I am trying to design forward and reverse primers for ~1000 loci for a multiplex PCR reaction. I am targeting the ends of fragments after RE digestion. If I am thinking about this correctly, I imagine to do this I would need a script that would write primers starting at the end of each fragment and add complementary nucleotides sequentially until it reached a desired GC content and melting temp (which would be similar for all primers.) In practice, I am not sure how to do this. Do you know of any software/scripts that will allow this type of high throughput design?
Thank you for your advice and help!