For instructions and hints, click here

Choose program to use and database to search:

Program Database

Enter sequence below in FASTA format

Or load it from disk

Set subsequence: From To

The query sequence is filtered for low complexity regions by default.
Filter Low complexity Mask for lookup table only

Expect Matrix Perform ungapped alignment

Query Genetic Codes (blastx only)

Database Genetic Codes (tblast[nx] only)

Frame shift penalty for blastx

Other advanced options:

Graphical Overview Alignment view
Descriptions Alignments Color schema


For your convenience we have pulled together all published chloroplast genomes, and offer a web interface to Blast against those sequences. Click here to get started.

The databases are available in a "genome", "nt",  and an "aa" version. The "genome" is the entire nucleotide sequence of each genome. The "nt" version is the nucleotide sequence that corresponds to identified ORFs. The "aa" is translated peptide sequence of the ORFs. Please note that each blast program has different requirements for nucleotide or amino acid input and databases. The following table is a guide:

Program Input Database
blastn nt
nt or genome
blastp aa aa
blastx nt
tblastn aa nt or genome
tblastx nt
nt or genome

The available databases are:

Database What it is:
Chloroplast_Public Blast against all published, whole, chloroplast genomes at once. See here to check when we last synced our database with NCBI