Prediction 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.
Brodin et al. BMC Bioinformatics 2013 14:255 doi:10.1186/1471-2105-14-255