Your option is to change the font size to a very small size so that the alignment diagonals look visible from the dots arrangement, that's what happens in dot plotter programs like EMBOSS, depending on the length of the sequences the viewing of the alignment can be adjusted by increasing/decreasing the font size and you have to deactivate word-wrapping as well just in case..
in reply to Dot-plot help please
Another option, if you can use any of the modules in the Bio::Align space...
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