PAGE 7 OF 12 Nucleic Acids Research, 2012, Vol. 40, No. 4 e29 A B C Figure 4. MTase speciﬁcities determined from SMRT sequencing. The sequence context 50-GATC-30 is methylated by (A) M.EcoKDam (m6A), (B) M.EsaLHCI (m4C) and (C) M.Sau3AI (m5C). The left panel shows IPD ratio data for both strands over the entire plasmid, with the inner and outer circles representing the reverse and forward DNA template strands, respectively. Template positions are indicated by the numbered track middle circle, with blue markers denoting occurrences of MTase target sequence contexts. The right panels show IPD ratios for two representative template positions containing the target context (bold letters), the methylated base is highlighted in red. Error bars represent the standard error of the ratio of means and is calculated as described in the ‘Materials and Methods’ section.