Diagonal Comparison Score

[Ne0tea]

Hi there!

Thanx for a such excellent software! It helps me a lot. I have a question about the value of diagonal alignment (self vs self). For me the self-comparison must be the best match, but in the Stainglass results the value is not always 100, nor is it always NA, it will probably be 80 90 which seems to depend on the similarity of the local regions. I'm very curious about how this part of the calculation works, and was hoping you could give some references, or if a handybook exists and I'm overlooking it.

Best regards, Yujie, Huang