Paste a template and get ranked PCR primer pairs. Tm uses the SantaLucia nearest-neighbor model, and every pair is checked for hairpins and primer dimers.
Positions are 1-based on the template. The reverse primer is shown 5′→3′ as you would order it. Dimer and hairpin values are the longest complementary run at the primer's 3′ end; 3 or fewer is ideal.
PrimerBench is a free online tool for PCR primer design. Design PCR primer pairs with nearest-neighbor Tm and dimer checks. It runs entirely in your browser, so there is nothing to install and your data stays on your device.
PrimerBench uses the SantaLucia 1998 unified nearest-neighbor parameters with a salt correction for your Na+ concentration and primer concentration. It doesn't correct for magnesium, so values can differ by a few degrees from tools that do.
Enter a target start and end. PrimerBench places the forward primer before the target and the reverse primer after it, within your product size range.
They are the longest run of complementary bases at a primer's 3' end, which is what matters most for mispriming. Three or fewer is ideal; pairs with five or more are excluded.