Use this to find restriction enzyme sites in a DNA sequence. It can show the sites on a linear or circular map and estimate digest fragments.
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.
Validated sequences 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
Use this to inspect crowded circular maps.
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.
Understanding The Results
The table shows enzyme names, cut counts, and positions.
The map shows where detected sites are located.
The digest preview estimates fragment sizes for selected enzymes.
The highlighted sequence shows sites in sequence context.
Accepted Input Formats
Raw DNA sequence.
FASTA.
GenBank where supported. Bases are read from the GenBank ORIGIN sequence section; feature annotations, including ori/origin-of-replication annotations, are ignored.
IUPAC-degenerate enzyme sites are supported.
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.
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.