Silent Mutator - Silent mutagenesis tool

A gene synthesis tool, with which you can easily introduce new restriction sites without changing the amino acid / protein sequence.


The genetic code used for translation of the input sequence is selected from the dropdown menu. Should other genetic code be used, a user can modify one of the selectable genetic codes by first selecting particular genetic code from the menu and then changing the selection to "User Provided". The genetic code table can be completely replaced, but the format must stay exactly the same. One can find and copy-paste genetic codes from the Genetic Codes NCBI webpage.


The sequence is:
linear circular
Restriction sites:
pre-set list of most commonly used enzymes (edit the list)
all commercially available enzymes (see the list)
exclude 4-cutters
exclude 5-cutters
exclude enzymes with degenerated recognition motifs
Dam/Dcm-methylated sites:
hide display
Genetic code: (display)
Save Fasta

Plain text, fasta or GenBank formats.

Plain text is just text without any formatting (i.e. from e.g. Notepad, but not MS Word). A fasta file is plain text sequence with a header in the form ">sequence name". A GenBank file contains a nucleotide sequence plus related information and feature definitions.


Sequence Name:
Translate & Analyze
Select All
Selection: - 0 bp %GC
Clear All
Apply & Process
Undo Changes
View Example
All fields will be erased, unsaved work will be lost!
Restriction Site:
Clear Search
Find Rev Compl


Restriction Endonucleases

To display the cutting pattern and positions, double-click the enzyme name.


Restriction endonucleases

To display the cutting pattern and positions, double-click the enzyme name. To apply changes made in the selection, press 'Enter' key or click the 'Apply' button.


Quick hints

Standard Genetic Code

genetic code

IUPAC Ambiguity Code

Symbol Bases represented Complement
R A, G Y
Y C, T R
K G, T M
M A, C K
S C, G S
W A, T W
B C, G, T V
D A, G, T H
H A, C, T D
V A, C, G B
N A, C, G, T N

Compatible Ends

Overhang Enzymes
N│G A T C N N C T A G│N BamHI, BglII
N│A A T T N N T T A A│N EcoRI, MfeI (MunI)
N│T C G A N N A G C T│N SalI, XhoI
N│C T A G N N G A T C│N AvrII (XmaJI), NheI, SpeI (BcuI), XbaI
N T G C A│N N│A C G T N NsiI (Mph1103I), PstI
N│G T A C N N C A T G│N Acc65I (Asp718I), BsiWI (Pfl23II), BsrGI (Bsp1407I)
N│C C G G N N G G C C│N AgeI (BshTI), BspEI (Kpn2I), XmaI (Cfr9I)
N│G G C C N N C C G G│N EagI (Eco52I), PspOMI (Bsp120I), NotI
N│C G C G N N G C G C│N AscI (SgsI), BssHII (PauI), MluI
N N│C G N N N N G C│N N AclI (Psp1406I), BstBI (Bsp119I), ClaI (Bsu15I), NarI
N N│T A N N N N A T│N N AseI (VspI), NdeI
N N A T│N N N N│T A N N PacI, PvuI
blunt ends AfeI (Eco47III), BsaBI (BseJI), DraI, EcoRV (Eco32I), Ecl136II, FspI (NsbI), HpaI (KspAI), MscI (MlsI), NaeI (PdiI), NruI (Bsp68I), PmeI (MssI), PmlI (Eco72I), PvuII, ScaI, SfoI (EheI), SmaI, SnaBI (Eco105I), SrfI, SspI, StuI (Eco147I), SwaI (SmiI), XmnI (PdmI), ZraI
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