Microhomology and comparison of insertion site characteristics of each locus. (a) An analysis of the microhomology of the six nucleotides adjacent to each insertion junction (with '1' indicating the nucleotide closest to the insert) to the corresponding sequence in the putative mRNA. Exclusion of a junction from analysis is indicated by a (-) and positions where microhomology is found are shaded grey. Those positions at which significant microhomology were found are highlighted in blue. (b) A binomial distribution analysis of the 6 bp at each junction revealed significant microhomology at both the 3' and 5' junctions of the insertions. No significant microhomology was found at the internal junction. P-values highlighted in blue are significant at p < 0.001. (c) A WebLogo analysis of the 6 bp found at the 3'junction. The logo supports our finding of microhomology at this junction, and is consistent with the expected motif at the L1 endonuclease cleavage site.