Ive been trying to optimize the PCR condition\mix for a few SSR primers I will be using for a population genetics study in insects , The primers were used only in one paper ( which is the same one where they isolated the microsatellites ) .
So I spent sometime troubleshooting My PCRs and I ended up with some of them working well, and other are showing very clear bands , but out of the expected size ( some times its about 100 bp ) , is it logical to have a band which is that far from the expected size ??
the expected size was mentioned in one paper only and were tested in a population in the Netherlands ( and I'm using them in a population from Germany ) .
so is it logical to find such differences in using SSRs ?? or in case of optimizing pcr for microsatellites and I end up with a band which is out of range ..should I assume that I'm amplifying something rather than the targeted sequence ?