Recognition Sequence Conservation as a Function of Peak Intensity

Conservation scores in predicted factor recognition sequences (p-value ≤ 0.001) (red lines), all remaining sequences (blue lines), and in sequences matching scrambled variants of the factors' recognition sequences (p-value ≤ 0.001) (green lines) in the 500-bp regions (±250 bp) around BCD1 and KR1 1% FDR peaks, in nonoverlapping windows of 250 peaks down the rank list to the 25% FDR cutoff. Panels in row (A) shows the mean PhastCons scores, and panels in row (B) the average pairwise differences per base pair between D. melanogaster and D. simulans. Gaps are ignored in the pairwise analysis. The 1% FDR cutoff is indicated by a vertical dotted line.