| blob | 03618af1e8789e9803d75cc3c1bc6c9c433a11aa |
1 YN00 examples/abglobin.nuc
3 ns = 5 ls = 285
5 Codon position x base (3x4) table for each sequence.
7 human
8 position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649
9 position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333
10 position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140
12 goat-cow
13 position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000
14 position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035
15 position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088
17 rabbit
18 position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140
19 position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684
20 position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439
22 rat
23 position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895
24 position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439
25 position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421
27 marsupial
28 position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439
29 position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333
30 position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123
32 Average
33 position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825
34 position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965
35 position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842
37 Codon usage for each species
38 --------------------------------------------------------------------------------------------------
39 Phe TTT 5 8 3 3 6 | Ser TCT 4 2 6 7 6 | Tyr TAT 3 2 3 1 1 | Cys TGT 2 1 1 2 2
40 TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3
41 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 1 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
42 TTG 0 2 1 4 5 | TCG 0 1 0 0 2 | TAG 0 0 0 0 0 | Trp TGG 3 3 3 3 4
43 --------------------------------------------------------------------------------------------------
44 Leu CTT 1 1 0 1 3 | Pro CCT 7 2 4 7 3 | His CAT 2 4 4 5 6 | Arg CGT 1 2 1 2 1
45 CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0
46 CTA 1 2 0 2 1 | CCA 2 0 1 0 0 | Gln CAA 0 0 0 0 1 | CGA 0 0 0 0 0
47 CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0
48 --------------------------------------------------------------------------------------------------
49 Ile ATT 0 0 1 4 1 | Thr ACT 3 4 4 3 10 | Asn AAT 1 5 5 3 2 | Ser AGT 2 3 5 2 1
50 ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3
51 ATA 0 0 0 1 0 | ACA 1 0 0 1 0 | Lys AAA 4 3 5 5 3 | Arg AGA 0 1 0 0 2
52 Met ATG 3 3 2 4 5 | ACG 0 0 0 0 0 | AAG 18 21 19 19 21 | AGG 4 3 4 4 2
53 --------------------------------------------------------------------------------------------------
54 Val GTT 5 5 4 4 6 | Ala GCT 8 11 8 13 10 | Asp GAT 5 8 1 11 6 | Gly GGT 5 4 5 6 10
55 GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5
56 GTA 0 0 0 1 1 | GCA 0 1 1 3 2 | Glu GAA 2 2 7 4 4 | GGA 0 1 0 3 3
57 GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2
58 --------------------------------------------------------------------------------------------------
61 Sums
62 --------------------------------------------------
63 Phe TTT 25 | Ser TCT 25 | Tyr TAT 10 | Cys TGT 8
64 TTC 51 | TCC 31 | TAC 19 | TGC 9
65 Leu TTA 0 | TCA 1 | *** TAA 0 | *** TGA 0
66 TTG 12 | TCG 3 | TAG 0 | Trp TGG 16
67 --------------------------------------------------
68 Leu CTT 6 | Pro CCT 23 | His CAT 21 | Arg CGT 7
69 CTC 24 | CCC 25 | CAC 68 | CGC 1
70 CTA 6 | CCA 3 | Gln CAA 1 | CGA 0
71 CTG 123 | CCG 5 | CAG 25 | CGG 2
72 --------------------------------------------------
73 Ile ATT 6 | Thr ACT 24 | Asn AAT 16 | Ser AGT 13
74 ATC 12 | ACC 53 | AAC 35 | AGC 19
75 ATA 1 | ACA 2 | Lys AAA 20 | Arg AGA 3
76 Met ATG 17 | ACG 0 | AAG 98 | AGG 17
77 --------------------------------------------------
78 Val GTT 24 | Ala GCT 50 | Asp GAT 31 | Gly GGT 30
79 GTC 19 | GCC 92 | GAC 48 | GGC 60
80 GTA 2 | GCA 7 | Glu GAA 19 | GGA 7
81 GTG 89 | GCG 14 | GAG 40 | GGG 7
82 --------------------------------------------------
85 Nei & Gojobori 1986. dN/dS (dN, dS)
86 human
87 goat-cow 0.251(0.0863 0.3443)
88 rabbit 0.263(0.0867 0.3301) 0.294(0.1054 0.3581)
89 rat 0.204(0.1261 0.6164) 0.246(0.1493 0.6065) 0.218(0.1348 0.6187)
90 marsupial 0.190(0.1931 1.0148) 0.189(0.1910 1.0099) 0.218(0.2111 0.9668) 0.272(0.2404 0.8852)
92 Estimation by the method of Yang & Nielsen (2000):
93 (equal weighting of pathways)
95 seq. seq. S N t kappa omega dN +- SE dS +- SE
97 2 1 183.7 671.3 0.5169 1.5804 0.1625 0.0818 +- 0.0115 0.5031 +- 0.0930
98 3 1 177.5 677.5 0.5033 1.5804 0.1642 0.0815 +- 0.0114 0.4967 +- 0.0927
99 3 2 180.1 674.9 0.5627 1.5804 0.1929 0.0997 +- 0.0128 0.5169 +- 0.0925
100 4 1 191.3 663.7 0.9075 1.5804 0.1308 0.1216 +- 0.0144 0.9301 +- 0.1987
101 4 2 192.4 662.6 0.9642 1.5804 0.1557 0.1447 +- 0.0159 0.9297 +- 0.2091
102 4 3 187.0 668.0 0.9790 1.5804 0.1262 0.1298 +- 0.0149 1.0286 +- 0.2614
103 5 1 189.3 665.7 2.1638 1.5804 0.0711 0.1853 +- 0.0184 2.6055 +- 3.9344
104 5 2 190.4 664.6 1.2984 1.5804 0.1416 0.1842 +- 0.0184 1.3008 +- 0.1995
105 5 3 185.2 669.8 1.3214 1.5804 0.1554 0.2023 +- 0.0194 1.3020 +- 0.2026
106 5 4 194.5 660.5 1.5554 1.5804 0.1591 0.2354 +- 0.0215 1.4797 +- 0.5173