Flanking sequence preferences of M.HaeIII. (A) Magnitude of the flanking sequence preferences for GGCC methylation at the −6 to +6 flank positions. Enrichment and depletion of bases at the positions in methylated substrate molecules were determined and the position-specific effect size plotted. Also see Supplementary Fig. S8B. (B) Enrichment and depletion of bases at the −6 to +6 flank positions in methylated substrate molecules were determined and plotted as o/e frequencies. (C) Average methylation levels of NNNGGCCNNN bins. (D) Flanking sequence preferences of M.HaeIII for methylation in AGCC context, taken from the methylation data obtained with the substrate library containing a CN site in randomized sequence context.