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Fragment analysis measures the size of DNA fragments by comparing the unknown fragment to DNA fragments with known lengths (the size standard). The size standard is combined with the sample of interest and co-injected into the capillary electrophoresis system. Common applications include: DNA fingerprinting, parentage analysis, microsatellites analysis, AFLP and ARISA.

To ensure that you obtain high quality data, it is essential that you have a robust PCR reaction that requires considerable dilution before running your samples on the AB3730 machine (e.g. 1 in 100). This will dilute out most of the excess PCR reagents, salt and potential contaminants in your samples. Excess reagents and salt can interfere with the electrokinetic injection of the machine and lower the quality of the data. Other contaminants, such as residual protein or detergents carried over from DNA extraction can adhere to the capillaries of the array thereby adversely reducing the quality and life span of the array. If considerable dilution of the sample is not possible we require our customers to perform a cleanup step (e.g. ethanol precipitation) prior to submission.

Very strong signals are difficult to analyse and can cause similar negative impacts on the array as other contaminants so it is suggested that a 1:20 to 1:150 dilution series is completed on a small number of samples to optimise prior to submitting large numbers of samples. If size ranges do not overlap within a dye colour PCR products may be pooled or multiplex PCR used.

Options for Fragment Analysis:

Size standards:
LIZ1200 – only available for plate submission (minimum sample number required). Please contact the Centre for further information.

Supported fluorescence labels:
6-FAM (blue)
VIC (green)
NED (yellow)
PET (red)
Primers with these labels are available from Life Technology.

Sample Submission Procedure

Please follow the sample submission guidelines carefully to ensure smooth processing and a quick turnaround time.

  • Create account/Login and submit samples online using the dnaLIMS system (refer to our LIMS User Guide). Please indicate the required size standard and the dye set(s) required in the submission process.

  • Prepare a 1-3ul aliquot of each sample in 1.5ml tubes or AB3730 compatible plates according to the service required. All samples are required to be diluted 10 fold or more, otherwise a cleanup step is required to remove excess dye and reagents.

  • It is important to select the correct “Service Request” option in the drop down menu, please select the Plate96- or Plate48- for plate submissions. 
    Screen Shot 2016-09-16 at 5.15.06 PM
  • Sample numbers for Fragment Analysis plate submissions are 40-48 for half plate (in odd columns) and 80-95 for full plate.
  • For individual samples, label tubes with the order number and consecutive numbering on the lid. For example, for order number 1234 with 3 samples, label tubes as “1234-1”, “1234-2” and “1234-3” (see below). Label plates with the order number or plate number.


  • Send samples by either courier or Express Post (Australia Post) to ensure prompt delivery. Please send samples and a copy of your submission confirmation to the address below. Alternatively, you can drop off your samples at our sample reception weekdays between 8am and 6pm.

  • You will receive an email when your results are available. You can access your results via dnaLIMS as per the LIMS user guide.


Courier Delivery Address:

The Ramaciotti Centre for Genomics
Upper Campus Store, Room LG018
E26, Bioscience South
LG018 Loading Dock,
Via Gate 11 Botany Street,
UNSW Sydney NSW 2052

Postal Address – Australia Post:
The Ramaciotti Centre for Genomics
Biological Sciences Building (D26)
UNSW Sydney, NSW 2052

In Person Drop Off:
Level 2
Biosciences South Building (E26)
Botany Street
UNSW Sydney, NSW 2052


Data Delivery:

Once sequencing is complete you will receive an email notification. You can access your data via an online account. The following files are available to download:

  • Raw trace (.ab1 file)
  • Raw, unfiltered basecall sequence (.seq file)
  • Text file of you sequence
  • FASTA Sequence
  • System QC score of the sequence

Quality Guarantee:

  • We include internal controls on all sequencing runs to ensure quality data
  • Batches of Core Prep include a pGem and M13 primer control reaction
  • All sequencing runs include a sequencing standard control
  • Free re-run service if results do not meet our quality standards

Note: Working days are Monday – Friday. Samples must be received by 12 noon to be included in the days processing list.

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