Table 3.

Site patterns observed across CpG censored alignments. Patterns were observed at sites classified as one of: ERV (PV); selfish DNA (RM+); or non-repetitive or repetitive but non-selfish (RM-)

Chimp:human	Autosomal			X-linked
	PV	RM+	RM-	PV	RM+	RM-
A:A	591392	1603551	1145366	26509	83350	43123
A:T	888	2496	1390	38	105	45
A:G	3650	8749	5067	112	335	155
A:C	1104	2678	1593	41	111	46
A:?	0	0	0	0	0	0
T:A	984	2572	1456	28	90	41
T:T	597941	1609580	1151417	26035	87639	43695
T:G	1197	2816	1527	57	109	62
T:C	3636	8534	4949	127	338	172
T:?	0	0	0	0	0	0
G:A	3294	8415	4950	131	389	144
G:T	1143	3034	1688	35	108	51
G:G	450769	1135140	703983	22571	56854	24790
G:C	974	2586	1439	29	105	51
G:?	0	0	0	0	0	0
C:A	1206	2935	1652	26	102	46
C:T	3394	8432	4957	120	328	183
C:G	986	2623	1400	31	91	55
C:C	460550	1128491	698783	18236	56537	25202
C:?	0	0	0	0	0	0
?:A	5	0	2	0	0	0
?:T	0	1	2	0	1	0
?:G	1	0	1	0	1	0
?:C	1	4	0	0	0	0
?:?	0	0	0	0	0	0
total	2123115	5532637	3731622	94126	286593	137861