User GuidesSnapGene PreferencesShow Full Structures for Primer-Template Duplexes

Show Full Structures for Primer-Template Duplexes

How do I show the most energetically favorable structures for primer-template duplexes?

By default, SnapGene shows the 5' tail of a primer as an unbound linear extension for display purposes. But primer annealing is calculated dynamically, and the lowest energy structure is often more complex.

Open Preferences

Click SnapGene → Preferences (macOS) or Edit → Preferences (Windows or Linux), and select "Primers" in the sidebar.

Check the box labeled "Show full structures of the most energetically favorable duplexes".

View the Primer

View the primer in Sequence view to see the full annealed structure that was calculated.