Detailed view of results for each sequence. The detailed view of matches highlights various types of cytosines (CG, CHG and CHH) and their fate under bisulfite treatment for each sequenced read. The first line, labeled in, of each set is the reference sequence with the cytosines colored to represent the type of cytosine (as in Figure 3), CG (red), CHG (blue) and CHH(green). The second line, labeled out, shows the result of bisulfite sequencing with colored T's, red for untransformed C's (which are protected by methylation) and tan for transformed C's (unmethylated). The mismatches number above each sequence gives the number of mismatches the sequence exhibited (besides the C to T conversions) and the total length of the particular sequence. This provides an estimate for sequence quality.