User GuidesSnapGene User Guide PrimersAdjust Primer Hybridization Parameters

Adjust Primer Hybridization Parameters

How can I adjust the hybridization parameters to see more or fewer primer binding sites?

Review the Primer Binding Sites

To show a synopsis of primer information, mouse over the primer name. Note the number of primer binding sites.

Alternatively, double-click the primer to open the Edit Primers dialog. If a primer has multiple binding sites, a warning message will be shown in a yellow box. The total number of binding sites is also shown. You can switch between different primer binding sites using the control button.

Adjust the Hybridization Parameters

SnapGene 5.3 and later allow detection of primers with mismatches within 3 nucleotides of the primer 3' end

To adjust the primer hybridization parameters, click Primers → Hybridization Parameters. The resulting dialog provides controls for adjusting the number of matching bases at the 3’ end of the primer as well as the minimum melting temperature.

Adjust the Default Hybridization Parameters for New Files

To adjust  the default primer hybridization parameters for new files, click SnapGene → Preferences (macOS) or Edit → Preferences (Windows or Linux), and select "Primers" in the sidebar. See Set the Default Primer Hybridization Parameters Used for New or Imported Sequences for more information.