How do I show the most energetically favorable structures for primer-template duplexes?
SnapGene calculates primer annealing dynamically but by default shows the tail of a primer (if present) as an simple unbound linear extension. The calculated lowest energy binding of the unbound tail is often more complex and can be displayed if required as detailed below.
See How does SnapGene estimate oligonucleotide (primer) melting temperatures (Tm)? 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". Note this option will apply for primers in all files subsequently viewed in SnapGene.
View a Primer
View primers in Sequence view to see the more detailed annealed structure for primers with unmatched regions.