Use this free online restriction site mapper to find restriction enzyme recognition sites in linear or circular DNA and estimate digest fragments for restriction digest planning.
Useful Checks
Use this before ligation setup to confirm enzyme sites and fragment sizes, then use the Ligation Calculator for insert-to-vector mass calculations.
The current sequence can be opened in Primer Designer or Primer Binding Checker, connecting restriction-site analysis with primer design and binding checks.
Minimum Inputs Needed
DNA sequence.
Optional Settings
Enzyme search (optional)
Type enzyme names or recognition sites to focus on specific enzymes. Use commas for more than one.
DNA topology
Use linear DNA for fragments. Use circular DNA / plasmid for plasmids. In circular mode, the coordinate origin means base 1 / the start of the entered sequence, not the biological ori.
Enzyme group
Use this to scan only common cloning enzymes, rare cutters, Type IIS enzymes, or degenerate-site enzymes.
Result filter
Show all enzymes, only enzymes that cut, or only enzymes that do not cut.
Max positions shown per enzyme
Keeps the table readable when an enzyme cuts many times.
Zoom
Zoom and drag crowded circular maps. Hover an enzyme to focus all of its labels and sites.
How To Use
Paste or upload the sequence.
Choose linear or circular topology.
Enter enzyme names only if you want to focus the scan.
Choose an enzyme group or result filter if needed.
Click Analyze restriction sites.
Click enzyme badges or map labels to add or remove enzymes from the digest preview. Select multiple enzymes for a combined digest.
Understanding The Results
The table shows enzyme names, cut counts, and positions.
The linear or circular map shows recognition-site start positions; circular mode also detects sites crossing base 1.
The digest preview estimates topology-specific fragment sizes for the selected enzyme set.
The virtual gel estimates the fragment pattern and shows a dashed uncut reference. An uncut circular plasmid is not represented as a simple linear fragment band.
The highlighted sequence shows sites in sequence context.
Copy summary preserves the selected digest, site counts, positions, and predicted fragments.
Accepted Input Formats
Raw DNA sequence.
FASTA.
GenBank text with an ORIGIN sequence section. Feature annotations, including ori/origin-of-replication annotations, are ignored.
Multiple FASTA records are concatenated for analysis and may create artificial junction sites. Analyze separate records one at a time.
IUPAC-degenerate enzyme recognition sites and reverse-complement site matching are supported.
.dna / SnapGene binary files are not supported. Export as FASTA or GenBank.
Assumptions And Limitations
The tool checks recognition sequences. It does not check methylation sensitivity or buffer compatibility.
Digest fragments are planning estimates.
For real digests, confirm enzyme details with supplier documentation.
The browser tool accepts sequence files smaller than 2 MB and sequences up to 100,000 bp.
Example
Paste a plasmid sequence, choose circular DNA, search EcoRI, BamHI, HindIII, and XhoI, and check which enzymes cut once.
Use note: These tools are for research and educational planning. Check important calculations and sequence designs before ordering reagents or running experiments.