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Table 1 Markov chain transition probabilities: probability for a nucleotide A, C, T or G to be: a) in the first position x1 of a codon, b) in the second position x2 of a codon given the nucleotide at x1, and c) in the third position x3 of a codon given the dinucleotide at x1x2

From: SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution

a)b)c)
x1ACTGx2ACTGx3ACTG
Start    x1    x1x2    
0.240.310.190.25A0.210.280.210.30AA0.160.350.130.36
     C0.270.380.210.14AC0.220.490.140.15
     T0.120.350.200.33AT0.020.410.140.43
     G0.290.300.190.22AG0.120.550.200.13
          CA0.090.220.120.57
          CC0.260.350.280.11
          CT0.070.260.120.55
          CG0.170.370.200.26
          TA0.010.640.340.01
          TC0.200.480.200.12
          TT0.100.480.220.20
          TG0.050.410.300.24
          GA0.210.250.180.36
          GC0.150.550.180.12
          GT0.080.300.160.46
          GG0.190.390.130.29