Silica: in-silico PCR amplification

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Paste primers in Fasta format

or upload Fasta file (.fa)

and select genome

Maximum Size of PCR Product (bp)

Minimal Primer Tm to Consider (°C)

Number of bp from the 3' End of the Primer Used to Seach for Matches (>14)

Maximal Allowed Number of Mutations in Matching Sequence (0 or 1)

Keep Only PCR Products with Penalty Below (-1 = keep all)

Penalty Factor for Single Primer Tm Mismatch to optimal Tm

Penalty Factor for Tm Mismatch of Primers in a Pair

Penalty Factor for PCR Product Length

Tm Calculation: Concentration of Monovalent Ions (mMol)

Tm Calculation: Concentration of Divalent Ions (mMol)

Tm Calculation: Concentration of Annealing(!) Oligos (nMol)

Tm Calculation: Concentration of the Sum of All dNTPs (mMol)

Load JSON file (.json)

Application Description

Silica runs a virtual insilico PCR with a set of primers on a selected genome. Multiple primer pairs are allowed, off target products will be shown if present. All primer combinations are tested, provided sufficiend binding to the DNA and reasonable amplicon size.

Accepted Input

Primers can be provided in fasta format or uploaded as a fasta file (*.fa).

Sample Data

The "Load Example" button loads an example primer set. Hit "Launch Analysis" to try the functionality.