Skip to main content
You are here
Nucleotide to Nucleotide BLAST (blastn)
Request a New BLAST
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
Show an Example Sequence
Enter FASTA sequence(s)
Enter query sequence(s) in the text area.
Or upload your own query FASTA:
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
Don't forget to press the Upload button before attempting to submit your BLAST.
Choose Search Target
Choose from one of the
BLAST databases listed below.
L. gibba Whole Genome Scaffolds 1.0
TAIR 10 cDNA
Select a Dataset
Max target sequences:
Select the maximum number of unique target sequences per query sequence to show results for.
e-Value (Expected Threshold)
Expected number of chance matches in a random model. This number should be give in a decimal format.
Expect value video tutorial
The length of the seed that initiates an alignment
Max matches in a query range
Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.
Reward and penalty for matching and mismatching bases.
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
Cost to create and extend a gap in an alignment. Linear costs are available only with megablast and are determined by the match/mismatch scores.