I have set of subject sequences (25 to 40 bps long). My query sequences are 200-300 bp long. I am trying to find the location of short subject sequences in long query sequences. This is the exact inverse of the alignment problem, where we have long reference and we have short reads that we align to that long reference sequence. I have tried creating a blast db using the short subject sequences (25 to 40 bp) and tried to query that blast db using the long (200-300 bp) sequences, I am getting good results, but the sensitivity is not that great. I have tried bowtie2 and bwa-mem, but the results are even worse. Does anyone know how to solve this problem other than doing global-local alignment against every subject sequence for every query sequence. Any help is appreciated.