(or use demo alignment - the raw sequences are available here.)






Similarity overlap
Tail length
Maximum primer length
Minimum primer length
Maximum melting temperature
Minimum melting temperature
Critical melting temperature
Minimum melting temperature with ambiguity positions
Minimum number of 3'-end matches
Maximum number of ambiguity positions
Minimum length with three or more ambiguity positions
Minimum length with two ambiguity positions
Critical ambiguity position distance from 3'-end
Maximum diversity per nucleotide position
Maximum number of ambiguity positions with maximum diversity
Minimum number of nucleotides per nucleotide position
Primer concentration in nanomolar
Salt concentration in molar
Maximum melting temperature difference
Optimal primer length interval
Optimal PCR product length interval
Minimum PCR product length
Maximum PCR product length
Optimal primer length dispensation with no ambiguity positions
Good conserved region length
Conservation window length
Minimum conservation-% in conservation window
Introns in sequences
At least one primer must be based on three sequences



© Jakob Fredslund 2005
If you would like to use PriFi for commercial purposes, please contact me.
If you found this application useful, please cite:
Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J. (2005)
PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W516-20
Abstract · Full text.
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