I tried to make sense of your output, but failed. Probably the fourth column of the second row was typoed, and should read 108. But I've no idea why the first three output lines all have the same value in the first column.

However, to count, that's trivial. Make a hash key from the primary key of your data, and just, uhm, count. You know, add one each time you see the same thing:

    $counts{$key,$start,$end}++;
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