Figure 1.

Why alignments matter and why determining the best alignment can be hard. Shown are several different alignments of two sequences, for which a mismatch is scored as -1 and a match is scored as +1. The vertical lines indicate exact matches. (a) A terrible alignment with five mismatches and no matches gives a score of -5. (b) A poor alignment with two mismatches and one match gives a score of -1. (c) The optimal alignment has one mismatch and three matches, and a score of +2.