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Table 2 Frequency of tetramers in MNase-digested LRs and CLRs

From: Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Naked DNA

ratio

p-val

Nucleosomal DNA

ratio

p-val

Common low regions (CLR)

ratio

p-val

AAAA.TTTT

3.87

< 10-18

TATA.TATA

4.06

< 10-18

AAAA.TTTT

4.48

< 10-18

TAAA.TTTA

2.38

< 10-18

ATAT.ATAT

3.09

< 10-18

TATA.TATA

3.18

< 10-18

TATA.TATA

2.38

9.05 × 10-4

AAAA.TTTT

2.91

< 10-18

TAAA.TTTA

2.67

< 10-18

AAAT.ATTT

2.16

< 10-18

ATAA.TTAT

2.21

< 10-18

ATAA.TTAT

2.62

< 10-18

ATAA.TTAT

2.13

< 10-18

AATA.TATT

2.08

< 10-18

ATAT.ATAT

2.57

< 10-18

TTAA.TTAA

2.10

7.54 × 10-3

ATTA.TAAT

1.99

10-4

AATA.TATT

2.43

< 10-18

AATA.TATT

2.02

< 10-18

TAAA.TTTA

1.84

7.04 × 10-4

TTAA.TTAA

2.29

3.22 × 10-3

ATAT.ATAT

2.00

4.62 × 10-3

AAAT.ATTT

1.62

4.22 × 10-3

AAAT.ATTT

2.27

< 10-18

AATT.AATT

1.84

5.53 × 10-3

   

ATTA.TAAT

2.15

< 10-18

ATTA.TAAT

1.79

3.62 × 10-3

   

AATT.AATT

1.81

1.30 × 10-2

GAAA.TTTC

1.45

3.44 × 10-2

      
  1. Experimentally detected and expected frequency ratios of different tetramers in MNase-digested LRs for naked (left) and nucleosomal (center) DNAs, and in CLRs (right). Displayed tetramers show a significant enrichment (p < 0.05) respect to genome average (Additional File 1: Additional Methods).
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BMC Genomics

ISSN: 1471-2164

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