Overview of repeats in <i>Xanthomonas</i> species <i>Xcc</i> and <i>Xac</i>.

<p>(A) Frequency plot [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144275#pone.0144275.ref049" target="_blank">49</a>] shows the consensus nucleotide sequence of a heptameric repeat unit in <i>Xcc</i> (top) and <i>Xac</i> (bottom). (B) Histogram shows the count of repeat iterations per repeat sequence in <i>Xcc</i> (dark blue) and <i>Xac</i> (light blue). (C) Examples of GGGAATC patterns in <i>Xcc</i>. Repeat #08 located upstream of the hypothetical gene xcc0178 is the longest, perfect repeat present (top). Repeat #03 and #04 represent an inverted repeat with two short repeat sequences located in convergent orientation on the plus and on the minus strand of the genome (bottom). (D) Distribution of GGGAATC on the <i>Xcc</i> (AE008922, top) and <i>Xac</i> (NC_003919, bottom) genomes. Repeats located on the plus strand are marked in blue (84 <i>Xcc</i>, 85 <i>Xac</i>), repeats on the minus strand in red (102 <i>Xcc</i>, 98 <i>Xac</i>). Locations of repeat associated genes <i>groES</i>, <i>dnaE</i>, <i>flgF</i>, <i>pilU</i>, <i>ruvA</i>, <i>pyrE</i> and <i>xpsF</i> have been marked for orientation. (E) Orientation of neighboring genes relative to repeat sequences in <i>Xcc</i> (left) and <i>Xac</i> (right). Intergenic repeats can be located on the same strand that will serve as the coding strand of the aligned ORFs (dark-blue) or on the non-coding strand (light blue), between convergent (dark green) or divergent (light green) ORFs. Intragenic repeats can be located on the coding strand (dark gray) or non-coding strand (light gray).</p>