At the top of the results page is a summary of your query, along with a link to go back to edit your search or save it to your My NCBI account.
In a box on the top right side of the results, you can filter by organism or by minimum percent identity, expect value, or query sequence coverage.
If you performed a PSI-BLAST, you will also have the option to set parameters for the next iteration of the PSI-BLAST.
Just above the main results section are three links (Other reports) to view a distance tree of results, multiple alignment, or a dynamic graphic view in NCBI's MSA Viewer.
The main section of the BLAST results page is organized by tabs
Additionally, if you have some low similarity matches, there will be a cutoff line in the listed results showing where the expect value (E-value) falls below the threshold.
Note: even if some matches fall below the E-value cutoff, you can still use them for PSI-BLAST iterations or for multiple sequence alignment. This is especially true if you are searching for orthologs to a conserved domain or fold, which may have low sequence identity but high functional or structural similarity.
On your BLAST results page, you can download the BLAST alignment in many formats (FASTA, Hit table, Text, XML, ASN.1, csv)
If want to run your own multiple sequence alignment from a subset of your results: