Best way to "fish" long reads that match a query sequence
I have seen the blasr aligner typically used for aligning PacBio reads to a reference.  Is there a reason why blasr would not be a good choice? I guess the very short sequence you are trying to align to might be an issue.  

Minimap2 is capable of mapping pacbio reads, and can also do pairwise mapping to see if reads overlap with each other, so this function might help you:
From https://github.com/lh3/minimap2

minimap2 -x ava-pb  reads.fq query_seq.fq &gt; ovlp.paf