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The number of mutations in DNA is compared between two species. With the molecular clock we basically compare the amount of mutations that took place.
I think you could use them as clocks by looking the length of the telomere strand that cap the chromosomes. According to Wiki, during cell division, enzymes that duplicate DNA cannot continue their duplication all the way to the end of chromosomes. If cells divided without telomeres, they would lose the ends of their chromosomes, and the necessary information they contain. So the answer is basically by looking at the telomeres that cap the DNA strands. The telomere tries its hardest to keep the most amount of DNA intact when the DNA gets replicated and "cap" the DNA to keep them from degenerating. So if you looked at how long the telomere strand is, you can see how much more until the DNA become disheveled and fall apart.