Analysis of global Alu methylation using the BISMA software for repetitive sequences. All methylated cytosines in CpG-context are presented and used for calculation. A) Graphical representation of the methylated CpG sites in all sequences of the Alu PCR products at the observed position in the alignment. Each line corresponds to one sequence. The methylated CpGs, which are found at the consensus positions, are represented by black boxes, while those CpGs at other positions are indicated by red boxes. The sequences are sorted according to the total number of methylated CpG. B) Frequency of methylated CpG sites in the sequences from individual clones in different samples. C) Frequency of methylated CpG per 100 bps in all clones in different samples.