Local sequence alignment without mismatches

ID: local-sequence-alignment-without-mismatches

Choose one contiguous substring from each string and align them under the same matching and gap rules as global sequence alignment without mismatches. Let maximize the score over aligned suffixes of the two prefixes. Zero permits a fresh empty alignment; the other cases extend one ending at adjacent prefix indices. The answer is the largest table entry, which can occur before either input ends. Starting all boundaries at zero yields time for positive lengths. Alignment traceback stops on reaching zero.

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