Table 5

Orientation of USS motifs and closely spaced USS pairs

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

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.

Kingsford et al. Genome Biology 2007 8:R22   doi:10.1186/gb-2007-8-2-r22