Update docs/usage.md

Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com>

Author: atrigila

docs/usage.md

@@ -47,7 +47,7 @@ If MirGeneDB should be used instead it needs to be specified using `--mirgenedb`
 
 See examples in: [the test-datasets repository of nf-core](https://github.com/nf-core/test-datasets/tree/smrnaseq/MirGeneDB).
 
-> [!NOTE] > `mirtop` is hard-coded to use the `pre` sequences rather than `pri`. Users must provide `pre` files from the start to ensure consistency between the FASTA and GFF files, as the coordinates in the GFF file are referenced to `pre` sequences. This also ensures that names in the BAM file will match those in the GFF.
+> [!NOTE] > `mirtop` is hard-coded to use the `pre` sequences, which originate from the hairpin FASTA, rather than the `pri` sequences, which come from the mature FASTA. Users must provide `pre` files from the start to ensure consistency between the FASTA and GFF files, as the coordinates in the GFF file are referenced to `pre` sequences. This also ensures that names in the BAM file will match those in the GFF.
 
 ### Genome