Guides for Sequencing, Fragment and Forensics

How to Analyze Microsatellites Using Capillary Electrophoresis

Written by SoftGenetics Team | Aug 7, 2025 12:13:52 PM

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

Issue

Description

Solution in GeneMarker®

Stutter Peaks

Shadow peaks from slippage

Motif-based stutter filters

Pull-Up

Dye bleed into other channels

Automatic pull-up suppression

Drift

Sizing inconsistency plate-to-plate

Internal control normalization 

Bin Misses

Ambiguous or shifted allele calls

Customizable allele bins

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

How SoftGenetics Helps?

  • GeneMarker®: high-performance sizing, binning, and allele calling plus embedded post-genotyping modules (MLPA/MS-MLPA, Aneuploidy, MSI, LOH…)

  • GeneMarker®HID: forensic-ready STR interpretation with mixture detection, database comparison, and visual QC tools

  • ChimerMarker®: Accurate, rapid genotyping, chimerism and MCC data analysis with documented time savings of up to 85%

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