Alignment signatures for C_INTER_RMD (Inter element recombination in the comparative genome). Two possible recombination scenarios and the possible alignments for R1 and R2, which recombine in the comparative genome to form R12 are shown. From left to right - Pink line - 5' flank of R1, blue triangles - target site duplications of R1, green arrow - first repeat copy (R1), brown line - intervening sequence, grey triangles - target site duplications of R2, light green arrow - second repeat copy (R2), orange line - 3' flank of R2. Region of homology between R1 and R2 shown in light green in top panel and dark green in bottom panel, R12 - recombined repeat with a consequential loss of one copy of the homologous region and the intervening sequence. Note that the 5' TSD of R12 comes from R1 (blue triangle) and the 3' TSD comes from R2 (grey triangle). Q1R1 - 5' flank of R1 with 50 bp repeat overhang, Q1R2-5' flank of R2 with 50 bp repeat overhang, Q2R1 - 3' flank of R1 with 50 bp repeat overhang, Q2R2 - 3' flank of R2 with 50 bp repeat overhang. As can be seen from the figure, the flank size should be sufficiently long to span the entire intervening region and other copy of the repeat to pick up such changes.