CutBench

Find restriction sites in your sequence, then pick enzymes to see the fragments and a virtual gel.

Sequence

Circular (plasmid)

Site map

Shows enzymes that cut once or twice. Positions are the base after which each enzyme cuts.

Enzymes

Tick enzymes to add them to the digest below.

Digest	Enzyme	Site	Cuts	Positions

Digest

About CutBench

CutBench is a free online tool for restriction enzyme mapping. Map restriction sites and preview digests on a virtual gel. It runs entirely in your browser, so there is nothing to install and your data stays on your device.

Features

Site map for 40+ common enzymes
Single, double, and non-cutters
Linear and circular (plasmid) DNA
Fragment sizes for multi-enzyme digests
Virtual gel with a 1 kb ladder
Save results as text, spreadsheet, or sequence files
Installs on your phone and works offline

Common questions

Which enzymes are included?

Over 40 commonly used enzymes, including EcoRI, BamHI, HindIII, XhoI, NotI, NcoI, NdeI, XbaI, and SpeI. Degenerate sites such as HincII (GTYRAC) are supported.

Does it handle plasmids?

Yes. Tick Circular to find sites that span the origin and to calculate fragments correctly for circular DNA.

How accurate is the virtual gel?

It approximates band positions on a 1% agarose gel with a log-scale model. Use it to plan and sanity-check digests, not as a substitute for running one.