What is a restriction enzyme?

A restriction enzyme (endonuclease) is a protein that recognizes a specific short DNA sequence (recognition site) and cuts the double-stranded DNA at or near that site. They are essential tools in recombinant DNA technology and cloning.

What does the cut position number mean?

The position reported is always the 1-based index of the first nucleotide of the matched recognition sequence as it appears on the input (top) strand. For a reverse-complement match, it is still the leftmost input-strand coordinate; the current results do not add a separate +/− strand label. The actual cleavage may occur within or outside the recognition sequence depending on the enzyme.

How are degenerate bases handled?

IUPAC ambiguity codes (R, Y, S, W, K, M, B, D, H, V, N) in the recognition sequences are expanded to all matching bases during the search, so degenerate motifs like RGATCY are correctly matched.

What does "unique cutter" mean?

A unique cutter cuts the sequence exactly once. These sites are especially useful for linearizing circular DNA or for inserting a single fragment at a defined position.

Are both strands searched?

Yes. The tool searches both recognition-sequence orientations against the input strand. Palindromic sites produce the same positions and are deduplicated; non-palindromic reverse-complement hits use the leftmost 1-based coordinate on the input strand.

Why might a familiar enzyme not appear in the results?

Either the recognition sequence is absent from your input, or the enzyme is not yet in the built-in library. The library currently covers 40+ widely used enzymes; rare cutters may be missing.

Restriction Enzyme Finder

Paste a DNA sequence to find all restriction enzyme cut sites from a library of 40+ common enzymes.

Enter DNA Sequence

0 bp

Filter Enzymes

Common Cloning 6-Cutters 4-Cutters Rare Cutters (8 bp)

Cut Site Results

Enzyme	Recognition Seq	Cuts	Positions (1-based)

Paste a DNA sequence above to find restriction sites.

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Summary

The Restriction Enzyme Finder scans any DNA sequence against a built-in library of 40+ common restriction enzymes and returns a complete cut-site map in seconds. Results show each enzyme, its recognition sequence, cut count, and exact positions — making it easy to plan cloning strategies, verify sequences, and identify unique sites for linearization.

How it works

Paste or type your DNA sequence into the input box.
Select which enzyme groups to include — popular cloning enzymes are checked by default.
The tool scans the sequence and lists every enzyme that cuts, along with the number of cut sites and their positions.
Click any enzyme row to see the cut positions highlighted in the sequence.
Use the filter to search for a specific enzyme by name.
Copy the results table to your clipboard for use in a lab notebook.

Use cases

Screen a cloning insert for compatible restriction sites.
Design a restriction digest map for gel verification.
Identify unique (single-cut) sites for linearizing a plasmid.
Find enzymes that do NOT cut your insert before cloning.
Quickly verify a published sequence by checking expected cut sites.
Select compatible cohesive ends for directional ligation.
Teach restriction enzyme biology with a hands-on visual tool.

Frequently Asked Questions

Last updated: 2026-09-30 · Reviewed by Nham Vu