Table 2

Comparison of expected and observed di-nucleotide frequencies and di-nucleotide PWM
1 2 3 4 5
AA 0 0 0 0 14
0 0 0 0 11.75
AT 0 0 72 0 10
0 0 71.04 0 5.88
AG 32 0 5 0 20
30.91 0 5.64 0 30.12
AC 0 0 0 0 4
0.46 0 0 0 2.2
TA 0 0 0 45 9
0 0 0 46.28 5.47
TT 0 0 1 24 0
0 0 1.08 21.53 2.73
TG 25 0 0 4 17
25.18 0 0.09 4.31 14.01
TC 0 0 0 1 0
0.38 0 0 1.08 1.03
GA 0 76 0 3 0
0 75.55 0 3.67 1.09
GT 0 1 1 2 0
0 1.14 1.08 1.71 0.55
GG 3 1 0 0 3
4.58 1.14 0.09 0.34 2.8
GC 1 0 0 0 1
0.07 0 0 0.09 0.21
CA 0 1 0 0 0
0 1.13 0 0 0.27
CT 0 0 0 0 0
0 0.02 0 0 0.14
CG 18 0 0 0 1
17.17 0.02 0 0 0.7
CC 0 0 0 0 0
0.26 0 0 0 0.05
AA -4.62 -5.66 -6.16 -5.81 -0.16
AT -4.14 -5.18 0.00 -5.33 -0.02
AG 0.00 -5.91 -3.39 -6.06 -0.05
AC -4.41 -5.45 -5.94 -5.60 -1.20
TA -4.02 -5.06 -5.55 0.00 0.00
TT -4.58 -5.62 -4.72 -1.20 -4.17
TG -0.09 -5.75 -6.24 -3.11 -0.06
TC -4.69 -5.73 -6.22 -4.48 -4.27
GA -4.69 0.00 -6.22 -3.38 -4.27
GT -4.44 -4.08 -4.57 -3.54 -4.02
GG -2.69 -4.83 -6.72 -6.38 -2.27
GC -3.70 -6.14 -6.63 -6.29 -3.29
CA -4.70 -4.34 -6.24 -5.89 -4.28
CT -4.84 -5.89 -6.38 -6.04 -4.43
CG -0.47 -5.80 -6.29 -5.95 -2.95
CC -5.17 -6.22 -6.71 -6.37 -4.76
AG/TG/CG GA AT TA TA/AT/AG/TG/AA

Optimized di-nucleotide frequency table and PWM. The observed frequencies are provided in the first line for each di-nucleotide, with the following line representing expected di-nucleotide frequencies (calculated from the mono-nucleotide frequencies). The presented are the frequencies of the di-nucleotides from the motifs selected from the interval -7 to 0.

Nandi and Ioshikhes

Nandi and Ioshikhes BMC Genomics 2012 13:416   doi:10.1186/1471-2164-13-416

Open Data