I'm trying to design some primers myself because all of the primer packages I've found are either web-based, are not very user friendly, cannot handle large numbers of sequence targets, can't take in multiple sequence alignments, cannot create just a forward primer, and/or are not easy to install.

I'm at the last stage but now I need to decide a threshold for when to use IUPAC degenerate bases. Here is an example of a few positions that are not definitely A, C, G, or T.

For position 2697 I'll keep T but maybe for 2689 it should be C or T.

What is best practice when using a degenerate base? Should it be like setting a threshold (e.g., 70%) and if a base isn't present in at least 70% then see if the cumulative frequency for one of the degenerates is higher then choose the degenerate?

Degenerate bases: https://www.bioinformatics.org/sms/iupac.html