Once your alignments are completed the next step is to analyze them.
a. How do the alignments look?
i. Are there large gaps in the sequence? If so do these gaps contain only one or a small number of nucleotides or amino acids on either side? If yes then this is an indication that the alignment is not good or the sequences are not very closely related to one another.
ii. Are there a lot of identical or similar nucleotides or amino acids? If so this is an indication that the genes/proteins are closely related.
b. If running the program were all that was required it would be easy to replace you and automate the process. Remember that one of your main assets as a bioinformatician is placing data in context.
c. Take a look at your alignments and ask yourself do these make sense? What looks "weird'? Can I change something to make the alignment better?
i. You should expect that the alignments of your TBP sequences will look similar, same for the TFB sequences. But, what about if you aligned the TBP and TFB sequences together?
ii. The more you practice the better you will get at spotting something weird