Figure 9.

Alignment signatures for insertion-mediated deletion concurrent with 3' flank transduction. Ancestral locus - from left to right - Pink line - 5' flank, turquoise line - sequence lost on L1 insertion, orange line - 3' flank. Green line - repeat sequence, brown line - transduced sequence, dotted lines - poly A tails. DS QFC - downstream sequence query first coordinate, DS SFC - downstream sequence subject first coordinate, Query1 - 5' or upstream flank with 50 bp repeat overhang, Query2 - 3' or downstream flank with 50 bp repeat overhang, RM - RepeatMasker start and end coordinates, USSLC - upstream sequence subject last coordinate. Insertion mediated deletion results in replacement of earlier sequence by the repeat with transduced flank (brown line) without the duplication of target site. On alignment at the orthologous locus in the comparative genome, no match is found for the repeat overhangs (represented by oblique green lines) and the transduced sequence, and the upstream and downstream flanks are separated by a sequence stretch representing the sequence lost upon insertion of the repeat in the main genome. Depending on the A and AT scores of the unmatched portion of the downstream flank, RISCI annotates the locus as INDEL_PAC or INDEL_PTS.