In CLC Main Workbench you have the possibility of matching known primers against one or more DNA sequences or a list of DNA sequences. This can be applied to test whether a primer used in a previous experiment is applicable to amplify e.g. a homologous region in another species, or to test for potential mispriming. This functionality can also be used to extract the resulting PCR product when two primers are matched. This is particularly useful if your primers have extensions in the 5' end.
To search for primer binding sites:
Toolbox | Primers and Probes ()| Find Binding Sites and Create Fragments ()
If a sequence was already selected, this sequence is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements.
Click Next when all the sequence have been added.
Note! You should not add the primer sequences at this step.