GC content across microinversion breakpoints and conserved sequence blocks. Top panel: 143 Drosophila melanogaster-D. pseudoobscura microinversions. For each microinversion breakpoint we extracted 200 bp flanking the breakpoint and 20 bp internal to the inversion as a contiguous section (we examined just 20 bp internal to each inversion breakpoint as the minimum inversion size was 40 bp). For each species, across all sequences for a given inversion breakpoint, we calculated GC content for all overlapping 5 bp windows. Each point in the plot represents the mean GC content for a single window. Vertical dashed lines indicate the inversion breakpoints. Note that the distance between these lines is variable across inversion events. Bottom panel: 774 Drosophila melanogaster-D. pseudoobscura conserved non-coding blocks. Using sliding-window BLAST data we identified all blocks of conserved non-coding sequence from the 93 genes harboring intronic microinversions (see Materials and methods for details). Sequence data were extracted from in/around the conserved blocks and analyzed as described for the microinversion data.