NCBI Blast:1945

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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

Search Parameters
Search parameter name	Search parameter value
Program	blastn
Word size	28
Expect value	1e-150
Hitlist size	500
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	Oct 27, 2017 8:42 AM
Number of letters	155,491
Number of sequences	183
Entrez query	Includes: Terebellidae (taxid:32261) Excludes: Polycirrus (taxid:516039) None

Karlin-Altschul statistics
Params	Ungapped	Gapped
Lambda	1.34025	1.28
K	0.623212	0.46
H	1.13145	0.85

Results Statistics
Results Statistics parameter name	Results Statistics parameter value
Length adjustment	18
Effective length of query	640
Effective length of database	152197
Effective search space	97406080
Effective search space used	97406080

Sequences producing significant alignments:
Select for downloading or viewing reports	Description	Max score	Total score	Query cover	E value	Ident	Accession
1Select seq gb\|HM473490.1\|	Neoamphitrite robusta CMC01 voucher BIOUG<CAN>:BAMPOL0406 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial	551	551	90%	1e-158	83%	HM473490.1
2Select seq gb\|HQ023927.1\|	Thelepus sp. CMC01 voucher TBLABR-062 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial	534	534	97%	1e-153	82%	HQ023927.1

Alignments

Download GenBank Graphics Next Previous Descriptions

Neoamphitrite robusta CMC01 voucher BIOUG:BAMPOL0406 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial

Sequence ID: HM473490.1Length: 616Number of Matches: 1

Related Information

Range 1: 16 to 609GenBank Graphics Next Match Previous Match

Alignment statistics for match #1
Score	Expect	Identities	Gaps	Strand	Frame
551 bits(298)	1e-158()	496/595(83%)	2/595(0%)	Plus/Plus

Query  7    TGAGGAGGATTATTAGGAACCTCTATAAGACKACTCATCCGAATTGAACTTGGCCAACCT  66
            |||||||||||| |||||||||||||||||| ||| |||||  | ||| | || ||||| 
Sbjct  16   TGAGGAGGATTACTAGGAACCTCTATAAGACTACTAATCCGTGTCGAATTAGGACAACCC  75

Query  67   GGTGCTTTTCTTGGAAGAGACCAATTATATAACACTATTGTAACTGCTCACGGGCTACTT  126
            || || |||||||||||||| ||||| ||||||||  | || || || || ||||| || 
Sbjct  76   GGAGCCTTTCTTGGAAGAGATCAATTGTATAACACAGTAGTTACAGCCCATGGGCTGCTA  135

Query  127  ATAATCTTTTTTCTTGTTATACCTGTACTTATTGGAGGTTTTGGAAACTGATTAATCCCA  186
            ||||| || ||| | ||||||||  | ||||| ||||| ||||||||||| ||| |||||
Sbjct  136  ATAATTTTCTTTTTAGTTATACCAATCCTTATCGGAGGATTTGGAAACTGGTTACTCCCA  195

Query  187  CTTATATTAGGCGCACCAGACATAGCCTTCCCACGAATAAACAATATAAGGTTTTGACTA  246
            ||||||||||| |||||||| ||||| ||||||||||||||||||||||| || ||| ||
Sbjct  196  CTTATATTAGGAGCACCAGATATAGCATTCCCACGAATAAACAATATAAGATTCTGATTA  255

Query  247  CTCCCTCCTGCACTACTTCTTCTCCTC-GCTTCCGCAGCAGTTGAAAAAGGAGTAGGAAC  305
            || || |||||  |||| || || ||| || || || |||||||||||||| | ||| ||
Sbjct  256  CTGCCCCCTGCTTTACTCCTGCTACTCAGC-TCAGCCGCAGTTGAAAAAGGTGCAGGGAC  314

Query  306  TGGTTGGACTCTTTACCCCCCTTTAGCAAGAAATCTAGCACATGCTGGACCCTCAGTAGA  365
             || || ||| | ||||||||  || ||||||||||||||||||| || || || |||||
Sbjct  315  AGGGTGAACTGTATACCCCCCACTATCAAGAAATCTAGCACATGCCGGTCCATCTGTAGA  374

Query  366  CCTTGCTATTTTTTCACTACATTTAGCTGGTATTTCCTCAATTTTAGGAGCTATTAACTT  425
            |||||||||||| || || ||||||||||| || ||||| ||| ||||||| ||||| ||
Sbjct  375  CCTTGCTATTTTCTCTCTTCATTTAGCTGGAATCTCCTCTATTCTAGGAGCAATTAATTT  434

Query  426  TATCACAACAGTAGCAAATATACGATGAAAAGGACTACGTCTAGAACGAGTTCCTTTATT  485
            ||| || || ||||| ||||||||||||||||| ||||| ||||||||| |||| |||||
Sbjct  435  TATTACCACCGTAGCTAATATACGATGAAAAGGGCTACGCCTAGAACGAATTCCATTATT  494

Query  486  TGTTTGAGCTGTAGATATCACTGTTGTTCTACTACTTTTATCCCTCCCTGTATTAGCCGG  545
            ||||||||||||  |||||||||| || ||||| ||  |||| || || ||  |||| ||
Sbjct  495  TGTTTGAGCTGTTAATATCACTGTAGTCCTACTTCTACTATCTCTGCCAGTTCTAGCAGG  554

Query  546  AGCAATTACTATATTATTAACAGACCGAAATGTTAACACATCATTCTTTGACCCT  600
            ||||||||||||||||||||||||||||||||| |||||||| || |||||||||
Sbjct  555  AGCAATTACTATATTATTAACAGACCGAAATGTAAACACATCTTTTTTTGACCCT  609

Download GenBank Graphics Next Previous Descriptions

Thelepus sp. CMC01 voucher TBLABR-062 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial

Sequence ID: HQ023927.1Length: 658Number of Matches: 1

Related Information

Range 1: 20 to 658GenBank Graphics Next Match Previous Match

Alignment statistics for match #1
Score	Expect	Identities	Gaps	Strand	Frame
534 bits(289)	1e-153()	524/641(82%)	4/641(0%)	Plus/Plus

Query  1    GGCGTATGAGGAGGATTATTAGGAACCTCTATAAGACKACTCATCCGAATTGAACTTGGC  60
            ||| | ||||| || ||| |||| ||||||||||| | ||| |||||||| ||| | || 
Sbjct  20   GGCATCTGAGGGGGGTTACTAGGTACCTCTATAAGGCTACTAATCCGAATCGAATTAGGA  79

Query  61   CAACCTGGTGCTTTTCTTGGAAGAGACCAATTATATAACACTATTGTAACTGCTCACGGG  120
            |||||||| || || ||||||||||||||| |||| |||||  | || || || || |||
Sbjct  80   CAACCTGGAGCCTTCCTTGGAAGAGACCAACTATACAACACAGTAGTCACCGCCCATGGG  139

Query  121  CTACTTATAATCTTTTTTCTT-GTTATACCTGTACTTATTGGAGGTTTTGGAAACTGATT  179
            || || ||||| ||| ||||| ||||||||  | || ||||| || ||||||||||||||
Sbjct  140  CTGCTGATAAT-TTTCTTCTTAGTTATACCAATCCTAATTGGGGGGTTTGGAAACTGATT  198

Query  180  AATCCCACTTATATTAGGCGCACCAGACATAGCCTTCCCACGAATAAACAATATAAGGTT  239
            |||||||||||||||||| |||||||| ||||| |||||||||||||| ||||| || ||
Sbjct  199  AATCCCACTTATATTAGGAGCACCAGATATAGCATTCCCACGAATAAATAATATGAGATT  258

Query  240  TTGACTACTCCCTCCTGCACTACTTCTTCTCCTC-GCTTCCGCAGCAGTTGAAAAAGGAG  298
             || ||  | ||||||||  ||||  | || ||| || || || ||||||||||||||||
Sbjct  259  CTGGCTGTTACCTCCTGCTTTACTATTACTACTCAGC-TCTGCGGCAGTTGAAAAAGGAG  317

Query  299  TAGGAACTGGTTGGACTCTTTACCCCCCTTTAGCAAGAAATCTAGCACATGCTGGACCCT  358
             ||| || || || ||  | ||||| || ||| |||||||||||||||||||||| || |
Sbjct  318  CAGGGACAGGATGAACCGTATACCCACCATTATCAAGAAATCTAGCACATGCTGGCCCAT  377

Query  359  CAGTAGACCTTGCTATTTTTTCACTACATTTAGCTGGTATTTCCTCAATTTTAGGAGCTA  418
            | |||||||| |||||||| || || ||||||||||| |||||||| ||| |||| || |
Sbjct  378  CTGTAGACCTAGCTATTTTCTCTCTTCATTTAGCTGGAATTTCCTCTATTCTAGGCGCAA  437

Query  419  TTAACTTTATCACAACAGTAGCAAATATACGATGAAAAGGACTACGTCTAGAACGAGTTC  478
            | |||||||| || || ||||| ||||||||||||||||||||||||||||||||| | |
Sbjct  438  TCAACTTTATTACCACTGTAGCCAATATACGATGAAAAGGACTACGTCTAGAACGAATCC  497

Query  479  CTTTATTTGTTTGAGCTGTAGATATCACTGTTGTTCTACTACTTTTATCCCTCCCTGTAT  538
            | ||||||||||| |||||| ||||||| ||  | || || || |||||  | || || |
Sbjct  498  CATTATTTGTTTGGGCTGTAAATATCACCGTAATCCTTCTTCTGTTATCTTTACCAGTTT  557

Query  539  TAGCCGGAGCAATTACTATATTATTAACAGACCGAAATGTTAACACATCATTCTTTGACC  598
            |||| ||||| |||||||||||||||||||| ||||||||||| ||||| || |||||||
Sbjct  558  TAGCAGGAGCTATTACTATATTATTAACAGATCGAAATGTTAATACATCTTTTTTTGACC  617

Query  599  CTAGAGGAGGAGGAGACCCAATTTTATATCAACACTTATTT  639
            |    ||||| |||||||||||  |||| ||||| ||||||
Sbjct  618  CGGCTGGAGGCGGAGACCCAATCCTATACCAACATTTATTT  658

Job title: 1945

Graphic Summary

Distribution of the top 2 Blast Hits on 2 subject sequences [?]

Descriptions

Alignments