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I have two genomes with high similarity. But I found out that one genome has a longer sequence of about 200 kbp. I try to align the sequence with Mauve. How can I extract this unique 200 kbp?

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    $\begingroup$ How is this region demarcated? Between certain features? A separate contig? How would you want the region identified for any such code to retrieve it? $\endgroup$
    – Joe Healey
    Dec 2, 2021 at 11:33

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I've found the answer.

I've aligned these genomes (gbk files) with Mauve Contig Mover, and then I exported the Gap File into a csv file. Then I used python pandas to analyze the region that is unique to each strand from the csv file.

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