Table 1.

Motif imbalance between human and chimpanzee. For the core motif and the degenerate motif, we analyzed cases where the motif occurs in exactly one of human and chimpanzee. Results are shown for the full set of non-shared motifs and stratified into five backgrounds which differ in average human recombination activity. Significance levels are calculated in two ways: p-values for ratios are based on a 1-sided exact binomial test of fewer human-only cases, as the motif is known to be active in humans. Empirical p-values are 1-sided and obtained by comparisons of counts for the core or degenerate motif to counts observed for motifs of the same length and GC content on the same backgrounds (8).

Sequence background	Core motif CCTCCCTNNCCAC				Degenerate motif CCNCCNTNNCCNC
	Human only	Chimp only	Ratio (p-value)	Empirical p-value	Human only	Chimp only	Ratio (p-value)	Empirical p-value
All	425	515	1.21 (0.0018**)	0.0033**	19448	20245	1.04 (3.2e-05**)	0.0020**
THE1	20	39	1.95 (0.0092**)	0.0050**	50	76	1.52 (0.0128*)	0.0093**
L2	30	47	1.57 (0.0338*)	0.0307*	432	496	1.15 (0.0193*)	0.0219*
AluY,Sc,Sg	-	-	-	-	3642	3924	1.08 (0.0006**)	0.1119
Other repeats	99	131	1.32 (0.0204*)	0.0346*	10126	10254	1.01 (0.1868)	0.4373
Non-repeats	276	298	1.08 (0.2135)	0.2206	5198	5495	1.06 (0.0021**)	0.0215*