SeWeR: PCR

primer3

Mispriming Library (repeat library)

Pick left primer or use sequence

Pick hybridization probe or use oligo

Pick right Primer or use sequence

Sequence Id (a name to identify your sequence)

Region the primers will flank
Formats: [base number],[number of bases] e.g. 50,2 or mark the sequence with []

Excluded Region
Formats:[base number],[number of bases] e.g. 401,7 68,3 or mark the sequence with <>

Product Size
Min Opt Max

Number of Return

Max 3' Stability

Max Mispriming

Pair Max Mispriming

General Primer Picking Conditions

Primer Size Min Opt Max

Primer Tm
Min Opt Max

Max Tm Difference

Product Tm
Min Opt Max

Primer GC%
Min Opt Max

Max Self Complementarity

Max 3' Self Complementarity

Max #N's

Max Poly-X

Inside Target Penalty

Outside Target Penalty

First Base Index

CG Clamp

Salt Concentration

Annealing Oligo Concentration

Liberal Base

Show Debuging Info

Other Per-Sequence Inputs

Included Region to pick primers
Format: Starting Base number, length e.g. 20,400 or mark the sequence with{}

Start Codon Position

Sequence Quality

Min Sequence Quality

Min End Sequence Quality

Sequence Quality Range Min

Sequence Quality Range Max

Objective Function Penalty Weights for Primers

Tm	Lt:	Gt:
Size	Lt:	Gt:
GC%	Lt:	Gt:

Self Complementarity
3' Self Complementarity
#N's
Mispriming
Sequence Quality
End Sequence Quality
Position Penalty
End Stability

Objective Function Penalty Weights for PrimerPairs

Product Size	Lt:		Gt:
Product Tm	Lt:		Gt:

Tm Difference
Any Complementarity
3' Complementarity
Pair Mispriming
Primer Penalty Weight
Hyb Oligo Penalty Weight

Hyb Oligo (Internal Oligo) Per-Sequence Inputs

Hyb Oligo Excluded Region

Hyb Oligo (Internal Oligo) General Conditions

Hyb Oligo Size:	Min	Opt	Max
Hyb Oligo Tm:	Min	Opt	Max
Hyb Oligo GC%	Min:	Opt:	Max:

Hyb Oligo Self Complementarity

Hyb Oligo Max 3' Self Complementarity:

Hyb Oligo DNA Concentration

Hyb Oligo Salt Concentration:

Hyb Oligo Min Sequence Quality

Hyb Oligo Mishyb Library

Hyb Oligo Max Mishyb:

Hyb Oligo Max Poly-X: Max #Ns

Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)

Hyb Oligo Tm Lt: Gt:
Hyb Oligo Size Lt: Gt:
Hyb Oligo GC% Lt: Gt:

Hyb Oligo Self Complementarity
Hyb Oligo #N's
Hyb Oligo Mishybing
Hyb Oligo Sequence Quality

codehop
Core (degenerate 3' region)
Degeneracy	Strictness
Clamp (non-degenerate 5' region)
Temperature	Poly-nuc
Primer concentration [in nM]
Codon usage table
Show the least degenerate, or show all overlapping primers
Use core strictness for the 3' base
Force the core/clamp boundary to be a codon boundary
Use the most common codons in the clamp

eprimer3

Your email:

Explain flag (-explainflag)

Create results files for each sequence (-fileflag)

Select task -- Task (-task)

Number of results to return (-numreturn)

First base index (-firstbaseindex)

Included region(s) (-includedregion)

Target region(s) (-target)

Excluded region(s) (-excludedregion)

Forward input primer sequence to check (-forwardinput)

Reverse input primer sequence to check (-reverseinput)

Pick anyway (-pickanyway)

Mispriming library (-mispriminglibrary)

Primer maximum mispriming (-maxmispriming)

Primer pair maximum mispriming (-pairmaxmispriming)

GC clamp (-gcclamp)

Primer optimum size (-osize)

Primer minimum size (-minsize)

Primer maximum size (-maxsize)

Primer optimum Tm (-otm)

Primer minimum Tm (-mintm)

Primer maximum Tm (-maxtm)

Maximum difference in Tm of primers (-maxdifftm)

Primer optimum GC percent (-ogcpercent)

Primer minimum GC percent (-mingc)

Primer maximum GC percent (-maxgc)

Salt concentration (mM) (-saltconc)

DNA concentration (nM) (-dnaconc)

Maximum Ns accepted in a primer (-numnsaccepted)

Maximum self complementarity (-selfany)

Maximum 3' self complementarity (-selfend)

Maximum polynucleotide repeat (-maxpolyx)

Product optimum size (-productosize)

Product size range (-productsizerange)

Product optimum Tm (-productotm)

Product minimum Tm (-productmintm)

Product maximum Tm (-productmaxtm)

Maximum 3' end stability (-maxendstability)

Internal oligo excluded region (-oligoexcludedregion)

Internal oligo input sequence (if any) (-oligoinput)

Internal oligo optimum size (-oligoosize)

Internal oligo minimum size (-oligominsize)

Internal oligo maximum size (-oligomaxsize)

Internal oligo optimum Tm (-oligootm)

Internal oligo minimum Tm (-oligomintm)

Internal oligo maximum Tm (-oligomaxtm)

Internal oligo optimum GC percent (-oligoogcpercent)

Internal oligo minimum GC (-oligomingc)

Internal oligo maximum GC (-oligomaxgc)

Internal oligo salt concentration (mM) (-oligosaltconc)

Internal oligo DNA concentration (nM) (-oligodnaconc)

Internal oligo maximum self complementarity (-oligoselfany)

Internal oligo maximum 3' self complementarity (-oligoselfend)

Internal oligo maximum polynucleotide repeat (-oligomaxpolyx)

Internal oligo mishybridizing library (-oligomishyblibrary)

Internal oligo maximum mishybridization (-oligomaxmishyb)

outfile (-outfile)

Primer3

Create PCR primers and Hybridization oligos from a DNA sequence. Input, DNA sequence. Required option-field, none.

CODEHOP

Pick primers from multiple alingnment of protein sequences. Input type, BLOCKS. Required option-field, none.

PRIMO

A primer design tool. Input type: . Required options: email input_file_name.

EPRIMER3

Picks PCR primers and hybridization oligos (EMBOSS). Input type: sequence -- dna [sequences] (-sequence). Required options: email sequence task outfile.

PRIMERSEARCH

Searches DNA sequences for matches with primer pairs (EMBOSS). Input type: sequences -- dna [sequences] (-sequences). Required options: email sequences primers mismatchpercent out.