Restriction Site Analyzer

Map restriction enzyme recognition sites in linear or circular DNA with this free online restriction site mapper for restriction digest planning, predicted digest fragments, and downstream primer design or binding validation.

Restriction site analyzer inputs

Accepted file types: .txt, .fa, .fasta, .fna, .ffn, .seq, .gb, .gbk, .genbank. Plain-text DNA, FASTA, or GenBank text only.

Use circular topology for plasmids if sites crossing base 1 or circular digest fragments matter.

Send sequence to another tool

Send the current sequence to another Mol Biology Tools page. The sequence will open in a new tab.

References

Sources for recognition sequences, strand-specific cleavage positions, Type IIS offsets, and compatible cohesive ends. Mapping and digest calculations use original Mol Biology Tools code and a versioned enzyme snapshot.

  1. Recognition sequences and cleavage positions: NEB recognition-sequence chart. The shared 81-enzyme dataset was verified on 14 September 2026 and retains per-enzyme manufacturer links. Each tool uses its supported subset; this is not a live REBASE download.
  2. Asymmetric recognition and Type IIS cleavage: NEB nonpalindromic enzyme chart. Cleavage offsets are applied to both strands; an incomplete linear cleavage region is excluded from the digest prediction.
  3. Restriction-modification database background: Roberts et al. (2023), REBASE. Consult the REBASE database and supplier documentation for methylation sensitivity and enzyme-specific requirements, which are not modeled here.
  4. Compatible restriction enzyme ends: New England Biolabs compatible cohesive ends chart.
  5. Degenerate recognition-site matching: NC-IUB/IUPAC nucleotide ambiguity recommendations.
  6. Sequence-file formats: NCBI FASTA documentation and GenBank sample record.