PrimerBench: PCR primer design, ranked and checked

PrimerBench scans your template for every workable primer, scores them by melting temperature, GC content, and 3′ stability, then returns the best-matched forward and reverse pairs for your product size.

Open PrimerBench All tools

Free, no sign-up, and installable on your phone. Runs in your browser at primers.gataca.com.

PrimerBench showing results for the built-in example — PrimerBench with its built-in example loaded.

What you can do with PrimerBench

Design primers to amplify a gene or exon for cloning
Flank a mutation or target region for sequencing
Build qPCR or colony PCR primer sets with matched Tm
Sanity-check a primer you already have

How to use it

Paste your template sequence (up to 50,000 bases).
Optionally set a target start and end, product size range, and Tm and GC limits.
Click Design primers to get the top five non-overlapping pairs.
Copy primers 5′→3′, ready to order, and view each pair on the template map.

Features

SantaLucia 1998 nearest-neighbor Tm with salt and primer concentration
GC content, GC clamp, and homopolymer run filters
3′ hairpin, self-dimer, and cross-dimer screening
Target region placement and product size control
Visual map of each pair on the template
Single-primer Tm calculator
Save results as reports, spreadsheets, or sequence files
Install it on your phone or computer; works offline

Frequently asked questions

Is PrimerBench a replacement for Primer3?

It covers the core of everyday primer design with transparent rules. For specialized needs such as probe design, mispriming libraries, or magnesium-corrected Tm, Primer3 offers more options.

Why are no pairs found?

Your constraints may be too tight for the sequence. Widen the Tm or GC range, the product size, or turn off the GC clamp requirement.

Does it check primer specificity against a genome?

No. PrimerBench checks primers against the template you paste. Use BLAST to confirm genome-wide specificity for critical assays.