Methylation levels, correlation within CGI. Since each CGI is a different length, each CGI was split into 40 equal-sized windows, and methylation levels and correlation were averaged within each window. (A) The x-axis is the mean β value within a window in the CGI, CGI shore, or CGI shelf regions across all sites in all individuals with a window size of 100 bp. (B) Methylation values of each CpG site in a CGI, CGI shore or CGI shelf Oxford, were compared with all other sites in the same CGI using MED. The x-axis and y-axis represent the genomic position of each CGI with a scale of 1:100, i.e. one unit in the matrix represents 100 bp distance. The MED of each unit cell was calculated for all pair-wise CpG sites corresponding to that matrix position and averaged over the 100 individuals. bp, base pair; CGI, CpG island; MED, mean squared Euclidean distance.