Figure 7.

SD-MMEJ repair can produce repair junctions without insertions, which may or may not have microhomology. If P1 and mh1 are directly adjacent, SD-MMEJ will not produce an insertion. To efficiently summarize the proposed SD-MMEJ mechanism, this ‘insertion’ of length zero is indicated by a box containing no sequence. In the case of ambiguous deletion breakpoints (junctional microhomologies), the ambiguous bases are flanked by boxes containing dots. Each panel shows alignment of the original sequence and repair product, the primer and microhomology repeats and the longer repeat created in the repair product. Notational conventions are as in Figures 5 and 6. (a and b) Apparent blunt joins consistent with SD-MMEJ repair. Box with dash indicates the point of ligation (0 bp insertion). (c and d) SD-MMEJ consistent repair products with junctional microhomologies. In both of these cases, SD-MMEJ results in annealing at longer microhomologies than would MMEJ at the microhomologies present in the repair product. a: sequence H, Supplementary Table S7. b: sequence B, Supplementary Table S7. c: sequence O, Supplementary Table S8. d: sequence F, Supplementary Table S8.