I have aligned two versions of the C. elegans genome together with Mauve. I am trying to understand how it works. Why are the blocks shown in different colours? Do I have two blocks of homology here? Can one block encompass more than one genome? What is the green line in the middle indicating? Are the red bars separating different sequences (chromosomes) in each genome?
I have exported the SNPs from this alignment and the file is empty except for the headers. Can I assume that the two genomes are exactly the same?