How to identify specific region using Mauve?

Question

[A_heath]

Hi all,

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:

[shenwei356]

see How to get the sequence differences between multiple bacterial genomes