The distribution of insertions, deletions and small interspersed repeats relative to RSSs.

The total numbers of core genome positions (i.e. the length excluding sequence insertions in either the donor or recipient strain) in the segments of imported donor sequence and BRs of secondary RSSs were separately calculated, as was the number of core genome positions that were not found to be affected by RSSs in any strain. These were compared with the number of repeats (counting only instances of these elements shared between donor and recipient), insertions and deletions relative to the recipient that were categorised in the same way. Where RSSs in different strains overlapped, bases and features were counted multiple times.