Integrated DNA Technologies acquires Archer™ next generation sequencing research assays to advance actionable scientific discoveries.

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PrimerQuest Tool

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

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

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IE >= 10
Firefox >= 3.6
Chrome >= 13
Safari >= 6
Opera >= 11.1

Hints

Download Template
Sequence length must be greater than 80 bases
PrimerQuest accepts only nucleic acid bases

Choose Your Design

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

Task Settings

Results

Results to Return

(1-50)

Vary Forward Primer Location

Vary Reverse Primer Location

Convert IUB/IUPAC to 'N'

Off

First Base Index

Avoid Lowercase Masking in 3' end of Primer

Off

Use Thermodynamic Alignment

Off

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 )

Primer GC ( % )

Primer Size ( nt )

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 )

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)

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For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.

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PrimerQuest Tool

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Running...

Loading...

Running...

Validating...

Loading...

Sequence Entry

Enter sequence(s) manually

Download sequence(s) using Genbank or Accession ID

Upload sequences in an Excel file

The current browser does not support this file upload feature. The following browsers are recommended for this feature:

Choose Your Design

Custom Design Parameters

Set Design Parameters for...

Task Settings

Results

Reaction Conditions

Primer Criteria

Primer Details

Misc Settings

Amplicon Criteria

Amplicon Details

Custom Target Region

Primer Focus Region

Partial Design Input

Design Across Junctions

Primer Force Location Settings

Batch Request

+32 (0) 16 28 22 60

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