The difference blastn output when using subject and db options

Question

[praasu]

I have blasted the candidate transposable element to my genome. When I use (db) command 1 (details below) then the output is small and different from the command 2 using subject parameter with same query . If anybody has idea why it is so, Please let me know, thank you very much for your time.

command 1

blastn -db 1621_genome.fa -query output_clusters.fa -num_threads 24 -outfmt "6 qseqid sseqid qstart qend sstart send score length mismatch gaps gapopen nident pident evalue qlen slen qcovs sstrand" >blast_mite_1621_repeat.csv

command 2

blastn -task blastn -query output_clusters.fa  -subject 1621_genome.fa -outfmt "6 qseqid sseqid qstart qend sstart send score length mismatch gaps gapopen nident pident evalue qlen slen qcovs sstrand" >blast_mite_1621_repeat.csv

output_cluster.fa consist of list of transposable element in fasta and 1621_genome.fa contains list of contig in fasta

Answer 1

[GenoMax]

Default task option is megablast for blastn which looks for highly similar sequences compared to blastn which is looking for somewhat similar sequences. Former is used in command 1.