A Regions are constructed by iteratively concatenating cytosines (and later clusters of cytosines) if they are less than 185 bp apart and their combined regions size does not exceed 185 bps (blue line on the left). Clusters further apart than 185 bp are kept separate (blue line on the right). The process starts with the cytosines that are closest together and iterates through increasing distances. B Autocorrelation of cytosines per context for MA line MA1_3. For the autocorrelation of the other MA lines see Figs. S1 and S2. The gray shading represents the variation caused by the different samples in the MA line pedigrees. The variation in CG context is included in the plot, but it is smaller than the line width and it is not visible. C Example snapshot from the integrative genome viewer (Robinson et al. 2011) showing a stretch of chromosome 1 from MA1_3. The top track shows the single CGs and the bottom track shows the regions. For both tracks, regions/cytosines are either Methylated (blue), unmethylated (red), or insufficiently covered (gray). For comparison, 100 bp bins are marked with vertical lines, showing how partitioning the genome with an arbitrary window size does not necessarily group close cytosines together. D Example snapshot of chromosome 1 from MA1_3 showing single CHGs and CHG regions. E Example snapshot of chromosome 1 from MA1_3 showing single CHHs and CHH regions.