PCR Primer Stats

How to check PCR primers

1. Paste primers one per line, with an optional name before each sequence, or as FASTA.
2. Set the primer and sodium concentrations used for the nearest-neighbor melting temperature.
3. Each primer is listed with its length, GC content, three melting temperatures, molecular weight and any warnings.

Frequently asked questions

Which melting temperature should I use?

The nearest-neighbor value is the most accurate. The basic formula is 2 °C per A or T and 4 °C per G or C for short primers, with a GC formula for longer ones; the salt-adjusted value corrects it for sodium.

What do the warnings check?

Length outside 18-30 bases, GC content outside 40-60%, no G or C at the 3' end, more than 3 G or C in the last 5 bases, runs of 5 or more of the same base, and self-complementary stretches that could form hairpins or primer dimers.

Is my sequence uploaded?

No. Everything runs in your browser, so your sequences never leave your device.