Viewing alignments
     
Alignments can be viewed, for example, using SeaView. The program color codes residues by type for easy sensemaking, and also allows you to manually edit alignments. SeaView's website provides executables for all major platforms.
   
To delete a couple of sequences, click on the name in the sequence name column, and choose "Delete sequence(s)" from the "Edit" menu. You can use the feature to get rid of alternative splices, fragments, and otherwise suspicious sequences.
   
To edit a sequence, tick "Allow seq. editing" from the "Props" menu, and type away in the alignment field itself. You can use it to fix small mistakes that the alignment program sometimes makes.
   
You can use the same editing feature to replace suspicious regions with an "XXXXX" stretch, for example. Though it would be better to go and see if a more complete version of the sequence from the same or closely related species can be found elsewhere on the internet.
   
There is a lot more stuff that SeaView can do - you are invited to explore on the SeaView's own help page.
   
Alternatively, Wikipedia lists many other programs that can be used to view and edit sequence alignments.
   
The alignments themselves can be found in the downloadable work directory on each results page that Cube produces. If you would like to try hand at making your own alignments, we suggest you download a program called MUSCLE, put the execultable in the same folder where you placed SeaView, and then follow the steps illustrated below: