BLAST Results
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Formatting options
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These options control formatting of alignments in results pages. The default is HTML, but other formats (including plain text) are available. PSSM and PssmWithParameters are representations of Position Specific Scoring Matrices and are only available for PSI-BLAST. The Advanced view option allows the database descriptions to be sorted by various indices in a table.


Choose how to view alignments. The default "pairwise" view shows how each subject sequence aligns individually to the query sequence. The "query-anchored" view shows how all subject sequences align to the query sequence. For each view type, you can choose to show "identities" (matching residues) as letters or dots. more...

  • Graphical Overview: Graphical Overview: Show graph of similar sequence regions aligned to query. more...
  • NCBI-gi: Show NCBI gi identifiers.
  • CDS feature: Show annotated coding region and translation. more...
  • Masking Character: Display masked (filtered) sequence regions as lower-case or as specific letters (N for nucleotide, P for protein).
  • Masking Color: Display masked sequence regions in the given color.
  • Descriptions: Show short descriptions for up to the given number of sequences.
  • Alignments: Show alignments for up to the given number of sequences, in order of statistical significance.
  • Line lenghth: Number of letters to show on one line in an alignment.
Type common name, binomial, taxid, or group name. Only 20 top taxa will be shown.
Add organism

Show only sequences from the given organism.


Show only those sequences that match the given Entrez query. more...


Show only sequences with expect values in the given range. more...


Show only sequences with percent identity values in the given range.

  • Format for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST) program performs iterative searches with a protein query, in which sequences found in one round of search are used to build a custom score model for the next round. more...
  • Inclusion Threshold: This sets the statistical significance threshold for including a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.
Search Strategies
PSSM to restart search
The Download link provides BLAST output that may be used as input to another program. This includes parseable formats such as the tabular report or XML as well as the Search Strategy files read by the BLAST+ applications. More details on the parseable (XML, tabular, and ASN.1) reports can be found at

The following formats are offered under the Alignment section:
1). "Text". Non-HTML standard BLAST report.
2). "XML". XML report based upon the DTD at
3). "ASN.1". Alignment written out in Abstract Syntax Notation 1.
4). "JSON Seq-align". Alignment written out in JSON.
4). "Hit Table(text)". The tabular report as text.
5). "Hit Table(csv)". The tabular report ready for import into spread-sheet programs like Excel.
6). "XML2". New XML format described at
7). "JSON". New JSON format described at
8). "SAM". Sequence Alignment Map format.

XML2 and JSON can be downloaded either as one file per query (multiple-file) or one file for all queries (single-file). These formats are listed as Multiple-file XML2 (and JSON) or Single-file XML (and JSON).

The following report is offered under the Search Strategy section:
1). "ASN.1" Search Strategy. A record of the parameters, query, and database used in the search. This file can be used to start a stand-alone BLAST search, see


Job title: gnl|VecScreen|Example Database sequence

Interpretation of VecScreen Results

Your BLAST job specified more than one input sequence. This box lets you choose which input sequence to show BLAST results for.

JGVZM27F015 (Expires on 11-05 13:55 pm)
Query ID
gnl|VecScreen|Example Database sequence with vector contamination
Molecule type
nucleic acid
Query Length
Database Name
UniVec (build 10.0)
BLASTN 2.16.0+

Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
Search Parameters
Search parameter name
Search parameter value
Word size11
Expect value700
Hitlist size1000
Match/Mismatch scores1,-5
Low Complexity FilterYes
Filter string L;m;
Genetic Code1
Database parameter name
Database parameter value
Posted dateMar 20, 2017 3:58 PM
Number of letters1,269,791
Number of sequences6,093
Entrez query
Karlin-Altschul statistics
Results Statistics
Results Statistics parameter name
Results Statistics parameter value
Length adjustment 14
Effective length of query 1043
Effective length of database 1184489
Effective search space 1235422027
Effective search space used 1750000000000