Primer3Plus

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Primer3Plus pick primers from a DNA sequence This instance of Primer3Plus will retire soon, please move to: https://www.primer3plus.com For similar results choose load server settings "P3W v0.4.0 Def" and press the button "activate settings"	Primer3Manager	Help
	About	Source Code

Task:

Select primer pairs to detect the given template sequence. Optionally targets and included/excluded regions can be specified.

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Main
General Settings
Advanced Settings
Internal Oligo
Penalty Weights
Sequence Quality

Sequence Id:

Paste source sequence below	Or upload sequence file:

Mark selected region:

Excluded Regions:

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:

Load and Save

Please select special settings here: (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:
Max #N's:		Salt correction formula:
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:

For Primers

For Primer Pairs

For Hyb Oligos

Lt:

Gt:

Product Tm

Lt:

Gt:

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.