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Table S1. Analysis of 4132 initial transcribed regions (see Cho et al., 2009) for putative σ70-dependent pause-inducing sequence elements. Summary of results nAnnnT and at least a 3/6 match to TATAAT in registers 1-9: 1654/4132 nAnnnT and at least a 4/6 match to TATAAT in registers 1-9: 817/4132 nAnnnT and at least a 5/6 match to TATAAT in registers 1-9: 200/4132 nAnnnT and a 6/6 match to TATAAT in registers 1-9: 12/4132 Key to table TSS Genomic coordinate of transcription start sites. The minus sign refers to the reverse strand. Position (minus sign refers to upstream and no sign refers to downstream) relative to 5'-end of Position nearest annoated coding sequence (CDS), non-coding RNA (NC), regulatory region (RR), tRNA or pseudogene. E. coli # Identifying number of the CDS, ncRNA, tRNA or pseudogene on the E. coli MG1655 chromosome Description Description of the CDS, ncRNA, tRNA or pseudogene ITR Sequence extending from +1 (the identified transcription start site) to +14 Match Number of matches to putative σ70-dependent pause-inducing sequence elements Register The first nucleotide of the putative σ70-dependent pause-inducing sequence element TSS Position E.

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