Alignment signatures for twin priming. Twin priming results in inversion of the 5' end of L1 (R1) as opposed to its 3' end (R2), the arrowheads indicating opposite orientations. Since Query1 R1 and Query2 R1 are in opposite orientation to Query1 R2 and Query2 R2, the alignment of query sequences at the orthologous empty locus in the comparative genome is in opposite orientations (indicated by opposite facing brown arrows). Also for Query1 R1, no match is found for 50 base overhang into R1, and the R2 sequence. Similarly, for Query1 R2, no match is found for 50 base overhang into R2, and the R1 sequence. Since the alignments are in opposite orientations, the TSDs identified are reverse complements of each other. From left to right - Pink line - 5' flank of the repeat, blue arrows and lines - target site duplication sequence, R1 - inverted 5' sequence, R2 - normal 3' sequence, orange line - 3' flank of the repeat. Query1 R1 - upstream flank of R1 with 50 base overhang into R1, Query2 R1, downstream flank of R1 with 50 base overhang into R1, Query1 R2 - upstream flank of R2 with 50 base overhang into R2, Query2 R2 - downstream flank of R2 with 50 base overhang into R2. In the final result file, inversions are indicated by '*' suffixed to the repeat name.