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.
Harmanci et al. BMC Bioinformatics 2011 12:108 doi:10.1186/1471-2105-12-108