Figure 4From: A multiple-alignment based primer design algorithm for genetically highly variable DNA targetsPrediction of dimerization risk. The dimerization risk is assessed by virtually sliding one primer (A) across another (B), reversed. Each potential overlap (1…n…N) is examined by i) a sliding window that tests if the two primers have an exact match within the window (user-specified parameter), and ii) a calculation of whether the fraction of matches in the overlap exceeds a certain ratio (user-specified). If either test indicates a potential dimer, the set is discarded. Primer-primer tests occur for all possible homo- and hetero-dimers.Back to article page