The most frequent short repeats in the fly genome. modENCODE A) and DGRP C) reads that mapped to a particular short repeat sequence were counted. Repeats were split into groups based on the number of reads that mapped to them. Repeat sequences in each group and the percentage of each group relative to the whole genome are indicated. B) and D) Repeats from the top groups shown in A) and C), respectively. The percentage of total reads mapped to each repeat over multiple experiments is shown in the form of boxplots. An asterisk (*) marks each repeat group identified in previous studies based on cloning and sequencing of CsCl gradient bands.