Fig. 3

Analysis of shorter mariner lineages made of rearranged sequences. a and b For the two examples presented here, copies where aligned and the hypothetical initial structure is shown above. The putative initial deletion event is shown in blue. For Rpmar17, the vertical blue line indicates the limit between the two non-overlapping regions, and blue horizontal arrows reflected the further internal deletions that could have take place after or during the amplification process. c Histograms showing the positions of the breakpoints in copies with a rearranged structure. The numbering is after the full-length non-rearranged copy (1319 bp). Copies were retrieved with megablastn using the full-length sequence as query, and were reversed-blasted against the full-length sequence. Only copies displaying hits on both plus and minus strands, and with no other deletions, were kept (227 copies). d Size distribution of the copies. e Scatter plot showing breakpoints in A part versus B part for each copy. The red dotted line represents a size limit of 938 bp