Table 1 List of high scoring clusters

194

3

3

-

-

-

201

-6.28

-12.94

+

yfr2, yfr3, yfr4

This paper

5

3

-

1

1

1

345

-7.58

-10.18

NT

rplCD operon leader, corresponds to Escherichia coli S10 r-operon

[61, 62]

92

5

1

1

1

2

756

-4.47

-9.9

NT

rrn operon leader

[63, 64]

112

2

2

-

-

-

1129

-8.15

-9.15

NT

Reciprocal coverage of 7.9%, artifact due to low-complexity sequences

-

229

2

-

-

1

1

161

-7.98

-4.90

NT

Hghly similar sequences, putative ncRNAs

This paper

227

2

-

-

1

1

229

-7.38

-7.32

NT

rplJ operon leader, corresponds to E. coli β r-operon

[65]

84

1

-

1

-

-

122

-6.27

-5.54

+

Yfr2

This paper

101

3

-

1

1

1

152

-5.77

-5.61

NT

Putative Cobalamin riboswitch

[39, 66]

226

2

-

-

1

1

142

-5.29

-5.28

NT

Possible bi-directional terminator of the rplKAJL operon

Predicted by TransTerm [67]

9

6

-

1

1

4

397

-4.38

-4.95

NT

No conserved position, no significant BLASTN hit to MED4

This paper

51

2

1

1

-

-

146

-0.84

-4.92

+

yfr7

This paper

53

9

2

2

1

4

697

-3.26

-4.59

+

yfr6 in MED4 and SS120 and a subgroup of 5' UTR regions to annotated genes and putative unannotated genes in all four strains

This paper

245

2

-

-

1

1

259

-3.7

-4.53

-

rpoBC operon leader, corresponds to E. coli attenuator separating the rpl genes from rpoBC in the rplKAJLrpoBC gene cluster

[37, 68]

217

1

1

-

-

-

153

-1.63

-4.28

-

Located between genes for a two-component sensor histidine kinase and a conserved hypothetical protein

This paper

87

2

-

-

1

1

336

-4.24

-3.64

NT

Region upstream of the rbcLS cluster containing conserved promoter

[51]

228

2

-

-

1

1

106

-0.67

-4.00

NT

Rpl11 operon leader, corresponds to E. coli L11 r-operon

[69, 70]

257

2

-

-

1

1

176

-3.42

-3.97

+

Yfr1

This paper

2

3

-

1

1

1

197

-3.93

-2.94

NT

Putative TPP riboswitch in front of thiC

[38]