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Table 4 Analysis of all USS hairpins in N. meningitidis Z2491

From: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

     Average no. of A/Ts
Region No. of reg No. of USS No. of hairpins A-tail T-tail
Tail-to-tail 268 375 94 3.33 3.18
Reverse tail-to-head 761 396 61 2.75 1.97
Forward tail-to-head 652 364 63 2.08 3.05
Intragenic 2,065 635 3 3.67 3.33
Head-to-head 270 104 10 2.40 1.70
  1. Analysis of all hairpins of the GCCGTCTGAA...TTCAGACGGC and TTCAGACGGC...GCCGTCTGAA motif in N. meningitidis Z2491. Hairpins were found by exhaustive search as described in the text. The pattern of conservation of nucleotides in the regions flanking the hairpins reflects that expected if the hairpins are being maintained to function as transcription terminators. The 'No. of reg' column gives the number of intergenic regions of positive length of each type. The 'No. of USS' column gives the number of USS instances (not necessarily paired) within each region type. The 'No. of hairpins' column lists the number of hairpin configurations of USS motifs (separated by ≤ 10 nt) that overlap each type of region. (For intragenic regions, we require that the hairpin be wholly contained within a gene.) The 'A-tail' column gives the average number of A residues in the five bases preceding the first occurrence of the motif in the pair. The 'T-tail' column gives the average number of T residues in the five bases following to the second occurrence of the motif in the pair.