MFE
primer
4.2.0
Doc
Publications
Hairpin analysis
* Primer sequences (<= 1000
?
) (
FASTA format
or just plain sequences one per line,
example
,
clear
)
Potential hairpin settings
Min loop size
Min
Max loop size
Max
Min double helix size
Min
Allowed max gaps for a hairpin
Max
Score (base pairs)
Min
Score cutoff value to filter hairpins
ΔG
Max
kcal/mol
ΔG cutoff value to filter hairpins
Thermodynamic settings
Concentration of monovalent cations (usually KCl)
mM
Concentration of divalent cations (usually MgCl
2
)
mM
Concentration of dNTPs
mM
Annealing oligo concentration
nM
Run
Specificity analysis
Dimer analysis
Hairpin analysis
Coverage analysis for various microbial strains
MP-Ref: Multiplex PCR Primer Design for Reference Genomes
Contact
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us.
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