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Figure 5. A pairwise sequence alignment from a BLAST report.

Figure 5A pairwise sequence alignment from a BLAST report

The alignment is preceded by the sequence identifier, the full definition line, and the length of the matched sequence, in amino acids. Next comes the bit score (the raw score is in parentheses) and then the E-value. The following line contains information on the number of identical residues in this alignment (Identities), the number of conservative substitutions (Positives), and if applicable, the number of gaps in the alignment. Finally, the actual alignment is shown, with the query on top, and the database match is labeled as Sbjct, below. The numbers at left and right refer to the position in the amino acid sequence. One or more dashes (–) within a sequence indicate insertions or deletions. Amino acid residues in the query sequence that have been masked because of low complexity are replaced by Xs (see, for example, the fourth and last blocks). The line between the two sequences indicates the similarities between the sequences. If the query and the subject have the same amino acid at a given location, the residue itself is shown. Conservative substitutions, as judged by the substitution matrix, are indicated with +.

From: Chapter 16, The BLAST Sequence Analysis Tool

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The NCBI Handbook [Internet].
McEntyre J, Ostell J, editors.
Bethesda (MD): National Center for Biotechnology Information (US); 2002-.

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