Both HpaII and MspI are unable to cut if the external cytosines are fully methylated. Selective amplification included a total of eight primer combinations per isoschizomer (Supplementary Table S1). HpaII (?2) primers were fluorescently labelled with 5-FAM or 5-HEX while EcoR1 (?3) remained unlabelled. The set of fragments from both digestions was grouped by primer combination,fragment size and sample to determine all individual profiles.