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Loading...

PrimerQuest
Name:
NCBI ID#	(NM_001111 or 301601652) Accession or Genbank ID
Input Sequence	Loading...
Sequence length must be greater than the current minimum product size of 80 bases. PrimerQuest accepts only nucleic acid bases.
Design For:	PCR Primers PCR Primers with Probe Forward Primer Only Reverse Primer Only Probe Only
Parameter Set:	General PCR Real-Time PCR Real-Time PCR (Fast Cycle) Pre-Amplification PCR For Human, Mouse, and Rat targets we highly recommend our Predesign Library which now supports intercalation dye assays (such as SYBR Green and EvaGreen). For other targets, we recommend our RealTime PCR program for design of gene expression assays.
Run PrimerQuest Design Parameters Start Over Running PrimerQuest...

Parameter Entry

Loading...

Design Task:

PCR Primers

Parameter Set:

Real-Time PCR

Sequence Name:

• Standard
• Advanced

TASK SETTINGS

Results to Return

(1-50)

SEQUENCE ANNOTATION SETTINGS

Design within Region

Avoidance Region List

Avoidance Region List - Probe

Design Focus Region List

PRIMER CRITERIA

	Opt

Primer Tm ( °C )

± 5

0

100

Primer GC ( % )

± 15

0

100

Primer Size ( nt )

± 6

1

36

PRODUCT CRITERIA

Product Size Range List

Task Settings Environment Settings Sequence Annotations Mispriming Criteria Quality Criteria Primer Criteria Product Criteria SHOW ALL

---

TASK SETTINGS

Solution Settings

Forward Min 3' Distance ( bp )

Results to Return

(1-50)

Reverse Min 3' Distance ( bp )

Convert IUB/IUPAC to 'N'

Off

On

First Base Index

Avoid Lowercase Masking in 3' end of Primer

Off

On

ENVIRONMENT SETTINGS

Monovalent Salt (Na⁺) ( mM )

Primer DNA Conc ( nM )

Divalent Salt (Mg⁺⁺) ( mM )

Probe DNA Conc ( nM )

dNTP Conc ( mM )

SEQUENCE ANNOTATION SETTINGS

Design within Region

Avoidance Region List

Avoidance Region List - Probe

Forward Primer Pair Ok Region List

Reverse Primer Pair Ok Region List

Design Focus Region Settings

Design Focus Region List

Primer Within Weight

Non-Overlapping Primer Weight

Primer Outside Weight

Overlap Junction Settings

Overlap Junction List

Min Overlap on 3' end of Primer

Min Overlap on 5' end of Primer

Partial Solutions Settings

Forward Primer Input

Probe Input

Reverse Primer Input

Primer Force Location Settings

Force Forward 5’ Location

Force Forward 3’ Location

Force Reverse 5’ Location

Force Reverse 3’ Location

MISPRIMING CRITERIA SETTINGS

Primer Max Mispriming

Weight(0-1)

Mispriming Library

None Human Rodent Rodent And Simple

Primer Pair Max Mispriming

Weight(0-1)

Primer Lib Ambiguity Codes Consensus

Off

On

Probe Max Mispriming

Weight(0-1)

QUALITY CRITERIA SETTINGS

Sequence Quality List

Primer Quality Range

-

Primer Min 3' End Quality

Weight(0-1)

Primer Min Quality

Probe Min Quality

Weight(0-1)

PRIMER CRITERIA

Primary Settings

	Min	Opt	Max	Wt

Primer Tm ( °C )

0

100

Primer GC ( % )

0

100

Primer Size ( nt )

1

36

Local Mispriming Settings

Max Mispriming

Weight(0-1)

Misc Settings

3' GC Clamp ( nt )

Max Stability in 3' 5 Bases

Weight(0-1)

Max GC Count in 3' 5 Bases

Max Ns Accepted ( nt )

Weight(0-1)

Max PolyN (A,C,G,T) Stretch ( nt )

Structure Align Settings

Max Homodimer

Weight(0-1)

Max Homodimer 3' End

Weight(0-1)

PRODUCT CRITERIA

Primary Settings

Product Size Range List

Primer Pair Max Delta Tm ( °C )

Weight(0-1)

	Min	Opt	Max	Wt

Product Tm ( °C )

0

100

Local Mispriming Settings

Primer Pair Max Mispriming

Weight(0-1)

Misc Settings

Probe Scoring Contribution Factor

Product Opt Size ( bp )

Weight(0-1)

Primer Pair Scoring Contribution Factor

Structure Align Settings

Max Heterodimer

Weight(0-1)

Max Heterodimer 3' End

Weight(0-1)

Run PrimerQuest

Advanced Params

Reset Defaults

Running PrimerQuest...

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