Isolating Symbols in Alignments

Problem

Say that we have two strings s and t of respective lengths m and n and an alignment score. Let's define a matrix M corresponding to s and t by setting Mj,k equal to the maximum score of any alignment that aligns s[j] with t[k]. So each entry in M can be equal to at most the maximum score of any alignment of s and t.

Given: Two DNA strings s and t in FASTA format, each having length at most 1000 bp.

Return: The maximum alignment score of a global alignment of s and t, followed by the sum of all elements of the matrix M corresponding to s and t that was defined above. Apply the mismatch score introduced in “Finding a Motif with Modifications”.