[BioC] Blast a BSgenome

[Ugo Borello]

Good morning,
I have a custom made Bsgenome data package and I would like to align a cDNA
sequence (~1kb) with the genome sequence of my Bsgenome, and retrieve the
aligned sequences.
Any suggestions? Any BLAST-like function in Bioconductor?
If I understand correctly Biostrings::matchPattern works with small
sequences, right? And I need in addition to account for gaps in the
alignment!
Does annotate::blastSequences could accept my Bsgenome genomic sequence as
argument? 
Thank you in advance for your help.

Ugo