My goal is to find specific genomic regions in a strain of interest in order to design specific primers.
To do that, I aligned multiple genomes closely related to the strain to see if there is any specificity. However I am having trouble interpreting Mauve data even with the user guide.
If I understood correctly the specific region are in white, right? Is there a way to get specific sequences in fasta format?
Here is what I obtained with Mauve: