Table 2

Microsatellite types with a significant difference in frequency either between hot and non-hot IGRs, or hot and non-hot ORFs, in the S. cerevisiae genome. Significance was inferred where p < 0.0026, with the level of alpha adjusted for 19 independent classes of repeat using Bonferroni's correction. The Mann-Whitney U Test or T Test was used, depending whether samples were normally distributed. The e value denotes the number of bases in any part of a repeat within which no more than one mismatch was allowed with respect to the consensus motif. A lower e value therefore results in the detection of more imperfect repeats.

Repeat type

IGRs

ORFs

Motif length

Copy number

Mis-matches allowed

Mean per kb freq.

Freq. ratio (hot/non hot)

P value

Mean per kb freq.

Freq. ratio (hot/non hot)

P value

Hot

Non hot

Hot

Non hot

1 (A)

3 to 5

perfect

35.0

39.9

0.88

< 0.0001

29.2

36.1

0.81

< 0.0001

e = 10

34.3

39.4

0.87

< 0.0001

29.1

36.0

0.81

< 0.0001

e = 6

31.8

36.7

0.87

< 0.0001

28.0

34.7

0.81

< 0.0001

6+

perfect

5.42

4.61

1.17

< 0.0001

0.981

1.64

0.60

< 0.0001

e = 10

5.24

4.50

1.16

< 0.0001

0.978

1.64

0.60

< 0.0001

e = 6

6.12

5.53

1.11

0.00173

1.28

2.13

0.60

< 0.0001

14+

perfect

0.418

0.171

2.45

< 0.0001

0.0134

0.00733

1.83

n/s

e = 10

0.733

0.311

2.36

< 0.0001

0.0182

0.0166

1.10

n/s

e = 6

0.854

0.377

2.26

< 0.0001

0.0218

0.0271

0.80

n/s

1 (G)

3 to 5

perfect

9.18

7.25

1.27

< 0.0001

12.9

10.1

1.28

< 0.0001

e = 10

9.16

7.24

1.27

< 0.0001

12.9

10.1

1.28

< 0.0001

e = 6

8.89

7.13

1.25

< 0.0001

12.6

9.93

1.27

< 0.0001

6+

e = 6

0.160

0.0931

1.72

0.00124

0.135

0.0798

1.69

n/s

14+

perfect

0.0035

0.000725

4.83

0.00179

0

0

n/a

n/a

e = 10

0.0035

0.000725

4.83

0.00179

0

0

n/a

n/a

e = 6

0.0035

0.000725

4.83

0.00179

0

0

n/a

n/a

2

3 to 5

perfect

4.67

3.96

1.18

< 0.0001

1.82

1.74

1.05

n/s

e = 10

4.34

3.68

1.18

0.000266

1.78

1.71

1.04

n/s

e = 6

6.17

5.52

1.12

0.000234

3.18

3.14

1.01

n/s

6+

perfect

0.368

0.196

1.88

0.000248

0.0405

0.00572

7.09

n/s

e = 10

0.599

0.356

1.68

< 0.0001

0.0720

0.0229

3.14

n/s

e = 6

0.797

0.529

1.51

< 0.0001

0.109

0.0398

2.73

n/s

10+

perfect

0.158

0.0606

2.62

n/s

0.0163

0.00173

9.44

< 0.0001

e = 10

0.221

0.0931

2.38

0.00164

0.0207

0.00275

7.53

< 0.0001

e = 6

0.252

0.109

2.32

0.00132

0.0159

0.00584

2.72

< 0.0001

6

6+

e = 6

0.00552

0.00341

1.62

n/s

0.0135

0.000877

15.40

< 0.0001

Bagshaw et al. BMC Genomics 2008 9:49   doi:10.1186/1471-2164-9-49