Design primers with the primer wizard

  • Updated

Open your sequence and click the Primer button on the right side bar. Select Create Primers > Wizard.

Select the region you want to target, adjusting the other default parameters as necessary.

We support designing PCR, qPCR and sequencing primers. Choose the primer type you want in the Task dropdown.

Work through each step in the Wizard to set your parameters:

  • Primer: Specify min, max and optimal primer parameters.

  • Amplicon: Specify amplicon min/max size.

  • Result Generation: Specify the number of possible primer results

  • Partial Design: Set part of the sequence included in the primer if desired.

  • Design Across Junctions: Design primers across junctions if desired.

  • Force Location: Specify the location of the primer.

Note: The default amplicon length range is 200 - 1000bp. If your amplicon length is outside of this range, please adjust the defaults. If your amplicon length does not fit within the selected range, Benchling will indicate that "no primers could be found."

Pro Tip: The easiest way to choose your target region is to select it on your sequence and click Use Selection.
When you are ready, click Generate Primers. Choose your primer / primer pair of interest and click Save Selected Primers.

Use the Export as CSV function to download your selected primers.

What do the Primer Wizard parameters mean?

We use Primer3 to create primers in our Wizard. For more information on how parameters are used in generating primers, refer to the official Primer3 manual:

Want to design primers manually?

Learn how to do it here!

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