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I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used:

progressiveMauve --output=outputfile --disable-backbone chl189.fas chl17415.fas chl50083.fas chlTAMOak81.fas

At the end, the resulting aligned genomes are not of the same length. What could be the potential problems?

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This is a global alignment. Which is why im surprised that they aren't all the same length after alignment? Also, while analysing the subsequent genomes, I noticed that some region which were present in only 2/4 genomes were misaligned in the end result. How do I proceed troubleshooting this problem?

I am a student and new to this field, could you please tell me how to proceed with manually checking to see whats wrong?

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