a = AGTAAAGATGAATCCAAATCAAAAGATAATAACGATTGGCTCTGTTTCTCTCACCATTTCCACAATATGCTTCTTCATGCAAATTGCCATCCTGATAACTACTGTAACATTGCATTTCAAGCAATATGAATTCAACTCCCCCCCAAACAACCAAGTGATGCTGTGTGAACCAACAATAATAGAAAGAAACATAACAGAGATAGTGTATTTGACCAACACCACCATAGAGAGGGAAATATGCCCCAAACCAGCAGAATACAGAAATTGGTCAAAACCGCAATGTGGCATTACAGGATTTGCACCTTTCTCTAAGGACAATTCGATTAGGCTTTCCGCTGGTGGGGACATCTGGGTGACAAGAGAACCTTATGTGTCATGCGATCCTGACAAGTGTTATCAATTTGCCCTTGGACAGGGAACAACAATAAACAACGTGCATTCAAATAACACAGCACGTGATAGGACCCCTCATCGGACTCTATTGATGAATGAGTTGGGTGTTCCTTTCCATCTGGGGACCAAGCAAGTGTGCATAGCATGGTCCAGCTCAAGTTGTCACGATGGAAAAGCATGGCTGCATGTTTGTATAACGGGGGATGATAAAAATGCAACTGCTAGTTTCATTTACAATGGGAGGCTTGTAGATAGTGTTGTTTCATGGTCCAAAGATATTCTCAGGACCCAGGAGTCAGAATGCGTTTGTATCAATGGAACTTGTACAGTAGTAATGACTGATGGAAATGCTACAGGAAAAGCTGATACTAAAATATTATTCATTGAGGAGGGGAAAATCGTTCATACTAGCAAATTGTCAGGAAGTGCTCAGCATGTCGAAGAGTGCTCTTGCTATCCTCGATACCCTGGTGTCAGATGTGTCTGCAGAGACAACTGGAAAGGATCCAACCGGCCCATCGTAGATATAAACATAAAGGATCATAGCATTGTTTCCAGTTATGTGTGTTCAGGACTTGTTGGAGACACACCCAGAAAAACCGACAGCTCCAGCAGCAGCCATTGCTTGAATCCTAACAATGAAAAAGGTGGTCATGGAGTGAAAGGCTGGGCCTTTGATGATGGAAATGACGTGTGGATGGGGAGAACAATCAACGAGACGTCACGCTTAGGGTATGAAACCTTCAAAGTCGTTGAAGGCTGGTCCAACCCTAAGTCCAAATTGCAGATAAATAGGCAAGTCATAGTTGACAGAGGTGATAGGTCCGGTTATTCTGGTATTTTCTCTGTTGAAGGCAAAAGCTGCATCAATCGGTGCTTTTATGTGGAGTTGATTAGGGGAAGAAAAGAGGAAACTGAAGTCTTGTGGACCTCAAACAGTATTGTTGTGTTTTGTGGCACCTCAGGTACATATGGAACAGGCTCATGGCCTGATGGGGCGGACCTCAATCTCATGCATATATAAGCTTTCGCAATTTTAGAAAAAACT
b = ACTGAGGCAAATAGGCCAAAAATGAACAATGCTACCTTCAACTATACAAACGTTAACCCTATTTCTCACATCAGGGGGAGTGTTATTATCACTATATGTGTCAGCTTCATTGTCATACTTACTATATTCGGATATATTGCTAAAATTTTCACAAACAGAAATAACTGCACCAATAATGCCATTGGATTGTGCAAACGCATCAAATGTTCAGGCTGTGAACCGTTCTGCAACAAAAGGGGTGACACTTCTTCTCCCAGAACCGGAGTGGACGTATCCTCGTTTATCTTGCCCGGGCTCAACCTTTCAGAAAGCACTCCTAATTAGCCCCCATAGATTCGGAGAAACCAAAGGAAACTCAGCTCCCTTGATAATAAGGGAACCTTTTATTGCTTGTGGACCAAAGGAATGCAAACACTTTGCTCTAACCCATTATGCAGCTCAGCCAGGGGGATACTACAATGGAACAAGAGAAGACAGAAACAAGCTGAGGCATCTAATTTCAGTCAAATTGGGCAAAATCCCAACAGTAGAAAACTCTATTTTCCACATGGCAGCTTGGAGCGGGTCCGCATGCCATGATGGTAGAGAATGGACATACATCGGAGTTGATGGCCCCGACAGTAATGCATTGCTCAAAATAAAATATGGAGAAGCATATACTGACACATACCATTCCTATGCAAAAAACATCCTAAGGACACAAGAAAGTGCCTGCAATTGCATCGGGGGAGATTGTTATCTTATGATAACTGATGGCCCAGCTTCAGGGATTAGTGAATGCAGATTCCTTAAGATTCGAGAGGGCCGAATAATAAAAGAAATATTTCCAACAGGAAGAGTAAAACATACTGAGGAATGCACATGCGGATTTGCCAGCAACAAAACCATAGAATGTGCCTGTAGAGATAACAATTACACAGCAAAAAGACCCTTTGTCAAATTAAATGTGGAGACTGATACAGCGGAAATAAGATTGATGTGCACAGAGACTTATTTGGACACCCCCAGACCAAATGATGGAAGCATAACAGGGCCTTGCGAATCTAATGGGGACAAAGGGAGTGGAGGCATCAAAGGAGGATTTGTTCATCAAAGAATGGCATCCAAGATTGGAAGGTGGTACTCTCGAACGATGTCTAAAACTAAAAGAATGGGGATGGGACTGTATGTAAAGTATGATGGAGACCCATGGACTGATAGTGAAGCCCTTGCTCTTAGTGGAGTAATGGTTTCAATGGAAGAACCTGGTTGGTATTCCTTTGGCTTCGAAATAAAAGATAAGAAATGTGATGTCCCCTGTATTGGGATAGAAATGGTACATGATGGTGGGAAAACGACTTGGCACTCAGCAGCAACAGCCATTTACTGTTTAATGGGCTCAGGACAACTGCTGTGGGACACTGTCACAGGTGTTGATATGGCTCTGTAATGGAGGAATGGTTGAGTCTGTTCTAAACCCTTTGTTCCTATTTTGTTTGAACAATTGTCCTTACTGAACTTAATTGTTTCTGAA
With the following code
pairalign(OverlapAlignment(), a, b, AffineGapScoreModel(EDNAFULL, gap_open=-25, gap_extend=-2))
The resulting alignment only aligns part of a, and is therefore not a global-global alignment.
Align these two sequences
With the following code
The resulting alignment only aligns part of
a
, and is therefore not a global-global alignment.