Protein Sequence

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Job name:

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Protein Sequence Enter protein sequence manually (formats)

Upload protein sequence file (formats)

Codon Frequency Table Choose from ONE of the following:

GCG CodonFrequency format only. For more organisms, check out the Codon Usage Database

Choice 1 - Choose a standard organism: E. coli class II H. sapiens D. melanogaster S. cerevisiae C. elegans X. laevis R. norvegicus M. musculus E. coli standard

Choice 2 - Enter custom codon frequency table manually:

Choice 3 - Upload codon frequency file:

Flanking Sequences (optional)

(formats)

Enter 5'-flanking sequence:

Enter 3'-flanking sequence:

Restriction Site Screen (optional)

Common sites: AflII BamHI ClaI EagI EcoRI EcoRV HindIII KpnI NcoI NdeI NheI NotI PstI SacI SalI SmaI SpeI SphI StuI XbaI XhoI XmaI

Non-degenerate sites: AatII Acc65I AclI AcuI AfeI AgeI AlwI ApaI ApaLI AscI AseI AsiSI AvrII BbsI BbvCI BbvI BccI BceAI BciVI BclI BfrBI BfuAI BglII BmgBI BmrI BmtI BpmI BpuEI BsaI BseRI BseYI BsgI BsiWI BsmAI BsmBI BsmFI BsmI BspCNI BspEI BspHI BspMI BsrBI BsrDI BsrGI BsrI BssHII BssSI BstBI BstZ17I BtgZI BtsI DraI EarI EciI FauI FokI FseI FspI HgaI HpaI HphI KasI MboII MfeI MluI MlyI MscI NaeI NarI NgoMIV NruI NsiI PacI PaeR7I PciI PleI PmeI PmlI PsiI PspOMI PvuI PvuII SacII SapI SbfI ScaI SfaNI SfoI SnaBI SspI SwaI TliI TspRI ZraI

Degenerate sites: AccI AflIII AhdI AleI AlwNI ApoI AvaI BaeI BanI BanII BcgI BglI BlpI Bme1580I Bpu10I BsaAI BsaBI BsaHI BsaJI BsaWI BsaXI BsiEI BsiHKAI BslI BsoBI Bsp1286I BsrFI BstAPI BstEII BstF5I BstXI BstYI Bsu36I BtgI Cac8I DraIII DrdI EaeI EcoNI EcoO109I HaeII HincII Hpy188III MmeI MslI MspA1I MwoI NlaIV NspI NspIII PflFI PflMI PpuMI PshAI RsrII SexAI SfcI SfiI SgrAI SmlI StyI Tth111I XcmI XmnI

Custom Site Screen (optional)

Enter name and sequence:

Parameters

Oligo Length: (format) (>20 nt)

Annealing Temperature: (format) (58-75*C)

Codon Frequency Threshold: (0-100)

Number of Solutions: (1-99)

Na+/K+ Concentration: 10 mM 25 mM 50 mM 75 mM 100 mM 150 mM 200 mM 250 mM 500 mM 750 mM 1 M

Mg2+ Concentration: 0 mM 0.5 mM 1.0 mM 1.5 mM 2 mM 3 mM 4 mM 5 mM 10 mM 20 mM 50 mM 100 mM 200 mM

Oligonucleotide Concentration: (1-100000 nM)

Thermodynamically Balanced Inside-Out Mode Output:

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E-mail Address:

Entering your e-mail address is entirely voluntary. The results will be made available online at the end of the program run, but if an address is entered, the results will also be sent to that address.

All runs will be terminated after 60 minutes.

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