Facing problems in analysis of bisulfite sequencing data

Question

[SHREYA]

Facing a lot of problem in analysing the bisulfite seqencing data, its not aligning with (bioinfomatically bisulfite converted) reference sequence. I can't identify the signature sequences so as to identify the CpG sites. Only reverse primer sequence is matching in all the clone sequencing data but the Guanines (G) are converted to Adenines (A).. Is it possible? I am very confused as usually I know that C is converted to T.. I have performed Sanger Sequencing. Can anyone please help me in this regards????