Transcription start site (TSS) classification. (A) Diagram showing all potential locations of TSS. In this report, they are categorized as primary (pTSS; most abundant transcript based on the highest number of cDNA reads) or secondary TSS (sTSS; all other transcripts) when located ≤300 bp upstream of a gene with transcription on the sense strand of that gene. They are categorized as internal TSS (iTSS) when located within an annotated gene and antisense TSS (aTSS) when located either in, or within ≤100 bp of a gene, on the antisense strand. A TSS not readily assigned to any of these categories was categorized as an orphan TSS (oTSS). (B) The distribution and overlap of the TSSs identified in each category. (C) The distribution of lengths of 5′-UTRs based on the combined number of pTSS and sTSS that initiate transcription at each position, with 0 being the first bp of the translation start codon. The numbers of TSS resulting in 5'-UTRs ≤8 nt, and so considered leaderless mRNAs, are indicated by the grey bars. The insert shows the consensus of the RBS identified in T. kodakarensis.