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linear circular


save fasta save gb clear All fields will be erased, unsaved work will be lost! reverse complement process to lowercase to uppercase
selection - 0 bp %GC select all crop aA Aa rev. compl. translate add feature forward primer reverse primer
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Display quick hints Change settings Display standard genetic code IUPAC ambiguous/degenerate positions Enzymes producing compatible ends Useful links Send feedback! Check for updates on Twitter User guide
new feature autodetect PCRproduct drawmap update uncheck all nothing selected
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© 2014 - 2017 Vladimír Čermák


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



Basic settings

Restriction sites:

display all sites
display only unique sites
display sites with maximum occurences

Restriction sites blocked by methylation (Dam or Dcm):

display and take into account

NEW! Selecting particular restriction sites for display is done here.

Genetic code:

mitochondrial (vertebrate)
mitochondrial (invertebrate)
mitochondrial (yeast)

Primer multi-match detection limit:

nucleotide perfect match at 3' end

Map drawing settings

Feature labels in maps:

with position values
without position values

Restriction sites in maps:

with position values
without position values

Basic circle diameter of plasmid maps:

240 px
300 px
360 px

Inside plasmid maps show:

plasmid name and length
1000 bp scale

genetic 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


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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