Figure 3.

Specificity of Alu junction enrichment. The average fraction of Alu sequence was computed in 10-bp windows for all 9,464 junctions. Junctions were oriented from external flanking sequence (white) to duplicated sequence (yellow). The X-axis represents base-pair position with respect to the junction point set at 0 (positive values are located internal to the junction, whereas negative values represent extension into flanking sequence). The greatest enrichment occurs specifically at the junction (23.9%) and dissipates within 300 bp (the size of an Alu repeat) on either side of the junction. This effect is asymmetric, with a more gradual bias observed within the duplicated portion of the alignment. Control (blue) and finished genome (gray) averages are shown as bold horizontal lines.