What does a primer penalty mean and what is good?

The primer penalty is a score assigned to an oligo depending on how well it conforms to the parameters you set and some set rules built into the system. The lower the number, the better the oligo according to the program. It is usually good to pick at least three sets and run a self-dimer, hairpin, and heterodimer analysis on the sets to make sure the primers do not have a lot of secondary structure. The OligoAnalyzer SciTool located on our website can be used to run these checks.

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