How to create an amplicon reference for Bismark analysis

[[email protected]]

I am working with a Miseq dataset on multiplex bisulfite amplicon sequencing. I have the sequences of the 30 amplicons. How can I make a fasta reference out of them to be used for Bismark alignment?
I have made a fasta file listing the amplicons as the following, but it didn't work with Bismark. I got 0% CpG methylation and 99% CHH methylation. Is there anything wrong with my amplicon reference? Thank you!

>Myh6_1
AATAACTGAGGTAAGGGCCTGGGTAGGGGAGGTGGTGTGAGACGCTCCTGTCTCTCCTCTATCTGCCCATCGGCCCTTTGGGGAGGAGGAATGTGCCCAAGGACTAAAAAAAGGCCATGGAGCCAGAGGGGCGAGGGCAACAGACCTTTCATGGGCAAACCTTGGGGCCCTGCTGTCCTCCTGTCACCTCCAGAGCCAAGGGATCAAAGGAGGAGGAGCCAGGACAGGAGGGAAGTGGGAGGGAGGGTCCCAGCAGAGGACTCCAAATTTAGGCAGCAGGCATATGGGATGGGATATAAAGGGGCTGGAGCACTGAGAGCTGTCAGACAGAGATTTCTCCAACCCAGGTAAGAGGGAGTTTCGGGTGGGGGCTCTTCACCCACACCAGACCTCTCCCCACCTAGAAGGAAACTGCCTTTCCTGGAAGT
>Myh6_2
CCTCCCATCAGGAGTGGAGGGTTGCAGAGGGAGGGTAAAAACCTACATGTCCAAACATCATGGTGCACGATATATGGATCAGTATGTGTAGAGGCAAGAAAGGAAATCTGCAGGCTTAACTGGGTTAATGTGTAAAGTCTGTGTGCATGTGTGTGTGTCTGACTGAAAACGGGCATGGCTGTGCAGCTGTTCAGTTCTGTGCGTGAGGTTACCAGACTGCAGGTTTGTGTGTAAATTGCCCAAGGCAAAGTGGGTGAATCCCTTCCATGGTTTAAAGAGATTGGATGATGGCCTGCATCTCAGGGACCATGGAAAATAGAATGGACACTCTATATGTGTCCCTAAGCCAAGGTAGCAAGGTCTTTGGAGGAC
>Myh7_1
GCTCAGAGCTGTGTTTGGGAAGAAAGGGGATTTCAAACTAAACCCTGAGTCTGTTGCCTAGACACCGAGCAGTGAAGCTTCTATAGCTGGAAGAACAAGAACGAGGCTGGGTGCCAGCGTTGCTCCCGGGGCCTGCAGGGGAAGACAAGGTCTCTCCTGTCCTGTCCCTCTCTCCACTAGGAAGAACAAAGATTGCACCCACGGCTAGACAGAGGCCAGGTGGACCAGGCAGCCGTAGCCATATCATCTACAGCCCTGGGTAACCCTGGGAGGCTCAGGCCTTGCGCCTCGAAAATCTGCAGGGCAGCGCTAGAACAGGAAAGGGCTCTAAAGCAGGACCATGAGCAACTGGTCCTCCTCCCCAAACAGCTTTGGCATACTTCTTAGCATCCCTAGCCCTCCTCCCCTGATTGGGATCAACTTCCTATCTGCTG

[dpryan]

When you get weird results it's always best to first look at the BAM files in IGV. Do the alignments look reasonable? Do they support the results? This will typically resolve residual doubts.