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Primer3Plus pick primers from a DNA sequence	Primer3Manager	Help
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Task:  Detection Cloning Sequencing Primer_List Primer_Check

Select primer pairs to detect the given template sequence. Optionally targets and included/excluded regions can be specified. Mark an included region to pick primers fixed at its the boundaries. The quality of the primers might be low. Pick a series of primers on both strands for sequencing. Optionally the regions of interest can be marked using targets. Returns a list of all possible primers the can be designed on the template sequence. Optionally targets and included/exlcuded regions can be specified. Evaluate a primer of known sequence with the given settings.

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• Main
• General Settings
• Advanced Settings
• Internal Oligo
• Penalty Weights
• Sequence Quality

Sequence Id:

Primer to test:

Paste source sequence below	Or upload sequence file:

Mark selected region:

Excluded Regions:

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>

Targets:

[

]

Included Region:

{

}

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'->3' on opposite strand).

First Base Index:		Sequence Quality:
Start Codon Position:
Min Sequence Quality:
Min End Sequence Quality:
Sequence Quality Range Min:
Sequence Quality Range Max:

Product Size Ranges

Primer Size	Min:	Opt:	Max:
Primer Tm	Min:	Opt:	Max:	Max Tm Difference:
Primer GC%	Min:	Opt:	Max:	Fix the prime end of the primer

Concentration of monovalent cations:		Annealing Oligo Concentration:
Concentration of divalent cations:		Concentration of dNTPs:

Mispriming/Repeat Library: NONE HUMAN RODENT_AND_SIMPLE RODENT DROSOPHILA

Load and Save

Please select special settings here:   Default qPCR Probe Use_Product_Size  (use Activate Settings button to load the selected settings)

To upload or save a settings file from your local computer, choose here:

Max Poly-X:		Table of thermodynamic parameters:	Breslauer et al. 1986 SantaLucia 1998
Max #N's:		Salt correction formula:	Schildkraut and Lifson 1965 SantaLucia 1998 Owczarzy et. 2004
Number To Return:		CG Clamp:
Max Self Complementarity:		Max 3' Self Complementarity:
		Max 3' Stability:
Max Repeat Mispriming:		Pair Max Repeat Mispriming:
Max Template Mispriming:		Pair Max Template Mispriming:
Left Primer Acronym:		Internal Oligo Acronym:
Right Primer Acronym:		Primer Name Spacer:

Product Tm

Min:

Opt:

Max:

Use Product Size Input and ignore Product Size Range			Warning: slow and expensive!
Product Size	Min:	Opt:	Max:

Liberal Base

Do not treat ambiguity codes in libraries as consensus

Use Lowercase Masking

Sequencing

Lead	Bp:		Spacing	Bp:
Accuracy	Bp:		Interval	Bp:
Pick Reverse Primers

Hyb Oligo Excluded Region:

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

Hyb Oligo Monovalent Cations Concentration:		Hyb Oligo DNA Concentration:
Hyb Oligo Divalent Cations Concentration:		Hyb Oligo [dNTP] Concentration:
Max #Ns:		Hyb Oligo Max Poly-X:
Hyb Oligo Self Complementarity:		Hyb Oligo Max 3' Self Complementarity:
Hyb Oligo Max Mishyb:		Hyb Oligo Min Sequence Quality:
Hyb Oligo Mishyb Library:	NONE HUMAN RODENT_AND_SIMPLE RODENT DROSOPHILA

For Primers

For Primer Pairs

For Hyb Oligos

Tm

Lt:

Gt:

Product Tm

Lt:

Gt:

Tm

Lt:

Gt:

Size

Lt:

Gt:

Product Size

Lt:

Gt:

Size

Lt:

Gt:

GC%

Lt:

Gt:

GC%

Lt:

Gt:

Mispriming		Pair Mispriming		Hyb Oligo Mishybing
Self Complementarity		Any Complementarity		Self Complementarity
3' Self Complementarity		3' Self Complementarity
Template Mispriming		Template Mispriming
#N's				Hyb Oligo #N's
Sequence Quality				Sequence Quality
End Sequence Quality
Position Penalty		Tm Difference
End Stability		Primer Penalty Weight
Inside Target Penalty:		Hyb Oligo Penalty Weight
Outside Target Penalty:
Set Inside Target Penalty to allow primers inside a target.