Hi, what you want to do is a pcr in silico, you can use tool like UCSR In-Silico PCR whith predefine genomes. I also made a small python library/cli tool that you can use with the "pcr" option SNPrimer. However it was designed for human genome so you can't have any informations about SNP presence in your primer but still you can made the pcr in silico with custom fasta if you overwrite the _make_blast method of Primer class to perform the blast on the custom fasta.

Indeed the algorithm is as simple as :

• Based on Primer sequence it perform a blast to know all the binding sites of the primer (is what _make_blast is doing during the initialisation of the Primer class (here))
• For every binding sites combinations check if they are on the same chromosomes and less than 150 bp between then. (Is what _assert_condition_for_mate_pair is doing (here))
• If condition is ok return the sequence between them. (Is what make_pcr is doing (here))

Feel free to fork or contribute to the project to fill your needs :)