Long inverted repeats are a source of small RNAs. (A) Small RNA distribution on IR3. Reads were distributed randomly on the two repeats during alignment. An enlargement of the region in-between the two repeats is shown below. (B) Low-molecular weight RNAs isolated from various cell lines as indicated above each lane were separated by denaturing gel electrophoresis and analyzed by Northern hybridization with an IR3-specific probe. Hybridization to 5S rRNA was used as a loading control (load, bottom panel). See additional file 5 for sequences of the hybridization probes.