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Format for	PSI-BLAST with inclusion threshold: [?] 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.

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Alignment Text XML ASN.1 JSON Seq-align Hit Table(text) Hit Table(csv) Multiple-file XML2 Single-file XML2 Multiple-file JSON Single-file JSON SAM	Search Strategies ASN.1	PSSM to restart search PSSM	[?]

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 https://www.ncbi.nlm.nih.gov/books/NBK153387/

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 https://www.ncbi.nlm.nih.gov/data_specs/dtd/NCBI_BlastOutput.dtd
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 ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf.
7). "JSON". New JSON format described at ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NEWXML/xml2.pdf.
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 https://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I455_BLAST_search_stra

Job title: E7Q0J:01365:11637

RID: VFT0UVZY014 (Expires on 09-13 21:41 pm)

Query ID: lcl|Query_191133; lcl|Query_191133
Description: E7Q0J:01365:11637
Molecule type: nucleic acid
Query Length: 157


Database Name: nr
Description: Nucleotide collection (nt) See details
Program: BLASTN 2.7.0+ Citation

Reference

Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.

Reference - database indexing

Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer (2008), "Database Indexing for Production MegaBLAST Searches", Bioinformatics 24:1757-1764.

Other reports: Search Summary [Distance tree of results]

Search Parameters
Search parameter name	Search parameter value
Program	blastn
Word size	28
Expect value	10
Hitlist size	100
Match/Mismatch scores	1,-2
Gapcosts	0,2.5
Low Complexity Filter	Yes
Filter string	L;m;
Genetic Code	1

Database
Database parameter name	Database parameter value
Posted date	Sep 10, 2017 7:25 AM
Number of letters	156,980,978,343
Number of sequences	44,402,363
Entrez query	none

Karlin-Altschul statistics
Params	Ungapped	Gapped
Lambda	1.33271	1.28
K	0.620991	0.46
H	1.12409	0.85

Results Statistics
Results Statistics parameter name	Results Statistics parameter value
Length adjustment	32
Effective length of query	125
Effective length of database	155560102727
Effective search space	19445012840875
Effective search space used	19445012840875

Graphic Summary

Distribution of the top 11 Blast Hits on 11 subject sequences [?]

The graphic is an overview of the database sequences aligned to the query sequence. These are represented horizontal bars colored coded by score and showing the extent of the alignment on the query sequence. Separate aligned regions on the same database sequence are connected by a thin grey line. Mousing over an alignment shows the database sequence title. Clicking an alignment displays a box with more details about the alignment and link to the sequence alignment itself in the Alignments section of the report.

Mouse over to see the title, click to show alignments

Color key for alignment scores

<40

40-50

50-80

80-200

>=200

Query

120

150

Descriptions

, Reading indexes 1-5, displaying indexes 1-5

Sequences producing significant alignments:

Select:All None Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reports	Description	Max score	Total score	Query cover	E value	Ident	Accession
1Select seq ref\|XM_011248941.2\|	PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X4, mRNA	272	272	100%	2e-69	98%	XM_011248941.2
2Select seq ref\|XR_879609.2\|	PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X3, misc_RNA	272	272	100%	2e-69	98%	XR_879609.2
3Select seq ref\|XM_011248940.2\|	PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X2, mRNA	272	272	100%	2e-69	98%	XM_011248940.2
4Select seq ref\|XM_011248939.2\|	PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X1, mRNA	272	272	100%	2e-69	98%	XM_011248939.2
5Select seq gb\|JN960751.1\|	Mus musculus targeted KO-first, conditional ready, lacZ-tagged mutant allele Cacnb1:tm1a(EUCOMM)Wtsi; transgenic	272	272	100%	2e-69	98%	JN960751.1
6Select seq dbj\|AK171194.1\|	Mus musculus NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630306P05 product:similar to ADP-ribosylation factor-like protein 8 [Homo sapiens], full insert sequence	272	272	100%	2e-69	98%	AK171194.1
7Select seq ref\|NM_207231.1\|	Mus musculus ADP-ribosylation factor-like 5C (Arl5c), mRNA	272	272	100%	2e-69	98%	NM_207231.1
8Select seq emb\|AL591209.17\|	Mouse DNA sequence from clone RP23-309H19 on chromosome 11, complete sequence	272	272	100%	2e-69	98%	AL591209.17
9Select seq ref\|XM_021175440.1\|	PREDICTED: Mus caroli ADP ribosylation factor like GTPase 5C (Arl5c), mRNA	244	244	100%	4e-61	95%	XM_021175440.1
10Select seq ref\|XM_021213782.1\|	PREDICTED: Mus pahari ADP ribosylation factor like GTPase 5C (Arl5c), mRNA	241	241	100%	5e-60	94%	XM_021213782.1
11Select seq dbj\|AK032519.1\|	Mus musculus adult male olfactory brain cDNA, RIKEN full-length enriched library, clone:6430578K18 product:unclassifiable, full insert sequence	106	106	40%	2e-19	97%	AK032519.1

Alignments

Download GenBank Graphics Next Previous Descriptions

PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X4, mRNA

Sequence ID: XM_011248941.2Length: 811Number of Matches: 1

Related Information

Range 1: 256 to 411GenBank Graphics Next Match Previous Match

Alignment statistics for match #1
Score	Expect	Identities	Gaps	Strand	Frame
272 bits(147)	2e-69()	155/158(98%)	3/158(1%)	Plus/Plus

Query  1    CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  256  CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  315

Query  61   GCGGGTCTGGCCCT-CCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  119
            |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  316  GCGGGTCTGGCCCTCCCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  375

Query  120  AGGCTGCTGACGCCCCGCCCGCCCCCAGCCTCCGGGAG  157
            |||||||||| |||||||||||||||||| ||||||||
Sbjct  376  AGGCTGCTGA-GCCCCGCCCGCCCCCAGC-TCCGGGAG  411

Download GenBank Graphics Next Previous Descriptions

PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X3, misc_RNA

Sequence ID: XR_879609.2Length: 1650Number of Matches: 1

Related Information

Range 1: 254 to 409GenBank Graphics Next Match Previous Match

Alignment statistics for match #1
Score	Expect	Identities	Gaps	Strand	Frame
272 bits(147)	2e-69()	155/158(98%)	3/158(1%)	Plus/Plus

Query  1    CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  254  CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  313

Query  61   GCGGGTCTGGCCCT-CCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  119
            |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  314  GCGGGTCTGGCCCTCCCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  373

Query  120  AGGCTGCTGACGCCCCGCCCGCCCCCAGCCTCCGGGAG  157
            |||||||||| |||||||||||||||||| ||||||||
Sbjct  374  AGGCTGCTGA-GCCCCGCCCGCCCCCAGC-TCCGGGAG  409

Download GenBank Graphics Next Previous Descriptions

PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X2, mRNA

Sequence ID: XM_011248940.2Length: 1209Number of Matches: 1

Related Information

Range 1: 214 to 369GenBank Graphics Next Match Previous Match

Alignment statistics for match #1
Score	Expect	Identities	Gaps	Strand	Frame
272 bits(147)	2e-69()	155/158(98%)	3/158(1%)	Plus/Plus

Query  1    CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  214  CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  273

Query  61   GCGGGTCTGGCCCT-CCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  119
            |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  274  GCGGGTCTGGCCCTCCCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  333

Query  120  AGGCTGCTGACGCCCCGCCCGCCCCCAGCCTCCGGGAG  157
            |||||||||| |||||||||||||||||| ||||||||
Sbjct  334  AGGCTGCTGA-GCCCCGCCCGCCCCCAGC-TCCGGGAG  369

Download GenBank Graphics Next Previous Descriptions

PREDICTED: Mus musculus ADP-ribosylation factor-like 5C (Arl5c), transcript variant X1, mRNA

Sequence ID: XM_011248939.2Length: 885Number of Matches: 1

Related Information

Range 1: 246 to 401GenBank Graphics Next Match Previous Match

Alignment statistics for match #1
Score	Expect	Identities	Gaps	Strand	Frame
272 bits(147)	2e-69()	155/158(98%)	3/158(1%)	Plus/Plus

Query  1    CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  246  CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  305

Query  61   GCGGGTCTGGCCCT-CCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  119
            |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  306  GCGGGTCTGGCCCTCCCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  365

Query  120  AGGCTGCTGACGCCCCGCCCGCCCCCAGCCTCCGGGAG  157
            |||||||||| |||||||||||||||||| ||||||||
Sbjct  366  AGGCTGCTGA-GCCCCGCCCGCCCCCAGC-TCCGGGAG  401

Download GenBank Graphics Next Previous Descriptions

Mus musculus targeted KO-first, conditional ready, lacZ-tagged mutant allele Cacnb1:tm1a(EUCOMM)Wtsi; transgenic

Sequence ID: JN960751.1Length: 40761Number of Matches: 1

Related Information

Range 1: 38720 to 38875GenBank Graphics Next Match Previous Match

Alignment statistics for match #1
Score	Expect	Identities	Gaps	Strand	Frame
272 bits(147)	2e-69()	155/158(98%)	3/158(1%)	Plus/Plus

Query  1      CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  60
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  38720  CCGGTGGGATTCCCAGGTCTCGAGGGTGACGCTTGGGGTTCCGCACATTTGATAGGAGCA  38779

Query  61     GCGGGTCTGGCCCT-CCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  119
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct  38780  GCGGGTCTGGCCCTCCCCCAGGCAGGGCTTTGAAGATTTGGGGCCAGACTCTGGTCCTGG  38839

Query  120    AGGCTGCTGACGCCCCGCCCGCCCCCAGCCTCCGGGAG  157
              |||||||||| |||||||||||||||||| ||||||||
Sbjct  38840  AGGCTGCTGA-GCCCCGCCCGCCCCCAGC-TCCGGGAG  38875