Best tool to view sequence alignment?

[cacti]

I blasted my de novo assembled RNA-Seq transcriptome for a particular protein using tblastn, and found three transcripts similar to this protein. The best hit matches with a 50% percent identity (e value 1E-11).

I would like to create a figure displaying the sequence alignment with the greatest match to this protein, or all three transcripts that matched. I used ClustalW and Clustal Omega to align the sequences of my transcripts to the mRNA transcripts of the known protein I pulled off of NCBI but I don't like the aesthetics of the output and I'm not sure if this is the best way to do it.

Any suggestions on a nice way to succinctly display sequence homology between my transcripts and this protein?

[GenoMax]

Have you looked at tools here: http://www.ebi.ac.uk/Tools/msa/

You can also try MEGA (http://www.megasoftware.net/).

The 50% identity over how many AA? You may only be looking at a similar/identical domain.