For my project I'm comparing the genomes of an outbreak strain with strains from it's own species. My goal is to identify possible unique regions in the outbreak strain. I use Mauve to compare the genomes.
As I read the Mauve official website, the .islands file (among the output from Mauve) seems to be the most interesting. It describes the regions where one or more genomes have an unique region where the others do not. However, I'm still having trouble fully understanding the file. The makers of Mauve, Darling lab, explains the file in the following way: link (Scroll down to the "The Islands file" paragraph).
My question is this: How can one derive unique regions from a file like this? It describes where two genomes align but that means it is, per definition, not unique right? Is it something I'm missing or simply not understanding?