Why is this different from my primer Tm?

Primer Tm models a short oligo binding its target; product Tm models the whole duplex. Length dominates: a 500 bp product melts ~80 °C, while its ~20 nt primers melt ~55–60 °C.

Does it handle very short products?

The formula is calibrated for products over ~50 bp. For short oligos use the Wallace-rule or nearest-neighbor primer Tm tools instead.

PCR product melting temperature calculator

Estimate the melting temperature of a full-length PCR product (amplicon) from its sequence and salt concentration, using the classic salt-adjusted formula for long dsDNA.

How it works

Formula

Tm = 81.5 + 16.6·log₁₀[Na⁺] + 0.41·(%GC) − 675 ÷ length. This salt-adjusted formula is for long double-stranded products (≳50 bp), not short primers.

Worked example

A 500 bp product that is 50% GC at 50 mM Na⁺ (0.05 M): 81.5 + 16.6·log₁₀(0.05) + 0.41·50 − 675 ÷ 500 = 81.5 − 21.6 + 20.5 − 1.35 ≈ 79.1 °C.

When to use it

To predict where an amplicon melts — for setting a qPCR melt-curve window, checking a high-resolution-melt design, or confirming a product is distinguishable from primer-dimers, which melt much lower.

Sensible defaults

Defaults use a 51 bp example at 50 mM Na⁺. Note the amplicon Tm (this tool) is very different from primer Tm — a long product melts far higher than the primers that made it.

FAQ

Why is this different from my primer Tm?: Primer Tm models a short oligo binding its target; product Tm models the whole duplex. Length dominates: a 500 bp product melts ~80 °C, while its ~20 nt primers melt ~55–60 °C.
Does it handle very short products?: The formula is calibrated for products over ~50 bp. For short oligos use the Wallace-rule or nearest-neighbor primer Tm tools instead.