This format, generated using -m 3, is similar to -m 1, with only one difference - all the alignment will be flattened out. The alignment gaps in the query will be presented as they are and there will be no insertion marks (\). The alignment may be difficult to read if the query is aligned to a divergent group of sequences with gaps in many different positions.
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Figure 6.3.4 Pairwise alignment (-m 3) display of a standalone
blastn search result.
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Note:
A - Deletions in the query are shown as they are
B - The filter masked region in the query is shown as Ns, sequences aligned to it are shown as they are
C - Insertions in the query are shown as deletions in the database sequences
D - Sequences different from the query are shown as they are