MFEprimer-4.1.0: PCR Primer Design and Quality Control Tools

Target settings

Genome database

Targets in BED format (<= 200, example, clear, SNP, Gene how-to)

STR mode: primers should be chosen around (not within) the regions.

Chromosome name examples

chrM    1000 1001
chrM    2000 2001
chrM    3000 3001

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).

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

Product settings

Product Min GC

Product Opt GC

Product Max GC

Product Min Size

Product Max Size

Advanced settings for thermodynamic analysis

Concentration of monovalent cations (usually KCl)

Concentration of divalent cations (usually MgCl₂)

Concentration of dNTPs

Annealing oligo concentration