Skip to main content
Toggle navigation
Species
Citrus clementina
Citrus ichangensis
Citrus sinensis
Citrus reticulata
Citrus maxima
Citrus medica
Poncirus trifoliata
Atalantia buxifolia
Ca. Liberibacter asiaticus
Ca. Liberibacter africanus
Ca. Liberibacter americanus
others
Data
Data Overview
Downloads
Data Submission
Marker Types
BIMS and Field Book
Publication Datasets
Trait Abbreviations
Search
Gene and Transcript Search
Germplasm Search
Map Search
Marker Search
Publication Search
QTL Search
Sequence Search
Cross Site Search
MegaSearch
Trait Descriptor Search
Trait Search
Tools
BLAST+
CitrusCyc
JBrowse
BIMS
MapViewer
Synteny Viewer
General
About CGD
Disclaimer
Mailing List
Presentations
Work Completed
Work In Progress
Steering Committee
Help
Contact Us
User Manual
Search
Login
Nucleotide to Nucleotide BLAST (blastn)
Request a New BLAST
Enter
Nucleotide
Query Sequence
Enter one or more queries in the top text box or use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. In both cases, the data must be in
FASTA format
.
Show an Example Sequence
Enter FASTA sequence(s)
Or upload your own query FASTA:
Upload
The file should be a plain-text FASTA (.fasta, .fna, .fa, .fas) file. In other words, it cannot have formatting as is the case with MS Word (.doc, .docx) or Rich Text Format (.rtf). It cannot be greater than
2048MB
in size.
Don't forget to press the Upload button before attempting to submit your BLAST.
Choose Search Target
Choose from one of the
nucleotide
BLAST databases listed below.
Nucleotide
BLAST Databases:
SELECT a Dataset
C. clementina v0.9 genome (JGI) CDS
C. clementina v0.9 genome (JGI) scaffolds
C. clementina v0.9 genome (JGI) transcripts
C. clementina v1.0 genome (JGI) CDS
C. clementina v1.0 genome (JGI) scaffolds
C. clementina v1.0 genome (JGI) transcripts
C. sinensis v1.0 genome (JGI) CDS
C. sinensis v1.0 genome (JGI) scaffolds
C. sinensis v1.0 genome (JGI) transcripts
C. sinensis v1.1 genome (JGI) CDS
C. sinensis v1.1 genome (JGI) scaffolds
C. sinensis v1.1 genome (JGI) transcripts
C. sinensis v2.0 genome (HZAU) CDS
C. sinensis v2.0 genome (HZAU) scaffolds
C. sinensis v2.0 genome (HZAU) transcripts
C. sinensis CGD RefTrans v1
C. clementina unigene v1.0 contigs
C. sinensis unigene v1.0 contigs
P. trifoliata unigene v1.0 contigs
C. clementina NCBI ESTs
C. reticulata NCBI ESTs
C. sinensis NCBI ESTs
C. trifoliata NCBI ESTs
Ca. L. asiaticus A4 CDS
Ca. L. asiaticus A4 genome
Ca. L. asiaticus Ishi-1 CDS
Ca. L. asiaticus Ishi-1 genome
Ca. L. asiaticus JXGC CDS
Ca. L. asiaticus JXGC genome
Ca. L. asiaticus gxpsy CDS
Ca. L. asiaticus gxpsy genome
Ca. L. asiaticus psy62 CDS
Ca. L. asiaticus psy62 genome
Ca. L. asiaticus-all strains CDS
Ca. L. africanus PTSAPSY CDS
Ca. L. africanus PTSAPSY genome
Ca. L. americanus Sao Paulo CDS
Ca. L. americanus Sao Paulo genome
Ca. L. solanacearum CLso-ZC1 CDS
Ca. L. solanacearum CLso-ZC1 genome
Liberibacter-all strains 16S rRNA
Liberibacter-all strains CDS
L. crescens BT-0 CDS
L. crescens BT-0 genome
L. crescens BT-1 CDS
L. crescens BT-1 genome
L. crescens-all strains CDS
Atalantia buxifolia v1.0 genome (HZAU) CDS
Atalantia buxifolia v1.0 genome (HZAU) scaffolds
Atalantia buxifolia v1.0 genome (HZAU) transcripts
C. ichangensis v1.0 genome (HZAU) CDS
C. ichangensis v1.0 genome (HZAU) scaffolds
C. ichangensis v1.0 genome (HZAU) transcripts
C. maxima v1.0 genome (HZAU) CDS
C. maxima v1.0 genome (HZAU) scaffolds
C. maxima v1.0 genome (HZAU) transcripts
C. medica v1.0 genome (HZAU) CDS
C. medica v1.0 genome (HZAU) scaffolds
C. medica v1.0 genome (HZAU) transcripts
C. reticulata v1.0 genome (HZAU) CDS
C. reticulata v1.0 genome (HZAU) scaffolds
C. reticulata v1.0 genome (HZAU) transcripts
Advanced Options
General parameters
Max target sequences:
10
50
100
250
500
1000
5000
10000
20000
e-Value (Expected Threshold)
Expected number of chance matches in a random model. This number should be give in a decimal format.
More Information
|
Expect value video tutorial
Word size:
7
11
15
16
20
24
28
32
48
64
128
256
Max matches in a query range
Scoring parameters
Match/Mismatch Scores:
1,-2
1,-3
1,-4
2,-3
4,-5
1,-1
Gap Costs:
Existence: 5 Extension: 2
Existence: 2 Extension: 2
Existence: 1 Extension: 2
Existence: 0 Extension: 2
Existence: 3 Extension: 1
Existence: 2 Extension: 1
Existence: 1 Extension: 1
BLAST