How do I show the predicted secondary structure of an oligonucleotide primer in SnapGene 7.1 or later?
Open a DNA Sequence
Open a sequence file that has associated primers. If required, add matching primers to the sequence - see Create a Primer (SnapGene 7.0 and later) or Import Primers.
Switch to Primers View
Switch to Primers view to see a list of all primers associated with the sequence.
Click the disclosure button (>) associated with any primer to see the primer details.
Click a Show Structure button to see the predicted secondary structure for that primer.
View the Predicted Structures for the Oligonucleotide Monomer
Use the "Monomer" tab to view the predicted structures of the oligonucleotide in the secondary structure viewer.
The temperature used for the predicted structure is shown in the window title.
Click the Calculation parameters button in the bottom left corner of the window to change parameters (including temperature) used for the structure prediction.
To learn more about other options in the secondary structure viewer window, see this guide article - View the Predicted Secondary Structure of Single Stranded Sequences.
View the Predicted Structure for the Oligonucleotide Homodimer
Click the "Homodimer" tab to view the predicted lowest free energy structure for the oligonucleotide homodimer.
The temperature used for the predicted structure is shown in the window title.
Click the Calculation parameters button in the bottom left corner of the window to change parameters (including temperature) used for the structure prediction.
To learn more about other options in the secondary structure viewer window, see this guide article - View the Predicted Secondary Structure of Single Stranded Sequences.