In the following you find a listing of options that influence the basic coverage of primers.

#### Binding region definition

You can either require primers to lie completely within the specified binding region or require that they only overlap with the target region.

#### Off-target binding

When the setting for Off-target ratio is greater than 0%, primers binding to non-target regions are also considered to cover these templates. However, if the ratio of primers binding to non-specified region exceeds the allowed ratio, a warning is shown to the user. For designing primers, the internal off-target binding ratio is automatically set to 0%.

#### Mismatch binding

By specifying the maximal number of mismatches, you can determine how many mismatches the string matching algorithm allows. Note that possible binding events above the specified maximal number of mismatches cannot be detected by openPrimeR. Note that the memory and runtime requirements increase with a larger number of allowed mismatches and that large settings require the use of an appropriate method for selecting putative binding events (e.g. free energy of annealing).