Primer Binding Checker

Check exact primer binding sites on linear or circular DNA with this free online primer binding checker and primer map, including orientation, additional template matches, 5' overhangs, and expected amplicon size.

Primer binding checker inputs
No template loaded.

Accepted file types: .txt, .fa, .fasta, .fna, .ffn, .seq, .gb, .gbk, .genbank. Maximum parsed template length: 500,000 bp.

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Primer pair 1

References

References for primer binding checker logic: degenerate-base matching, reverse-complement primer mapping, primer-binding Tm calculations, salt and magnesium correction, and linear or circular DNA amplicon interpretation. Mol Biology Tools implementation code is original.

  1. Degenerate-base matching and reverse-complement logic: NC-IUB/IUPAC nucleotide ambiguity recommendations.
  2. Primer-binding Tm calculations: SantaLucia J. (1998), unified nearest-neighbor DNA thermodynamics.
  3. Salt and magnesium correction for DNA duplex Tm: Owczarzy et al. (2008), DNA duplex stability in magnesium and monovalent cation solutions.