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Figure 1. Different alignments of footprinted E. coli Fur binding sites. Sequence alignments were done using the program malign with different window sizes [from (–15, +15) to (–5, +5)] (17) on 11 footprinted E. coli Fur binding sequences and their complements (see Supplementary Figure S1 for sequences). Three classes of alignments, M12 (A), M9 (B) and M6 (C) were obtained by using window sizes of (–12, +12), (–9, +9) and (–6, +6), respectively. In these logos, the height of each letter is proportional to the frequency of that base at each position, and the height of the letter stack is the conservation in bits (18). The dashed sine wave on each logo represents the 10.6 base helical twist of B-form DNA (31,81). The double dashed arrows on the top of each logo mark the inverted repeats in each model. Note that the M12 logo corresponds to two overlapping M9 sites, as indicated by the two red double dashed arrows below the M12 logo. A similar relationship occurs between the M9 and M6 logos.
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