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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?

enter image description here

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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I’ve seen cases like this. For me, there were plasmids at end that didn’t get aligned.

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    $\begingroup$ Your answer could be improved with additional supporting information. Please edit to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center. $\endgroup$
    – Community Bot
    Mar 14, 2022 at 20:40
  • $\begingroup$ Hi @SethCommichaux please do remember to provide supporting information for your answer, i.e. not simply to confirm the OP's observation but offer a solution. $\endgroup$
    – M__
    Sep 6, 2023 at 14:41

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