The flat query-anchored alignment format. In this format, all sequences above the E value threshold are aligned beneath the query. In the "with identity" format, identical residues are shown as dots. Gaps in the alignment are shown as dashes. Using this format it is easy to visualize the extent to which specific residues are conserved among BLAST hits. In this example, the E value threshold was set very stringently and the four BLAST sequences that were better than threshold are aligned beneath the query (blast_tmp). The first three sequences align starting at position 4 of the query, while the fourth aligns starting at position 106. Identities shared by all four sequences can be readily spotted.
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