I am working on some closely related bacterial species (complete genomes from NCBI). I would like to extract the sequence differences between them. To be more specific, I want to find unique sequences (50 -100 nts) in each of the bacterial species (n=6) under my study. I found many other related posts suggesting tools like Mauve, Mummer, Artemis ACT etc.. and I tried all of them. Mauve gave pretty good results, but when I extracted the sequences in the range as suggested to be different from other genomes under comparison, and performed blast, I got multiple hits to other bacterial species.
Thanks in advance.