In -m 2, or query anchored no identities, the query sequence, along with the aligned region of the database sequences, is kept as it is. Alignment gaps in the database sequence are shown as -, while alignment gaps in the query will be shown as insertions in the database sequence(s). We will be able to see what the aligned sequence is for a matching database entry. This display, however, obscures the differences.
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Figure 6.3.3 Pairwise alignment (-m 2) display of a standalone
blastn search result.
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Note:
A - The filter masked region in the query is shown as Ns
B - Deletions in the query are shown as insertions in database sequences (after the first t)
C - Insertions in the query are shown as deletions in the database sequences
D - partial alignments to the query