Why are the primers used to amplify the d1s80 region complementary to unique sequence outside the actual repeats, instead of using primers that would be directly complementary to the actual repeats?

Explanation:

D1S80 is a VNTR locus (a locus with a variable number of tandem repeats). It's a widely-used polymorphic locus used to differentiate individuals. At the moment 29 alleles for this locus are described, with a length ranging between 200bp to 800bp, depending on how many repetitions of a 16 bp sequence are there.

If primers complementary to the 16bp repeats were used, they could bind any of the repetitions, so in an agarose gel you would see a smear because after the PCR you would amplify in each cycle a product of different length, depending on where the primers bound to the template.

The goal is to detect the polymorphism between individuals, which depends on the length of the sequence that contains the tandem repeats. To obtain only one PCR product that contains all the repeats in the allele, flanking primers are used.

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