Alternatively, you can open a second browser window and copy sequences from one browser window into the alignment server in the other. I decided to use the default parameters for protein alignment and selected Perform Search. Here is another example involving dopamine receptor sequences. I just used default values for the gap penalty terms. The figure following the alignment is a dendrogram showing sequence similarities.
Horizontal distance indicates sequence similarity, and vertical lines show the order of alignment.
You can add your consensus sequence to the sequences in your Sequence Manager if you wish. The favorite choice among molecular biologists I have talked to is ClustalX . You can download your own copy of the latest version from the authors in Strasbourg , France. They have versions for Windows, Mac, and various flavors of Unix. Multiple sequence alignments can be used in many ways, and there are several very useful databases containing multiple sequence alignments.