Once primers are annotated on a sequence, the resulting PCR product can be extracted by selecting Primers → Extract PCR Product. If only a single pair of primers are annotated on a sequence then these will automatically be chosen as the Forward and Reverse primer. If multiple primers are annotated on a sequence, then the drop down menus allow you to choose which primers to use for extracting a single PCR product, or alternatively you can choose to Extract PCR products from all primers.
When you click OK a new sequence document is produced containing only the sequence spanning (and including) the PCR primers. Any 5’ extensions on the primers will also be included.
PCR products can also be extracted directly from the annotated sequence by selecting a forward and reverse pair of primers while holding down the shift key to select the sequence bounded by the primers. Then click the Extract button. You will be given the option to either extract the PCR product, or the Selected region. If PCR product is selected, the resulting product will include any 5’ extensions on the primers.