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
  • Tm
  • Oligoanalyzer