a–c, DNA methylation, by CG (red), CHG (blue) and CHH (+ strand, − strand) context (green) and cytosine context (scale: 1 = methylated cytosine; 0 = unmethylated cytosine) at ATCOPIA93 (AT5G17125) (a), the ATMU5 (AT4G08680) DNA transposon and the surrounding region (b) and the ATHILA6A (AT4TE15030) retrotransposon and the surrounding region (c). Twenty-one-nucleotide and 24-nucleotide siRNAs, represented as a histogram of read density (grey bars). sRNA reads: unique (U), mapping to one location of the genome; and multiple (M), mapping to more than one location of the genome. PARE read density. Track order for panels Col-0 (1), ddm1-2 (2), rdr6-15 (3) and ddm1-2 rdr6-15 (4).