When piecing together a puzzle, it can be beneficial to have some reference point. If the only guide you had to piece the puzzle together was how the pieces themselves fit together and there were several pieces that fit the same other piece, it would be nearly impossible to put the puzzle together correctly. Even if you did put it together right, it would be challenging to be sure that was what you had done.
Sequence Tagged Sites can help give more perspective to the puzzle so it is less of a chance effort. They range from 200 to 500 base pairs long and have a known sequence. This known sequence can act as a guide when analyzing the DNA fragments and trying to find how they all go back together.
The Human Genome Project and Cancer 