Overview of repeats in Xanthomonas species Xcc and Xac.

(A) Frequency plot [49] shows the consensus nucleotide sequence of a heptameric repeat unit in Xcc (top) and Xac (bottom). (B) Histogram shows the count of repeat iterations per repeat sequence in Xcc (dark blue) and Xac (light blue). (C) Examples of GGGAATC patterns in Xcc. 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 Xcc (AE008922, top) and Xac (NC_003919, bottom) genomes. Repeats located on the plus strand are marked in blue (84 Xcc, 85 Xac), repeats on the minus strand in red (102 Xcc, 98 Xac). Locations of repeat associated genes groES, dnaE, flgF, pilU, ruvA, pyrE and xpsF have been marked for orientation. (E) Orientation of neighboring genes relative to repeat sequences in Xcc (left) and Xac (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).