Figure 2.

Banding by a reference multiple alignment. The reference alignment (A) is progressively realigned within a limited deviation of Δ = 1, resulting in F. First, the most similar sequences X and Y are aligned such that the alignment lies within the band in B composed of black matrix entries, corresponding to the original alignment of X and Y in the reference; and gray entries, corresponding to deviations of Δ = 1. Next, the intermediate alignment (C) is aligned with sequence Z under the constraints of the band in E. This band is the intersection of the two bands in D generated from the alignment string of X in alignment (C) versus sequence Z, and the alignment string of Y in C versus Z.