Why do different tools report different Tm values for one oligo?

Because the value depends on the thermodynamic table, the salt correction and the stated ion and oligo concentrations. Each of those is selectable here, and a preset quotes its source, so a value can be reproduced.

Does it handle magnesium?

Yes. The Owczarzy 2008 correction for magnesium is one of the selectable methods, alongside the monovalent corrections.

Amplify

Melting Temperature

Compute the melting temperature of an oligo under conditions you state, rather than under conditions a tool assumed. The salt correction is selectable across the published methods, each named with its source, and every field maps to a real parameter of the underlying model.

Open Melting Temperature Open the Primer test sample

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

What it does

01Nearest-neighbour Tm with selectable thermodynamic tables
02Eight salt-correction methods, each named with its publication, from Schildkraut and Lifson 1965 through Owczarzy 2008 for magnesium
03Published condition presets, with every value quoted from its source
04Monovalent and divalent ion, dNTP and oligo concentration inputs
05Self-complementary oligo handling, which halves the concentration term
06GC-percentage formulas as an alternative model, including McConaughy 1969 and Blake and Delcourt 1996
07Fields the chosen model does not use are marked as unused rather than left to imply an effect

What it runs on

The Tm engine ports the nearest-neighbour tables and salt corrections and is golden-validated against the reference implementation. The panel runs on @ports/melt, @ports/tm.

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

Why do different tools report different Tm values for one oligo?: Because the value depends on the thermodynamic table, the salt correction and the stated ion and oligo concentrations. Each of those is selectable here, and a preset quotes its source, so a value can be reproduced.
Does it handle magnesium?: Yes. The Owczarzy 2008 correction for magnesium is one of the selectable methods, alongside the monovalent corrections.

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