Distributions of Substitution Rates in Cattle, Dog and Human. (A) Histograms of the local substitution rates in aligned sequences (84 loci, 5.5 Mb aligned bases, 1,794 windows). (B) Histograms of the local substitution rates in aligned ancestral repeats (84 loci, 1.2 Mb aligned bases, 353 windows). All measures were computed in non-overlapping 3-kb sliding windows for cattle-dog-human multiple sequence alignments. These rates were calculated in multiple comparisons assuming branch times of the cattle, dog and human lineages from the LCA of cattle and dog of 83, 83 and 101 mya, respectively. Suboptimal alignments were excluded. The cattle branch: blue; the dog branch: green; and the human branch: red. The dashed lines were computed after removing CpG dinucleotides.