text: user10309: I have 7 RefSeq accessions which I performed multiple sequence aligment on it using CLUSTALO. These are the following:
  NC_026431.1
  NC_007363.1
  NC_004907.1
  NC_007377.1
  NC_007367.1
  NC_002016.1
  NC_026427.1
  
  I input the fasta sequence of those 7 accessions on CLUSTALO under this link. I get the result in either the msf format or clustal format with characters. The result looks like the following:
  CLUSTAL O(1.2.4) multiple sequence alignment
  
  
  NC_002016.1      -------AGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_007377.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_007367.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_004907.1      GGGGAATTCCAAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   60
  NC_026427.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
  NC_007363.1      -------AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_026431.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
                                                   ***** **********************
  
  I'm aware that the * symbols means a highly conserved region and that's exatcly what I'm looking for , however I need the highly conserved regions relative to a specific accession, namely NC_007367.1. I'm not sure how to do that. I'm also not sure what the - represents.
  
  user3541: You can opt for a similarity matrix as output (here is an example). The fact that you would like to judge conservation "relative to a given sequence", you can use this matrix to rank similarities of different sequences with respect to any of these sequences.
  I would advise visualizing these similarities, for example in terms of a heatmap, and seeing if anything stands out (with respect to your sequence of interest). And I would advise against selecting an arbitrary threshold (i.e. 90% or 95%), this would trigger questions based on the selection criteria of such a cutoff and this is understandable, such arbitrary cut-offs often do not mean much in biology.
  
original_text: 10309: <p>I have 7 <code>RefSeq</code> accessions which I performed <code>multiple sequence aligment</code> on it using <code>CLUSTALO</code>. These are the following:</p>
  <pre><code>NC_026431.1
  NC_007363.1
  NC_004907.1
  NC_007377.1
  NC_007367.1
  NC_002016.1
  NC_026427.1
  </code></pre>
  <p>I input the fasta sequence of those 7 accessions on <code>CLUSTALO</code> under this <a href="https://www.ebi.ac.uk/Tools/msa/clustalo/" rel="nofollow noreferrer">link</a>. I get the result in either the <code>msf</code> format or <code>clustal</code> format with characters. The result looks like the following:</p>
  <pre><code>CLUSTAL O(1.2.4) multiple sequence alignment
  
  
  NC_002016.1      -------AGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_007377.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_007367.1      -------AGCAAAAGCAGGTAGATATTGAAAGATGAGCCTTCTAACCGAGGTCGAAACGT   53
  NC_004907.1      GGGGAATTCCAAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGT   60
  NC_026427.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
  NC_007363.1      -------AGCAAAAGCAGGTAGATATTGAAAAATGAGTCTTCTAACCGAGGTCGAAACGT   53
  NC_026431.1      --------------------------------ATGAGTCTTCTAACCGAGGTCGAAACGT   28
                                                   ***** **********************
  </code></pre>
  <p>I'm aware that the <code>*</code> symbols means a highly conserved region and that's exatcly what I'm looking for , however I need the highly conserved regions relative to a specific accession, namely <code>NC_007367.1</code>. I'm not sure how to do that. I'm also not sure what the <code>-</code> represents.</p>
   3541: <p>You can opt for a similarity matrix as output (<a href="https://biology.stackexchange.com/questions/46049/how-to-interpret-percent-identity-matrix-created-by-clustal-omega">here is an example</a>). The fact that you would like to judge conservation &quot;relative to a given sequence&quot;, you can use this matrix to rank similarities of different sequences with respect to any of these sequences.</p>
  <p>I would advise visualizing these similarities, for example in terms of a heatmap, and seeing if anything stands out (with respect to your sequence of interest). And I would advise against selecting an arbitrary threshold (i.e. 90% or 95%), this would trigger questions based on the selection criteria of such a cutoff and this is understandable, such arbitrary cut-offs often do not mean much in biology.</p>
  