I am trying to find low similarity DNA sequences from two genomes of very closely related fungal species. Blast+ alignment of concatenated genomic sequences showed hits with identities around 70~80%. However, when I retrieved these DNA sequences of the both query and subject and made blastn search against genomes of each other, I was able to see hits with 100% identities.
What do you recommend to improve the accuracy of alignment results?
Command used to produce the alignment was:
$ blastn -db db_file -query input_file.txt -out output.txt -max_target_seqs 100 -outfmt 7