Comparison of the human and mouse genomes led
to the unexpected result that 40% of the human
genome basepairs can be aligned to the mouse ge-
nome at the nucleotide level (Waterston et al. 2002).
Insights from human/mouse genome comparisons.Mamm Genome . 2003 Jul;14(7):429-36.
Initial sequencing and comparative analysis of the mouse genome .
http://www.ncbi.nlm.nih.gov/pubmed/12925891
This image shows the 95% of the chimpanzee genome that maps to identical sequence in the human genome. The consistency of the color indication demonstrates the close identity between the two genomes since their last common ancestor, approximately 5 million years before present. (reference) The human chromosome 2 actually aligns to two separate chimp chromsomes, now called chr2a and chr2 and represented here by the same color. These chromosomes were formerly named chr12 and chr13 but have been renamed by the Chimp Sequencing Consortium to reflect the fact that they share a common origin with human chr2.
At the nucleotide level, approximately 40% of the human genome
can be aligned to the mouse genome. These sequences seem to
represent most of the orthologous sequences that remain in both
lineages from the common ancestor, with the rest likely to have been
deleted in one or both genomes.