BioinformaticsBrowser-side scanStarter enzyme set

Restriction Site Finder

Paste a DNA sequence and scan for common restriction enzyme sites in your browser. Built for quick cloning checks, plasmid map review, and sequence prep before deeper analysis.

Scan sequenceRead FAQ
Runs locally in your browserFASTA and raw input supportedCommon enzymes first
Sequence input
Paste raw DNA or FASTA text. Whitespace is stripped, U is converted to T, and the scan stays in your browser.
Starter set
Analyzed bases: 102Enzymes scanned: 8
FASTA headers and whitespace are removed automatically
Why this page exists
A quick restriction digest check is a natural first step before cloning notes, notebook work, or sequence prep.
Restriction map summary

See which enzymes match, where they cut, and how many sites appear in the sequence.

Browser-side scanning

The sequence is normalized locally, so you can use it for quick checks without a server round-trip.

Built for lab workflows

Designed to support cloning prep and the bioinformatics workflows that later move into Runcell notebooks.

Browse bioinformatics resourcesOpen Runcell
Restriction map
Starter enzymes sorted by site count in the current sequence.
Sites found
6
Enzymes matched
6
Sequence length
102
Enzyme
Motif
Cut site
Hits
Positions
BamHI
Common vector mapping enzyme.
GGATCCG^GATCC
1
12
EcoRI
Classic cloning site.
GAATTCG^AATTC
1
4
HindIII
Standard insert checking site.
AAGCTTA^AGCTT
1
22
NheI
Popular directional cloning site.
GCTAGCG^CTAGC
1
62
PstI
Useful for restriction maps.
CTGCAGCTGCA^G
1
39
XhoI
Frequent cloning and screening site.
CTCGAGC^TCGAG
1
30
EcoRV
Blunt-end enzyme for quick checks.
GATATCGAT^ATC
0
—
NdeI
Start-codon-adjacent cloning site.
CATATGCA^TATG
0
—
Restriction map preview
Highlighted bases show every matched recognition motif in the sanitized sequence.
MatchNon-match
1
TTTGAATTCGCGGATCCAAAGAAGCTTCCCTCGAGGGTCTGCAGGGGCGGCCGCATGCAT
61
GGCTAGCGGTACCGAGCTCCCGGGGTCGACAGATCTCATATC
Starter set

This page intentionally focuses on a compact enzyme set so the results stay fast, readable, and useful for quick cloning checks.

How the scanner works

1. FASTA headers and whitespace are removed.

2. Lowercase input is normalized and U is converted to T.

3. The sequence is scanned against the starter enzyme motifs in the browser.

What the results mean

Each row shows the recognition motif, the cut pattern, the number of hits, and the 1-based start positions.

Use the copy button to move the table into notes, notebook cells, or a cloning checklist.

Useful next step

After a quick site check, many users move into reverse-complement, GC-content, or concentration calculations before analysis.

Open reverse complementBrowse bioinformatics hub
Related bioinformatics tools
These are the next pages in the same sequence-analysis cluster.
Reverse Complement

Flip sequence orientation before downstream checks.

GC Content Calculator

Measure sequence composition and quality at a glance.

DNA Concentration Calculator

Convert DNA quantities while you prepare cloning inputs.

Protein Concentration Calculator

Continue into protein-side planning after sequence prep.

Restriction Site Finder FAQ

Answers to the most common sequence-scanning questions.

It scans a DNA sequence for enzyme recognition motifs and reports where each site appears. That makes it easier to plan cloning, digest checks, and plasmid map validation.