Location of transposable elements, CMT3, KYP and DRM1/2 targets along chromosome arms. (a) Transposable elements and CMT3 targets. (b) Comparison of KYP, DRM1/2 and CMT3 DRM1/2 targets to CMT3 targets. (c) Comparison of all CMT3 targets to the subset of CMT3 targets that are not also KYP targets, and comparison of CMT3 targets to the subset that are not also CMT3 DRM1/2 targets. To map repeats relative to the centromere, Repbase library sequences were searched using BLASTN with default Repbase parameters against TIGR Release 5 of the Arabidopsis genome sequence. All CMT3 targets, single-copy CMT3 targets and DRM1/2 targets from the gene-oligo array (Figure 2b) were also mapped on the same scale. The fraction of the total number of hits within each 1 Mb bin is shown. To compensate for differences in oligo abundance on the array, bins were normalized by dividing each raw fraction by the fraction of oligos in the bin.