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Try to use an aligner, bwa for instance.
Sounds like a bit of an overkill for a single fasta sequence. Why not a pairwise alignment with EMBOSS-Needle?
OP wants bam file.
Suggesting an alternative.
You can use
bbmap.shfrom BBMap suite. Something like this:if you have
samtoolsavailable in your$PATHthen you can directly output a BAM file.