MFEprimer-3.0: PCR Primer Quality Control - Specificity, Hairpins & Dimers

Dimer

Primer sequences (multiplex PCR primers supported, example ) *Number of primer sequences: 1 (min) - 50 (max). 2 (max) primers for degenerate bases.

Score cutoffMinimum score value required for a dimer.

Maximum mismatchHow many mismatches allowed in a dimer?

3'end key basesIn default, the last 3 bases at the 3'end are treated differently and there should be zero mismatches among these bases.

Maximum mismatch allowd in 3'end key basesHow many mismatches allowed in 3'end key bases in a dimer?

Gap/mismatch runMaximum continuous mismatches allowed in a dimer.

Temperature

°C

Temperature for thermodynamics calculation.

Concentration of monovalent cations (usually KCl) *

Concentration of divalent cations (usually MgCl₂) *

Concentration of dNTPs *

Annealing oligo concentration *

MFEprimer-3.0