Which melting-temperature model does it use?

A nearest-neighbour model, with the salt correction method selectable, so a reported Tm can be traced to the published method that produced it.

Can I check primers I already have?

Yes. Primer Check scans a primer set against the open sequence using 3-prime anchored identity and grades each primer, and it reports amplicon length for a pair.

Amplify · experimental

Primer Designer

Design primers against a region of an open sequence and see the numbers that decide whether they will work: nearest-neighbour melting temperature under stated salt conditions, GC content, and the free energy at the 3-prime end. Existing primers can be checked against the sequence instead, which is the faster path when the oligos are already in a freezer.

Open Primer Designer Open the Primer test sample

Real sequences (GenBank plasmid, FASTA, and a protein family) for the Primer Designer

What it does

01Primer pair design over a selected region
02Nearest-neighbour Tm with a stated salt correction, not a single fixed formula
03GC content, length and 3-prime end free energy per primer
04Primer checking against the open sequence with 3-prime anchored identity, graded per primer
05Amplicon length for a pair
06A primer library with import from an order CSV, so a real oligo order can be checked as a set

What it runs on

Thermodynamics run on the Tm engine in packages/ports, which ports the nearest-neighbour tables and salt corrections and is golden-validated against the reference implementation. The panel runs on @ports/enzymes, @ports/oligo-structure, @ports/primer.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Which melting-temperature model does it use?: A nearest-neighbour model, with the salt correction method selectable, so a reported Tm can be traced to the published method that produced it.
Can I check primers I already have?: Yes. Primer Check scans a primer set against the open sequence using 3-prime anchored identity and grades each primer, and it reports amplicon length for a pair.

Also searched as

primer design online · PCR primer designer · primer3 alternative online · primer Tm calculator · check primers against template · amplicon length calculator · primer binding site finder · free primer design software · Primer3Plus alternative · Primer-BLAST alternative · design cloning primers with overhangs · sequencing primer design · design primers from a plasmid map