After performing multiple sequence alignment, how do i analyze the conserved motifs and domains?

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Brian Thomas Foley

The ConSurf server maps the rate of evolution of each codon or amino acid onto the 3D structure of the protein.

https://consurf.tau.ac.il/consurf_index.php

Jobin Thomas

Since you have used Clustal omega you can upload your data to UGENE and calculate for the conserved domains and other parameters also.

Regards