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PrimerQuest Tool
Assay Design
Results
About
Help
Assay Design
Results
About
Help
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Sequence Entry
Enter sequence(s) manually
Hints
Paste your sequence into the Textbox
Add up to 50 sequences in
FASTA
format
Sequence length must be greater than 80 bases
PrimerQuest accepts only nucleic acid bases
Sequence Name
Clear Sequence Entry
Download sequence(s) using Genbank or Accession ID
NCBI ID#
Hints
Enter Genbank or Accession ID
NM_001111 or 301601652
Comma Separated for Batch
NM_001234, 301601652
Sequence length must be greater than 80 bases
PrimerQuest accepts only nucleic acid bases
Upload sequences in an Excel file
Upload Sequence File
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Hints
Download Template
Sequence length must be greater than 80 bases
PrimerQuest accepts only nucleic acid bases
Choose Your Design
PCR
2 Primers
qPCR
2 Primers + Probe
qPCR
2 Primers
Intercalating Dyes
Show Custom Design Parameters
Custom Design Parameters
Set Design Parameters for...
General PCR (Primers Only)
qPCR (2 Primers + Probe)
qPCR Intercalating Dyes (Primers only)
Forward Only - Sequencing
Reverse Only - Sequencing
Standard
Advanced
Task Settings
Reaction Conditions
Custom Target Region
Primer Criteria
Amplicon Criteria
SHOW ALL
Task Settings
Results
Results to Return
(1-50)
Vary Forward Primer Location
Vary Reverse Primer Location
Convert IUB/IUPAC to 'N'
Off
On
First Base Index
Avoid Lowercase Masking in 3' end of Primer
Off
On
Use Thermodynamic Alignment
Off
On
Reaction Conditions
Monovalent Salt (Na
+
) ( mM )
Primer DNA Conc ( nM )
Divalent Salt (Mg
++
) ( mM )
Probe DNA Conc ( nM )
dNTP Conc ( mM )
Primer Criteria
Primer Details
Min
Opt
Max
Primer Tm ( °C )
45
75
Primer GC ( % )
20
80
Primer Size ( nt )
12
45
Misc Settings
3' GC Clamp ( nt )
Max Stability in 3' 5 Bases
id="DIVprimerMaxEndGC">
Max GC Count in 3' 5 Bases
Max Ns Accepted ( nt )
Max PolyN (A,C,G,T) Stretch ( nt )
Amplicon Criteria
Amplicon Details
Primer Pair Max Delta Tm ( °C )
Min
Opt
Max
Product Tm ( °C )
35
85
Amplicon Size ( bp )
-1
2147483647
Probe Scoring Contribution Factor
Primer Pair Scoring Contribution Factor
Custom Target Region
Included Region
Excluded Region List
Excluded Region List - Probe
Forward Primer Pair Ok Region List
Reverse Primer Pair Ok Region List
Primer Focus Region
Target Region List
Primer Within Weight
Non-Overlapping Primer Weight
Primer Outside Weight
Partial Design Input
Forward Primer Input
Probe Input
Reverse Primer Input
Design Across Junctions
Overlap Junction List
Min Overlap on 3' end of Primer
Min Overlap on 5' end of Primer
Primer Force Location Settings
Force Forward Start Position (5' End)
Force Forward Stop Position (3' End)
Force Reverse Start Position (5' End)
Force Reverse Stop Position (3' End)
Get Assays
Batch Request
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