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name:
LOCUS
DEFINITION
ACCESSION
SOURCE
COMMENT

Click on "name" to edit.

linear circular

length:

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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quick hints quick hints genetic code genetic code compatible ends useful linx send feedback twitter logo user guide
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
translation feature labels restriction sites

© 2014 - 2016 Vladimír Čermák

RESTRICTION ENDONUCLEASES

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.

QUICK HINTS

SETTINGS

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
ignore


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


Genetic code:

standard
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

STANDARD 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 C A T G│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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