Figure 3.

Sequence conservation properties of the REDfly analysis CRMs. (a) Average fraction of aligned bases between D. melanogaster and each of the other species for the CRMs (blue), CRM flanking sequences (green; ± 1 kb to each side of the CRM; see text), coding regions (orange; based on 2,000 genes; see Materials and methods), and size-matched randomly selected non-coding sequences (red). Dashed lines indicate the 20% and 80% percentile values for the CRMs and random sequences. Also indicated are the 'differences' in conservation between CRMs and random non-coding sequences (black) and between coding sequences and random non-coding sequences (pink). Species abbreviations are as given in the legend to Figure 3. A similar graph showing the fraction of aligned 'identical' bases is given in Figure S3-1 in Additional data file 3. (b) Histogram of the conservation fraction for CRMs (black bars) and random non-coding sequences (white bars) for D. melanogaster aligned with D. pseudoobscura. Histograms for the other species are shown in Figure S3-2 in Additional data file 3. (c) Median conserved block density for each of the species aligned to D. melanogaster. Blocks are defined as ungapped regions of seven or more nucleotides with ≥75% identity. Shown are block densities for CRMs (blue), CRM flanking regions (green), and size-matched randomly selected non-coding sequences (red). (d) Histogram of the distribution of conserved block density for CRMs (black bars) and random non-coding sequences (white bars) for D. melanogaster aligned with D. pseudoobscura. Histograms for the other species are shown in Figure S3-3 in Additional data file 3.