Primer designing procedure/Help Report bugs/Request features Run this program locally Change log
Target selection
Select genome
AND
Select gene to design primers within ± X Kb around transcription start site from the dropdown menu?
Gene selected
none
Distance around the TSS to scan
bp upstream to 
bp downstream
or
 Enter genomic coordinate in the format chr1:1234-5678 ?
none
 
or
Enter nucleotide sequence
Fragment selection parameters
Minimum fragment length (bp)
Maximum fragment length (bp)
Size of sub-fragment to choose non-reading primer from (bp)
Reading primer length (bp)? bp to bp
Try all primer lengths in selected range No | Yes
Annealing temperature parameters
Minimum TM (Celsius)
Maximum TM (Celsius)
Maximum TM difference (Celsius)
Primer selection parameters
Number of primers to return per fragment
Maximum number of 3' end hits with 100% identity (may cause mispriming)
Enzyme search mode all combinations
specify primary and secondary enzymes
limit enzymes


Last updated Jan 25, 2018.

Initial primer designer code written by Alex Gileta under guidance of Scott Smemo and Noboru Sakabe. Definitive designer written by Noboru Sakabe. Web interface and service created, provided and maintained by Noboru Sakabe.
Nobrega lab - Department of Human Genetics - University of Chicago, Chicago, USA.