I have a primer pair and I want to test it against a given set of many target genes. How can I do that while allowing some mismatches?
I tried using primer3 (and primer-blast), but it only found matches where the exact primer sequence is contained in the target sequence. Even if the target sequence contained an 'N', the primer sequence had to also contain an 'N' at the same location to be found by primer3.
To be clear, I don't want to test the primers against some online data base, but against my own local database.
Thanks in advance for your advice!! Rotem