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Table 5 Orientation of USS motifs and closely spaced USS pairs

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

Organism Total + Total - ++ -- +- -+
Neisseria       
   N. meningitidis Z2491 958 934 0 0 226 5
   N. meningitides MC58 966 969 0 0 229 4
   N. gonorrhoeae FA 1090 1,011 954 1 1 215 5
Pasteurellaceae       
   H. influenzae 737 734 1 0 50 25
   H. influenzae 86 028NP 734 782 0 0 52 23
   P. multocida 468 459 0 0 13 8
   M. succiniciproducens MBEL55E 730 755 0 0 31 20
   H. ducreyi 35000HP 717 654 0 2 6 8
  1. For the organisms listed in the table, the USS motif occurs with approximate equal frequency on each strand. The 'Total +' and 'Total -' columns give the number of times the motif occurs on the reference strand as deposited in GenBank (+) and how many times it occurs on the complementary strand (-). The '++' and '--' columns count the number of occurrences in which the motifs occurred on the same strand within 10 nt of each other. As expected, since these configurations do not induce hairpins, they are relatively rare. The '+-' and '-+' columns give the number of occurrences of the USS motifs on opposing strands separated by ≤ 10 nt. There is an overabundance of +- pairs, representing, for example, a preference for the GCCGTCTGAA...TTCAGACGGC hairpin over the TTCAGACGGC...GCCGTCTGAA hairpin.