Association of epigenetic marks with repeat classes. For each Chip-Seq replicate k-mer frequencies were determined for both input and IP sequences. For each k-mer present in both input and IP at least twice, the enrichment of IP over input was calculated. K-mers were grouped by enrichment. Left: Distribution of counts in each group. Middle: K-mers in each group were classified as short repeats, 359 bp repeats, transposons, assembled genome or unmapped. The percentage of k-mers classified in each repeat class is shown. Some k-mers were classified as both short repeats and transposons, and they are included in both groups. Right: Percentage of A + T in short repeat k-mers. For all graphs the median between experimental replicates is shown. The number of replicates was two for all modifications.