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Table 1.

Observed Changes in Aligned Sites

A. Observed Changes in 4D Sites
		Mouse
		A	C	G	T
Human A	0.1779	0.0246	0.0499	0.0192
Human C	0.0135	0.1597	0.0169	0.0348
Human G	0.0358	0.0169	0.1641	0.0134
Human T	0.0187	0.0495	0.0257	0.1793

B. Observed Changes in AR Sites
		Mouse
		A	C	G	T
Human A	0.2163	0.0198	0.0508	0.0207
Human C	0.0160	0.1184	0.0116	0.0463
Human G	0.0463	0.0116	0.1183	0.0159
Human T	0.0207	0.0509	0.0199	0.2166

[i] Frequency of observed changes in (A) 4D sites and (B) ancestral repeat sites in 100-kb windows with medium human GC content (between 36.2% and 41.2% G or C). GC content was calculated using all aligned bases in the window. Frequencies are expressed as the fraction of the total observed changes.