Clustalw will mark out your sequence of interest alone in the aligned sequences. You are rigtht, that in clustalw you have to feed all the sequences of interest as a single file in a FASTA format. But one of the parameters will ask you for your sequence of interest and that sequence will then appear in reverse shading. You can also specify the consensus blocks and the percent of identity or similarity. I pointed that software out to you, since you asked for an alignment tool and clustalw is one of the best alignment tools in the market. I think it uses the popular near neighbourhood algorithm.
But in case you just want a more complete identity search, you should try out FASTA and point out your database to it. I believe that FASTA is more global than BLAST (Basic local alignment search tool) which is more localized.
I you want to have whole sequences aligned but in pairs, you can try out GAP which is one of the applications in the wisconsin package. GAP will give you a very good identity and similarity scores.
best of luck