CENP-A occupies DNA sequences within putative centromere contigs.

Organization of each CENP-A-enriched island corresponding to centromere candidates: (A) CenX, (B) Cen4; (C) CenY; (D) Cen3; (E) Cen2. Different repeat families are color coded (see legend; note that Jockey elements are shown in one color even though they are distinct elements). Shown are the normalized CENP-A enrichment over input (plotted on a log scale) from one replicate (replicate 2, other replicates are in S4 Fig) colored in gray for simple repeats and black for complex island sequences. Although the mapping quality scores are high in simple repeat regions, we do not use these data to make inferences about CENP-A distribution (see text for details). The coordinates of the significantly CENP-A-enriched ChIPtigs mapped to these contigs (black), and the predicted ChIP peaks (orange) are shown below each plot. See also S4 Fig and S3 and S4 Tables. Cen2, centromere 2; Cen3, centromere 3; Cen4, centromere 4; CENP-A, centromere protein A; CenX, X centromere; CenY, Y centromere; ChIP, chromatin immunoprecipitation; IGS, intergenic spacer of the ribosomal genes; LTR, long terminal repeat; Prodsat, Prod satellite.