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When calculating the Tm of my oligo, should I only use the bases which are complementary to my target or should I also include any sticky overhangs on the primer?
To determine the relative Tm of primers with non-complementary overhangs, only the complementary region should be taken into account. You can obtain the Tm using the free, online OligoAnalyzer tool found at www.idtdna.com/scitools.