Restriction Enzyme Site Finder
Find recognition and cut sites for common restriction enzymes.
🔒 Nothing you paste is logged or stored
A standalone restriction site finder: paste DNA and all 49 curated common restriction enzymes are scanned at once, with IUPAC-aware matching for degenerate recognition sequences like HinfI G^ANTC. The table lists each enzyme, its recognition sequence with the cut point marked, how many times it cuts, and every 1-based site position, so you can plan a restriction digest or build a restriction map.
0 bp · 0 sites from 0 enzymes
Enter a sequence to scan.
Working on a whole construct rather than a single digest check? Open SeqStudio — the full editor, with live feature annotation, plasmid maps, restriction and primer panels, undo/redo, multi-document tabs and GenBank / SnapGene import and export.
How to use the Restriction Sites tool
- 1Paste DNA (raw or FASTA) into the DNA sequence box, or click Load example to try a polylinker packed with common sites.
- 2Check the line under the box for sequence length, total sites found and how many enzymes were scanned.
- 3Leave the Show only enzymes that cut checkbox ticked for a short hit list, or clear it to also list the enzymes with zero sites.
- 4Read the results table: enzyme, recognition site with a caret marking where it cuts, cut count, and the 1-based positions. Use Share to copy a link that restores the sequence and the checkbox.
- 5Need more than a cut site finder? Open SeqStudio from the link below the tool to edit the construct itself.
Frequently asked questions
Which enzymes are included?
A curated set of ~50 commonly used enzymes (EcoRI, BamHI, HindIII, NotI and many more), including some with degenerate recognition sequences.
Are degenerate recognition sequences handled?
Yes. Enzymes with IUPAC codes (e.g. HinfI G^ANTC) are matched correctly using the full ambiguity alphabet.
Can I edit the sequence, not just scan it?
Not on this page. This is a read-only scanner: paste a sequence and read the table. If you need to edit the construct itself, open SeqStudio from the link under the tool. That is SeqBench's full editor, where every keystroke remaps features live, with undo/redo, auto-annotation, plasmid maps, multi-document tabs, and GenBank / SnapGene import and export.
More
Guides
References
Common restriction enzymes: recognition sites, cut positions, NEB buffer activity, star activity and an interactive double-digest buffer finder.
Nucleotide ambiguity codes and their complements.
Selection markers, mechanisms and working concentrations for cloning.
Related tools
Pick two restriction enzymes and get the single buffer that runs both, each enzyme's activity in every buffer, and a straight answer on when to digest sequentially instead.
Summarise and validate FASTA or FASTQ: counts, N50, GC, quality.
Convert between mass, moles, molarity and copy number for DNA/RNA.