Figure 2. Repeats in 4-kb CNV breakpoint regions.

The location of tandem repeats (red), G-quadruplexes (green), Alus (light blue) and 50-bp motif (dark blue) sequences are shown for a subset of terminal deletion (A), inverted duplication adjacent to terminal deletion (B) and interstitial deletion (C) breakpoint regions. Repeats on the positive (+) and negative (−) strands are shown on the top and bottom of the black line, respectively. Arrows point to sequenced breakpoint junctions. The breakpoint region from EGL108 underlies terminal deletions and one interstitial duplication. Black Xs show Alu-Alu recombination sites for sequenced junctions (C).