How do I show the most energetically favorable structures for primer-template duplexes?
SnapGene calculates primer annealing dynamically, but by default shows the 3' tail of a primer as an simple unbound linear extension. The calculated lowest energy structure is often more complex and can be displayed if required as detailed below.
See this support article for more information on how annealing and Tm are calculated.
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.