DeadlineWasYesterday

Pairwise2 gets stuck forever

2

Biopython 1.79, pairwise2 alignment with the following two sequences runs forever: seqA = 'ATGAGACCATCAATACCTCTTGACTATGCTCTCTTCCAACTCTCCCCAAAGCGGTCAAGATGTGAATTGTTTGTCTCTACTGCGGGGTATACTGAGAAGATTGCTTCTGGACTGGTCAAACCGTTTGTTGCTCATTTGAAAGTCGCTGAAGAGCAGGTGGCCAGGGAAGCTCTGTCTATAAGGCTACAAGTTGAGAGCAGCAAAAATGCTGGAACTTGGTTTACTAAAGCGACGCTCGAGAGGTTTGTACGCTTTGTTAGTACCCCAGAGGTTCTGGAATTGGTTAGCGCTTTGGATGAGGAAATGTCTCAGTTAGAGGCTGCCCGTAAAATATACGGCGAGGGGACTGGTGACCAGCGATCTGGTGCAAAAGATGGCACAGAAACTACACCAGCGGCTGATGTGACAAAGAAGGAGCTACTGAGAGCTATTGATTTACGGCTTGCAGCAGTTAGACAGGACTTGGAAACTGCTTGTAATCGTGCTTCTGCTGCTGGTTTTAACCCAATCACTGTCCCCGAACTTACTCAATTTGCTGATCGATTTGGAGCCAGTCGCTTGAATGACGCATGCACCAAGTTTATAGCAGTTTGCCAGAGAAGGCCAGAGCTTATGAGCTCTTGGAGGTTGTTCAATCAGGAACAAGAAGCTATACGTTCGTCATGGGAATCTGATATGTCAATTGATGATCCCACTGAAGATCCATCCAAAAACCTGGGAAGTGGTATGGAAGAGAAAAGTGTAACAGCGACCAGATACTCCCAGCAAGAAGCAAAGCTTATGCCACAGAGTAGTCATGGTGAAAAGGATGAAGAAGAGGAAAAAACTCCTGTGCAAAACGAGCCATTAGCAAGCCAGACTAGGCAACTAACGAGACGGCTCAGTGTGCAGGAGAGGATCAACCTATTTGAAAACAAGCAGAAAGAAAACTCTGGAGGGAAAACAGCTGTGGTGGTGAAACCCACTGATCTGAAAAGGCTCTCTTCTGATTTATCATCTTCCGCAGGGGTGGAAAAAGCTGTGGTACGGAGATGGAGTGGTGCTAGTGACATGAGCATTGATTTGGGAAATGATAGGAAGGATGTGGCTGGTGATAGTCCCTCGTCGTCATCAGTGTCCAAAGATGGAAGTGGTGGTATATCTTCAAAACAATCTGTTGGATGCAATAAAAGAGAGCATAACGGGTTGAGTCATACTGAGAATCCTCATAAGAATGAAGATGAATGTAGTTCCAACAGTACTGGTGACATGGGAACGGATAAAGTAGAGTCCCATAAATCAAGCTCTCCTTTCTTACGGAAAGACAAGGAGGTAGACTTGAAGGTGCCTTTGGATTACTCAGGGAATGCAAATATAGATGATGAGTCCAATAACAAAATTGGAGATTTTGAATCAGATAAGCAGGATCAAATACAGTTTAGAGATCCTCGGAGTCATTCATTGTCTACATTACATCAGTTAAGTGGTACTGAATCTAGTCTCACTAGTGTTCGGAGCAATGGAGGAACTGCGGAGTCTCCTAGGAGAGAATCTTCAGCTACTAGGCAATCACCACCAGCTGAGGATCGCCAGGGAAAGACACAACTCTATGGAGGTACTGAACAGATGAGAAGACCACATGGTAGAAGGGCTGAAACTGGTTCTGCCGATGTAAATAAAAAGCCACCTTCAGCCATTAATATTAGTGTGTCAGACATCTCAGAGAGTGATACTTTGAACCAAATGTCCCCGGCAGAGCAAGTTCAAAGGGCCAGAGCCTCTAAGGGAAGTCAAGAGCTGAATGATGAATTGAAAGTGAAAGCAAACGAGCTTGAAAAGCTATTTGCTGAACACATGCTCCGTGTCCCCGGGGATCAATCCAGTTCTGTCCGTAGAGGCAAGCCTGTAAAGCCGAGTGAACAAGCTGTGACGTCACAGCTCAGAAGACCTGTAGCAGAGGATCTAATCACAAGTTCAAATGATGAAGACAAGTTCAAAACTCCACCAACTGTGAAGGCGGTTGCTAACAGTGACTATGGAGACACCACAAGGCAAAAACTTCCAGAAATCAGCTTTTCAGATAGCTCTAGAGGAAAGTTCTATGAGGAGTATATGCAGAAGAGAGACGCCAAGCTGAAGGAAGACTGGAGTTCAAGAAGGACCGAGAAGGAAGCCAAGTTGAAGGTGATGCAAGATGTACTTGATCGCAGTAACGCTGAGATGAAAACCAAGTTTTCTCAGTCTACTGCAAGACGTGACTCAGATGCTAGACGTGCAGAGAAGCTTGTGTACTTCAACTCTAGGCTTAGTGCTAGACAGGATCAGCATCCAATTAGCTCATTCCAGAGTGAAGAAGAGGAAGATGTTTCCAGGAGCACACAGAATACGAAGCTACAACAAAACAAAAACACTTCTCGAACCATTACTACATCAGCTTCACGCTCTGCAGCCAAAGTGTCTACACCCAGTTCCGCTAGGCGGAGAGGACAAGACAAGCTTCTTGCACAGTCAGTCCCTAACTTCGCCGAGTTCAAGAAGGAAGGCATGAAGCAACCATCCTCAGGAGTTGGGAGAAATGGTGTCCGCTCACAGGCGAGAAGCTCCGTGAGACCGAAGGCTGTAATAACTGAAGAAGAGAAGCTGAGAAGGCCGACAAACTTCAGAAAAGTTGCTGCTGAAGCTGCTGCTCCAGAGGATGATGCTGTTTCTGTACCTCTGAATCTTGAGCAAGAGCAAAGCGGGAGAAAGGCTTCAGAAGGATCCGATGCATCAGACGAAATGGAGAAAGAGGAGGTGGAAGATGTGCTTGGTGATGACACAGAAGCTGAAGCTTTTACTGACGCAGAAAACGAGAAGTCAAGACTTAGTCAAGACTTTGAAGATGGTGAATCTATAGCTTCTCAGCTTGACCCTGGTTCAAACGCTGAGTTACCTATAGCTTCTAGGCATCACCAAACCATCGGTTCGTTTCTGGATGCACGAGTGAAGCAGCAGCAGTATCAAAACGAGGCATCTGAGCTTGATGCTTCAGTGGACTCTCCAGTGGACAGTCCTACTTTCTGGAGCCTTAGCCACACAGAGAATGATACAACTCAAATGAGAAAGAAATGGGGAGCTGCTGAGAATAAACAAGATGTGACGAAAGGGTTGAAAAGGCTTTTGAACTTTGGAAGGAAGAACCGTGCGGCTGAGAATTTGGCTGACTGGATATCCGCTACGACCTCTGAAGGGGATGATGATACCGAAGATGGAAAAGATCTCGCGTATAGATCATCAGAAGACTTGAGAAAGTCGAGATTCTTACAAACTCAGCCCTCTGATGATAGCTTCAACGAGAGTGAGCTATTCAATGAACAAGCACGAACCACTAGCGCACCATTGAGCTTTAAACTGAAGGAGGATCAGATGTCTGGAGCTTCTGTAAAAGCACCAAGGTCATTCTTTTCACTCTCCAATTTTCGAAGCAAGGGGAAATGA' SeqB = 'ATGAGACCAGCTGCTGCTATACCTCTTGACTATGCTGTCTTCCAACTCTCTCCAAAGCGCTCAAGATGTGAATTGTTTGTCTCTACTGCGGGGAACACTGAGAAGCTTGCTTCTGGTTTGGTCAAACCTTTTTTTGCTCATTTGAAAGTCGCTGAAGAGCAGGTCGCCAGGGAAGCTCGGTCTATAAGGCTACAAGTTCAAAGCTGCGAGAATGCTGCAACTTGGTTTACTAAAGGGACACTCGAGAGGTTTGTACGCTTTGTTAGTACCCCAGAGGTTCTGGAATTGGTTAGCGCTTTGGATGAGGAAATGTCTCAGTTAGAGGCTGCCAGAAAAATATATGGCGAGgGGACTGGTGATCAGCGATCTGGTGCAAAAGATGGCACAGAAACTACAACAGCAGCTGATGTGACAAAGAAAGAGCTACTTAGAGCTATTGATTTAAGGCTTGCAGCAGTTAAACAAGACTTGGCAACTGCTTGTAATCGTGCATCTGCTGCTGGTTTCAACCCAGTCACTGTCCCCGAGCTTAGTCAATTTGCTGATCGATTTGGGGCCAATCGCTTGAATGAAGCATGCGCCAAGTTTATTGCACTTTGCCAGAGAAGGCCAGAGCTTATGAGCTCTTGGAGGTTCAAtcaggaagaagaagctataCGTTCGTCTTGGGAATCTGATATGTCAATTGATGATCCCGGTGAAGTCCCATCCAAAAACCTCGCAACTGATAGAACCCAACAACATAGAGAACATCGAACTGATATGCAACAGCAAAGTGCAACAGGAAGCAGTTACTCCCAACAAGAAGCAAAGGTGGTGATGCCACAAAGTAGCCATGATGAAAAGgttgaagaagaggaaaaaagcCCTGTGCCGAATGAGCCGTTAGCAAGTCAGACTAAGCAACTCACGAGACGGCTCAGTGTGCAGGAGAGGATCAACCTGTTTGAAAACAAGCAGAAAGAGAACTCCGGAGGGAAAACAGCTGTGGTGAAATCCACTGAGCTGAAAAGGCTCTCTTCTGATCTATCATCTTCTGTACGAAGATGGAGTGGGGCTAGTGACATGAGCATTGATTTGGGGAATGATAGGAAGGATGGTACTGGTGATAGTCCATTGTGCACTCCTCCTCCGGCATCATCAGTGTCCAAAGACGGAAGTGGTATGTCTTCAAAACAATCTGTCGGCTTCAAGCAGACTGGATTGAGTCATGTTGAGAATCCTAACAGGAATGAGGACGAATGTAGTTCCAGCAATCTTGCTGACTGGGGAACTGACAAAGCAGAGCCCCAGAAAGACAAGGAGGTAGACTTGAAGATGCCATTGGATGGTTTGTTGGAGAAGACTTCTAAGTTTCCATTCTCAGGGAATGCAAATAGAGATGATGAGTCTGATAACAAAACGGGCGAATTTGAATCAAATAAGCAGGACCAAATACAGTTAAGAGTTCCTCGGAGTCATTCATTGTCTACATTACAGCAGTTAAGTGGTGCTGAATCAAATGGAGGAACTGCGGAGTCTCCTAGGAAAGAACCGTTGGCTAGGCAATCACCACCGGTTGAGGATCGTCAGAGAAAGACACAAGTGTATGGAGGAGGATCTGAACAGATGAAAAGAAGAGAGCATGGTAGAAGGGCTGAAGTTGGTTCTGCTGATGTAAATAAAAAGCCACCTGCAGCCGTTAATAGTGTGTCAGATATTTCCGAGAGTGATACTTTGAGCCAAATGGCCCCAGCAGAGCAAGTTCAAAGGGCTAGAGCGTCTAAGGGAAGCCAAGAGCTGAATGATGAATTGAAAGTGAAAGCAAATGAGCTTGAAAAGCTATTTGCTGAACACATGCTCCGTGTGCCGGCTGGGGATCAATCCAGTTCTGCCCGTAGAGGTAAGCCCGGAAAGCCAAGTGAACAGACTAGAAGACCTGTAGCAGAGGATCTATCTTCTGCAAATCACAAGACCCCAACAACAACGCCAACTTTAAACTCAAATGATGAAGACAGGTTCAAAACTCCGCCAACAATGAAGGTGGTGGTTTCTAACAATGACTATGGAGATACCACAAGGCAGAAACTTTCAGAAATCAGCTTTTCAGATAACTCTAGAGGGAAGTCGTATGAGAAATATATGCAGAAGAGAGACGTGAAGCTGAAGGAAGACTGGAGTTCAAGAAGGACCGAGAAGGAAGCCAAGTTGAAGGTGATGCAAGACATGCTTGATCGCAGTAACGCTGagatgaaaaccaaaatttctcAGTCTTCGGCAAGACGTGACTCAGATGCCAGACGTGCAGAGAAGCTTGTATACTTCAATTCTAGGCTGAGTGCTAAAAAGGATCAGCATCCAATTAGCTCATTCcaaagtgaagaagatgaagatgttaCCAGGAGCACCCAGAATAAGAAgccacaacaaaacaaaaacagttccTTGACTGCTCGAACCACTGCTACATCAGCTTCACGCTCTGCAGCGAAAGTTTCTACACCCGGTGCTGTTAGGCGGAGAGGACAAGAAAAACTTCTTGCACAGTCAGTCCCTAATTTCGCCGAATTCAAGAAGGAAGGCATGAAGGGAGTTGGAAAAAATGGTGTCCGCTCACAGGTGAGAAGCTCTGTCCGACCAAAGGCTGTAACTGAAGAAGAGAAGCCGCGAAGACCGACGAGTATCAGGAAAGTTGCTGCTGAAGCTGCAGAGTTGGCAGATGTTTCTCAGTTAAAGTCAGAGGAAATTGTCATCAGCTCTGATGATGTGCAGCTTAAGGCTTCAGAAGGATCGGATGCATCAGGGGAAATGGATAAGGAGGAGATGGAAGAAGTGTTTGACGACACAGAAGAAGCTTTTACGGACGCAGAAAACGACAAGTCAAGACTTAGTCAAGAGTTTGAAGAATGGGATGGTAACGAGGTTGCAAATGGTGAATCCGTTACTCAGCTTGACACTGGTTCAAACGCTGAGTTACCTACTGCTGCTATAGCTTCCAGGCATCATCAAACCATCGGTTCATTCCTGGATTCACGAGGAGCATCTGAACTGGATGCTACAGTGGACTCTCCTGCTTTCTGGAACTTGTCTTCCCTTAACCAACCAGAGAATAATGAGATAAGTCAGATGAGGAAGAAATGGGGAGCTGCTCAGAAACGGCTTGGCGCTGGTAGTAATCAATCTCAAAGCCAGTGCCAGCAGGATGTGACTAAAGGGTTGAAAAGGCTGTTGAATTTTGGAAGGAAGAACCGTGCGGCTGAGAATTTGGCTGACTGGATCTCTGCTACAACCTCTGAAGGGGATGATGATACTGAAGACGGACGAGATCTTGCAAATCGATCATCAGAAGACTTGAGGAAGTCGAGAATGGGATTTTTACAGACACAGGCCTCTGATGATAGTTTCAACGAGAGTGAGCTATACAATGAACAAGCCCAAAACACTAGTGCACCATTAAGCTTTAAACTGAAGGAGGATCAGGTGTCAGGAGCTTCTGTAAAAGCACCAAGGTCATTCTTTTCACTCTCCAATTTTCGTAGCAAAGGAAAATGA' Code: ``` align1 = pairwise2.align.localms(seqA, seqB, 1, -3, -5, -2) ``` ### Expected...

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1

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3

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1

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1

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1

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1

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