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Problems in PCR "microsatellites" trubleshooting

Problems in PCR "microsatellites" trubleshooting - Molecular Biology Techniques

Problems in PCR "microsatellites" trubleshooting - Molecular Biology Forum. Includes forums for common molecular biology techniques.

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Old 11-15-2012, 01:55 PM
Pipette Filler
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Default Problems in PCR "microsatellites" trubleshooting

Greetings .
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 ?

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entomology , microsatellites , pcr , pcr troubleshooting , population genetics , problems , ssr , trubleshooting

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