Figure 6.

Adaptation of SIMPLE to detect L1 3’ ends. (A) CLC Genomics Workbench window view of a representative fixed human specific L1 element (L1Hs) detected by 3’-SIMPLE. L1Hs represents a known human specific L1 element on chromosome 1. Small red lines at bottom are reverse 3’-SIMPLE reads, reading into the3 end of the L1Hs element. (B) Frequency distribution of the number of reference L1Hs elements detected by 3’-SIMPLE versus the number of independent 3’-SIMPLE hits detected for that element. On average, a reference L1Hs element was assayed by seven independent 3’-SIMPLE reads, with the vast majority of reference L1Hs elements assayed by at least two independent reads.