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BLASTn output format start position larger than stop position

Dear Community,

I am currently running an experiment to identify gene expansion in parasite genomes. I have collected respected gene sequences and created a blast database of my parasite reference genomes using blast db function.

I use blastn and search against my parasite reference genome with my collected gene sequences as query using the command: 

blastn -query HSP_collectedseqs.fa -db parasite_database -outfmt 6 -out experiment1.blast -task blastn -evalue 0.0001

I noticed in my output fmt 6 blast file that some of the hits have start positions that are larger than their end positions. For example: 

human-HSP8 pathogen_contig_019288 73.71 175 46 0 1076 1250 7 181 6e-22 109

So you can see that for subject start and subject end respectively its 7 and 181.

How is this possible? Is there an error in my code? I have searched through the documentation/manual and turned to the internet but cannot find a definitive answer as to what this could mean.

Any guidance is greatly appreciated!

blast blastn blastn output blast outfmt 6
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updated by Sej Modha Sej Modha • written by nataliagru1 nataliagru1

1 answer

Default BLAST settings will perform searches in both strands. As shown in blastn -help

 -strand <String, `both', `minus', `plus'>
   Query strand(s) to search against database/subject
   Default = `both'
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written by Sej Modha Sej Modha

Thank you very much for your response. It seems as though I didn't intuitively read the manual. Its clear to me now! Greatly appreciated

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written by nataliagru1 nataliagru1

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