGTCCGGAAAACTCTGTATCATGGGATTTCTCATAGTCCGGAAAGGGGTATCGGAATAGTCCGGAAAGGACATAGTCCGGAAAAAACATTATGCCGTATAGTCCGGAAAGTGACCGGCATAGTCCGGAAATAATAGTCCGGAAAAGGTGTGGATATGTTTTTCACATAGTCCGGAAAATAGTCCGGAAAAATCAAACTCAAACTCGCTCTGTATAGTCCGGAAACACCCAGAATAGTCCGGAAAAATCTGTATAGTCCGGAAACTCTCTAGCAACTATGTCGTATAGTCCGGAAAAAAATTTCCGGTCCCATCCATAGTCCGGAAACTATAGTCCGGAAAGTCCGGAAAGGAATCGAATTCAGTGTGACGCAGACCGATGTTGTTTCCAGGGAGTGTTTCCAGGGAATTGTTCTAATGGTGGATTCAGAGAACTTAGAGTTCTTACCCCGCGTGAACAATGTGCCAGTCTGTTTCCAGGGATCCAGGGAGAACTAAACCTGTTGTTTCCAGGGAGGCTGATTCATAATCAATCGCGTGTTTCCATGTTTCCAGGGATATGTCGGGACTCATAAGATCATCCGGGTAACGTTTTTGTTTCCAGGGAGTTTCTGTTTCCAGGGATTGTTTCCAGGGAGTATATGTTTCCAGGGATCCATGTTTCCAGGGACACACCCGACTAAGTGTTTCTGTTTTGTTTCCAGGGATCTTGTCGTCCCTCTTTCCAGGGATGTCGTCCCTCTTACTGTGAATGTTTGTCTGTCGTCCCTCTTTATGTTTCCAGGGATTGCGACTGTCGTCCCTCTTGTCGTCCCTCTCCTCTCCCTCTCTTCCTCTTCTTGTTTCCAGGGATTCGTGTCGTCCCTCTACGCAGATTACTGTCGTGTCGTCCCTCTCTGTCGTGTTGTCGTCCCTCTAGGTTGTCGTCCCTCTGTCGTCCCTCTTCCCTCTCTCTTCTTAGGTTGCAGCGAGAGTCGATGTCGTTGCCTGACAACTCGGGCTACGCATTCCCCTTGGTCTGTCGTGTCGTCCCTCTCAATAAACAAGCTGTCGTCCCTCTTGTCGTCCCTCTATACCTATTTTCGGTTGGTGACACAAATGGCATTTTGTCGTCCCTCTTGTCGTCCCTCTTCCCTCTTCTGTCGTCCCTCTTTGGATGGTAATCCATTAGCACCTAATCCATTAGCACCATTAATCCATTAGCACTGATGGGCTGTTATCCATTAGCAATCCATTAGATCCATTAGCACGTCCCTATCCATTAGCACCGTACTGTCGTCCCTCTCCATGATGTGATGGCCAATCCATTAGCACATCCATTAGCACATGATGCTGAACCCCTTTATTGCTCTCAGGAAGCCAATCAATCCATTAGCACTAGCACCATCATCCATTAGCACACGGCCATGATGGATATCCATTAGCAATCCATTAGCACCATCCATTAGCACCCCATGATAATCCATTAGCACATGTTTCTACGCCATGATCCATTATCCATTAGCACATGCATGATCCATTAGCACCACGATGGCCATGATGGCCATGATGTGATGCGGAATGGCCATGATGCATATGTGCCGACGCGCTACGTGACCACTCCCATTGTAGCAATCCATTAGCACCATCCATTAGCACCACCCGGCCCCCAACTGTCCTTGCGAGACTATCCATTAGCACATGAGTATCCATTAATCCATTAGCACATGATGCTCTCTATCCATTAGCACGATGGCCATGATGGGCAGTCAATTCTAGAAGCTCTCTCTAGACATACGATCGCTTGCTATAATTATCCTGGGCGAGTAAAGCTCATTAAGAGATACATTGATAGGACATAAGCTAGTCGCTTAGGTATCTTCCGCCACGACCAAAGGTGCATCACGATACTCTTTTAAGAAAGGAGAAAAGCTTGCGCAAAGTCCCTAAGCGTCCGAGAGGCAAGGTTTCTGTCTAACAATATCAAGCCGTCCCCCATGGCAGAGGGAGATCGCCACAGGAGCGCAGGTGATGGTAAGCATCCCCCGGGAACGTGAGACCGCGAACGCCGCACTTACTGGAGGGATTTATCCTTTATCCCGTCCAACAACCATGGAGACAAGAGGAATAGGAATCATCTACCAGCGGTTACTGATCCTGCGATCCCATGTGTTTGGTTTGGGTCTGCCGGATCATCATTCCCGAACCGCCCCATGGAGAGTTTAAAAAGGGAGGTAGTAATACTGGGTCAAGTTGGCCACCTCATAAACCCCTCATAAACTTTTCTGTGTACGGGACGACTGCCCGCTCCCCTCATAAACTTGTACATTACTGATATAATCTAGATGCTCCCCTCATAAACCCTCATAAACTTCTCCTCATAAACCTCATAAACTTGGCCCGCACAGCATAAGCCTCATAAACTTATTAGCGGGAATTTTTTTATTCCCTCATAAACTTTGTAGAAAGGACTTCTTGTTTGCCTTCCTCATAAACTTCCTCATAAACTTCGCAGACACCCTCATAAACTTATAAACTTCATAAAGTCAGCCTCATAAACTTTCATAAACTTTTGCAAACCTCATAAACTTAGCGCTGCGTAAGAAGACTTAAACCTCATAAACTTAATTAGCGCTGCGCGCTGCGTAAGTCATAAACTTGGCGCTGCGTAAGGGTCATACATACAGTAAGGGGGTTCAAGAATAGGAGTAACCAACCGGGTGCCTCATAGCGCTGCGTAAGTGCGTAAGGGCTGCGTAAGATAACCTCATAAACTTAGACGCGCTGCGTAAGTTCGTCTACCCTCATAAACTCCTCATAAACGCGCTGCGTAAGGCGCTGCGTAGCGCTGCGTAAGGCGGCGCTGCGTAAGCTGCGCGCTGCGCGCTGCGTAAGATATTTGTTAGGCGCTGCGTAAGCGTAAGGCGCGCGCTGCGTAAGGCGTAAGTGCGTAAGTCCAAATCATCCCGTGCATGGTTCTCCGCGCTGCGTGCGCTGCGTAAGTAGCGCTGCGTAAGAACAGGGGATTAGTTGGCCCTTCTCAGGTGACTATGCGCTGCGTAAGCTGCGTAAGTACCTGCCCCGCGCTGCGTAAGGCCAGCTGCGCTGCGTAGCGCTGCGTAAGCTGCGTAAGCTTCTGCGGCCCCCACACTGTTCTGCGGCCCCCTGCGGCCCCCCATCTGGTGTCAGACCGACGGCTCTTCTTTCTGCGGCCCCGGCCTTCTGCGGCCCCGAGGATTCAACCATTTTCTGCGGCCCCCCCCCTCCTCGGTTCTGCGGCCCTTCTGCGGCCCCCTTCTGCGGCCCCTTTCTGCGGCCCCCTGCGGCCCCCGCGCTTCTGCGGCCCCACTATTGTAATGCAGATTCTGCGGCTTCTGCGGCCCCCTGCCGGTCTACGTCACGTGTCAAGGGATGGACATTCTGCGGCCCCTTATTTCTTCTGCGGCCCCAGCGTTCGAATCCTCCCAAATCCCGGCTAGACACGTTCTGCGGCCCCAGTTCTGCGGCCCCGCTTCTGCTTCTGCGGCCCCTAAGGTTCTGCGGCCCCGTTCACACATATAGTTCTGCGGCCCCTCGCGCTTTCTGCGGCCCCCGGCCCCAGTAAAAGATTGTTCCAACTCATATCAACACGCAGAAATTCTGCGGCCCCCGGCGTTACCGCCTAGCCATAAAATAGGCGGCCAAGCCGAGTCTACCGCAGTTCTCGTTACTAATACCTGGACACTACTAATGACTGCAGAATAATACGGCCGCCCGAGACTGTAGAAACAGACTCATCTAGGGGCAATGTTGCGCCCCTAAGGGGAGGTCGACAGTTACCTACCCCACTAGACCTTAGGCGATAGGCGTGGGCGATA'
k, L, t = 12, 492, 17

out=[]
for i in range(len(genome)-L+1):
    string = genome[i:i+L]
    c={}
    for j in range(len(string)-k+1):
        kmer = string[j:j+k]
        if kmer in c:
            c[kmer] += 1
        else:
            c[kmer] = 1
    for key, v in c.items():
        if v >= t:
            out.append(key)

print(' '.join(set(out)))