Mauve Alignment Viewer: similarity profile

[Tiglat12]

Mauve Alignment Viewer: similarity profile
Hi,
I hope this is not too obvious a question, but so far I was just not able to solve it myself:
In the Mauve Alignment Viewer, one sees these colored blocks and inside each block, Mauve draws a similarity profile of the genome sequence.

I don't understand what this similarity profile actually shows: I have a reference genome, and one genome aligned to it. Why is there a similarity profile shown for both genomes (is the similarity shown of genome 1 to 2 and vice versa?), and more importantly, why do they look DIFFERENT in homolog blocks? Shouldn't they be exactly equal in homologs?

Any help with this is greatly appreciated!

[jnfass]

Are you sure the plot is different for aligned sequence? Wherever you're looking, if you left-click on a location in one or the other sequence, the other sequence(s) will shift to line up with the location you've clicked. You'll probably see more similar profiles, at least locally speaking, in both or all of your sequences.

The plot is something related to entropy, IIRC (don't take my word on that).