FastPCR is an integrated tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching

  • The FastPCR software is an integrated tools environment that provides comprehensive and professional facilities for designing any kind of PCR primers for standard, long distance, inverse, real-time PCR (TaqMan, LUX-primer, Molecular Beacon), multiplex PCR, Xtreme Chain Reaction (XCR®); single primer PCR (design of PCR primers from close located inverted repeat); automatically detecting Simple sequence repeat (STR) loci and direct PCR primer design; amino acid sequence degenerate PCR.
  • Loop-mediated Isothermal Amplification (LAMP).
  • Primer design and fragment assembly using Gibson Assembly.
  • Fragment assembly using Polymerase Chain Assembly (PCA).
  • Design multiplexed of overlapping and non-overlapping DNA amplicons that tile across a region(s) of interest for targeted next-generation sequencing (Molecular Tagging).
  • The competitive allele-specific TaqMan™ PCR (castPCR™ Technology), allele-specific TaqMan PCR utilizes an allele-specific primer for mutant allele detection that competes with an MGB blocker oligonucleotide to suppress the wild-type background and enable specific-allelic scoring of single nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels) at specific loci.
  • Allele-Specific PCR (AS-PCR) - KASP™ (Kompetitive Allele Specific PCR) or PACE™ (PCR Allele Competitive Extension) based genotyping assay design for biallelic discrimination of single nucleotide polymorphisms (SNPs) and small/large insertions and deletions (Indels) at specific loci.
  • The SNaPshot® Multiplex System primer extension-based method enables multiplexing SNPs genotyping.
  • The Invader® assay for SNP genotyping - uses a structure-specific flap endonuclease to cleave a three-dimensional complex formed by hybridization of allele-specific overlapping oligonucleotides to target DNA containing a single nucleotide polymorphism (SNP) site.
  • Multiplex Ligation Assay (MLA) design - MLPA® (Multiplex Ligation-dependent Probe Amplification) is a technology designed for detection of SNPs/Indels, analysis of DNA methylation, relative mRNA quantification, detection of gene copy number.
  • The “in silico” (virtual) PCR primers or probe searching or in silico PCR against whole genome(s) or a list of chromosome - prediction of probable PCR products and search of potential mismatching location of the specified primers or probes. Searching multiple targets simultaneously within a certain range. The “in silico” oligonucleotide search is helpful for discovering target binding sites with the temperature melting and PCR annealing temperature calculation.
  • A long oligonucleotide can be designed for microarray analyses and dual-labeled oligonucleotides for probes such as molecular beacons.
  • Comprehensive primer test, the melting temperature calculation for standard and degenerate oligonucleotides, primer's PCR efficiency and linguistic complexity, dilution and resuspension calculator.
  • Primers (probes) are analyzed for all primer secondary structures including the alternative hydrogen bonding to Watson-Crick base pairing such as G-quadruplexes or wobble base pairs (like G-G, G-T, G-A), hairpins, self-dimers and cross-dimers in primer pairs. The software utilizes combinations of normal and degenerated primers for all tools and for the melting temperature calculation are based on the nearest neighbour thermodynamic parameters.
  • The program includes various bioinformatics tools for analysis of sequences with GC or AT skew, GC% and GA% content and purine-pyrimidine skew, the linguistic sequence complexity; generation random DNA sequence with Tm or GC% control; restriction I-II-III types enzymes analysis, find or create restriction enzyme recognition sites for coding sequences.
  • Sequence alignment tools, supports the assembly of a set of contiguous sequences (contigs), k-mer based distance calculation and consensus sequence generation and sequences similarity and conservancy analysis.
  • Efficient and complete detection of different types of repeats and any type of tandem repeats, from short tandem repeats (microsatellites) to large satellite sequences with a summary table of the types and locations of the found repeats.

If you’re looking for a special feature or features that are not realized in the current version of the FastPCR software, please get in touch with us and we will customize the product specifically to your needs.

System requirements

FastPCR software can be installed exclusively on Microsoft Windows platform and properly works only on computers that meet the minimum technical specifications outlined below:


In case your computer does not meet any of the minimum system requirements you may have trouble using certain features of the software.

Current version: 6.8.66
License type: trial


Once the program is downloaded, please follow the steps listed below to get FastPCR installed on your computer:


  • To install the program, save the FastPCR.msi file in your computer.
  • Run the FastPCR.msi file that starts the Installation Wizard.
  • Follow all steps suggested by the wizard. This is a "local" software installation and require administrator rights to install.

When you complete these steps, the software will be activated for 7 days. During this period of time, the full set of latest release's features will be available to you.

After the evaluation period, the program can be removed via Add/Remove Program in the Windows control panel.

FastPCR training & certification

The comprehensive FastPCR software and PCR application development training solutions, which now include training for FastPCR and WebTools. Additionally, our industry-leading enterprise development certifications validate skills in FastPCR software and PCR application development.
Please contact us (free email accounts will not be accepted) for course dates by

Guided video tour of the FastPCR