= Solution
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 \b[508]. The following are one-based inclusive coordinates; the aligned strings and all percentages are given in parts (a) and (b).
|| Query
|| Query length
|| Query interval
|| Reference interval
|| Columns
|| Score
| baboon
| 65
| 1–65
| 241–306
| 66
| 314
| squirrel monkey
| 56
| 1–56
| 61–116
| 58
| 278
| dingo
| 66
| 1–66
| 1–66
| 71
| 301
| goldfish
| 63
| 2–63
| 248–315
| 72
| 190
For example, the goldfish <local sequence alignment> excludes its first query residue and aligns residues 2–63. As a check, removing gaps from each aligned string gives exactly the sequence slice determined by its reported interval.
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