I have one primer and a list of sequences. I want to check to which of the sequences (if any) the primer could bind to. It's like an in-silico PCR (so mismatches should be more penalized at the 3' end of the primer than at the 5' one etc.), but with only one primer.
I can't seem to find a tool that accepts only one primer instead of a pair. Anyone has any suggestion? Possibly, I would like to integrate this tool in a Python script.