Figure 4.

The Consensus 13-mer, CCNCCNTNNCCNC, Associated with Meiotic Recombination/NAHR Hotspots Is Present at Breakpoint Alus of Some Alu-Mediated CNVs

(A) CNVs (black bars) displayed with breakpoint Alus (pentagons; filled and intersected by a colored line if they contain the consensus 13-mer [CCNCCNTNNCCNC] associated with meiotic recombination/ NAHR hotspots⁴², ⁴³). This motif is present at a single breakpoint Alu of ten Alu-mediated CNVs, at both breakpoint Alus of one CNV (Park 3), and in the Alu from which inserted breakpoint sequence is derived in one apparently complex rearrangement (A2). Abbreviation: Dup, duplication.

(B) All instances of the 13-mer (black arrowheads).

(C) SINE elements (RepeatMasker track via UCSC Genome Browser).