BLAST isn't appropriate for multiple sequence alignment.
BLAST generates pairwise alignments. Furthermore, the aligning regions shown in a BLAST report only include subsets of the hit sequences.
To create multiple sequence alignment of hits you want to:
- run blast
- extract the hit sequences
- perform multiple-sequence-alignment (e.g., using MAFFT)
Extracting hit sequences can be done using the command-line. Check the docs for
If you prefer a point-and-click interface, you can also do this using my lab's SequenceServer BLAST software by simply selecting the hits that you want to retain, and in the Download section, clicking "FASTA of selected hits". Or if you want all of them, click "FASTA of all hits".