Analysis of hits. Hits can be viewed in A) HTML output, showing all hits listed in order of descending score, followed by a pairwise Needle alignment of the query and target sequence. The Info hyperlink links to the NCBI entry for the target sequence, and the score hyperlink takes the user to the Needle alignment. B) The Hits Manger window, which allows the user to sort hits and view pairwise or multiple alignments, or view selected sequences in FASTA format. A global alignment is shown between the query sequence and the top scoring new hit.