Ok, what I make of that tool is that it is used to just align TWO sequences, so naturally it just ignores the rest. Adding to @Ram 's answer, you want to create a database for your fasta using makeblastdb (is as easy as makeblastdb -in file.fa -dbtype nucl -out database), once you have your database set, you can go on and run blastn (blastn -query file.fa -db database -out file.out -outfmt 6). Now, it depends on how you want your output (option -outfmt), I recommend reading more. This will give you a text output that can be more easily searched than using webtools. Hope it helps :)