In order to display the alignment of two paralogs:
Select the gene of interest.
Scroll to the bottom of the Gene Detail page.
Under "Homolog Display", you will find a "Homolog selection" dropbox.
Select "Paralogs / Orthologs."
Be sure that the box is checked off next to "Include current query gene ########## in this page for adding to gene cart."
Check off the box next to the paralog of interest.
Click "Add Selections To Gene Cart."
Under "Sequence Alignment," click "DNA" and uncheck "Color Alignments with Mview."
Click "Do Alignment."
The resulting page displays the alignment of the two sequences in ClustalW, a widely used alignment format.