How to find conserved sequences relative to a specific accession

Question

[alexmondaini]

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.

[GenoMax]

- represents gaps. You could simply edit this alignment file and move the accession you need to the top. Clustal omega does not seem to allow one sequence to be used as a reference. Moving the sequence you want to the top of the input file will also be easier as you run the alignment.

[alexmondaini]

Ok, if I move the desired sequence to the top means this sequence is the "anchor/consensus" and all the rest is relative to it ?

[GenoMax]

No that is just a visual representation. You will need to use a different program if you want to designate a particular sequence as reference. I think MAFTT or MEGA11 allow you to do that.