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Fragment Length Analysis (FLA)
High-quality fragment length analysis for STR, microsatellite and DNA fingerprinting applications. Microsynth offers flexible service options ranging from raw fragment separation to fully analyzed results and customized project workflows.
Microsynth provides fragment length analysis services for STR analysis, microsatellite analysis and DNA fingerprinting applications.
Why Choose Microsynth?
- Accredited quality – ISO/IEC 17025:2017 accredited workflows
- Reliable technology – ABI 3730XL platform with GeneMarker analysis
- Fast turnaround – results available within 1–2 working days (raw data)
- Flexible service models – from raw data to fully analyzed reports
- Expert support – experienced scientists for assay design and troubleshooting
Service Options
Microsynth offers three fragment length analysis service models depending on your workflow:
Fragment Length Analysis – Labeled PCR Products
Submit diluted, fluorescently labeled PCR products. Microsynth adds the size standard and performs capillary electrophoresis.
Includes:
- Fragment separation on ABI 3730XL
- Raw data delivery (FSA files)
- Optional GeneMarker data analysis
Turnaround time:
- 1–2 working days (raw data only)
- 2–6 working days (with data analysis/reporting)
Fragment Length Analysis – Ready-to-load
Submit PCR products already mixed with size standard and HiDi formamide.
Includes:
- Direct fragment analysis without additional preparation
- Raw FSA files
- Optional GeneMarker analysis and reporting
Turnaround time:
- 1–2 working days (raw data only)
- 2–6 working days (with data analysis/reporting)
Fragment Length Analysis – Customized
Microsynth supports complete workflows from DNA isolation and PCR optimization to fragment analysis and reporting.
Ideal for complex or large-scale projects requiring tailored solutions.
Output & Reporting
You can choose between raw data delivery and fully analyzed results:
- FSA raw data files
- Allele calling (bp size and allele name)
- Excel-based result tables
- JPEG visualization of allele peaks
- Additional signal metrics (height, area, ratio) on request
Example Results
Figure 1. Excerpt from the result Excel with the determination of the allele name and the bp size.
Figure 2. JPEG export of the allele calling (FSA files).
Applications
STR & Microsatellite Analysis
- Cell line authentication
- Human, animal and plant genotyping
- Linkage mapping
- Animal and plant breeding
- Pathogen sub-typing
- Genetic diversity studies
- Microsatellite instability
- Loss of heterozygosity (LOH)
- ISSR and MLVA
- Paternity testing
- Population genetics
DNA Fingerprinting & AFLP
- Microbial genome typing
- Genetic variation analysis
- Strain differentiation
- Biodiversity studies
- Forensic and traceability applications
Detection & Technical Specifications
Microsynth supports a range of fluorescent dye chemistries for fragment length analysis.
Filter sets define which fluorescent dyes can be detected during capillary electrophoresis and are relevant for multiplex assay design.
Show me filter sets
| Dye Set Name | Matrix Type | Blue | Green | Yellow | Red | Orange |
| Powerplex_4C | 4 dye | FAM | JOE | TAMRA | size standard* |
N/A |
| DS-30_D | 4 dye | 6-FAM | HEX | NED | size standard* |
N/A |
| DS-33_G5 | 5 dye | 6-FAM | VIC | NED | PET | size standard** |
| Mic-G5 | 5 dye | FAM | ATTO532 | ATTO550 | ATTO565 | size standard** |
* Reserved dyes for specific size standards (e.g. ILS 600 CXR, GeneScan 350/400/500 ROX, MapMarker 1000 ROX).
** For LIZ-based standards: GeneScan 120/500/600/1200 LIZ.
** For LIZ-based standards: GeneScan 120/500/600/1200 LIZ.
RCT option: All dye sets are available with RCT signal setting upon request. Due to reduced signal intensity, use of RCT is recommended only after consultation with our technical experts.
Ready-to-load service:
Any size standard can be added upon request. Please indicate the standard used for fragment sizing.
Forward primers can be synthesized with the dyes listed above (except PET and LIZ).
Cost-effective alternative dyes with comparable performance are available.
Cost-effective alternative dyes with comparable performance are available.
Show me size standards
The table below lists the size standards compatible with each dye set.
| Size Standard | Size Standard Range | Fluorophor | ABI Channel | Compatible Filter Set |
| GeneScan 120 LIZ | 15 - 120 nt | LIZ | Orange | |
| GeneScan 350 ROX | 35–350 nt | ROX / CXR | Red | Powerplex_4C DS-30_D |
| GeneScan 400 HD ROX | 50–400 nt | ROX / CXR | Red | Powerplex_4C DS-30_D |
| GeneScan 500 LIZ | 35–500 nt | LIZ | Orange | DS-33_G5 Mic-G5 |
| GeneScan 500 ROX | 35–500 nt | ROX / CXR | Red | Powerplex_4C DS-30_D |
| GeneScan 600 LIZ | 20–600 nt | LIZ | Orange | DS-33_G5 Mic-G5 |
| ILS 600 CXR | 60–600 nt | ROX / CXR | Red | Powerplex_4C DS-30_D |
| MapMarker 1000 ROX | 50–1000 nt | ROX / CXR | Red | Powerplex_4C DS-30_D |
| GeneScan 1200 LIZ | 20–1200 nt | LIZ | Orange | DS-33_G5 Mic-G5 |
RCT option: Dye sets using the RCT signal setting use the same size standards as the corresponding standard dye sets.
How to Order
1. How to order labels (non-prepaid):
- Enter our webshop
- Click on "Plates" under Fragment Length Analysis and follow the further instructions
2. How to register your samples:
- Prepare your samples arrayed in a 96-well plate according to our sample requirements.
- Fill the order form on our webshop.
- Print the order form and put it together with the samples in a plastic bag or envelope. Drop the samples in the next Microsynth collection box. To find the closest collection point please login our online shop and click “Options & Preferences” under DNA Sequencing and find details under “Collection Points”. In case there is no collection box in your vicinity, ship your samples to Microsynth in Balgach, Switzerland. See here for your shipment options.
- New customers will get an introductory discount of 50% for the first plate to be analyzed at Microsynth.