Hi Telesto, and welcome to the fray.
First of all. There is no ONE result number. The algorithm compared about 650000 sequences with about 400 million bases in summary (Human Y is 60 million bases long, Chimp Y is about 20 million bases long). So compared sequences overlaped many times. I also got mismatch bases. Each sequence had (in my case) percentage identity, sequence length and number of mismatch bases. For example:
97.3% 4552 105
My guess is that the algorithm is similar to other matching algorithms (such as tree rings) ...
So they take one as the baseline and then compare the second one starting with matching both at one end and then shifting the second one along the first one base at a time, recording the degree of matching for each step.
The DNA likely has a lot of regions that were duplicated and then modified, so those would produce matches with lower percentages.
Enjoy
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