Clustal Omega on uniprot

Question

[kodo64]

Hi,

Iv got two alignments (two sets of alignments (A and B)) that I have generated using clustal omega on uniport. I have selected the similarity check box to find conserved amino acid sequences between these two alignment sets. Now I want to compare these two alignment sets so to find a region that is not conserved in A but conserved in alignment set B and vice versa. Is there a way of doing this besides a manual approach. I.e. I want to find a difference in the pattern of conservation between these alignment sets if there is one.

thanks