EMBOSS explorer


Pick PCR primers and hybridization oligos (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Pick PCR primer(s)?
Select task
Pick hybridization probe?
Primer3 internal oligo mishybridizing library file (optional):
Primer3 mispriming library file (optional):
Additional section
Program options
Number of results to return
Sequence options
Included region(s)
Target region(s)
Excluded region(s)
Forward input primer sequence to check
Reverse input primer sequence to check
Primer options
GC clamp
Primer optimum size
Primer minimum size
Primer maximum size
Primer optimum Tm
Primer minimum Tm
Primer maximum Tm
Maximum difference in Tm of primers
Primer optimum GC percent
Primer minimum GC percent
Primer maximum GC percent
Salt concentration (mM)
DNA concentration (nM)
Maximum polynucleotide repeat
Product options
Product optimum size
Product size range
Product optimum Tm
Product minimum Tm
Product maximum Tm
Internal oligo input
Internal oligo excluded region
Internal oligo input sequence (if any)
Internal oligo options
Internal oligo optimum size
Internal oligo minimum size
Internal oligo maximum size
Internal oligo optimum Tm
Internal oligo minimum Tm
Internal oligo maximum Tm
Internal oligo optimum GC percent
Internal oligo minimum GC
Internal oligo maximum GC
Internal oligo salt concentration (mM)
Internal oligo DNA concentration (nM)
Internal oligo maximum self complementarity
Internal oligo maximum 3' self complementarity
Internal oligo maximum polynucleotide repeat
Internal oligo maximum mishybridization
Advanced section
Explain flag?
Create results files for each sequence?
First base index
Pick anyway?
Primer maximum mispriming
Primer pair maximum mispriming
Maximum Ns accepted in a primer
Maximum self complementarity
Maximum 3' self complementarity
Primer penalty weights
Maximum 3' end stability
Output section
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.