### Coverage model

Based on our experimental results, we have trained a logistic regression model based on the free energy of annealing and the position of 3' mismatches between primers and templates. The model outputs an estimated false positive rate for every prediction, which indicates the likelihood that the model would falsely predict a coverage event when there is none. For designing primers, low cutoffs on the false positive rate should be used to ensure that all template sequences can actually be amplified.