BLAST is a tool for comparing sequences that relies on local sequence alignment. The Web BLAST (webBLAST) service is useful for quickly generating alignments for your sequences. This guide will help you align two protein sequences using the BLAST web service provided by NCBI.
Navigate to https://blast.ncbi.nlm.nih.gov/ in your web browser.
Hit the "Protein BLAST" button. The Standard Protein BLAST form will appear.
Select the "Align two or more sequences" checkbox.
Paste one of your sequences into the "Query Sequence" textbox and the other one into "Subject Sequence".
Hit the BLAST button at the bottom of the page. This will generate the pairwise alignment of your sequences, and you will be taken to the page that gives you the results.