MFEprimer-4.1.0: PCR Primer Design and Quality Control Tools

Target settings

* Species list Multiple selection of the species (<= 5) of interest.

Targets selected

Primer settings

Primer Min Size

Primer Opt Size

Primer Max Size

Primer Min GC

Primer Opt GC

Primer Max GC

Primer Min T_m

°C

Primer Opt T_m

°C

Primer Max T_m

°C

Dimer Min ΔG

kcal/mol

Hairpin Min Score

Probe settings

Probe Min T_m

°C

Probe Opt T_m

°C

Probe Max T_m

°C

Product settings

Product Min GC

Product Opt GC

Product Max GC

Product Min Size

Product Max Size

Nonspecific analysis settings for background databases

Background database (e.g., host genome, hg38, mm10)

T_m

Min

°C

Minimum Tm value required for the binding stability between primer and its binding sites.

Nonspecific Amplicon Size (bp)

From

Product size: 0 (min) - 1000000 (max).

Advanced settings for thermodynamic analysis

Concentration of monovalent cations (usually KCl)

Concentration of divalent cations (usually MgCl₂)

Concentration of dNTPs

Annealing oligo concentration