It seems like it's actually differentially expressed over time (note, bottom graph is log scale) which is why I chose to closely look at this region in particular. The coverage is strikingly consistent at it's peak. I put the sequence into Rfam and I got a single result for the 3' end: C4 antisense RNA. It appears to target the ant (adenine nucleotide translocator) gene and originates from a phage. As far as I know, Haemophilus influenzae does not have an ant gene. It does appear to mostly follow the structural template for this RNA as seen below:
I hope to find other possible sRNA using a similar technique. Stay tuned.
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