Although repeats are considered junk , they do have their uses. Generally, genes are no good for fingerprinting. Although most genes have several versions or alleles, most are not very common. Any changes in genes will probably result a change in the function of the gene product, so is almost always selected against. Analysis of 10 or more VNTRs is usually enough for a fingerprint.
Repeats also have another interesting consequence for sequencing.
The chemical reactions used to read off the bases are stalled by highly repetitive regions. The situation is worse in the case of the privately funded Celera Genomics sequencing program. Celera uses a shotgun sequencing technique. Overlaps between the ends of these sequences are looked for so that they can be fitted together like a jigsaw. The nature of this technique is that there will be gaps where a section hasn t been successfully sequenced.