NetPrimer is a gratis web-based tool used for analysing primers used in PCR to amplify a DNA sequence.
The accurate prediction of the melting temperature (Tm) is one of the most important factors that governs the success of a PCR reaction.
[3] NetPrimer also analyzes the thermodynamically important secondary structures such as hairpins, self and cross dimers, runs and repeats.
[4] These structures significantly affect the primer efficiency and therefore the success[clarification needed] of a PCR reaction.
In addition to the primer quality, its molecular weight and optical activity (both in nmol/A260 and μg/A260) are also presented for quantitation.