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Fragment Analysis

Fragment Analysis Submission Policies

Our DNA Analyzer uses fluorescence based detection to determine the size of DNA fragments. We will add the size standard and perform the electrophoresis on the samples.


The minimum number of samples for a Fragment Analysis submission is 24 samples. You may submit fewer, but you will still be charged for 24 wells.

For pricing, please visit our fees page.

Standard Turn Around Time

Standard turnaround time is 1 business day. Yale users will receive priority over non-Yale users. You can check the status of your order on the sample submission page by selecting CHECK EXISTING ORDERS. If you have not received your results in 2 business days, feel free to reach out to us at

**If your samples are RUSH samples, please make us aware of this before we receive your submission. We will work to accommodate your request without compromising the lab’s workflow requirements.

Plasticware Requirements

All samples must be submitted in a [non fully-skirted] 96-well optical plate with clear 2mL wells. It must be sealed properly with strip caps or sealing film. It should be wrapped in foil due to it being light sensitive.

Here are some examples of acceptable plate types:

  • ABI MicroAmp Optical Plates, part #N801-0560.
  • USA Scientific TempPlate #1402-9596
  • Thomas Scientific Non-Skirted PCR Plates #1148A37

**Fast plates will not work with our instrumentation and will require samples transfer to a compatible plate. There is a fee associated with the sample transfer.

ABI #4346907 and VWR 82006-664 are two examples of incompatible plates.

If you have questions about plates other than those listed above, please contact and we can determine compatibility.**

Dye Sets

Please check the compatibility of your dyes and filter sets to our offerings.

Applied Biosystems Standard Dye Sets for Genotyping Applications
Dye Set DS-02 DS-30 DS-33
Filter Set E5 D G5
Dye Set Components dR110, dR6G, dTAMRATM, dROXTM, LIZ© 6-FAMTM, HEXTM, NEDTM, ROX 6-FAM, VIC, NED, PET©, LIZ
Applied Biosystems Kits and Other Products for Genotyping SNaPshot© Primer Focus© Kits, SNaPshot Multiplex Kits Custom Oligos AmpFLSTR Identifiler© Kits1, AmpFLSTR YfilerTM Amplification Kits, Custom Oligos, LMS v2.5, Mouse Mapping Primers, StockMarks Kits

1AmpFLSTR 4- and 5-dye kits are not supported on the Applied Biosystems 3730/3730xl instruments.

These are the current size standard sets we offer:

Fragment Analysis Submission Protocol

(1) Before pooling multiplex PCR products:

  • We recommend running a mini-gel to verify that your PCR product works.
  • Determine optimal PCR concentration by serial dilution.
  • Example of possible Microsatellite optimized concentration: pre-PCR = 50ng/µl, post amplification 25ng/µl
  • To avoid Plus A problem order primer with tails. See User Bulletin: Plus A Artifacts for more information.

(2) Submission:

  • Yale Internal Users: 1-2 µl of each fluorescently labeled PCR product brought to a final volume of 10µl with water or HiDi Formamide.
  • External User: 1-2µl of each fluorescently labeled PCR product brought to a final volume of 10µl with water.

We will add the size standard of your choosing to your submission.

After the order is placed online, please fill out the Sample Sheet Template and email it to If a sample sheet is not supplied, your sample files will be named Plate Name-Well number.

  • Please fill your plate by column; i.e: A1-H1, A2-H2, and so on.

Analysis Software

Results for Yale researchers can be viewed using GeneMarker or GeneMapper software through a remote desktop connection. Please email us at for login instructions.

If you need more options, please see the Freeware tab on our webpage.

GeneMapper Tutorial

GeneMarker Tutorial