Honestly, it's not going to be easy. The shorter product will be more efficiently amplified simply because it is shorter. You can try increasing the extension time.

Or you might have to design allele-specific primers.

Good luck!

Thank you Katie!

Let's see how it goes.

Best

If you just need to sequence once or a few times, you could try a nested PCR - physically separate the larger band using reverse SPRI or a gel cut, then isolate that product and use it as a template for a second PCR.

Thanks! That is a good option, will try Laura Leighton