Internal transcription start sites. The genome organizations surrounding (A) rpoL (TK1169) and (B) rpoN (TK1499). The promoter motifs for the pTSS of TK1169 and TKt26 and for the iTSS identified for rpoL and rpoN are shown below the panels. The abundances of transcripts present in T. kodakarensis cells growing exponentially (Sexp; blue) and in stationary phase (Sstat; red) in sulfur medium, growing exponentially in pyruvate medium before (Pexp; green) and 20 min after sulfur addition (PS; orange) are given by the peak heights. Data from the control library (C) not digested with TEX are shown in grey. The position of the sequence near the 3′-terminus of rpoL that, when transcribed, is predicted to form a stable RNA hairpin structure is indicated (see also Additional file 7: Figure S3). The black scale bar in the top right corner of each panel is corresponds to 100 nt.