The traditional alignment display format, generated by -m 0, is Pairwise. In this format, the query is aligned to matching database sequences one at a time. The HSPs from the same database sequence are sorted in descending significance and listed together. Database sequences with alignment(s) to the query are listed in descending significance and the upper limit of database sequences shown is determined by the -b parameter.
For nucleotide alignment, as shown below, the midline of the alignment display uses pipe symbol (|) to indicate identity and space to indicate mismatch. For protein alignment, the midline will contain letter, +, and space representing identity, positive substitution, and negative substitution, respectively. Which pair up in the alignment to get the + will depend on the protein scoring matrix used.
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Figure 6.3.1 Alignment (-m 0) display of a standalone blastn
search result.
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Note:
A - defline of the matching database sequence and its length
B - alignment statistics and orientation for this HSP
C - gaps in the alignment
D - filter masked low complexity region (with -F T) E - mismatch in the alignment