Please select the Task here:   Detection Cloning Sequencing Primer_List Primer_Check

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Detection:	Pick primers anywhere in the Sequence using targets and regions.
Cloning:	Pick primers exactly at the border of included region.
Sequencing:	Pick primers for sequencing along the sequence using targets and regions
Primer List:	Pick a list of primers along the sequence using targets and regions
Primer Check:	Check a primer provided in left primer input

Sequence Id:	Mispriming/Repeat Library: NONE HUMAN RODENT_AND_SIMPLE RODENT DROSOPHILA
A name to identify your output.	Or N-out undesirable sequence (vector, ALUs, LINEs...)

To upload or save any sequence from your local computer, choose here:

Paste source sequence below:

5'->3', as ACGTNacgtn -- other letters treated as N -- numbers and blanks ignored FASTA format ok.

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).

Excluded Regions:	<  >
E.g. 401,7 68,3 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68. Or mark the source sequence with < and >: e.g. ...ATCT<CCCC>TCAT.. forbids primers in the central CCCC.
Targets:	[  ]
E.g. 50,2 requires primers to surround the 2 bases at positions 50 and 51. Or mark the source sequence with [ and ]: e.g. ...ATCT[CCCC]TCAT.. means that primers must flank the central CCCC.
Included Region:	{  }
E.g. 20,400: only pick primers in the 400 base region starting at position 20. Or use { and } in the source sequence to mark the beginning and end of the included region: e.g. in ATC{TTC...TCT}AT the included region is TTC...TCT.

Please select special settings here:   Default qPCR Probe Use_Product_Size

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

Product Size Ranges

Primer Size	Min:	Opt:	Max:
Primer Tm	Min:	Opt:	Max:	Max Tm Difference:
Primer GC%	Min:	Opt:	Max:

Salt Concentration:		Fix the prime end of the primer
Annealing Oligo Concentration:		Select which end of the primer is fixed and which end can be extended or shortened by Primer3Plus fo find optimal primers.
(Not the concentration of oligos in the reaction mix but of those annealing to template.)

General Sequencing Conditions

Lead	Bp:		Space between primer binding site and the start of readable sequencing
Spacing	Bp:		Space between the primers on one DNA strand
Accuracy	Bp:		Space in which Primer3Plus picks the optimal primer
Pick Reverse Primers			Pick also primers on the reverse DNA strand
Interval	Bp:		Space between primers on the forward and the reverse strand

Max #N's:		Max Poly-X:
Number To Return:		CG Clamp:
Max Self Complementarity:		Max 3' Self Complementarity:
		Max 3' Stability:
Max Mispriming:		Pair Max 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!
Select box to specify the min, opt, and max product sizes only if you absolutely must! Using them is too slow (and too computationally intensive for our server).
Product Size	Min:	Opt:	Max:

Liberal Base

Show Debuging Info

Do not treat ambiguity codes in libraries as consensus

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

Hyb Oligo Salt Concentration:		Hyb Oligo DNA 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

Hyb Oligo (Internal Oligo) Per-Sequence Inputs

Hyb Oligo Excluded Region:

Other Per-Sequence Inputs

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

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		Self Complementarity		Self Complementarity
3' Complementarity		3' Complementarity
#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.

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