PRIMER DESIGN FORM


This service uses the Primer3 Software (through EMBOSS primer3 interface) to design two sets of primers for doing a nested PCR.
The input can either be in Fasta format or in GENOTRACE output format.
You will have to indicate with square brackets [atcgt] which region should be included in the amplicon.
Primers for multiple amplicons (for example all exons) can be designed in a single run.


 1. Paste your preformatted sequence(s) here:

 

  Or select the file containig preformatted sequence(s):

 


 2. Select type of PCR:

   Single PCR.

   Nested PCR.

   Nested PCR for tilling:
  Organism:
  Gene name: (max. 5 symbols, capitals recommended)
  Amplicon id:  (starting amplicon if several)
  Oligo 2 5'tail: (defaults to M13F)
  Oligo 3 5'tail: (defaults to M13R)



 3. Primers can be checked to avoid priming in repetitive elements. Note that this filtering could substantially slow down the search and affect results. If you are sure your input sequence doesn't containg repetitive elements, it's better to skip mispriming check.

Select the relevant RepBase (v.7.8) mispriming libraries:

   Reference collection of C. elegans repetitive elements.

   Reference collection of zebrafish repetitive elements.
   Reference collection of fugu repetitive elements.
   Reference collection of vertebrate repetitive elements; not including zebra fish.

   Reference collection of human repetitive elements.
   Reference collection of pseudogene repetitive elements.

   Reference collection of mammalian repetitive elements.

   Reference collection of rodent repetitive elements.
   Rat repetitive elements (manual selection from rodent collection).

   Reference collection of D. melanogaster repetitive elements.
   Reference collection of invertebrate repetitive elements; not including C. elegans or D. melanogaster.

   Reference collection of A. thaliana repetitive elements.
   Reference collection of O. sativa repetitive elements.
   Reference collection of plant repetitive elements; not including A. thaliana or O. sativa.

  Or provide the file with your own mispriming library:

 


 


Contact: Eugene Berezikov