| blob | 6b4edfc922f5616b6fabcd2f41f18a8a34412065 |
1 2 195
3 seq1 GTT ACC GGT CTT GAC ATG AAC ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTT TTA GGT
4 seq2 GTT GCT GGT CTT GAC ATG AAT ATC AGC CAA TTT CTA AAA AGC CTT GGC CTT GAA CAC CTT CGG GAT ATC TTT GAA ACA GAA CAG ATT ACA CTA GAT GTG TTG GCT GAT ATG GGT CAT GAA GAG TTG AAA GAA ATA GGC ATC AAT GCA TAT GGG CAC CGC CAC AAA TTA ATC AAA GGA GTA GAA AGA CTC TTA GGT
8 Printing out site pattern counts
11 2 111 P
13 seq1 AAA AAC AAT ACA ACC AGA AGC ATA ATC ATG ATT CAA CAC CAG CAT CGC CGG CTA CTT CTT GAA GAC GAG GAT GCA GCT GGA GGC GGG GGT GTA GTG GTT TAT TTA TTG TTT
14 seq2 ... ..T ... ... G.T ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 4 1 1 2 1 1 2 1 4 2 1 1 3 1 1
17 1 1 2 1 4 6 1 1 3 1 1 1 2 1 3
18 1 1 1 1 2 2 2
20 CODONML (in paml version 4.5, December 2011) /var/folders/pr/wb88nxq93xn7hdhgr2_bjd5w0000gn/T/UIa4SSyGGv/Bw_1hNQpYZ
21 Model: One dN/dS ratio for branches kappa = 2.000 fixed
23 Codon frequency model: F3x4
24 ns = 2 ls = 65
26 Codon usage in sequences
27 --------------------------------------------------------------
28 Phe TTT 2 2 | Ser TCT 0 0 | Tyr TAT 1 1 | Cys TGT 0 0
29 TTC 0 0 | TCC 0 0 | TAC 0 0 | TGC 0 0
30 Leu TTA 2 2 | TCA 0 0 | *** TAA 0 0 | *** TGA 0 0
31 TTG 2 2 | TCG 0 0 | TAG 0 0 | Trp TGG 0 0
32 --------------------------------------------------------------
33 Leu CTT 5 4 | Pro CCT 0 0 | His CAT 1 1 | Arg CGT 0 0
34 CTC 0 1 | CCC 0 0 | CAC 3 3 | CGC 1 1
35 CTA 2 2 | CCA 0 0 | Gln CAA 1 1 | CGA 0 0
36 CTG 0 0 | CCG 0 0 | CAG 1 1 | CGG 1 1
37 --------------------------------------------------------------
38 Ile ATT 1 1 | Thr ACT 0 0 | Asn AAT 1 2 | Ser AGT 0 0
39 ATC 4 4 | ACC 1 0 | AAC 1 0 | AGC 2 2
40 ATA 1 1 | ACA 2 2 | Lys AAA 4 4 | Arg AGA 1 1
41 Met ATG 2 2 | ACG 0 0 | AAG 0 0 | AGG 0 0
42 --------------------------------------------------------------
43 Val GTT 1 1 | Ala GCT 1 2 | Asp GAT 3 3 | Gly GGT 3 3
44 GTC 0 0 | GCC 0 0 | GAC 1 1 | GGC 2 2
45 GTA 1 1 | GCA 1 1 | Glu GAA 6 6 | GGA 1 1
46 GTG 1 1 | GCG 0 0 | GAG 1 1 | GGG 1 1
47 --------------------------------------------------------------
49 Codon position x base (3x4) table for each sequence.
51 #1: seq1
52 position 1: T:0.10769 C:0.23077 A:0.30769 G:0.35385
53 position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462
54 position 3: T:0.29231 C:0.23077 A:0.33846 G:0.13846
55 Average T:0.25641 C:0.17949 A:0.33846 G:0.22564
57 #2: seq2
58 position 1: T:0.10769 C:0.23077 A:0.29231 G:0.36923
59 position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462
60 position 3: T:0.30769 C:0.21538 A:0.33846 G:0.13846
61 Average T:0.26154 C:0.17436 A:0.33333 G:0.23077
63 Sums of codon usage counts
64 ------------------------------------------------------------------------------
65 Phe F TTT 4 | Ser S TCT 0 | Tyr Y TAT 2 | Cys C TGT 0
66 TTC 0 | TCC 0 | TAC 0 | TGC 0
67 Leu L TTA 4 | TCA 0 | *** * TAA 0 | *** * TGA 0
68 TTG 4 | TCG 0 | TAG 0 | Trp W TGG 0
69 ------------------------------------------------------------------------------
70 Leu L CTT 9 | Pro P CCT 0 | His H CAT 2 | Arg R CGT 0
71 CTC 1 | CCC 0 | CAC 6 | CGC 2
72 CTA 4 | CCA 0 | Gln Q CAA 2 | CGA 0
73 CTG 0 | CCG 0 | CAG 2 | CGG 2
74 ------------------------------------------------------------------------------
75 Ile I ATT 2 | Thr T ACT 0 | Asn N AAT 3 | Ser S AGT 0
76 ATC 8 | ACC 1 | AAC 1 | AGC 4
77 ATA 2 | ACA 4 | Lys K AAA 8 | Arg R AGA 2
78 Met M ATG 4 | ACG 0 | AAG 0 | AGG 0
79 ------------------------------------------------------------------------------
80 Val V GTT 2 | Ala A GCT 3 | Asp D GAT 6 | Gly G GGT 6
81 GTC 0 | GCC 0 | GAC 2 | GGC 4
82 GTA 2 | GCA 2 | Glu E GAA 12 | GGA 2
83 GTG 2 | GCG 0 | GAG 2 | GGG 2
84 ------------------------------------------------------------------------------
87 Codon position x base (3x4) table, overall
89 position 1: T:0.10769 C:0.23077 A:0.30000 G:0.36154
90 position 2: T:0.36923 C:0.07692 A:0.36923 G:0.18462
91 position 3: T:0.30000 C:0.22308 A:0.33846 G:0.13846
92 Average T:0.25897 C:0.17692 A:0.33590 G:0.22821
94 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
95 0.01224357 0.00910419 0.01381326 0.00565088
96 0.00255074 0.00189671 0.00287776 0.00117727
97 0.01224357 0.00910419 0.00000000 0.00000000
98 0.00612179 0.00455210 0.00000000 0.00282544
99 0.02623622 0.01950899 0.02959984 0.01210903
100 0.00546588 0.00406437 0.00616663 0.00252271
101 0.02623622 0.01950899 0.02959984 0.01210903
102 0.01311811 0.00975449 0.01479992 0.00605451
103 0.03410709 0.02536168 0.03847979 0.01574173
104 0.00710564 0.00528368 0.00801662 0.00327953
105 0.03410709 0.02536168 0.03847979 0.01574173
106 0.01705355 0.01268084 0.01923990 0.00787087
107 0.04110342 0.03056408 0.04637309 0.01897081
108 0.00856321 0.00636752 0.00966106 0.00395225
109 0.04110342 0.03056408 0.04637309 0.01897081
110 0.02055171 0.01528204 0.02318654 0.00948540
114 Nei & Gojobori 1986. dN/dS (dN, dS)
115 (Note: This matrix is not used in later ML. analysis.
116 Use runmode = -2 for ML pairwise comparison.)
118 seq1
119 seq2 0.0913 (0.0066 0.0726)
121 pairwise comparison, codon frequencies: F3x4.
124 2 (seq2) ... 1 (seq1)
125 lnL = -272.706911
126 0.06846 0.10294
128 t= 0.0685 S= 51.9 N= 143.1 dN/dS= 0.1029 dN = 0.0069 dS = 0.0668