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Region of differences using Mauve

I want to find region of difference (RDs) in my bacterial genomes. I came across on literature suggesting that Mauve output was used to extract genome regions differentially present among the strains.What does this mean and how to do it? I am able to do mauve alignment but what after that. I am beginner in bioinformatics so can anyone help me in finding this.

genome sequencing alignment

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