Figure 3

Normalised counts of nucleotide matches over the percentage of genomes in which the nucleotides match. Shown are the count distributions form SWGA (black), SW+ (blue), and SWGA+ (red), minus the counts for SW. All three scoring schemes exhibit a pronounced shift into the higher percentage bins compared to SW, with aligning fewer nucleotides that match fewer genomes (most notably the drop at the 50% mark), and more nucleotides that match in 80-100% of the genomes.