I have two fasta files from WormBase. One is the coding transcripts, the other is ncRNA. When I BLAST (using NCBI Blast+) 44k 60-mers against just the transcripts, I get 37,216 hits. When I concatenate the ncRNA fasta file to the transcripts file (and do makeblastdb again) I get 33,572. I know that several of these 60-mers hit both the transcripts and the ncRNA so I need to BLAST them together. How do I do that without losing ~4k hits?