Figure 1.
Description of data sets used in this study, which represent specific subsets of sites of the MLAGAN whole-genome alignments (Brudno et al. 2004). One hypothetical alignment is shown; (H) human; (M) mouse; (R) rat. Excluded sites are shaded gray. The remainder is kept, with the final number of sites in each set shown. Dotted lines represent gaps, which are not drawn to scale. Dataset 1 consists of all those regions that are shared among all three species. Excluded are regions that are gapped in human, or in one or both rodents, for at least 20 consecutive bases. The number of positions shown refers to those scored in the microindel analysis; for analyses of rates of substitution, gapped sites were eliminated, leaving 1,071,376,029 sites. Dataset 2 consists of “rodent-specific” sites, explicitly defined as those regions in our global alignments across from a human gap of at least 20 bases in length, and in which the rodent sequences contain less than 10% gap characters. Note that these two data sets are mutually exclusive, and therefore constitute independent sites.