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Set the Default Primer Hybridization Parameters Used for New or Imported Sequences

How do I set the default primer hybridization parameters for newly entered or imported sequences?

Open Preferences

The hybridization settings referenced below are for new or imported sequences only. To set the hybridization parameters for an existing sequence file, open the file and click Primers → Hybridization Parameters. See  Adjust Primer Hybridization Parameters for more information.

To adjust  the default primer hybridization parameters for new or imported sequences files, click SnapGene → Preferences (macOS) or Edit → Preferences (Windows or Linux), and select "Primers" in the sidebar.

SnapGene "Add Primers" is a live tool, it may find more than one binding site on a sequence if you reduce the allowed 3' match or reduce the  required melting temperature.

We provide separate hybridization settings for short sequences and long sequences.

Settings for long sequences allows you to use more stringent settings so that fewer lower quality "off-site" binding sites are detected.

Set the Hybridization parameters for Smaller DNA Sequences

  1. Use the dropdown menu to specify the minimum match length required at the 3' end of the primer (minimum 8 , maximum  35 nucleotides. If required set to allow a "single isolated mismatch" within the 3' binding region.
  2. Set a minimum melting temperature (minimum 10°C, maximum 50°C).

Set the Hybridization parameters for Larger DNA Sequences

  1. Set the size threshold for sequences to be considered large (minimum 10,000 bp, maximum 1,000,000,000 bp).
  2. Use the dropdown menu to specify the minimum match length required at the 3' end of the primer (minimum 8 , maximum  35 nucleotides. If required set to allow a "single isolated mismatch" within the 3' binding region.
  3. Set a minimum melting temperature (minimum 10°C, maximum 50°C).

Set Hybridization Parameters for Oligonucleotides That Don't Match at their 3' Ends

Set this option  to allow detection of oligonucleotides that can bind but are mismatched at their 3' ends.

Use the dropdown menu to specify the minimum match length required for the oligonucleotide at the 5' end (minimum 8 , maximum  35 nucleotides.

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