Fig. 4

Distribution of PSSM scores for three different TFBSs along CPR sequences for CHKov1 and CG33506. PSSM scores (log odds scoring matrix) for the binding sites of BREd (a for CHKov1 and d for CG33506), DCE S II (b for CHKov1), DCE S III (c for CHKov1), DPE (e for CG33506), and TATA box (f for CG33506) at all positions in CPR sequences on the strand are shown. Gray dotted horizontal lines indicate a PSSM score of zero and black horizontal lines indicate PSSM scores at threshold values above which each transcription factor is likely to bind. Black dashed vertical lines indicate the position of SNPs found in the population. Black triangles indicate positions where PSSM scores for one or more alleles were larger than the threshold value (closed triangle), while other alleles had PSSM scores smaller than the threshold value (open triangle). Gray shading indicates the range of positions at which PSSM score are changed by mutations. Different colors (red, blue, and green) indicate differences in TFBS patterns caused by sequence variations. The color and alphabet (a-f) correspond with alleles shown in Fig. 2