User guide

Differential Display and VNTRs

18-5

In the text box next to the Flanking Region Size prompt, enter the size (in base

pairs or other repeated units) of the part of the fragment that does not include

any repeated elements. This would include primer length and the length of

any sequences that fall between the end of the primer region and the

beginning of the stretch of repeats.

Fig. 18-4. Diagram of components of a DNA fragment.

Next to the Repeated Unit Size prompt, 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 that deviate

from the nearest whole number. These values may warrant further review.

The Test for ambiguity? prompt allows you to ﬂag values that deviate from a

whole number. If you select Yes, you must specify what constitutes ambiguity.

Next to the “Ambiguous if rounded >” prompt, specify how much the

calculated value must deviate from the nearest whole number for it to be

ﬂagged.

PCR Primer

Sequence between primer and VNTR

VNTR repeat unit