User GuidesSnapGene User Guide PrimersAnalyze Primer Sequences

Analyze Primer Sequences

How do I analyse primers (oligonucleotides) to obtain extinction coefficient, hairpin formation, self-dimerization or hetero-dimerization information?

SnapGene reports %GC, molecular weight and Tm in Primer view. To access further information about primers SnapGene can pass your primer sequences to the IDT "OligoAnalyzer" form.

You can create a free login at IDT, via, to use IDT "OligoAnalyzer".

Open a DNA sequence

Open a DNA sequence that has primers annotated on the sequence. See the User Guide chapter on Primers to learn more about creating, adding and using primers in SnapGene.

Select one or more primers for analysis in Map view, Sequence view or Primers view.

Analyse Selected Primers

Click Primers → Analyse Selected Primers.

Log into the IDT Website

SnapGene will open a separate Tab in your default web browser for each primer and automatically fill each IDT form with a primer sequence.

1. Use the buttons to the right of the window to obtain detailed information about each primer.

2. Use the modifications "drop-downs" to add chemical modifications to your primer, then click "Analyze" to obtain detailed information about the modified primer.