Evolutionary conservation of sequence elements. The core promoter sequences surrounding each D. melanogaster TSS were mapped to orthologous locations in the 12 Drosophila genomes. (a) Conservation of sequence elements across the 12 fruit fly genomes. The set of D. melanogaster promoters having an element present in its preferred window was selected, and the fraction of all orthologous sequences with the motif present was assessed in a pairwise fashion with the other 11 species. The figure indicates a sharp decline in the conservation of the elements outside of the melanogaster subgroup. (b) Enrichment of conserved motif matches in promoters over random sequences. The plot shows the fold enrichment of the fraction of total D. melanogaster motif matches conserved in the preferred window of 100-bp sequences surrounding detected TSSs compared to random intergenic locations. For clarity, the plot shows only five out of the eleven species in the total pairwise comparisons. (c) Differences in conservation of canonical elements between peaked versus broad promoters. After splitting the motif matches used in (a) by their occurrence in peaked versus broad promoters, there are noticeable differences between the conservation levels of motifs. For clarity, we again only show five out of the eleven pairwise species comparisons. D. mel, D. melanogaster; D. sim, D. simulans; D. sec, D. sechellia; D. yak, D. yakuba; D. ere, D. erecta; D. ana, D. ananassae; D. pse, D. pseudoobscura; D. per, D. persimilis; D. wil, D. willistoni; D. moj, D. mojavensis; D. vir, D. virilis; D. gri, D. grimshawi.