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Table 1 Frequency of MNase-preferred tetramers at the cutting sites

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
TATA.TATA 13.28 < 10-18 CTAG.CTAG 4.07 < 10-18
ATAG.CTAT 8.45 < 10-18 ATAG.CTAT 3.93 < 10-18
CTAA.TTAG 7.90 < 10-18 CAAG.CTTG 3.57 < 10-18
CTAG.CTAG 6.80 < 10-18 CTTA.TAAG 3.52 < 10-18
ATTA.TAAT 5.74 < 10-18 CATG.CATG 3.42 3.01 × 10-4
CATA.TATG 5.62 < 10-18 CATA.TATG 3.11 < 10-18
ATAA.TTAT 5.14 < 10-18 CTAA.TTAG 3.00 < 10-18
CTTA.TAAG 4.92 < 10-18 CTAC.GTAG 2.98 < 10-18
TTAA.TTAA 4.64 < 10-18 ATTG.CAAT 2.96 < 10-18
ATAT.ATAT 4.52 < 10-18 AAAG.CTTT 2.82 < 10-18
TAAA.TTTA 3.48 < 10-18 CTTC.GAAG 2.79 < 10-18
ATTG.CAAT 3.25 < 10-18 AATG.CATT 2.50 < 10-18
GTAA.TTAC 2.64 1.01 × 10-4 CATC.GATG 2.24 6.03 × 10-4
ATAC.GTAT 2.39 2.01 × 10-4 CAAC.GTTG 2.19 10-3
    CAAA.TTTG 2.17 < 10-18
  1. Experimentally detected and expected frequency ratios of MNase-preferred tetramers at the cutting sites for naked (left) and nucleosomal (right) DNAs. Displayed tetramers are observed in at least two-fold higher frequency than expected, with a statistically significant difference (p < 10-3) (Supplementary Methods). Ratios for d(TAAA)·d(TTTA) and d(GTAA)·d(TTAC) tetramers in nucleosomal DNA are 1.39 (p < 0.08) and 1.6 (p < 0.03) respectively.