Diagnostic digest of pEGFP-N1
Compare single and double digests of a fluorescent protein vector.
Restriction Digest Simulator
FigranPaste a DNA sequence, choose enzymes and see the restriction enzyme digest on a virtual gel.
- Single, double and triple digests
- Virtual gel with real ladders
- Free SVG and 300 DPI PNG
Restriction Digest Simulator
Sequence
4,733 bp · Circular · GC 53%
Enzymes
| Enzyme | Site | Cuts | Positions | Ends | Add |
|---|---|---|---|---|---|
| BamHI | G↓GATCC | 1 | 660 | 5′ | |
| BsaI | GGTCTC(1/5) | 1 | 3746 | 5′ | |
| EcoRI | G↓AATTC | 1 | 629 | 5′ | |
| HindIII | A↓AGCTT | 1 | 622 | 5′ | |
| NheI | G↓CTAGC | 1 | 591 | 5′ | |
| NotI | GC↓GGCCGC | 1 | 1401 | 5′ | |
| XhoI | C↓TCGAG | 1 | 613 | 5′ | |
| SalI | G↓TCGAC | 1 | 639 | 5′ | |
| SacI | GAGCT↓C | 1 | 620 | 3′ | |
| NdeI | CA↓TATG | 1 | 234 | 5′ | |
| XbaI | T↓CTAGA | 1 | 1411 | 5′ | |
| BglII | A↓GATCT | 1 | 609 | 5′ | |
| KpnI | GGTAC↓C | 1 | 649 | 3′ | |
| PstI | CTGCA↓G | 1 | 638 | 3′ | |
| SmaI | CCC↓GGG | 1 | 658 | blunt | |
| HpaI | GTT↓AAC | 1 | 1520 | blunt | |
| SacII | CCGC↓GG | 1 | 652 | 3′ | |
| ClaI | AT↓CGAT | 1 | 2597 | 5′ | |
| StuI | AGG↓CCT | 1 | 2578 | blunt | |
| MfeI | C↓AATTG | 1 | 1507 | 5′ | |
| AflII | C↓TTAAG | 1 | 1639 | 5′ | |
| AseI | AT↓TAAT | 1 | 7 | 5′ | |
| BmtI | GCTAG↓C | 1 | 595 | 3′ | |
| AccI | GT↓MKAC | 1 | 640 | 5′ | |
| Acc65I | G↓GTACC | 1 | 645 | 5′ | |
| AflIII | A↓CRYGT | 1 | 4675 | 5′ | |
| AgeI | A↓CCGGT | 1 | 666 | 5′ | |
| ApaI | GGGCC↓C | 1 | 657 | 3′ | |
| ApaLI | G↓TGCAC | 1 | 4361 | 5′ | |
| EcoO109I | RG↓GNCCY | 1 | 3855 | 5′ | |
| Eco53kI | GAG↓CTC | 1 | 618 | blunt | |
| PciI | A↓CATGT | 1 | 4675 | 5′ | |
| PflFI | GACN↓NNGTC | 1 | 2875 | 5′ | |
| FspI | TGC↓GCA | 1 | 2859 | blunt | |
| MscI | TGG↓CCA | 1 | 2839 | blunt | |
| SexAI | A↓CCWGGT | 1 | 2346 | 5′ | |
| SfiI | GGCCNNNN↓NGGCC | 1 | 2532 | 3′ | |
| PaeR7I | C↓TCGAG | 1 | 613 | 5′ | |
| PspOMI | G↓GGCCC | 1 | 653 | 5′ | |
| RsrII | CG↓GWCCG | 1 | 3273 | 5′ | |
| TspMI | C↓CCGGG | 1 | 656 | 5′ | |
| XmaI | C↓CCGGG | 1 | 656 | 5′ | |
| KasI | G↓GCGCC | 1 | 2756 | 5′ |
Lanes
Gel options
Fragments
3 lanes · 5 fragments · 4,733 bp circular
| Lane | # | Size (bp) | From–To | Left end | Right end |
|---|---|---|---|---|---|
| EcoRI | 1 | 4,733 | 630–629 | EcoRI 5′ AATT | EcoRI 5′ AATT |
| PvuII | 1 | 608 | 2256–2863 | PvuII blunt | PvuII blunt |
| PvuII | 2 | 4,125 | 2864–2255 | PvuII blunt | PvuII blunt |
| NheI + NotI | 1 | 810 | 592–1401 | NheI 5′ CTAG | NotI 5′ GGCC |
| NheI + NotI | 2 | 3,923 | 1402–591 | NotI 5′ GGCC | NheI 5′ CTAG |
Methylation may block overlapping sites: EcoRI · CpG, NheI · CpG, NotI · CpG
Restriction digest examples
Explore common digests and load one to get started.
pUC19 restriction map and digests
Inspect PvuII, EcoRI + HindIII and AseI digests.
Empty vector vs construct: plasmid digest check
Compare an empty vector with a construct containing a synthetic insert.
PCR-RFLP genotyping with HinfI
Compare different HinfI band patterns, including a mixed sample.
Type IIS sites for Golden Gate screening
Inspect external cleavage sites in a synthetic sequence.
Lambda DNA EcoRI digest beside a λ–HindIII marker
Compare EcoRI and HindIII fragments with a λ–HindIII marker.
How to simulate a restriction digest
Go from a sequence to a virtual gel in four steps.
1Enter a sequence
Paste DNA or open a sequence file and set its topology.
2Find enzymes
Search for sites and add an enzyme to a lane.
3Arrange lanes
Choose digest combinations and gel settings.
4Export
Download the figure or copy the fragment list.
How to read a virtual restriction digest gel
Compare each lane with the marker to interpret expected fragment sizes.
- 1The ladder provides size references.
- 2Lane labels identify each digest.
- 3Within a lane, brighter bands represent more DNA mass.
- 4Small fragments may run off the gel.
- 5Fragments close in size may merge into one band.
Restriction map and fragment sizes
Fragments are measured between adjacent cut positions.
A circular molecule with n cuts yields n fragments; a linear molecule yields n + 1. For pUC19, PvuII cuts after bases 308 and 630, giving 322 bp and 2,364 bp. The Map view shows cut sites for the selected lane.
References: REBASE · NEB agarose gel resolution
Restriction digest FAQ
How do I simulate a restriction digest online?
Paste or open a sequence, select its topology, add enzymes to lanes, and view the fragments, gel and map. The calculation stays in your browser.
How are restriction enzyme cutting sites numbered?
A cut position is the number of the base immediately before the top-strand cut. Both strands are searched; circular sequences can wrap across the origin.
Can I get a plasmid map with genes and features?
This map shows cut sites and fragment sizes. Use Plasmid Map Maker for annotated genes and features.
Why does my real gel look different from the simulation?
Migration is approximate and band intensities are normalized within each lane. Uncut plasmid topology, partial digestion, loading and gel conditions can change observed bands.
Which DNA ladder should I choose?
Choose a ladder that covers the expected fragment sizes, such as a 1 kb ladder for plasmid fragments or a 100 bp ladder for short products.
Which buffer should I use for a double digest?
Check the current supplier compatibility information for both enzymes; a sequential digest may be needed. Use the Ligation Calculator for the next step.
Will Dam or Dcm methylation block my digest?
It depends on the enzyme, overlapping sites and DNA source. Consult the supplier for methylation sensitivity.
Does the simulator show star activity or partial digestion?
No. These depend on reaction conditions and cannot be inferred from sequence alone.
How do results compare with NEBcutter, SnapGene and SMS?
The same sequence and cut positions yield the same fragment sizes. This tool places multiple digest lanes on one virtual gel.