How to Analyze Microsatellites Using Capillary Electrophoresis

Microsatellites, or SSRs, are short tandem repeats used to assess genetic variation across individuals or populations. When analyzed via CE, they provide high-resolution, reproducible data ideal for breeding, biodiversity, and conservation genetics.

How Microsatellite Analysis Works

1. Design primers flanking the repeat
   
   
2. Amplify via PCR with fluorescent dye labels
   
   
3. Run on a CE system with size standard
   
   
4. Call alleles using binning software
   

Expert Insight: Quality Matters

Accurate microsatellite genotyping depends on:

• Motif-specific stutter correction
  
  
• Adjusting bin width to repeat type
  
  
• Managing PCR artifacts (e.g., plus-A, pull-up)
  
  
• Using reference controls across batches
  

GeneMarker’s auto binning engine includes motif-aware stutter filters and repeat-specific calibration, improving confidence in large-scale studies.

Batch & Drift Management

Experts analyzing hundreds of samples benefit from:

• Batch binning with drift correction
  
  
• Plate normalization tools
  
  
• Automated allele table exports for downstream stats (e.g., GenAlEx, STRUCTURE, Cervus)
  
  
• LOD filters to clean noisy peaks

Common Issues and Fixes

Ready-to-Go with GeneMarker®

Whether you’re a breeder screening 96-well plates or a conservation biologist managing endangered species diversity, GeneMarker® gives you:

• Accurate allele calls

• Robust QC visualization

• Streamlined reporting in one tool

Why Choose SoftGenetics for Variant Detection Analysis?

• Comprehensive Solutions: Support for Sanger, NGS, and long-read sequencing.
• User-Friendly Design: Simplifies workflows, even for non-experts.
• Trusted in Clinical and Research Labs: Proven accuracy and reliability.

Start your journey with a free  35-day trial of SoftGenetics software and experience the difference in variant detection analysis.