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)

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 2MB 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:

Advanced Options

General parameters

Max target sequences:

Select the maximum number of unique target sequences per query sequence to show results for.

Max HSP Alignments

Select the maximum number of HSP alignments per target 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. More Information | Expect value video tutorial

Word size:

The length of the seed that initiates an alignment

Scoring parameters

Match/Mismatch Scores:

Reward and penalty for matching and mismatching bases.

Gap Costs:

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.

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SIMRbase Genome

Nucleotide to Nucleotide BLAST (blastn)

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SIMRbase Genome

Nucleotide to Nucleotide BLAST (blastn)

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