Primers and multimapping ?

Question

[Picasa]

Hi,

I am trying design primer using primer3.

Maybe a stupid question but I was wondering if the forward primer map in multiple location on the genome but the reverse map in one uniq location, will I still got a pcr product ?

[Pierre Lindenbaum]

unrelated to bioninformatics. You'll get any PCR product if any of the multiple location of the foward is close to the revere on the same chromosome on the complementary strand.

[ATpoint]

If you want to design primers properly in this regard use PrimerBLAST which extends Primer3 by BLASTing hits against a genome to avoid exactly what you describe.