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I need to design oligos that will be used as PCR and sequencing primers and it is important thet they do not bind anywhere in mouse genome. These should be single oligos, not a pair. I want to get PCR products where one primer is specific for a defined sequence (I already have some good primers for this) and the other has to be non-mouse.
I designed some primers in Roche Design Center (other organism) using some plant specific genes. But when I blast the primers against mouse genome, I always get hits e.g. 16 from 20 nucleotides primer show max identity with some mouse genes. I'm afraid this may be enough to cause unspecific PCR products.
Is there any website or any program, that would generate primers that definitely do not bing anywhere in mouse genome?
