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!