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Table 24 Top entropy hits in B. subtilis filtered for GC-comp. and uracil-comp.

From: Secondary structural entropy in RNA switch (Riboswitch) identification

B. subtilis

Start

End

Strand

Upstream operon

Upstream gene

Dist. to upstream

MFE

MFE p. Val.

GC

RND

RND p. Val.

Uracil

Dist. to downstream

Downstream gene

Downstream operon

Probability

157 nt

191850

192006

forward

BSU01590

ybaS

-12186

-54.16

0.01

0.4904

94.7470016

0.0359

0.3057

2277

trnSL-Glu2

BSU_tRNA_75

0.8561704159

157 nt

749147

749303

forward

BSU06780

yeeC

-3069

-49.19

-

0.4458

94.8936005

0.0310

0.3630

550

yeeG

BSU06820

0.8463344574

157 nt

665425

665581

forward

BSU06130

ydjC

-677

-51.50

-

0.4968

95.6813965

0.0169

0.3439

1963

gutB

BSU06150

0.8462108970

157 nt

1017114

1017270

forward

BSU09400

spoVR

18

-53.10

-

0.4968

94.5084991

0.0412

0.3376

1806

lytE

BSU09420

0.8305525184

157 nt

823013

823169

forward

BSU07480

yfmG

-604

-48.60

-

0.5032

94.2139969

0.0507

0.2866

4161

yfmA

BSU07540

0.7458834648

157 nt

3421066

3421222

reverse

BSU33340

sspJ

-320

-49.40

-

0.4713

97.1984024

0.0049

0.3312

79

lysP

BSU33330

0.8851321340

157 nt

3158851

3159007

reverse

BSU30890

ytxO

-328

-48.50

-

0.4395

95.1657028

0.0250

0.3630

3376

ytdA

BSU30850

0.8522043228

157 nt

736435

736591

reverse

BSU06740

yefB

-2481

-50.51

-

0.4904

95.0205994

0.0279

0.3376

3690

yerO

BSU06700

0.8204180002

157 nt

201248

201404

reverse

BSU01800

alkA

-1220

-49.46

-

0.4968

95.0683975

0.0269

0.2930

7301

ybbK

BSU01720

0.8003951907

157 nt

4129689

4129845

reverse

BSU40200

yydD

-810

-48.40

-

0.4904

94.8125000

0.0332

0.3567

2120

yydF

BSU40180

0.7834032774

150 nt

4134601

4134750

forward

BSU40190

fbp

-4483

-50.91

-

0.4733

91.2214966

-

0.3800

677

yycS

BSU40240

0.8779885173

150 nt

3359819

3359968

forward

BSU32650

yurS

-5258

-46.80

-

0.4600

92.3918991

-

0.3600

12677

yuzL

BSU32849

0.8770275712

150 nt

749175

749324

forward

BSU06780

yeeC

-3102

-46.50

-

0.4600

92.0363998

-

0.3867

527

yeeG

BSU06820

0.8652582169

150 nt

1958237

1958386

forward

BSU18190

yngC

-9899

-48.30

-

0.4733

90.9682007

-

0.3533

44327

iseA

BSU18380

0.8436317444

150 nt

1540761

1540910

forward

BSU14680

ykzC

-1995

-46.42

-

0.4333

90.3455963

-

0.3400

1052

ylaA

BSU14710

0.8428211212

150 nt

3199841

3199990

forward

BSU31170

yulF

-1875

-47.20

-

0.4467

89.9530029

-

0.3733

12677

tgl

BSU31270

0.8267914653

150 nt

3421066

3421215

reverse

BSU33340

sspJ

-325

-49.40

-

0.4800

93.4540024

-

0.3333

74

lysP

BSU33330

0.9072541595

150 nt

933665

933814

reverse

BSU08620

yfhP

-718

-49.54

-

0.4600

89.9813995

-

0.3733

5474

sspK

BSU08550

0.8426564932

200 nt

3359769

3359968

forward

BSU32650

yurS

-5183

-66.40

-

0.4600

123.4530029

-

0.3450

12702

yuzL

BSU32849

0.9236087203

200 nt

339225

339424

forward

BSU03130

nadE

-20

-63.60

-

0.4700

121.1809998

-

0.3250

702

aroK

BSU03150

0.8414211273

200 nt

1678852

1679051

reverse

BSU17060

ymzD

-101667

-62.81

-

0.4750

122.0299988

-

0.3300

7299

ylqB

BSU15960

0.8517054319

200 nt

3717398

3717597

reverse

BSU36100

ywrD

-1637

-51.30

-

0.3650

130.8540039

-

0.3950

399

cotH

BSU36060

0.9702541828

200 nt

198226

198425

reverse

BSU01800

alkA

-4222

-30.81

-

0.3750

130.7449951

-

0.5150

4299

ybbK

BSU01720

0.8267450333

157 nt

235800

235956

reverse

BSU02180

ybfE

-2285

-54.99

-

0.3312

66.4815979

01

0.3439

550

glpT

BSU02140

0.0401644297

200 nt

3236257

3236456

forward

BSU31500

yuxK

61

-82.70

-

0.4200

93.3933029

02

0.2650

802

yufL

BSU31520

0.0853443071

  1. Significant hits of the forward and reverse strands of the B. subtilis intergenic regions having significantly high RND entropy (p-Val. <0.0500), significantly low (p.Val. <0.050), GC and uracil compositions within the range of those for known riboswitches Threshold values and their corresponding p-values have been calculated separately for each genome-wide test. No overlap used for 157 nt scan (28340 segments). 175 nt overlap used for 150 nt scan (60204 segments). 100 nt overlap used for 200 nt scan (44847 segments). Distance from upstream and downstream operons are the distance from the center of the hit to the stop and start codons of upstream and downstream operons, respectively. Probability denotes the multinomial regression likelihood of being a riboswitch under the LMFEGCRND model. Negative values indicate distance to upstream operon. Columns Upsream/Downstream Operon show gene ID within the operon.
  2. 1Table 24: The entropy of this sequence is the lowest within the test. The significance of this value is also shown in Figure 5 as the lowest blue point on the graph.
  3. 2Table 24: The entropy of this sequence is the lowest within the test.
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BMC Bioinformatics

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