The latest human (hg18), chimpanzee (panTro2), rhesus macaque (rheMac2), mouse (mm8), rat (rn4), and dog (canFam2) genome assemblies were obtained from the University of California, Santa Cruz (UCSC) Genome Browser. Humanreferenced whole-genome alignments were constructed from syntenic pairwise alignments with human (the ''syntenic nets'') using the UCSC/MULTIZ alignment pipeline [80, 81] . Low quality bases (Phred score ,20) from the chimpanzee, macaque, rat, and dog genomes were converted to 'N's in these alignments.