✂️ Restriction Enzyme Digest Calculator
Pick your enzymes and paste a DNA sequence to find every recognition site, the cut positions and the resulting fragment sizes — for a linear fragment or a circular plasmid.
54 bp · 3 enzymes selected
4 cuts → 5 fragments
30 bp · 11 bp · 6 bp · 6 bp · 1 bp
Cut positions (linear)
- EcoRI — site @ 1, cuts after base 1
- BamHI — site @ 7, cuts after base 7
- HindIII — site @ 13, cuts after base 13
- EcoRI — site @ 43, cuts after base 43
Finds each enzyme's recognition site (IUPAC ambiguity supported) in your sequence and reports the cut positions and resulting fragment sizes. The ·N on a chip is how many sites that enzyme has. Recognition sites and cut points are standard NEB/REBASE values. Enter a circular sequence as a plasmid to wrap the fragments. 🔒 Computed in your browser.
How the restriction enzyme digest calculator works
Each restriction enzyme cuts double-stranded DNA at a specific recognition sequence. The tool scans your sequence for the sites of the enzymes you select (IUPAC ambiguity codes are supported), marks where each cuts the top strand, then sorts the cut positions and reports the fragment lengths — the pieces you would see on a gel. Choose "circular" for a plasmid so the fragments wrap around the origin. Each enzyme chip shows how many sites it has in your sequence, so you can spot single-cutters and non-cutters at a glance.
Recognition sequences and cut positions are the standard NEB/REBASE values for 26 common enzymes. This predicts the digest from the sequence alone; real digests also depend on methylation (Dam/Dcm), star activity, buffer compatibility for double digests and complete vs partial cutting. Your sequence never leaves the browser — the right default for unpublished constructs.
Frequently asked questions
What is a restriction digest?
Cutting DNA with one or more restriction enzymes, each of which recognises a specific short sequence and cuts there. The result is a set of fragments whose sizes depend on where the sites fall — used for cloning, mapping and screening.
How do I predict fragment sizes?
Find every recognition site for your enzyme(s), note the cut position of each, and the fragments are the distances between consecutive cuts (plus the ends for a linear molecule, or wrapping around for a circular plasmid). This tool does it automatically for the enzymes you select.
What is the difference between a linear and circular digest?
A linear fragment with N cuts gives N+1 fragments (the two ends are free). A circular plasmid with N cuts gives exactly N fragments, because the molecule wraps around — a single cut linearises it into one fragment. Toggle "circular" for plasmids.
Why does EcoRI leave sticky ends?
EcoRI cuts G^AATTC off-centre on each strand, leaving a 5′ AATT single-stranded overhang — a "sticky end" that can base-pair with any fragment cut by the same enzyme. Blunt cutters like SmaI (CCC^GGG) cut straight across, leaving no overhang.
Which enzymes are included?
Twenty-six common ones — EcoRI, BamHI, HindIII, NotI, XhoI, SalI, PstI, SmaI, KpnI, SacI, SpeI, XbaI, NheI, NcoI, NdeI, EcoRV, BglII, ClaI, AflII, ApaI, DraI, HaeIII, AluI, MspI, TaqI and HinfI — with their standard recognition sites and cut positions.
Does it account for methylation or star activity?
No — it predicts the digest from the DNA sequence alone. Real results can differ because of Dam/Dcm methylation blocking some sites, star activity under non-ideal conditions, or partial digestion. Use the prediction as your expected pattern, then verify on a gel.
Is my sequence uploaded?
No. The scan and fragment calculation run entirely in your browser, so the sequence — often an unpublished construct — is never sent to a server.