The maximum-scoring cell records the inclusive end position in each sequence. During traceback, moving left consumes a reference residue, moving up consumes a query residue, and moving diagonally consumes both; when traceback stops, the remaining prefix lengths are one less than the corresponding one-based starts. Consequently
i+1 and j+1 are the correct starts returned in part (a), without counting any inserted gaps as sequence residues.The following report joins these coordinates to the alignments and sequence identity/sequence similarity values already calculated:
for name, a in alignments.items():
print(f"{name}: query length={a['query_length']}, "
f"reference length={a['reference_length']}, "
f"alignment columns={a['alignment_length']}, score={a['score']}")
print(f"Query {a['query_start']} {a['query']} {a['query_end']}")
print(f"Ref {a['reference_start']} {a['reference']} {a['reference_end']}")
print(f"Identity {a['identity_percent']:.2f}%; "
f"similarity {a['similarity_percent']:.2f}%; "
f"gaps {a['gap_percent']:.2f}%")All reference sequences have length 508. The following are one-based inclusive coordinates; the aligned strings and all percentages are given in parts (a) and (b).
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