Primer 3


Sequence Id:
A string to identify your output.
Targets:
E.g. 50,2 requires primers to surround the 2 bases at positions 50 and 51.
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.

Product Size Ranges:

Number to Return (max 10):
Max 3' Stability:
Max Repeat Mispriming:
Pair Max Repeat Mispriming:
Max Template Mispriming:
Pair Max Template Mispriming:

General Primer Picking Conditions

Primer Size
Primer Tm
Max Tm Difference
Product Tm
Table of Thermodynamic Parameters
Primer GC%

Max Self Complementarity:
Max 3' Self Complementarity
Max #N's:
Max Poly-X:
Inside Target Penalty:
Outside Target Penalty:
First Base Index:
GC Clamp:
Concentration of monovalent cations:
Salt correction formula:
Concentration of divalent cations:
Concentration of dNTPs:

Annealing Oligo Concentration:
(Not the concentration of oligos in the reaction mix but of those annealing to template.)

Other Per-Sequence Inputs

Included Region:
E.g. 20,400: only pick primers in the 400 base region starting at position 20.
Start Codon Position:

Sequence Quality

Min Sequence Quality:
Min End Sequence Quality:
Sequence Quality Range Min:
Sequence Quality Range Max:

Penalties

Objective Function Penalty Weights for Primers

Tm
Size
GC%

Self Complementarity:
3' Self Complementarity:
#N's:
Mispriming:
Sequence Quality:
End Sequence Quality:
Position Penalty:
End Stability:
Template Mispriming:

Objective Function Penalty Weights for Primer Pairs

Product Size
Product Tm

Tm Difference:
Any Complementarity:
3' Complementarity:
Pair Mispriming:
Primer Penalty Weight:
Hyb Oligo Penalty Weight:
Primer Pair Template Mispriming Weight:


Hyb Oligos (Internal Oligos)

Hyb Oligo (Internal Oligo) Per-Sequence Inputs

Hyb Oligo Excluded Region:

Hyb Oligo (Internal Oligo) General Conditions

Hyb Oligo Size
Hyb Oligo Tm
Hyb Oligo GC%

Hyb Oligo Self Complementarity:
Hyb Oligo Max 3' Self Complementarity:
Max #N's:
Hyb Oligo Max Poly-X:
Hyb Oligo Mishyb Library:
Hyb Oligo Max Mishyb:
Hyb Oligo Min Sequence Quality:
Hyb Oligo Conc of Monovalent Cations:
Hyb Oligo DNA Concentration:
Hyb Oligo Conc of Divalent Cations:
Hyb Oligo [dNTP]:

Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)

Hyb Oligo Tm
Hyb Oligo Size
Hyb Oligo GC%

Hyb Oligo Self Complementarity:
Hyb Oligo #N's:
Hyb Oligo Mishybing:
Hyb Oligo Sequence Quality:


Copyright Notice and Disclaimer

Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007 Whitehead Institute for Biomedical Research, Steve Rozen, and Helen Skaletsky All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

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