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Primer3

Primer3 is a free online tool to design and analyze primers for PCR and real time PCR experiments. Primer3 can also select single primers for sequencing reactions and can design oligonucelotide hybridization probes. The online tool constitutes some important features like primer detection, cloning, sequencing and Primer listing.


 INPUT
a sequence: a file:
Mark:   Target   Included Region   Excluded Region   Clear
   
Pick Left Primer
or Enter Left Primer Sequence
Pick Hybridization Probe
or Enter Probe Sequence
Pick Right Primer
or Enter Right Primer Sequence
     
 

GENERAL PARAMETERS    
PRODUCT SIZE RANGES
  MINIMUM OPTIMUM MAXIMUM
PRIMER SIZE
PRIMER Tm
PRIMER GC%
PRODUCT Tm
PRODUCT SIZE
       
MAX Tm DIFFERENCE FIX THE ......
MISPRIMING/REPEAT LIBRARY    
       
CONCENTRATION SETTINGS      
MONOVALENT CATION ANNEALING OLIGOs
DIVALENT CATION dNTPs
       
ADVANCE SETTINGS    
MAX POLY-X TABLE OF THERMODYNAMIC PARAMETERS
MAX #Ns 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
LEFT PRIMER ACRONYM INTERNAL OLIGO ACRONYM
RIGHT PRIMER ACRONYM PRIMER NAME SPACER
       
SEQUENCING SETTINGS      
  BASE PAIR   BASE PAIR
LEAD SPACING
ACCURACY INTERVAL
PICK REVERSE PRIMERS    
       
INTERNAL OLIGO PARAMETERS    
HYB OLIGO EXCLUDED REGION
  MINIMUM OPTIMUM MAXIMUM
HYB OLIGO SIZE
HYB OLIGO Tm
HYB OLIGO GC%
       
MAX #Ns HYB OLIGO MAX POLY-X
HYB OLIGO SELF COMPLEMENTARITY HYB OLIGO 3' SELF COMPLEMENTARITY
HYB OLIGO MAX MISHYB HYB OLIGO MIN SEQUENCE QUALITY
HYB OLIGO MISHYB LIBRARY    
       
INTERNAL OLIGO CONCENTRATION SETTINGS    
HYB OLIGO MONOVALENT CATION HYB OLIGO DNA
HYB OLIGO DIVALENT CATION HYB OLIGO dNTP
       
PENALTY WEIGHTS FOR PRIMERS    
  LESS THAN GREATER THAN  
Tm  
SIZE  
GC%  
       
MISPRIMING TEMPLATE MISPRIMING
SELF COMPLEMENTARITY 3' SELF COMPLEMENTARITY
#Ns SEQUENCE QUALITY
POSITION PENALTY END STABILITY
INSIDE TARGET PENALTY OUTSIDE TARGET PENALTY
       
PENALTY WEIGHTS FOR PRIMER PAIRS    
  LESS THAN GREATER THAN  
PRODUCT Tm  
PRODUCT SIZE  
       
Tm DIFFERENCE    
ANY COMPLEMENTARITY 3' SELF COMPLEMENTARITY
PRIMER PENALTY WEIGHT HYB OLIGO PENALTY WEIGHT
       
PENALTY WEIGHTS FOR HYB OLIGOS    
  LESS THAN GREATER THAN  
Tm  
SIZE  
GC%  
       
HYB OLIGO MISHYBING SELF COMPLEMENTARITY
HYB OLIGO #Ns SEQUENCE QUALITY
       
SEQUENCE QUALITY PARAMETERS    
FIRST BASE INDEX SEQUENCE QUALITY
START CODON POSITION
MIN SEQUENCE QUALITY
MIN END SEQUENCE QUALITY
       
 
 

 


 
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