Noguera Research Group at UW-Madison

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Supplementary Material For

Yilmaz L.S. and D. R. Noguera (2004).  A mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization.  Applied and Environmental Microbiology, 70(12): 7126-7139.

 

Table of Calculated Free Energy Changes (DG0) and Solvent Accessible Surface Area (DASAts) for All Probes in the 16S rRNA Accessibility Maps of Fuchs et al. (1998) and Behrens et al. (2003).

Probe characteristics

Flourescein-labeled probes*

Cy3-labeled probes**

Gibbs free energy changes  (kcal/mol)

DASAts

Name

5'

3'

Sequence

Intensity

Brightness Class

Intensity

Brightness Class

DG01

DG02

DG03-i

DG03-ii

DG03-iii

DG03-iv

DG0overall-i

DG0overall-ii

DG0overall-iii

DG0overall-iv

(Ĺ/residue)

Eco1

1

19

TGATCAAACTCTTCAATTT

1

VI

0.68

II

-12.4

1.6

-2.8

-1.5

-2.8

-2.8

-9.5

-10.7

-9.5

-9.5

63.51

Eco13

13

31

CAATCTGAGCCATGATCAA

35

IV

0.58

III

-16.2

1.0

-3.2

-3.2

-3.9

-3.9

-12.9

-12.9

-12.2

-12.2

18.78

Eco20

20

37

AGCGTTCAATCTGAGCCA

44

III

1.15

I

-19.0

0.9

-6.2

-6.2

-2.9

-2.9

-12.6

-12.6

-15.9

-15.9

23.57

Eco32

32

47

GCCTGCCGCCAGCGTT

42

III

0.54

III

-24.3

-0.0

-6.5

-7.2

-17.9

-27.2

-17.4

-16.7

-6.0

3.3

27.28

Eco38

38

54

GTGTTAGGCCTGCCGCC

68

II

0.55

III

-24.1

-1.2

-5.4

-4.3

-10.7

-20.8

-17.4

-18.5

-12.1

-2.0

7.15

Eco48

48

65

TCGACTTGCATGTGTTAG

76

II

0.54

III

-16.1

1.0

-6.1

-1.2

-10.0

-13.0

-9.9

-14.7

-6.0

-3.0

2.82

Eco55

55

72

TTACCGTTCGACTTGCAT

56

III

0.74

II

-17.7

1.8

-3.3

-1.2

-8.7

-12.6

-14.4

-16.4

-9.0

-5.1

2.59

Eco60

60

77

TCCTGTTACCGTTCGACT

66

II

-

-

-19.7

1.8

-3.3

-2.8

-4.2

-15.0

-16.4

-16.9

-15.5

-4.7

2.59

Eco63

63

80

GCTTCCTGTTACCGTTCG

67

II

-

-

-20.9

1.8

-3.1

-5.9

-16.3

-15.0

-17.7

-14.9

-4.6

-5.9

0.00

Eco66

66

83

GCTGCTTCCTGTTACCGT

62

II

0.77

II

-22.4

1.8

-4.4

-5.9

-6.1

-6.1

-18.0

-16.5

-16.3

-16.3

0.00

Eco70

70

88

AGCAAGCTGCTTCCTGTTA

48

III

-

-

-20.8

-1.1

-8.7

-6.4

-7.0

-7.0

-10.9

-13.2

-12.6

-12.6

0.00

Eco73

73

90

GCAGCAAGCTGCTTCCTG

27

IV

0.27

IV

-21.5

-1.9

-8.0

-6.1

-7.0

-7.0

-11.6

-13.5

-12.6

-12.6

0.00

Eco79

79

96

CAGCAAAGCAGCAAGCTG

3

VI

-

-

-16.9

-1.6

-12.3

-7.4

-7.0

-7.0

-3.0

-7.8

-8.3

-8.3

0.00

Eco84

84

101

TCGTCAGCAAAGCAGCAA

6

V

0.18

V

-17.0

0.0

-12.5

-9.0

-7.0

-7.0

-4.1

-7.5

-9.6

-9.6

0.96

Eco87

87

104

CACTCGTCAGCAAAGCAG

10

V

-

-

-17.1

0.4

-11.8

-8.3

-8.6

-8.6

-5.0

-8.5

-8.2

-8.2

9.40

Eco89

89

106

GCCACTCGTCAGCAAAGC

41

III

-

-

-20.2

1.0

-9.5

-8.3

-16.4

-21.6

-10.6

-11.8

-3.7

1.5

12.15

Eco91

91

108

CCGCCACTCGTCAGCAAA

70

II

0.82

I

-20.8

0.2

-9.1

-6.8

-12.0

-16.5

-11.4

-13.7

-8.5

-4.0

17.17

Eco102

102

118

ACTCACCCGTCCGCCAC

46

III

0.75

II

-23.6

1.8

-6.7

-5.6

-6.5

-8.6

-16.8

-17.9

-17.0

-14.9

22.93

Eco109

109

126

CAGACATTACTCACCCGT

40

IV

0.82

I

-18.5

1.4

-10.3

-5.4

-14.5

-14.5

-8.2

-13.1

-4.0

-4.0

5.47

Eco119

119

136

GGCAGTTTCCCAGACATT

27

IV

0.78

II

-20.2

1.0

-8.1

-9.1

-20.7

-22.1

-12.0

-11.0

0.6

2.0

21.69

Eco127

127

144

CTCCATCAGGCAGTTCC

47

III

0.73

II

-23.0

0.3

-6.6

-8.8

-21.6

-25.2

-16.1

-13.8

-1.1

2.5

24.50

Eco137

137

154

AGTTATCCCCCTCCATCA

35

IV

0.71

II

-22.8

2.5

-8.9

-9.8

-18.3

-24.7

-13.9

-13.0

-4.5

1.9

3.35

Eco145

145

162

TTTCCAGTAGTTATCCCC

66

II

0.79

II

-20.1

2.0

-9.0

-3.1

-10.4

-19.6

-11.1

-16.9

-9.7

-0.5

0.50

Eco155

155

172

TTAGCTACCGTTTCCAGT

46

III

0.99

I

-19.3

1.9

-8.4

-7.6

-7.6

-7.6

-10.9

-11.7

-11.7

-11.7

0.00

Eco163

163

180

ATGCGGTATTAGCTACCG

30

IV

0.32

IV

-18.0

-2.6

-8.2

-7.6

-14.7

-19.6

-7.2

-7.8

-0.7

4.2

10.19

Eco173

173

190

TTGCGACGTTATGCGGTA

39

IV

0.39

IV

-18.0

-0.4

-4.4

-4.5

-3.8

-14.0

-12.9

-12.8

-13.5

-3.3

21.54

Eco181

181

198

CTTTGGTCTTGCGACGTT

65

II

0.77

II

-18.7

0.3

-4.2

-3.7

-9.7

-10.1

-14.2

-14.8

-8.7

-8.3

24.79

Eco191

191

209

AAGGTCCCCCTCTTTGGTC

76

II

0.75

II

-24.5

-0.5

-4.5

-12.0

-10.9

-10.1

-19.3

-11.8

-12.9

-13.7

12.73

Eco199

199

215

GGCCCTAAGGTCCCCCT

61

II

0.67

II

-26.1

-0.2

-9.0

-8.3

-10.8

-10.9

-16.5

-17.2

-14.7

-14.6

0.00

Eco210

210

226

CGATGGCAAGAGGCCCG

5

VI

0.17

V

-19.9

-1.8

-12.2

-13.2

-18.7

-29.5

-5.8

-4.8

0.7

11.5

1.27

Eco216

216

233

GCACATCCGATGGCAAGA

21

IV

0.29

IV

-18.8

0.4

-11.1

-12.2

-27.1

-30.7

-7.4

-6.3

8.6

12.2

16.23

Eco227

227

243

TCCCATCTGGGCACATC

26

IV

0.32

IV

-20.3

-1.2

-12.9

-12.9

-22.0

-29.5

-6.1

-6.1

3.0

10.5

32.45

Eco234

234

251

CTAGCTAATCCCATCTGG

27

IV

0.63

II

-18.2

0.6

-12.1

-12.1

-22.3

-28.5

-5.9

-6.0

4.3

10.5

15.62

Eco244

244

261

ACCCCACCTACTAGCTAA

41

III

0.56

III

-20.3

1.9

-12.7

-14.5

-11.4

-11.4

-7.6

-5.7

-8.9

-8.9

27.14

Eco252

252

268

AGCCGTTACCCCACCTA

62

II

1.02

I

-22.6

2.2

-9.8

-9.7

-9.8

-9.8

-12.8

-12.9

-12.8

-12.8

44.51

Eco262

262

279

TCGCCTAGGTGAGCCGTT

19

V

0.16

V

-22.7

0.6

-12.0

-12.2

-11.4

-11.4

-10.5

-10.3

-11.1

-11.1

28.38

Eco269

269

285

GGATCGTCGCCTAGGTG

27

IV

0.32

IV

-19.8

1.5

-13.8

-14.8

-21.4

-26.8

-6.0

-4.9

1.6

7.0

21.63

Eco280

280

297

CAGACCAGCTAGGGATCG

25

IV

0.48

III

-19.0

-0.3

-13.3

-15.0

-14.4

-21.2

-5.1

-3.5

-4.0

2.8

6.94

Eco285

285

302

CCTCTCAGACCAGCTAGG

53

III

0.7

II

-20.9

0.0

-13.7

-14.7

-14.4

-20.9

-6.8

-5.7

-6.1

0.4

3.39

Eco298

298

315

TGTGGCTGGTCATCCTCT

56

III

0.82

I

-21.9

0.3

-8.3

-8.1

-8.2

-18.2

-13.3

-13.6

-13.4

-3.4

11.09

Eco303

303

320

TCCAGTGTGGCTGGTCAT

25

IV

0.52

III

-21.6

-2.1

-10.3

-10.6

-12.0

-26.9

-9.1

-8.8

-7.4

7.5

7.69

Eco316

316

333

ACCGTGTCTCAGTTCCAG

62

II

0.54

III

-20.7

2.0

-5.8

-6.1

-12.8

-12.8

-14.9

-14.6

-7.9

-7.9

20.84

Eco321

321

338

TCTGGACCGTGTCTCAGT

71

II

0.78

II

-20.7

0.4

-5.8

-6.1

-12.8

-12.8

-14.6

-14.3

-7.6

-7.6

20.84

Eco334

334

350

CTCCCGTAGGAGTCTGG

27

IV

0.48

III

-20.3

-1.3

-9.8

-10.0

-14.3

-21.4

-9.1

-8.9

-4.6

2.5

0.36

Eub338

338

353

GCTGCCTCCCGTAGGAGT

58

III

-

-

-22.2

-1.6

-5.4

-5.8

-10.1

-10.1

-15.2

-14.7

-10.5

-10.5

0.38

Eco343

343

359

CACTGCTGCCTCCCGTA

64

II

0.73

II

-22.8

1.9

-9.1

-5.4

-14.4

-19.2

-13.7

-17.4

-8.4

-3.6

0.36

Eco351

351

369

CAATATTCCCCACTGCTGC

33

IV

0.66

II

-21.3

1.6

-5.3

-5.0

-13.1

-14.4

-16.0

-16.3

-8.2

-6.9

13.50

Eco360

360

377

CCATTGTGCAATATTCCC

35

IV

0.69

II

-18.1

0.4

-10.1

-10.0

-12.6

-13.2

-7.8

-7.8

-5.3

-4.7

33.79

Eco370

370

386

GGCTTGCGCCCATTGTG

52

III

0.54

III

-21.9

-0.8

-11.5

-9.9

-11.0

-11.0

-9.4

-11.0

-9.9

-9.9

22.00

Eco378

378

394

CTGCATCAGGCTTGCGC

32

IV

1.09

I

-20.6

-0.3

-8.9

-10.1

-11.0

-11.0

-11.1

-9.9

-9.0

-9.0

13.18

Eco387

387

403

GCGGCATGGCTGCATCA

39

IV

0.4

IV

-21.4

-1.7

-6.1

-4.5

-14.0

-25.7

-13.5

-15.1

-5.6

6.1

26.12

Eco395

395

412

TTCATACACGCGGCATGG

35

IV

1.06

I

-18.3

1.4

-4.5

-4.4

-19.7

-24.5

-13.7

-13.8

1.5

6.3

46.11

Eco404

404

421

AAGGCCTTCTTCATACAC

37

IV

0.64

II

-17.0

0.5

-3.3

-4.9

-10.8

-17.2

-13.5

-11.9

-6.0

0.4

39.48

Eco413

413

429

TACAACCCGAAGGCCTTC

62

II

0.69

II

-17.9

-0.7

-4.8

-4.7

-4.7

-4.7

-12.3

-12.4

-12.4

-12.4

24.59

Eco422

422

439

AAAGTACTTTACAACCCG

37

IV

0.66

II

-13.5

0.6

-6.1

-4.9

-13.1

-17.2

-7.2

-8.5

-0.2

3.9

32.84

Eco431

431

448

TCCCCGCTGAAAGTACTT

42

III

0.33

IV

-19.2

0.7

-8.8

-8.1

-23.0

-27.2

-10.2

-10.9

4.0

8.2

11.30

Eco439

439

455

CCCTTCCTCCCCGCTGA

53

III

-

-

-26.1

2.1

-11.2

-10.0

-16.4

-22.7

-14.9

-16.1

-9.7

-3.4

10.21

Eco440

440

456

TCCCTTCCTCCCCGCTG

83

I

0.94

I

-26.0

4.6

-11.2

-10.0

-18.0

-24.3

-14.8

-16.1

-8.0

-1.7

8.58

Eco443

443

460

TTACTCCCTTCCTCCCCG

62

II

-

-

-24.9

4.6

-12.6

-11.8

-21.8

-32.3

-12.3

-13.1

-3.1

7.4

8.10

Eco446

446

463

ACTTTACTCCCTTCCTCC

64

II

-

-

-21.7

4.6

-10.3

-10.3

-10.3

-10.3

-11.4

-11.4

-11.4

-11.4

8.10

Eco449

449

467

ATTAACTTTACTCCCTTCC

35

IV

0.47

III

-18.1

1.8

-6.7

-6.8

-6.7

-6.7

-11.3

-11.2

-11.3

-11.3

7.53

Eco455

455

473

AAAGGTATTAACTTTACTC

3

VI

0.01

VI

-11.4

0.4

-6.7

-6.8

-6.7

-6.7

-4.4

-4.2

-4.4

-4.4

0.15

Eco468

468

486

AACGTCAATGAGCAAAGGT

3

VI

0.03

VI

-14.6

1.2

-6.7

-6.8

-6.7

-6.7

-7.9

-7.7

-7.9

-7.9

6.24

Eco474

474

491

CGGGTAACGTCAATGAGC

3

VI

0.25

IV

-16.4

0.3

-9.8

-10.3

-24.1

-28.8

-6.3

-5.8

8.0

12.7

9.00

Eco478

478

495

TCTGCGGGTAACGTCAAT

20

V

-

-

-17.2

-0.2

-6.0

-7.7

-17.1

-18.9

-10.6

-9.0

0.5

2.3

4.15

Eco481

481

498

TCTTCTGCGGGTAACGTC

21

IV

-

-

-18.9

-0.2

-6.0

-7.7

-17.1

-18.9

-12.3

-10.7

-1.3

0.5

5.28

Eco484

484

501

GCTTCTTCTGCGGGTAAC

60

III

-

-

-19.4

1.6

-6.9

-9.7

-21.5

-25.5

-12.5

-9.7

2.1

6.1

9.72

Eco487

487

504

GGTGCTTCTTCTGCGGGT

54

III

0.72

II

-22.8

1.0

-8.1

-8.8

-21.2

-29.0

-14.5

-13.8

-1.5

6.3

17.70

Eco492

492

509

TAGCCGGTGCTTCTTCTG

46

III

0.63

II

-20.7

-1.0

-7.5

-8.2

-15.2

-15.2

-12.1

-11.4

-4.4

-4.4

23.88

Eco499

499

516

ACGGAGTTAGCCGGTGCT

25

IV

-

-

-21.7

-1.3

-7.8

-8.5

-18.4

-22.7

-12.5

-11.9

-1.9

2.4

29.55

Eco505

505

522

GCTGGCACGGAGTTAGCC

56

III

0.4

IV

-22.4

-0.8

-8.9

-9.0

-4.3

-4.3

-12.5

-12.4

-17.1

-17.1

36.75

Eco510

510

527

CGGCTGCTGGCACGGAGT

37

IV

0.41

III

-23.2

-0.5

-6.8

-8.2

-4.3

-4.3

-15.7

-14.3

-18.2

-18.2

41.27

Eco523

523

540

CTCCGTATTACCGCGGCT

54

III

0.76

II

-22.2

-0.8

-6.3

-8.2

-4.3

-4.3

-14.9

-13.0

-16.9

-16.9

35.70

Eco528

528

545

GCACCCTCCGTATTACCG

42

III

0.49

III

-22.4

0.8

-9.1

-9.4

-13.5

-27.4

-13.1

-12.8

-8.7

5.2

40.06

Eco541

541

558

CCGATTAACGCTTGCACC

96

I

0.66

II

-18.8

-0.0

-2.2

-2.2

-2.8

-4.0

-16.1

-16.1

-15.5

-14.3

44.70

Eco548

548

566

CAGTAATTCCGATTAACGC

42

III

0.45

III

-15.3

-0.0

-0.2

-1.0

0.1

0.1

-14.3

-13.7

-14.4

-14.4

38.23

Eco559

559

576

GCTTTACGCCCAGTAATT

46

III

0.49

III

-18.5

0.0

-4.1

-4.9

6.3

6.3

-14.0

-13.2

-18.1

-18.1

24.39

Eco567

567

584

CTGCGTGCGCTTTACGCC

44

III

0.73

II

-22.7

-2.2

-4.1

-4.1

0.7

0.7

-16.3

-16.3

-20.3

-20.3

14.98

Eco577

577

594

AACAAACCGCCTGCGTGC

42

III

0.78

II

-19.8

0.2

-7.0

-6.1

-13.4

-24.1

-12.4

-13.3

-6.0

4.7

35.16

Eco585

585

602

TCTGACTTAACAAACCGC

2

VI

0.14

V

-14.3

1.9

-10.1

-8.4

-19.8

-28.7

-4.2

-5.9

5.5

14.4

43.04

Eco595

595

613

GGGATTTCACATCTGACTT

2

VI

0.1

V

-17.5

0.5

-13.3

-15.0

-20.5

-28.7

-4.0

-2.2

3.3

11.4

27.60

Eco603

603

620

GAGCCCGGGGATTTCACA

4

VI

0.19

V

-21.7

0.5

-13.2

-13.2

-13.2

-13.2

-8.3

-8.3

-8.3

-8.3

26.13

Eco614

614

631

GTTCCCAGGTTGAGCCCG

25

IV

0.34

IV

-24.3

0.2

-8.3

-8.3

-8.5

-8.5

-15.6

-15.6

-15.4

-15.4

34.45

Eco621

621

638

AGATGCAGTTCCCAGGTT

2

VI

0.04

VI

-20.5

2.0

-12.3

-15.8

-17.5

-17.5

-8.2

-4.7

-3.0

-3.0

24.20

Eco627

627

644

AGTATCAGATGCAGTTCC

1

VI

0.18

V

-17.5

1.6

-9.6

-15.7

-19.5

-17.5

-7.8

-1.7

2.1

0.1

26.58

Eco632

632

649

TTGCCAGTATCAGATGCA

2

VI

0.04

VI

-18.1

0.5

-8.3

-11.0

-22.6

-17.5

-9.6

-6.8

4.7

-0.3

24.93

Eco639

639

656

CTCAAGCTTGCCAGTATC

4

VI

0.09

V

-18.4

0.9

-10.1

-12.2

-19.3

-21.0

-8.2

-6.1

1.1

2.7

27.99

Eco645

645

662

ACGAGACTCAAGCTTGCC

22

IV

0.81

I

-18.5

0.9

-10.1

-10.8

-17.4

-25.3

-8.3

-7.6

-1.0

6.9

23.03

Eco650

650

667

CCTCTACGAGACTCAAGC

13

V

0.36

IV

-17.7

0.2

-11.7

-12.1

-22.8

-26.1

-5.6

-5.3

5.4

8.8

32.53

Eco654

654

671

CCCCCCTCTACGAGACTC

17

V

-

-

-23.7

0.2

-8.0

-10.9

-26.8

-31.4

-15.3

-12.4

3.5

8.1

36.56

Eco657

657

674

CTACCCCCCTCTACGAGA

19

V

0.47

III

-22.9

0.2

-6.6

-10.9

-29.3

-33.5

-15.9

-11.6

6.8

11.0

45.39

Eco661

661

678

AATTCTACCCCCCTCTAC

22

IV

-

-

-20.9

3.2

-7.8

-13.1

-23.7

-29.5

-13.1

-7.8

2.8

8.6

44.34

Eco665

665

682

CTGGAATTCTACCCCCCT

21

IV

1.14

I

-22.2

1.2

-11.9

-16.1

-27.7

-35.6

-10.2

-6.0

5.5

13.4

40.01

Eco668

668

685

CACCTGGAATTCTACCCC

12

V

0.82

I

-20.3

1.2

-10.5

-14.6

-27.3

-32.7

-9.7

-5.5

7.1

12.5

43.17

Eco675

675

692

ACCGCTACACCTGGAATT

50

III

0.62

II

-18.6

0.2

-7.3

-7.7

-11.9

-11.9

-10.9

-10.5

-6.3

-6.3

44.85

Eco681

681

698

CATTTCACCGCTACACCT

55

III

1.3

I

-19.5

4.6

-7.3

-6.7

-7.2

-7.2

-12.2

-12.8

-12.2

-12.2

43.74

Eco686

686

703

CTACGCATTTCACCGCTA

40

IV

0.67

II

-18.8

0.9

-2.2

-2.2

-2.2

-2.2

-16.4

-16.4

-16.4

-16.4

34.68

Eco690

690

707

ATCTCTACGCATTTCACC

60

III

1.27

I

-17.7

3.2

-4.3

-4.3

-4.3

-4.3

-13.4

-13.4

-13.4

-13.4

37.38

Eco693

693

710

CAGATCTCTACGCATTTC

29

IV

0.44

III

-16.2

0.8

-4.8

-6.7

-10.7

-10.7

-11.1

-9.3

-5.3

-5.3

29.86

Eco704

704

721

CGGTATTCCTCCAGATCT

38

IV

0.75

II

-19.7

0.6

-7.5

-5.5

-15.1

-16.7

-11.9

-13.9

-4.4

-2.7

51.11

Eco711

711

728

TCGCCACCGGTATTCCTC

62

II

0.65

II

-22.7

0.3

-7.8

-5.0

-4.3

-4.3

-14.6

-17.4

-18.1

-18.1

36.28

Eco722

722

737

GGGCCGCCTTCGCCTC

21

IV

0.64

II

-24.9

-0.6

-8.4

-8.5

-11.7

-11.7

-15.6

-15.5

-12.4

-12.4

32.46

Eco729

729

744

GTCCAGGGGGCCGCCT

37

IV

0.25

IV

-25.3

0.0

-8.4

-9.8

-16.1

-11.7

-16.4

-15.0

-8.7

-13.2

55.59

Eco738

738

755

CGTCAGTCTTCGTCCAGG

19

V

0.67

II

-20.9

1.5

-6.0

-7.3

-24.8

-30.7

-14.8

-13.5

4.0

9.8

48.87

Eco745

745

762

ACCTGAGCGTCAGTCTTC

19

V

0.33

IV

-20.2

-0.4

-9.0

-6.5

-15.7

-22.5

-10.6

-13.0

-3.8

2.9

24.53

Eco756

756

773

CACGCTTTCGCACCTGAG

15

V

0.53

III

-20.0

0.1

-11.1

-9.5

-14.8

-28.1

-8.5

-10.2

-4.8

8.4

6.15

Eco763

763

780

TGCTCCCCACGCTTTCGC

77

II

0.79

II

-24.8

0.1

-8.3

-9.8

-20.1

-23.9

-16.1

-14.5

-4.2

-0.5

14.22

Eco774

774

791

CTAATCCTGTTTGCTCCC

52

III

0.57

III

-20.1

1.3

-6.5

-7.2

-5.7

-5.7

-13.5

-12.8

-14.3

-14.3

9.76

Eco781

781

799

CAGGGTATCTAATCCTGTT

4

VI

0.25

IV

-18.1

-1.2

-5.2

-3.2

-4.6

-4.6

-11.6

-13.6

-12.2

-12.2

4.02

Eco792

792

809

CGTGGACTACCAGGGTAT

2

VI

0.35

IV

-19.0

-0.1

-8.2

-9.5

-14.3

-15.1

-10.4

-9.1

-4.2

-3.4

6.56

Eco800

800

817

GTTTACGGCGTGGACTAC

31

IV

0.37

IV

-18.1

1.3

-5.2

-6.4

-10.8

-16.7

-12.9

-11.6

-7.3

-1.4

2.32

Eco810

810

827

AGTCGACATCGTTTACGG

38

IV

0.5

III

-16.5

0.0

-7.1

-8.1

-15.3

-15.3

-9.0

-8.0

-0.8

-0.8

13.64

Eco818

818

835

AACCTCCAAGTCGTCATC

10

V

0.62

II

-18.2

1.3

-7.0

-8.5

-17.5

-25.8

-11.1

-9.6

-0.6

7.7

30.61

Eco828

828

845

TCAAGGGCACAACCTCCA

6

V

0.56

III

-19.8

-0.4

-7.0

-11.4

-18.9

-25.8

-12.1

-7.7

-0.3

6.7

23.66

Eco836

836

852

CCACGCCTCAAGGGCAC

8

V

0.15

V

-21.2

-1.9

-10.1

-10.1

-9.4

-9.4

-9.2

-9.2

-9.9

-9.9

10.00

Eco846

846

862

GCTCCGGAAGCCACGCC

42

III

0.39

IV

-23.5

-0.4

-11.8

-11.8

-10.6

-11.0

-11.1

-11.0

-12.2

-11.8

6.19

Eco853

853

870

ACGCGTTAGCTCCGGAAG

52

III

0.21

IV

-19.5

0.1

-8.7

-10.1

-12.0

-12.0

-10.4

-9.0

-7.1

-7.1

5.74

Eco863

863

880

GGTCGACTTAACGCGTTA

42

III

0.39

IV

-17.0

0.7

-6.4

-5.3

-12.9

-15.3

-10.4

-11.5

-4.0

-1.6

26.90

Eco871

871

888

CCCCAGGCGGTCGACTTA

87

I

0.73

II

-23.6

0.6

-5.9

-6.3

5.2

5.2

-17.5

-17.1

-23.4

-23.4

30.71

Eco881

881

897

GGCCGTACTCCCCAGGC

77

II

0.77

II

-25.4

-0.6

-8.4

-8.7

1.7

1.7

-16.2

-15.8

-24.5

-24.5

6.84

Eco889

889

906

TAACCTTGCGGCCGTACT

85

I

0.62

II

-20.5

0.4

-4.9

-6.2

-4.1

-4.1

-15.4

-14.0

-16.2

-16.2

0.00

Eco898

898

916

ATTTGAGTTTTAACCTTGC

73

II

0.52

III

-15.4

1.0

-5.4

-5.5

-3.4

-4.2

-9.9

-9.8

-11.9

-11.1

13.73

Eco907

907

925

CGTCAATTCATTTGAGTTT

40

IV

1.01

I

-14.9

-0.3

-1.3

-2.9

1.7

1.7

-12.9

-11.3

-14.2

-14.2

21.00

Eco917

917

933

CGGGCCCCCGTCAATTC

69

II

0.6

III

-23.1

-1.0

-9.1

-8.2

-10.3

-10.3

-12.8

-13.7

-11.6

-11.6

16.28

Eco926

926

941

CGCTTGTGCGGGCCCC

38

IV

0.53

III

-24.2

-1.4

-10.9

-10.0

-20.6

-28.9

-11.8

-12.8

-2.1

6.1

18.28

Eco934

934

951

CATGCTCCACCGCTTGTG

50

III

0.88

I

-21.7

-0.1

-10.4

-9.3

-19.5

-27.5

-10.8

-11.8

-1.6

6.3

27.44

Eco942

942

959

TTAAACCACATGCTCCAC

46

III

0.72

II

-16.3

1.9

-7.6

-4.8

-17.1

-21.5

-8.7

-11.4

0.9

5.3

34.53

Eco952

952

969

TTGCATCGAATTAAACCA

4

VI

0.25

IV

-12.8

1.9

-5.5

-6.2

-11.3

-21.5

-7.3

-6.5

-1.4

8.7

26.77

Eco960

960

977

TCTTCGCGTTGCATCGAA

60

III

0.46

III

-18.1

0.0

-5.9

-2.1

-11.3

-21.5

-11.8

-15.5

-6.4

3.8

35.35

Eco970

970

987

CAGGTAAGGTTCTTCGCG

33

IV

0.47

III

-18.1

0.9

-7.4

-5.0

-9.8

-21.5

-10.5

-12.9

-8.1

3.5

44.99

Eco978

978

995

GTCAAGACCAGGTAAGGT

27

IV

0.22

IV

-17.3

-0.3

-8.2

-4.1

-15.9

-15.9

-8.5

-12.6

-0.8

-0.8

24.80

Eco988

988

1005

TTCCGTGGATGTCAAGAC

8

V

0.26

IV

-17.0

1.0

-7.2

-5.3

-17.0

-20.4

-9.6

-11.5

0.1

3.5

4.03

Eco996

996

1013

CTGAAAACTTCCGTGGAT

10

V

0.2

V

-14.7

0.8

-8.3

-8.3

-19.5

-25.0

-6.3

-6.2

5.0

10.4

0.00

Eco1006

1006

1023

ATTCTCATCTCTGAAAAC

4

VI

0.06

V

-12.2

0.8

-6.7

-6.2

-7.3

-7.3

-5.4

-5.8

-4.7

-4.7

6.09

Eco1014

1014

1031

GAAGGCACATTCTCATCT

8

V

0.16

V

-16.8

1.3

-8.4

-7.2

-6.3

-7.4

-8.3

-9.5

-10.4

-9.3

6.09

Eco1024

1024

1041

CACGGTTCCCGAAGGCAC

31

IV

0.6

III

-21.1

-1.6

-10.1

-4.6

-10.3

-10.3

-9.3

-14.8

-9.2

-9.2

0.00

Eco1032

1032

1049

ACCTGTCTCACGGTTCCC

52

III

0.57

III

-23.0

0.6

-10.1

-5.1

-14.6

-20.7

-12.7

-17.7

-8.2

-2.1

7.85

Eco1042

1042

1059

GCCATGCAGCACCTGTCT

48

III

0.6

III

-23.5

0.5

-9.7

-5.6

-10.5

-17.1

-13.5

-17.6

-12.7

-6.1

31.83

Eco1050

1050

1067

TGACGACAGCCATGCAGC

6

V

0.35

IV

-20.0

0.4

-6.6

-3.5

-8.6

-15.7

-13.2

-16.2

-11.1

-4.0

38.27

Eco1060

1060

1077

CAACACGAGCTGACGACA

2

VI

0.15

V

-16.1

-0.3

-9.7

-6.3

-14.5

-24.0

-5.8

-9.1

-1.0

8.6

37.71

Eco1068

1068

1085

ACATTTCACAACACGAGC

12

V

0.2

V

-14.8

2.1

-6.4

-6.9

-17.6

-17.6

-8.4

-7.8

2.8

2.8

39.39

Eco1078

1078

1095

ACTTAACCCAACATTTCA

6

V

0.18

V

-14.7

1.9

-3.2

-4.5

-2.7

-2.7

-11.4

-10.1

-11.9

-11.9

18.94

Eco1086

1086

1103

GTTGCGGGACTTAACCCA

10

V

0.27

IV

-20.1

-0.9

-5.1

-6.6

-8.5

-9.8

-13.9

-12.4

-10.5

-9.2

23.91

Eco1097

1097

1112

GTTGCGCTCGTTGCGGG

6

V

0.27

IV

-19.7

-2.2

-6.8

-5.5

-11.3

-20.5

-10.6

-11.9

-6.1

3.0

53.14

Eco1104

1104

1121

AGGATAAGGGTTGCGCTC

8

V

0.38

IV

-18.6

1.6

-6.2

-8.9

-22.5

-27.0

-12.3

-9.7

4.0

8.5

51.16

Eco1113

1113

1130

TGGCAACAAAGGATAAGG

2

VI

0.03

VI

-12.4

-0.2

-4.7

-6.5

-14.7

-23.1

-7.1

-5.3

2.8

11.2

49.19

Eco1122

1122

1139

CCGGACCGCTGGCAACAA

15

V

0.27

IV

-21.1

-0.2

-7.6

-8.1

-8.2

-8.2

-12.9

-12.5

-12.4

-12.4

29.36

Eco1131

1131

1146

TTCCCGGCCGGACCGC

40

IV

0.48

III

-24.0

-1.7

-6.1

-6.1

-4.6

-4.6

-16.1

-16.1

-17.6

-17.6

4.33

Eco1140

1140

1157

TCTCCTTTGAGTTCCCGG

46

III

0.77

II

-21.5

0.1

-6.8

-9.3

-14.7

-4.6

-14.3

-11.8

-6.4

-16.5

26.39

Eco1147

1147

1165

ACTGGCAGTCTCCTTTGAG

13

V

0.19

V

-20.8

0.3

-5.7

-11.9

-15.5

-4.6

-14.7

-8.6

-4.9

-15.8

26.91

Eco1158

1158

1175

CCAGTTTATCACTGGCAG

2

VI

0.03

VI

-18.2

-2.3

-6.9

-6.9

-8.9

-8.9

-8.9

-8.9

-6.9

-6.9

4.86

Eco1166

1166

1183

ACCTTCCTCCAGTTTATC

10

V

0.32

IV

-19.7

2.0

-6.9

-6.9

-8.9

-8.9

-12.8

-12.8

-10.7

-10.7

13.74

Eco1176

1176

1193

CGTCATCCCCACCTTCCT

50

III

0.84

I

-24.8

2.5

-7.8

-7.8

-10.3

-13.0

-17.0

-16.9

-14.5

-11.8

45.86

Eco1184

1184

1201

TGACTTGACGTCATCCCC

6

V

0.12

V

-20.3

-0.7

-6.8

-8.2

-9.2

-12.8

-12.6

-11.2

-10.2

-6.6

42.32

Eco1194

1194

1211

AGGGCCATGATGACTTGA

10

V

0.25

IV

-18.2

1.1

-11.3

-7.1

-10.9

-17.1

-6.8

-10.9

-7.2

-1.0

30.36

Eco1202

1202

1219

TGGTCGTAAGGGCCATGA

2

VI

0.05

VI

-19.5

-0.8

-9.5

-6.6

-17.0

-24.1

-9.0

-12.0

-1.6

5.5

31.92

Eco1212

1212

1229

TGTGTAGCCCTGGTCGTA

25

IV

0.63

II

-21.8

1.8

-7.0

-8.3

-14.7

-22.9

-14.8

-13.4

-7.0

1.2

53.30

Eco1220

1220

1237

GTAGCACGTGTGTAGCCC

58

III

0.62

II

-21.9

0.5

-7.0

-8.3

-15.8

-24.4

-14.7

-13.4

-5.9

2.7

55.66

Eco1230

1230

1247

ATGCGCCATTGTAGCACG

35

IV

0.36

IV

-19.6

-0.1

-6.4

-7.7

-22.6

-31.9

-12.7

-11.4

3.5

12.9

31.10

Eco1238

1238

1255

CTCTTTGTATGCGCCATT

31

IV

0.68

II

-18.8

0.8

-5.1

-5.9

-15.6

-21.5

-13.6

-12.7

-3.1

2.9

41.47

Eco1248

1248

1265

GAGGTCGCTTCTCTTTGT

58

III

0.61

II

-19.8

0.6

-1.3

-5.9

-5.9

-5.9

-18.2

-13.7

-13.7

-13.7

24.35

Eco1256

1256

1273

GCTCTCGCGAGGTCGCTT

62

II

0.58

III

-23.1

-1.8

-5.0

-5.9

-6.2

-6.2

-16.3

-15.4

-15.1

-15.1

2.36

Eco1266

1266

1283

AGGTCCGCTTGCTCTCGC

58

III

0.52

III

-23.9

0.6

-4.1

-5.9

-5.9

-5.9

-19.5

-17.7

-17.7

-17.7

13.36

Eco1274

1274

1291

ACTTTATGAGGTCCGCTT

15

V

0.26

IV

-18.4

0.4

-2.4

-5.1

-5.9

-5.9

-15.7

-13.0

-12.2

-12.2

22.08

Eco1284

1284

1301

ACTACGACGCACTTTATG

15

V

0.33

IV

-14.9

1.0

-3.2

-5.3

-15.6

-19.8

-11.6

-9.5

0.9

5.0

20.87

Eco1292

1292

1309

CAATCCGGACTACGACGC

23

IV

0.42

III

-17.9

-0.7

-5.6

-7.4

-16.3

-20.2

-11.4

-9.5

-0.7

3.2

40.13

Eco1302

1302

1319

TTGCAGACTCCAATCCGG

33

IV

0.56

III

-19.2

0.5

-7.8

-8.3

-8.7

-17.3

-11.1

-10.6

-10.3

-1.7

59.20

Eco1310

1310

1327

GAGTCGAGTTGCAGACTC

2

VI

0.02

VI

-18.1

-0.9

-9.3

-8.3

-10.8

-10.8

-7.8

-8.7

-6.3

-6.3

51.13

Eco1320

1320

1337

CGACTTCATGGAGTCGAG

6

V

0.01

VI

-16.7

-2.9

-6.7

-8.8

-6.8

-17.3

-7.1

-5.0

-7.0

3.5

36.55

Eco1328

1328

1345

AGCGATTCCGACTTCATG

65

II

0.65

II

-17.5

-0.4

-8.6

-8.4

-9.7

-13.7

-8.2

-8.4

-7.1

-3.1

30.73

Eco1338

1338

1355

CACGATTACTAGCGATTC

15

V

0.16

V

-14.7

0.1

-4.4

-11.7

-10.2

-16.4

-9.9

-2.6

-4.1

2.1

43.64

Eco1346

1346

1363

TTCTGATCCACGATTACT

12

V

0.51

III

-15.9

0.8

-0.4

-7.5

-14.2

-16.4

-15.1

-8.2

-1.5

0.7

40.24

Eco1356

1356

1373

CACCGTGGCATTCTGATC

19

V

0.43

III

-19.3

0.9

-6.7

-7.5

-15.6

-16.4

-12.5

-11.6

-3.6

-2.7

51.27

Eco1364

1364

1382

GAACGTATTCACCGTGGCA

21

IV

0.56

III

-19.6

-0.2

-8.4

-10.3

-9.6

-16.4

-10.6

-8.7

-9.4

-2.6

70.54

Eco1374

1374

1391

AAGGCCCGGGAACGTATT

52

III

0.58

III

-19.2

-0.9

-1.3

-3.2

-18.4

-21.1

-16.7

-14.9

0.3

3.0

35.85

Eco1383

1383

1400

GGTGTGTACAAGGCCCGG

65

II

0.58

III

-21.9

0.8

-4.0

-5.5

-10.3

-10.3

-17.7

-16.2

-11.4

-11.4

6.11

Eco1392

1392

1409

GTGACGGGCGGTGTGTAC

67

II

0.48

III

-20.8

0.2

-5.2

-5.1

0.4

0.4

-15.3

-15.4

-20.2

-20.2

4.13

Eco1401

1401

1418

TCCCATGGTGTGACGGGC

67

II

0.64

II

-22.7

-0.3

-6.1

-5.7

-5.3

-5.3

-16.0

-16.4

-16.8

-16.8

2.51

Eco1410

1410

1427

GCAACCCACTCCCATGGT

90

I

0.52

III

-23.4

0.1

-9.2

-8.8

-25.3

-5.3

-13.8

-14.2

2.4

-17.6

2.51

Eco1419

1419

1436

ACTTCTTTTGCAACCCAC

23

IV

0.46

III

-18.0

1.5

-5.6

-6.2

-23.5

-5.3

-12.3

-11.8

5.6

-12.6

1.18

Eco1428

1428

1445

AAGCTACCTACTTCTTTT

38

IV

0.66

II

-15.8

1.0

-5.9

-7.2

-16.0

-5.3

-9.8

-8.5

0.3

-10.4

7.78

Eco1437

1437

1454

CCGAAGGTTAAGCTACCT

4

VI

0.04

VI

-17.7

-0.6

-8.4

-8.2

-10.2

-10.2

-8.5

-8.8

-6.8

-6.8

6.60

Eco1446

1446

1463

AGCGCCCTCCCGAAGGTT

44

III

0.59

III

-24.8

-0.7

-7.4

-7.3

-9.1

-9.1

-16.6

-16.6

-14.8

-14.8

18.42

Eco1455

1455

1472

AAAGTGGTAAGCGCCCTC

31

IV

0.69

II

-19.0

0.6

-10.0

-8.5

-10.5

-10.5

-8.8

-10.2

-8.2

-8.2

18.42

Eco1464

1464

1481

ATGAATCACAAAGTGGTA

4

VI

0.03

VI

-12.0

0.3

-4.5

-3.1

-24.5

-10.5

-7.2

-8.6

12.8

-1.1

0.00

Eco1473

1473

1490

ACCCCAGTCATGAATCAC

65

II

0.66

II

-18.6

0.6

-4.6

-3.1

-24.2

-10.5

-13.8

-15.3

5.9

-7.8

0.83

Eco1482

1482

1499

TACGACTTCACCCCAGTC

100

I

0.56

III

-20.3

0.5

-4.7

-4.2

-3.4

-5.3

-15.4

-15.8

-16.6

-14.7

5.81

Eco1491

1491

1508

TTACCTTGTTACGACTTC

31

IV

0.39

IV

-15.6

1.0

-7.0

-7.5

-4.0

-4.0

-8.5

-7.9

-11.5

-11.5

4.98

Eco1500

1500

1517

CCCCTACGGTTACCTTGT

92

I

0.51

III

-22.3

0.9

-12.3

-14.3

-12.5

-14.4

-9.8

-7.9

-9.7

-7.7

0.00

Eco1509

1509

1525

CGCAGGTTCCCCTACGG

4

VI

0.13

V

-22.3

-0.6

-12.3

-14.4

-17.5

-17.5

-9.2

-7.1

-4.0

-4.0

6.84

Eco1518

1518

1535

GTGATCCAACCGCAGGTT

17

V

0.17

V

-20.3

-2.5

-11.8

-13.8

-13.8

-14.4

-6.1

-4.0

-4.0

-3.4

6.84

Eco1526

1526

1542

TAAGGAGGTGATCCAAC

25

IV

0.29

IV

-14.0

-1.0

-5.0

-5.8

-5.2

-5.2

-7.9

-7.1

-7.6

-7.6

0.00

* Fuchs, B., Wallner, G., Beisker, W., Schwippl, I., Ludwig, W., and Amann, R. (1998). "Flow Cytometric Analysis of the In Situ Accessibility of Escherichia coli 16S rRNA for Fluorescently Labeled Oligonucleotide Probes." Applied and Environmental Microbiology, 64(12), 4973-4982.

** Behrens, S., Rühland, C., Inácio, J., Huber, H., Fonseca, A., Spencer-Martins, I., Fuchs, B., and Amann, R. (2003). "In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucleotide Probes." Applied and Environmental Microbiology, 69, 1748-1758.

 


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This page was created on March 24, 2004. Last revision was on December 06, 2008