Region

OK, so you have DNA sequences from related species which are somewhere diverse, somewhere are identical. For example the region coding for active site will be probably conserved, while some loops on surface of the protein will be divergent. Both on DNA and amino acid level. You can ...

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... amino acids are identical, the DNA sequences are probably also very similar (but does not have to be identical!), thus primer annealing to this region may be used for several species. It can be used either as unspecific primer for known species or it can be used even for so far unsequenced species.

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Why would the identical amino acids region of certain species be used as a basis for a primer design? I know they share homology and are very conserved but why is it used as a primer?

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... band mass variation. When you are using 12 pairs of primers, they are targeting 24 different binding loci. Each forward and reverse pair spans a region that has a variable number of base pairs between individuals, but a given individual will have a definite base distance between each pair of ...

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I realise that each of the 12 primer pairs bind to a different region of human genome; the VNTR's within each region, and that is how 12 distinct bands can be detected after PCR. But what i don't know is why the exact same primers that target the same location ...

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