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

Sources for DNA strand notation, sequence formats, and restriction-end warnings. Exact A/C/G/T binding is checked in the supplied primer orientations using original Mol Biology Tools code; Tm, mismatches and degenerate-base binding are not modeled.

  1. DNA base and strand notation: NC-IUB (1985), nucleotide sequence nomenclature. This checker's accepted sequence alphabet is A, C, G, and T.
  2. FASTA and GenBank input: NCBI FASTA documentation and GenBank sample record. GenBank annotations are not treated as sequence.
  3. Recognition sites and cleavage offsets: NEB recognition-sequence chart. The shared enzyme snapshot was verified on 14 September 2026.
  4. Compatible restriction enzyme ends: New England Biolabs compatible cohesive ends chart.