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Copyright © 2000, 2003, 2004 Malay Kumar Basu
Send your comments/suggestions/bug-report to me:
malay@bioinformatics.org
Disclaimer


Program Name

primer3
Mispriming Library (repeat library)
Pick left primer or use sequence
Pick hybridization probe or use oligo
Pick right Primer or use sequence
Sequence Id (a name to identify your sequence)
Region the primers will flank
Formats: [base number],[number of bases] e.g. 50,2 or mark the sequence with []
Excluded Region
Formats:[base number],[number of bases] e.g. 401,7 68,3 or mark the sequence with <>
Product Size
Min Opt Max
Number of Return Max 3' Stability
Max Mispriming
Pair Max Mispriming
General Primer Picking Conditions
Primer Size Min Opt Max
Primer Tm
Min Opt Max
Max Tm Difference
Product Tm
Min Opt Max
Primer GC%
Min Opt Max
Max Self Complementarity Max 3' Self Complementarity
Max #N's Max Poly-X
Inside Target Penalty Outside Target Penalty
First Base Index CG Clamp
Salt Concentration Annealing Oligo Concentration
Liberal Base Show Debuging Info
Other Per-Sequence Inputs
Included Region to pick primers
Format: Starting Base number, length e.g. 20,400 or mark the sequence with{}
Start Codon Position
Sequence Quality
Min Sequence Quality Min End Sequence Quality
Sequence Quality Range Min Sequence Quality Range Max
Objective Function Penalty Weights for Primers
Tm Lt: Gt:
Size Lt: Gt:
GC% Lt: Gt:
Self Complementarity
3' Self Complementarity
#N's
Mispriming
Sequence Quality
End Sequence Quality
Position Penalty
End Stability
Objective Function Penalty Weights for PrimerPairs
Product Size Lt: Gt:
Product Tm Lt: Gt:
Tm Difference
Any Complementarity
3' Complementarity
Pair Mispriming
Primer Penalty Weight
Hyb Oligo Penalty Weight
Hyb Oligo (Internal Oligo) Per-Sequence Inputs
Hyb Oligo Excluded Region
Hyb Oligo (Internal Oligo) General Conditions
Hyb Oligo Size: Min Opt Max
Hyb Oligo Tm: Min Opt Max
Hyb Oligo GC% Min: Opt: Max:
Hyb Oligo Self Complementarity
Hyb Oligo Max 3' Self Complementarity:
Hyb Oligo DNA Concentration
Hyb Oligo Salt Concentration:
Hyb Oligo Min Sequence Quality
Hyb Oligo Mishyb Library
Hyb Oligo Max Mishyb:
Hyb Oligo Max Poly-X: Max #Ns
Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)
Hyb Oligo Tm
Lt: Gt:
Hyb Oligo Size
Lt: Gt:
Hyb Oligo GC%
Lt: Gt:
Hyb Oligo Self Complementarity
Hyb Oligo #N's
Hyb Oligo Mishybing
Hyb Oligo Sequence Quality
codehop
Core (degenerate 3' region)
Degeneracy Strictness
Clamp (non-degenerate 5' region)
Temperature Poly-nuc
Primer concentration [in nM]
Codon usage table
Show the least degenerate, or show all overlapping primers
Use core strictness for the 3' base
Force the core/clamp boundary to be a codon boundary
Use the most common codons in the clamp
Primer3
Create PCR primers and Hybridization oligos from a DNA sequence. Input, DNA sequence. Required option-field, none.
CODEHOP
Pick primers from multiple alingnment of protein sequences. Input type, BLOCKS. Required option-field, none.