when using a Kiusalas perforation gauge .....

Given the gauge uses dots I had always assumed they are aligned with the perforations.

The specialty gauge measures the distance between the center of one perf hole to the next, in thousandths of an inch. The gauge has the proper spacing between perforations and the dots are the same diameter as the perf hole size. That said, the correct use of the gauge is to place the dots in the perf holes, rather than on the teeth. Make all measurements under magnification and the match should be the same along the entire length of the side being measured.