Table 1

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

Sequence
background
Core motif CCTCCCTNNCCACDegenerate motif CCNCCNTNNCCNC
Human onlyChimp onlyRatio (P value)Empirical P valueHuman onlyChimp onlyRatio (P value)Empirical P value
All4255151.21 (0.0018**)0.0033**19448202451.04 (3.2e-05**)0.0020**
THE120391.95 (0.0092**)0.0050**50761.52 (0.0128*)0.0093**
L230471.57 (0.0338*)0.0307*4324961.15 (0.0193*)0.0219*
AluY,Sc,Sg364239241.08 (0.0006**)0.1119
Other repeats991311.32 (0.0204*)0.0346*10126102541.01 (0.1868)0.4373
Non-repeats2762981.08 (0.2135)0.2206519854951.06 (0.0021**)0.0215*

*P < 0.05.**P < 0.01.