Answers.Body: <p>I’ve seen cases like this. For me, there were plasmids at end that didn’t get aligned.</p>
  
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Answers.Text: 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.
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Body: <p>I am aligning 4 genomes of <em>Psuedomonas chlororaphis</em> using progressive mauve software. Command used:</p>
  <pre><code>progressiveMauve --output=outputfile --disable-backbone chl189.fas chl17415.fas chl50083.fas chlTAMOak81.fas
  </code></pre>
  <p>At the end, the resulting aligned genomes are not of the same length. What could be the potential problems?</p>
  <p><a href="https://i.sstatic.net/sfV99.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/sfV99.png" alt="enter image description here" /></a></p>
  <p>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?</p>
  <p>I am a student and new to this field, could you please tell me how to proceed with manually checking to see whats wrong?</p>
  
Tags: <phylogenetics><genome><mauve>
Title: What does it mean if aligned genomes are not of the same length?
ThreadText: # What does it mean if aligned genomes are not of the same length?
  
  (Asked by: username_0 on 2020-05-01)
  
  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](https://i.sstatic.net/sfV99.png)](https://i.sstatic.net/sfV99.png)
  
  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?
  
  **Tags:** phylogenetics, genome, mauve
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-03-14. Score: 1
  
  I’ve seen cases like this. For me, there were plasmids at end that didn’t get aligned.
  
  > **Comments:**
  > **username_3**: 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](/help/how-to-answer).  
  > **username_2**: Hi @username_1 please do remember to provide supporting information for your answer, i.e. not simply to confirm the OP's observation but offer a solution.  
  
  ---
  
  