Identification of sequence divergence by aCGH. D. melanogaster compared with D. sechellia (A), D. simulans (B) and D. yakuba (C). The percent of array features that were identified as "diverged" based on statistical analysis of hybridization ratio (y-axis) is reported as function of actual sequence divergence (x-axis). Grey points indicate the percentage for a moving window of 51 array features at P < 0.1, corrected for false discovery. Lowess-smoothed curves summarize these values for P < 0.1 FDR (solid), P < 0.05 FDR (dashed) and P < 0.01 FDR (dotted).