I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?

To identify unique regions in your aligned bacterial genomes using the Mauve plugin in Geneious, follow these enhanced steps based on the provided research articles:

By integrating these steps, you can effectively identify and extract unique genomic regions without needing coding expertise, leveraging the powerful features of Geneious and related tools.

Reference

[1] Darling, A., Mau, B., & Perna, N. (2010). progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLoS ONE, 5.

[2] Rissman, A. I., Mau, B., Biehl, B. S., Darling, A., Glasner, J., & Perna, N. (2009). Reordering contigs of draft genomes using the Mauve Aligner. Bioinformatics, 25, 2071 - 2073.

[3] Ågren, J., Sundström, A., Håfström, T., & Segerman, B. (2012). Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups. PLoS ONE, 7.

[4] Ryoo, S., Lee, J., Oh, J. Y., Kim, B. K., Kim, Y., Kim, J. H., Shin, C., & Lee, S. H. (2018). Comparing Two Mycobacterium tuberculosis Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments. Tuberculosis and Respiratory Diseases, 81, 216 - 221.