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Primer3引物设计
基因组浏览器
BLAST
多重序列比对
序列提取
GO富集分析
Primer3引物设计
e-PCR
友情链接
生信工具
基因组浏览器
BLAST
多重序列比对
序列提取
GO富集分析
Primer3引物设计
e-PCR
友情链接
Primer3引物设计
Select the
Task
for primer selection
Generic
Template masking
before primer design
Select species
None
Primer failure rate cutoff
Nucleotides to mask in 5' direction
Nucleotides to mask in 3' direction
Paste source sequence below (5'->3', string of ACGTNacgtn -- other letters treated as N -- numbers and blanks ignored). FASTA format ok. Please N-out undesirable sequence (vector, ALUs, LINEs, etc.) or use a
Mispriming Library (repeat library)
NONE
Pick left primer, or use left primer below
Pick hybridization probe (internal oligo), or use oligo below
Pick right primer, or use right primer below (5' to 3' on opposite strand)
Pick Primers
Load Example
Reset Form
+More config
Sequence Id
A string to identify your output.
Targets
E.g. 50,2 requires primers to surround the 2 bases at positions 50 and 51.
Overlap Junction List
E.g. 27 requires one primer to overlap the junction between positions 27 and 28.
Excluded Regions
E.g. 401,7 68,3 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68.
Pair OK Region List
See manual for help.
Included Region
E.g. 20,400: only pick primers in the 400 base region starting at position 20.
Start Codon Position
Internal Oligo Excluded Region
Force Left Primer Start
Force Right Primer Start
Force Left Primer End
Force Right Primer End
Sequence Quality
Min Sequence Quality
Min End Sequence Quality
Sequence Quality Range Min
Sequence Quality Range Max
Pick Primers
Load Example
Reset Form
General Primer Picking Conditions
Upload the settings from a file
upload
Primer Size
Min
Opt
Max
Primer Tm
Min
Opt
Max
Max Tm Difference
Table of thermodynamic parameters
SantaLucia 1998
Product Tm
Min
Opt
Max
Primer GC%
Min
Opt
Max
Product Size Ranges
Number To Return
Max 3' Stability
Max Library Mispriming
Pair Max Library Mispriming
Thermodynamic Secondary Structure Alignments
Use Thermodynamic Oligo Alignment
TH: Max Self Complementarity
TH: Max 3' Self Complementarity
TH: Max Pair Complementarity
TH: Max 3' Pair Complementarity
TH: Max Primer Hairpin
Old Secondary Structure Alignments
Max Self Complementarity
Max 3' Self Complementarity
Max Pair Complementarity
Max 3' Pair Complementarity
Thermodynamic Template Alignments
Use Thermodynamic Template Alignment
TH: Max Template Mispriming
TH: Pair Max Template Mispriming
Old Template Alignments
Max Template Mispriming
Pair Max Template Mispriming
Max #N's accepted
Max Poly-X
Inside Target Penalty
Outside Target Penalty
Note: you can set Inside Target Penalty to allow primers inside a target.
First Base Index
CG Clamp
Max GC in primer 3' end
3' End Distance Between Left Primers
3' End Distance Between Right Primers
5 Prime Junction Overlap
3 Prime Junction Overlap
(Distance of the primer ends to one overlap position.)
Concentration of Monovalent Cations
Salt Correction Formula
SantaLucia 1998
Concentration of Divalent Cations
Concentration of dNTPs
Annealing Oligo Concentration
(Not the concentration of oligos in the reaction mix but of those annealing to template.)
Sequencing Spacing
Sequencing Interval
Sequencing Lead
Sequencing Accuracy
Liberal Base
Print Statistics
Treat ambiguity codes in libraries as consensus
Lowercase masking
Pick anyway
Objective Function Penalty Weights for Primers
Size
Lt
Gt
Tm
Lt
Gt
GC%
Lt
Gt
TH: Self Complementarity
TH: 3' End Self Complementarity
TH: Hairpin
TH: Template Mispriming
Self Complementarity
3' End Self Complementarity
Template Mispriming
#N's
Library Mispriming
Sequence Quality
End Sequence Quality
Position Penalty
End Stability
Primer failure rate
Objective Function Penalty Weights for Primer Pairs
Product Size
Lt
Gt
Product Tm
Lt
Gt
TH: Any Complementarity
TH: 3' End Complementarity
TH: Template Mispriming Weight
Any Complementarity
3' End Complementarity
Template Mispriming Weight
Tm Difference
Library Mispriming
Primer Penalty Weight
Internal Oligo Penalty Weight
Internal Oligo (Hyb Oligo) General Conditions
Internal Oligo Size
Min
Opt
Max
Internal Oligo Tm
Min
Opt
Max
Internal Oligo GC%
Min
Opt
Max
TH: Internal Oligo Self Complementarity
TH: Internal Oligo Max 3' End Self Complementarity
TH: Internal Oligo Hairpin
Internal Oligo Self Complementarity
Internal Oligo Max 3' End Self Complementarity
Internal Oligo Min Sequence Quality
Max #Ns
Internal Oligo Max Poly-X
Internal Oligo Mishyb Library
NONE
Internal Oligo Max Library Mishyb
Internal Oligo Conc of monovalent cations
Internal Oligo DNA Concentration
Internal Oligo conc of divalent cations
Internal Oligo [dNTP]
Objective Function Penalty Weights for Internal Oligos (Hyb Oligos)
Internal Oligo Size
Lt
Gt
Internal Oligo Tm
Lt
Gt
Internal Oligo GC%
Lt
Gt
TH: Internal Oligo Self Complementarity
TH: Internal Oligo 3' End Complementarity
TH: Internal Oligo Hairpin
Internal Oligo Self Complementarity
Internal Oligo 3' End Complementarity
Internal Oligo #N's
Internal Oligo Library Mishybing
Internal Oligo Sequence Quality
Internal Oligo Sequence End Quality
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