6.3.7 Flat query-anchored, no identities and blunt ends

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6.3.7 Flat query-anchored, no identities and blunt ends

This alignment display, generated by -m 6, is similar to the alignment generated by -m 4 with one difference: partial alignments to the query are all extended or filled with dashes to generate blunt ends. See C in the figure below.

Image m6

Figure 6.1.3.5 Pairwise alignment (-m 6) display of a standalone blastn search result.


Figure 6.1.3.5 Pairwise alignment (-m 6) display of a standalone blastn search result.

Note:

A - Alignment gaps in the query

B - Alignment gaps in the database sequence

C - Dash files the regions with no alignment to the query

Tao Tao 2006-12-29