Hi, I would like to check if there is any homology between 2 sets of primers for my TaqMan qPCR. I've checked homology of primer set for target and for endogenous control individually in the Primer-Blast using nr and RefSeq databases. Each pair set was OK individually and it will amplify only target or endogenous control.

How can I put them together and see if there is any chance that they bind to each other? And, is it any point to align them in e.g. EndNote?

Thanks. Yael