Rsequence can be used to investigate relationships between different sites. First, one may ask which binding site has more information than another. For example, ribosome binding sites contain, on the average, less information (11 bits) than do EcoRI sites (12 bits). When repressors are compared, Rsequencevaries between 16 and 23 bits (Table 1), in every case representing an information content higher than for ribosome binding sites. Indeed, individual repressors regulate transcription at a subset of the E. coli genes.
Secondly, the information patterns are different for the various repressors. LexA and TrpR have high peaks 3 bases wide while ArgR has double spikes and cI/cro have single spikes. These distinctive morphological differences probably reflect the location and strength of structural contacts between the different repressors and their cognate sites.
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