Structure of recombinations within the primary locus.

<p>(A) Annotation of two sections immediately flanking the <i>cps</i> locus, within the primary locus. The position of the <i>cps</i> locus is marked by a horizontal black bar, with a vertical grey shaded band underneath; this locus, across which all recombinations span, is not shown to scale relative to the flanking regions. The extent of an IS element insertion in <i>S. pneumoniae</i> 23F-R, not present in <i>S. pneumoniae</i> TIGR4<b>Δ</b><i>cps</i>, is marked by a second grey vertical band within the 5′ flank. A scale bar, labelled with the genome coordinates and with tick marks every 1 kb, is displayed beneath the annotation. (B) A plot of sequence identity showing the level of similarity between the donor and recipient throughout the locus. The value on the graph represents the proportion of the aligned flanking 100 bp that is identical in both strains for each base in the displayed region. (C) Distribution of recombination sizes. The selected RSSs spanning the <i>cps</i> locus from each of the sequenced 84 isolates are displayed as explained in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002745#ppat-1002745-g002" target="_blank">Figure 2A</a>. At the <i>cps</i> locus itself, all 84 isolates have the donor allele. On the left side, in (i), the RSSs are ordered by their 5′ boundary, while on the right side, in (ii), they are independently ordered by their 3′ boundary. The positions of these boundaries can be modelled as an exponential decay, which is represented by the red line and displayed rate parameter for each flank.