I'm running blastn from the command line and keep getting weird results -- about half of the sequences have terrible alignments to the query, but have the same scores and E values as perfect matches. Using the -perc_identity option doesn't seem to change anything. I've tried changing just about everything except for the blast database.
If anyone has any advice I'd be very grateful.
ETA: This is using BLASTN 2.2.30+.
command line used: blastn -db ../i20.fasta -query query1.txt -out test.txt -perc_identity 100
Example of results:
>HS3:591:C5VMVACXX:4:1101:10795:94073 1:N:0:CTAAGGTC Length=100 Score = 102 bits (55), Expect = 2e-20 Identities = 12/55 (22%), Gaps = 0/55 (0%) Strand=Plus/Plus Query 1 GTATTTTTCAATTCTATTTACGCGTATAATATATCTTCGTCAACTATTGTGGAGT 55 | | | | || || | | | | Sbjct 33 GGTGGTAAGATTCAATAAATACAATACAAGACACACATTATCTAATGGCTCTTTT 87 >HS3:591:C5VMVACXX:4:2316:8876:76137 1:N:0:CTAAGGTC Length=100 Score = 102 bits (55), Expect = 2e-20 Identities = 55/55 (100%), Gaps = 0/55 (0%) Strand=Plus/Plus Query 1 GTATTTTTCAATTCTATTTACGCGTATAATATATCTTCGTCAACTATTGTGGAGT 55 ||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 41 GTATTTTTCAATTCTATTTACGCGTATAATATATCTTCGTCAACTATTGTGGAGT 95