Fig. 2.

An example alignment extension procedure. The arrows point at each step to the position currently considered in both sequences. First, there are two matches and the arrows move to the right by two positions on both sequences. When a mismatch (T-G) is encountered the algorithm tries alignment operations and conditions. The first operation: a substitution, which requires nine matching bases following the mismatch, fails. The second operation, an insertion which requires ten matches succeeds and is applied to the alignment. In the last step there is a match (G-G)