| blob | 62a7593ffd9dbfe3d7589dcea48e1f4106d539ff |
1 CODONML (in paml 3.15, November 2005) /tmp/I7ZhE4PgvE/V8dSv7iz0l Model: One dN/dS ratio
2 Codon frequencies: F3x4
3 ns = 4 ls = 573
5 Codon usage in sequences
6 --------------------------------------------------------------------------------------
7 Phe TTT 4 4 5 3 | Ser TCT 16 15 11 15 | Tyr TAT 11 11 14 14 | Cys TGT 2 1 2 1
8 TTC 7 7 8 8 | TCC 12 8 16 8 | TAC 14 14 10 11 | TGC 1 2 1 2
9 Leu TTA 1 1 1 2 | TCA 5 7 3 6 | *** TAA 0 0 0 0 | *** TGA 0 0 0 0
10 TTG 5 5 8 7 | TCG 5 5 8 6 | TAG 0 0 0 0 | Trp TGG 6 6 6 6
11 --------------------------------------------------------------------------------------
12 Leu CTT 7 7 10 8 | Pro CCT 22 21 18 17 | His CAT 5 3 3 5 | Arg CGT 3 2 2 2
13 CTC 14 15 13 17 | CCC 11 13 12 16 | CAC 4 3 5 5 | CGC 4 5 5 4
14 CTA 1 1 0 2 | CCA 12 13 14 11 | Gln CAA 38 38 40 38 | CGA 4 3 4 2
15 CTG 7 7 4 4 | CCG 14 13 12 13 | CAG 33 34 28 31 | CGG 2 3 4 5
16 --------------------------------------------------------------------------------------
17 Ile ATT 3 4 4 3 | Thr ACT 6 8 4 5 | Asn AAT 9 10 9 6 | Ser AGT 3 3 5 3
18 ATC 11 11 9 10 | ACC 5 4 7 7 | AAC 14 13 12 15 | AGC 4 4 5 6
19 ATA 1 2 2 2 | ACA 4 3 9 8 | Lys AAA 6 7 5 4 | Arg AGA 6 7 7 7
20 Met ATG 9 9 11 8 | ACG 10 9 5 5 | AAG 16 15 17 19 | AGG 7 7 4 5
21 --------------------------------------------------------------------------------------
22 Val GTT 3 4 5 5 | Ala GCT 16 16 16 18 | Asp GAT 14 14 15 18 | Gly GGT 17 16 17 18
23 GTC 8 8 8 8 | GCC 19 18 15 18 | GAC 13 15 13 10 | GGC 8 9 10 9
24 GTA 7 6 7 6 | GCA 16 17 11 14 | Glu GAA 16 17 19 15 | GGA 7 7 4 6
25 GTG 5 7 6 7 | GCG 10 8 18 10 | GAG 24 22 21 23 | GGG 6 6 6 6
26 --------------------------------------------------------------------------------------
28 Codon position x base (3x4) table for each sequence.
30 #1: R265
31 position 1: T:0.15532 C:0.31588 A:0.19895 G:0.32984
32 position 2: T:0.16230 C:0.31937 A:0.37871 G:0.13962
33 position 3: T:0.24607 C:0.26003 A:0.21640 G:0.27749
35 #2: WM276
36 position 1: T:0.15009 C:0.31588 A:0.20244 G:0.33159
37 position 2: T:0.17103 C:0.31065 A:0.37696 G:0.14136
38 position 3: T:0.24258 C:0.26003 A:0.22513 G:0.27225
40 #3: H99
41 position 1: T:0.16230 C:0.30366 A:0.20070 G:0.33333
42 position 2: T:0.17627 C:0.31239 A:0.36824 G:0.14311
43 position 3: T:0.24433 C:0.26003 A:0.21990 G:0.27574
45 #4: JEC21
46 position 1: T:0.15532 C:0.31414 A:0.19721 G:0.33333
47 position 2: T:0.17452 C:0.30890 A:0.37347 G:0.14311
48 position 3: T:0.24607 C:0.26876 A:0.21466 G:0.27051
50 Sums of codon usage counts
51 ------------------------------------------------------------------------------
52 Phe F TTT 16 | Ser S TCT 57 | Tyr Y TAT 50 | Cys C TGT 6
53 TTC 30 | TCC 44 | TAC 49 | TGC 6
54 Leu L TTA 5 | TCA 21 | *** * TAA 0 | *** * TGA 0
55 TTG 25 | TCG 24 | TAG 0 | Trp W TGG 24
56 ------------------------------------------------------------------------------
57 Leu L CTT 32 | Pro P CCT 78 | His H CAT 16 | Arg R CGT 9
58 CTC 59 | CCC 52 | CAC 17 | CGC 18
59 CTA 4 | CCA 50 | Gln Q CAA 154 | CGA 13
60 CTG 22 | CCG 52 | CAG 126 | CGG 14
61 ------------------------------------------------------------------------------
62 Ile I ATT 14 | Thr T ACT 23 | Asn N AAT 34 | Ser S AGT 14
63 ATC 41 | ACC 23 | AAC 54 | AGC 19
64 ATA 7 | ACA 24 | Lys K AAA 22 | Arg R AGA 27
65 Met M ATG 37 | ACG 29 | AAG 67 | AGG 23
66 ------------------------------------------------------------------------------
67 Val V GTT 17 | Ala A GCT 66 | Asp D GAT 61 | Gly G GGT 68
68 GTC 32 | GCC 70 | GAC 51 | GGC 36
69 GTA 26 | GCA 58 | Glu E GAA 67 | GGA 24
70 GTG 25 | GCG 46 | GAG 90 | GGG 24
71 ------------------------------------------------------------------------------
74 Codon position x base (3x4) table, overall
76 position 1: T:0.15576 C:0.31239 A:0.19983 G:0.33202
77 position 2: T:0.17103 C:0.31283 A:0.37435 G:0.14180
78 position 3: T:0.24476 C:0.26222 A:0.21902 G:0.27400
81 Nei & Gojobori 1986. dN/dS (dN, dS)
82 (Note: This matrix is not used in later m.l. analysis.
83 Use runmode = -2 for ML pairwise comparison.)
85 R265
86 WM276 0.2264 (0.0186 0.0821)
87 H99 0.1481 (0.0586 0.3959) 0.1481 (0.0611 0.4126)
88 JEC21 0.1112 (0.0421 0.3787) 0.1173 (0.0466 0.3970) 0.1419 (0.0380 0.2679)
90 pairwise comparison, codon frequencies: F3x4.
93 2 (WM276) ... 1 (R265)
94 lnL =-2569.912690
95 0.10404 3.29148 0.32693
97 t= 0.1040 S= 541.4 N= 1177.6 dN/dS= 0.3269 dN= 0.0210 dS= 0.0644
100 3 (H99) ... 1 (R265)
101 lnL =-3019.970151
102 0.43604 3.31017 0.20554
104 t= 0.4360 S= 540.2 N= 1178.8 dN/dS= 0.2055 dN= 0.0656 dS= 0.3193
107 3 (H99) ... 2 (WM276)
108 lnL =-3036.174074
109 0.45547 3.63495 0.20989
111 t= 0.4555 S= 547.4 N= 1171.6 dN/dS= 0.2099 dN= 0.0691 dS= 0.3290
114 4 (JEC21) ... 1 (R265)
115 lnL =-2937.357570
116 0.38462 2.95077 0.15134
118 t= 0.3846 S= 530.2 N= 1188.8 dN/dS= 0.1513 dN= 0.0470 dS= 0.3104
121 4 (JEC21) ... 2 (WM276)
122 lnL =-2966.384266
123 0.41002 3.25414 0.16413
125 t= 0.4100 S= 538.1 N= 1180.9 dN/dS= 0.1641 dN= 0.0527 dS= 0.3210
128 4 (JEC21) ... 3 (H99)
129 lnL =-2844.283241
130 0.29120 4.67661 0.21504
132 t= 0.2912 S= 566.5 N= 1152.5 dN/dS= 0.2150 dN= 0.0441 dS= 0.2049