NCBI blast vs blast+ @ Galaxy

Hi all!

I have a bunch of sequences, in fasta format, like


I used NCBI BLAST+ blastn to blast this against following databases:

A) Homo Sapiens GRCh37 (hg19) ncRNA+CDS
>>> which had been imported from “Shared data” to my history
B) Homo_sapiens.GRCh38.cdna.all and Homo_sapiens.GRCh38.ncrna.fa
which I had uploaded in .gz format from Ensembl (

I choose BlastN among blast flavors. However, when I blast this very same set of sequences at NCBI, I get full length alignments (query coverage=100) with no mismatches. This is not the case with galaxy version of blast. Where am I going wrong?

Blastn @ NCBI gives


All three with no mismatches and 100% query cover.

Galaxy Blast+ blastn against Homo_sapiens.GRCh38.cdna.all.fa gives ensemble transcripts with query cover of 38/60.

Is this issue related to databases or am I doing something wrong in galaxy?

Thank you very much.