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PrimerQuestSM

HeatMap Options

   Basic | Standard | Advanced  Display All Values | About | Quick Start Guide  
Show All | Sequence Details | Primer Conditions | Primer Product Details | Probe Details
Calculate


Advanced Sequence Design
Number of Primer Sets to Return:  (Limit 50 Primer Sets)
Use Mispriming Library:
Forward Primer Sequence Input:  
Probe Sequence Input:  
Reverse Primer Sequence Input:  
Targets:   (start,length)  
Excluded Regions:   (start,length)  
Included Regions:   (start,length)  
Start Codon Position:  
Mixed Bases         Force Primer Pick         Show Detailed Info    
Sequence Quality: (PHRED Scores)
 
Min Sequence Quality:     Min End Sequence Quality:  
Sequence Quality Range Min:     Sequence Quality Range Max:  


Primer Conditions
Min Optimum Max
Primer Size:  nt  nt  nt
Primer TM:  °C  °C  °C
Primer GC%:  %  %  %
Max TM: Difference:  °C Max # of N's:
Max Self Comp:  nt Max 3' Self Comp:  nt
Inside Target Penalty:   Outside Target Penalty:  
Max Poly-X:   GC Clamp:  
Na+ Concentration:  mM   Annealing Oligo Concentration:  mM  
Mg++ Concentration:  mM   dNTPs Concentration:  mM  
Max Mispriming:   Pair Max Mispriming:  
Max 3' Stability:   First Base Index:  


Primer Product Details
Product Size Ranges:  bp
Min Optimum Max
Product TM:  °C  °C  °C
Product Size:  bp

Objective Function Penalty Weights for Primers
TM: Less Than:   TM: Greater Than:  
Size Less Than:   Size Greater Than:  
GC% Less Than:   GC% Greater Than:  
Self Comp:   3' Self Comp:  
Sequence Quality:   End Seq. Quality:  
Position Penalty:   End Stability:  
# of N's:   Mispriming:  

Objective Function Penalty Weights for Primer Pairs
Product TM: LT:   Product TM: GT:  
Product Size LT:   Product Size GT:  
Any Comp:   3' Comp:  
Pair Mispriming:   TM: Difference:  
Primer Penalty Weight:  


Probe Conditions
Min Optimum Max
Probe Size:  nt  nt  nt
Probe TM:  °C  °C  °C
Probe GC%:  %  %  %
Probe Self Comp:   Probe Self Comp End:  
Max # of N's:   Max Poly-X:  
Probe Max Mishybrid:   Probe Min Sequence Quality:  
Probe Na+ Concentration:  mM   Probe DNA Concentration:  mM  
Probe Mg++ Concentration:  mM   Probe dNTPs Concentration:  mM  

Objective Function Penalty Weights for Probes
Probe TM: LT:   Probe TM: GT:  
Probe Size LT:   Probe Size GT:  
Probe GC% LT:   Probe GC% GT:  
Probe Self Comp:   Probe 3' Comp:  
Probe Sequence Quality:   Probe End Sequence Quality:  
Probe # of N's:  
Probe Terminal Position Specifications
Bases 5' End 3' End
A
C
G
T

Clear All
     
Reset Defaults
Calculate
1. Paste in a sequence
2. Configure primer/probe options
3. Calculate!
4. Select the set(s) or oligos you like
5. Order your primers
 
 
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