Bio-Rad Quantity One 1-D Analysis Software - Manual (Page 208)

Chapter 9. Differential Displays and VNTRs
9-5
Fig. 9-3. Diagram of components of a DNA fragment.
In the Repeated Unit Size field, enter the size in base pairs of the repeated element
(e.g., if you are working with (CA) repeats, enter “2”).
Testing for Ambiguity
The number of repeats calculated by the software may not be a whole number, due to
the limitations of exact band size determination. Since the number of times an
element is repeated must be a whole number, the calculated value is rounded to the
nearest whole number.
In the dialog box, you have the option to “flag” those numbers
Select Yes after Test for ambiguity? to flag values that deviate from the nearest
whole number by a certain fraction. These values may warrant further review. In the
Ambiguous if rounded > field, specify how much the calculated value must deviate
from the nearest whole number for it to be flagged.
Finally, specify how to identify the ambiguous values using the Flag with * button or
the Leave Blank button.
When you have entered all the information in the dialog box, click on the Done
button. The number of tandem repeats will be displayed next to the bands. (Note that
if no standards have been defined on the gel, no numbers will be displayed.)
If the numbers have been concealed (e.g., by the Hide Overlays command), you can
redisplay them by selecting VNTR Display.
PCR Primer
Sequence between primer and VNTR
VNTR repeat unit