Sequence composition of selected regions of the D. melanogaster Y Chromosome, along with a control euchromatic region (white gene). Coding exons are shown as numbered black rectangles (unlabeled when pseudogenes), transposable elements in pink, simple satellites in blue (with darker shades indicating higher AT-richness), and single-copy sequences as a thin black line. The top six regions all have very low read coverage, whereas the bottom five have approximately normal coverage. All regions are represented at approximately the same scale. In the region containing ORY exons 1–2, we could not determine which copy is functional, so we labeled both. The most abundant satellites were identified as described in the Supplemental Methods.