Figure 1.

Nucleotide coincidence. Example illustrating nucleotide co-incidence. (a) a sample alignment for two hypothetical sequences x₁ and x₂, and (b) representation of the alignment as an array where i denotes the nucleotide index for sequence x₁ and k the nucleotide index for the sequence x₂. The co-incident nucleotide positions are indicated by black and cross-hatched squares, where the black squares indicate aligned positions and the cross-hatched squares indicate inserted positions.