I am struggling with some primer design and my training in molecular biology is limited. After designing a primer to select for Shiga toxin 1 for several strains and serotypes of E. coli, I noticed after blasting my primer sets that I was also matching Enterobacter phage and Stx 1 converting phage. What I am trying to determine is, if doing traditional PCR, will I end up selecting for both my target sequence in E. coli as well as where my primers anneal (100% match through blast) to the phage? There is a slight variation in amplicon size but perhaps this is something I really don't need to worry about?
Any info would be helpful