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Biology Tools · Updated October 21, 2026 · Reviewed by FormatFlow Editorial

Restriction Enzyme Digest Calculator

You can map restriction sites and fragment sizes for linear or circular DNA in your browser, choosing from common enzymes and seeing every cut position in the entered sequence.

Runs in your browserFree · No sign-up · No watermark
DNA + ENZYMES → FRAGMENTSRuns in your browser
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Everything runs locally in this tab. No file is uploaded while the tool loads.

This tool runs in your tab. Nothing is uploaded and no copy is stored.

How files are handled

At a glance

Works with
DNA + ENZYMES → FRAGMENTS
Processing
In your browser
Price
Free, no account
Updated
October 21, 2026
All Biology Tools

About Restriction Enzyme Digest Calculator

A restriction digest turns a DNA molecule into defined fragments by cutting at recognition sequences. Mapping those sites is a routine step in cloning: it confirms a plasmid's identity, predicts band sizes on a gel and shows whether an insert is present in the expected orientation.

This calculator searches the entered sequence for the recognition site of each selected enzyme, reports cut positions using each enzyme offset, and lists fragment sizes for linear or circular molecules, including a combined digest when several enzymes are chosen. The per-enzyme and combined tables make it easy to compare what one cutter would produce with the pattern from a multi-enzyme digest, which is the comparison a cloning check usually needs.

What this tool does

The details that matter when you use Restriction Enzyme Digest Calculator for real work.

  • Sixteen common enzymes

    EcoRI, BamHI, HindIII, XhoI, SalI, PstI, NotI, SmaI, KpnI, SacI, XbaI, NdeI, NheI, BglII, MluI and AgeI, with recognition sites and cut offsets.

  • Linear or circular molecules

    Fragment sizes stop at the ends for linear DNA and wrap around the origin for plasmids, which changes the expected set of bands.

  • Per-enzyme and combined views

    See each enzyme's sites, cut positions and fragments, then read the combined digest when several enzymes are selected.

  • Cut positions with offsets

    Staggered enzymes such as EcoRI and NotI report the cut at the correct position within the recognition site.

  • FASTA and ambiguity handling

    Headers and formatting are stripped; ambiguity codes are allowed with a warning that sites spanning them cannot be detected.

  • Input validation

    Empty input, RNA letters, unknown enzymes and an empty selection are rejected with clear messages.

How to use Restriction Enzyme Digest Calculator

No account, no installation — the whole job happens in this browser tab.
  1. 01

    Paste the DNA sequence

    Paste raw DNA or a FASTA record; headers, spaces, digits and punctuation are removed before the search.

  2. 02

    Choose the topology

    Select linear for a restriction fragment or PCR product, or circular for a plasmid, so fragment sizes are calculated correctly.

  3. 03

    Select one or more enzymes

    Tick each enzyme, use the common set for a quick plasmid check, or clear the selection and start again.

  4. 04

    Read the per-enzyme table

    Each enzyme row shows the number of sites, cut positions and the fragment sizes produced by that enzyme alone.

  5. 05

    Check the combined digest

    The combined cut list and fragment sizes show what a multi-enzyme digest would produce, assuming complete digestion.

How this tool works

Works with
DNA + ENZYMES → FRAGMENTS
Processing
Client-side, in your browser. Nothing is uploaded.
Requirements
Chrome, Edge, Firefox or Safari · JavaScript enabled

Limitations worth knowing

  • Assumes complete digestion at every detected site; methylation sensitivity, star activity, partial digests and enzyme kinetics are not modelled.
  • Fragment sizes are calculated on the entered top strand using each enzyme's cut offset, so staggered cuts leave overhangs and the two strands differ by a few bases.
  • Ambiguity codes are accepted but sites spanning them are not detected, and gel migration does not map linearly to fragment length.

Privacy and file handling

The DNA sequence you paste stays in this browser tab. Site searching, cut mapping and fragment calculations run with JavaScript on your device, so nothing is uploaded, stored or logged, and closing the page discards the input.

Read the full privacy policy

Restriction Enzyme Digest Calculator FAQ

Short, direct answers to the questions people ask before using this tool.
How do I find restriction sites in a DNA sequence?
Search the sequence for the enzyme's recognition site and for its reverse complement, because the enzyme can bind either strand. This calculator does that search for every selected enzyme and reports each match with its cut position.
What are cut offsets and why do they matter?
The cut offset is the number of bases within the recognition site before the enzyme cuts the top strand. EcoRI cuts after the first base of GAATTC, leaving a four-base overhang, while SmaI cuts in the middle of CCCGGG and leaves a blunt end, so the offset decides where the fragment boundary falls.
How are fragment sizes calculated for circular DNA?
For a circular molecule the cut sites are treated as points around a circle, and each fragment is the distance from one cut to the next, wrapping around past the origin at the end. A single cut linearizes the circle and gives one fragment equal to the full length.
Why is one fragment listed when there are no sites?
If none of the selected enzymes cuts the sequence, the molecule remains intact. The fragment list therefore contains one item at the full sequence length, which is also what you would see on a gel for an uncut linear or circular sample.
Do I need to check the reverse complement of each site?
For the 16 enzymes in this dataset it makes no difference because all of their recognition sequences are palindromic, so the site reads the same on either strand. The search still checks the reverse complement so the calculation stays correct if the enzyme set is extended.
Why might my gel show different fragment sizes?
Fragment sizes depend on complete digestion, methylation and star activity, and a supercoiled plasmid migrates differently from a linear one. The calculator predicts ideal cut positions, so compare it with a properly linearized or digested sample and treat gel migration as an approximate check.
Does the calculator model methylation-sensitive enzymes?
No. The embedded dataset contains recognition sites and cut offsets but does not include methylation sensitivity or blocked-site information. Dam or CpG methylation can prevent cutting at a site that the calculator still predicts, so check the enzyme's methylation notes for your strain.
Does my DNA sequence leave this browser during a digest?
No. Searching, cut mapping and fragment sizing all run with JavaScript in this browser tab, so the sequence is never uploaded, stored or logged, and closing the page discards it.

Background reading

Format guides that explain the trade-offs behind Restriction Enzyme Digest Calculator.