Fragment Analysis

Fragment Analysis

Service Description

As part of our Sanger Service offerings, we have a variety of fragment analysis services to help with sizing of fluorescently labeled products of 100-600bp. You run the assays in your lab and can bring them over as “Ready to Go” or we can add the ladder before running.

Generation of labeled fragments

You will run all the PCR reactions in your lab prior to submission. We encourage you to run the reaction out on an agarose gel before submitting to ensure the existence and rough concentration of the products.


The capillary instrumentation is spectrally calibrated to detect various fluorophores within filter sets D or G5.

Dye Color Dye Set D Dye Set G5
 6-FAM Blue Product Product
HEX/VIC Green Product Product
NED Yellow Product Product
ROX Red Ladder Product
LIZ Orange N/A Ladder
You can pool products by different colors and sizes, but each well must have an internal molecular weight (ladder) and the entire plate can only be a single dye set. For custom sized products, 6-FAM labeled primers are a good place to start because that label is the most robust (the brightest, and most stable) and can be made cheaply.

Getting Started

To discuss a project or acquire a quote, please contact us! For new clients, please set up an account (see New Lab or Customer Access below). All projects must be discussed before samples are submitted.

If you would like to initiate a project or get more information, please use the following contact information, and a member of our group will get in touch with you directly.

Next Generation Sequencing:

New Lab or Customer Access

We MUST have this information before we can proceed with your request.

Adding a new lab:

    • Name, address, phone number, UW NetID and email of the Principal Investigator (PI) or Primary scientific contact person.
    • Name, address, phone number, FAX number and email of he financial contact person.
    • Name, UW NetID, phone number and email of all individuals who will be using our service.
    • Payment information: For campus users this should be a direct charge number, e.g. a 144 or 133 prefixed account (please send the whole string of characters). For off campus users you can set up a PO or we can send the financial contact person a bill — your choice. Non-UW system users are charged an additional institutional overhead.

Adding a member to an existing lab:

    • Name of the PI whose lab you are joining.
    • Your name, UW NetID, phone number and email.

Sanger Sequencing Submission Guidelines

Please contact Samples can also be dropped off in Room 1259.

Submission Forms and Guidelines

Please check the service page guidelines for specific Submission Forms and Guidelines that need to be included with your samples.

Submitting Samples/ Shipping Instructions

After setting up a customer account, filling out submission form, and reviewing submission guidelines, you can now submit or send samples. *We require customers to submit electronic Submission Forms!*

In Person Submission

Please give advance notice of submission date and time so staff can be prepared to receive samples. Schedule a time for drop off with a staff member at Samples can be dropped off in Room 1259.

Shipping Submission

Please send the tracking information to:

Seal tubes and plates with the matching manufacture caps. Pad the samples to protect against the shipping abuse. Shipping on dry ice is ideal, but for most room temperature is okay. Next Morning delivery is not necessary.

If shipping samples from outside UWBC, ship via express shipping carrier on dry ice to the address below:

Sanger Sequencing

UW DNA Sequencing Facility

Attn: Sanger Sequencing

425 Henry Mall

1240 Biotechnology

Madison WI, 53706

Fragment Analysis Pricing

EXTERNAL RATES: Clients not affiliated with UW Madison or the University of Wisconsin system are charged a 55% surcharge for all labor and incidentals provided; prices are as listed above.  This surcharge is subject to change.

Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequencing Facility are intended for research purposes only. They are not intended nor certified for diagnostic or clinical use. Clinical services are provided through our collaboration with the UW Collaborative Genomics Core.