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1 CODONML (in paml 3.12 February 2002) abglobin.nuc Model: several dN/dS ratios for branches
2 Codon frequencies: F3x4
4 ns = 5 ls = 285
5 # site patterns = 223
6 9 2 1 1 1 4 3 1 1 1 2 1 1 3 1
7 7 1 1 1 1 1 1 1 1 1 1 1 1 1 1
8 1 1 5 1 1 1 4 2 2 1 6 1 1 1 1
9 1 3 1 1 3 1 1 1 2 3 1 1 1 1 1
10 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1
11 1 1 6 1 1 1 1 1 1 1 1 1 1 1 1
12 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1
13 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1
14 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1
15 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
16 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1
17 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1
18 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
19 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
20 1 1 1 1 1 1 1 1 1 1 1 1 1
22 1
23 human GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC CCC ACC ACC TAC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG GTG GCC GAC GCG CTG ACC AAC GCC GTG GCG GTG GAC ATG CCC AAC GCG CTG TCC GCC CTG AGC CTG CAC GCG CTT CGG GAC CCG GTC AAC TTC CTC CTA AGC TGC CTG CTG GCC GCC CTC CCC GCC GAG TTC ACC CCT GCG GTG CAC GCC TCC CTG GCT TCT AGC ACC TCC AAA TAC CGT CTG ACT CCT GAG GAG TCT GCC GTT ACT GCC CTG GGC AAC GTG GAT GAA GTT GGT GGT CTG AGG CTG GTG GTC CCT ACC CAG TTC TTT GAG TCC TTT GGG GAT CTG TCC ACT CCT GAT GCT GTT ATG GGC AAC CCT GTG AAG GCT CAT AAG AAA CTC GGT GCC TTT AGT GAT GGC CTG GCT CAC CTG GAC AAC CTC AAG TTT GCC ACA CTG AGT GAG TGT CAC GAT CCT AAC AGG CTC GGC AAC GTG CTG GTC TGT GTG GCC CAT CAC TTT AAA GAA TTC ACC CCA CCA GTG GCT GCC TAT GTG GGT AAT GCC AAG TAT CAC
24 goat-cow ... ... ... G.C ... ... ... T.. ..T ... ... ... ... ... ... ... ... ... .GC A.. ... ..A .CT ... ..C ..A ... ..T ... ... ... ... ... ... AG. ... ... ... ... ..C ... ... ... ... ... ... ... ..G ... ... ..C ... ... ... ... G.. ... ... .C. ... ... ... ..A ..G ... .GC C.. ... C.. ... GGT A.T ... ..T .AT ... ..T ... ... ..C ..G ..T ... ... ... ... ..T ..T ..G ... .C. ... ... ... TG. ... ... AAT ..T ... ... ..C ... ..C ... ... ... T.. ..C AAC ... ... ... ... ... ... ... ... G.. ... ... G.. ... ..C ..C ... T.T ... ..A ... ... ... ... ... ... ... ... ... ..T ... ..C ..T ... ... ... ... ... ... ... ..C T.. ... ... G.. ... ... ... ... AA. ... ... ... ... ..C ... ... ..G ..A .A. T.. ... ... A.. ... A.. AAG ..T ..C ..T G.. ... ... ... ..T G.G ... ... ... ... ..T ... ... ... .A. ... ... ... ... ..A ..G GT. ... ..T .GC A.T ... ..G ... ... ... ..G GTG C.. ... .A. .T. ... ... ... ... .GA ... ..T
25 rabbit ... ... ... ..C ..T ... ... ... ... A.. ... A.T ... ... .AA ... A.C ... AGC ... .G. ... ... ... ..C ..C ... ... G.. ... ... ... ... T.. GG. ... ... ... ... ..C ... ... ... T.C .C. ... ... ... .AG ... A.C ..A .C. ... ... ... ... T.. ..A ..C ... ... ..G ... ... .GC C.. ... C.. ... GG. ..C ... ..T A.T ..C ... ... ... ... ..G ... ... ... ..G ..T ... ... ..G TC. ... ... ... ... AA. .A. ... AGT ..A ... ... ... ... ... ..T ... ... ... ..C AAC ... ... ... ... ..T ... ... T.C AG. ... ... ... ..G ..C ... ... ... ... ..T ... ..A ... ... ... ... ... ... ... ..T ... ..A ... ... ... ..C ... ... ... ... ..C ... ... T.. G.A A.. ... ... ... AA. ..T ... ... ... ... ... ... ..G ..G .C. ... ..C ... ..G ..T ... AG. ... ... ... ... ... ..A ... ..T .AG ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T AT. ... T.T ... ..T ... ... ... ... ..T ..T .AG ... ... ... ... ... ... ... ..T ..A ..C ...
26 rat ... ..C ... G.A .AT ... ..A ... ... A.. ... AA. TG. ... ..G ... A.. ..T .GC ..T .G. ..T ..A ... ..C .A. ... ... ..A C.. ... ... ... GCT G.. ... ... ... ... T.T ... A.T ..T G.A ... .C. ... ... ... ... ..C ... .CT ... ... ... ..T ..T ..T ..C T.. G.. ..A ..T .CA .AC ..C ..A C.. ..T GGT ..C ... ... A.T ... ... ... ..T ..C ..G ..T ..T ..T ... ... ... T.. ..G ... ... ... T.. ..T TG. .A. ..T .GA ..T ... ..A ..C ..C A.. ... ... ..T ..T ..C ... ... ..T ... ..G ... ... ..A ... GA. .CT ... G.. ..T ... .A. ... ... ..A ... CCT ... ..T ... ... ..C ... ... ... ..T ... ... ... ... .A. ... ..T AG. ... ... ..C ... ... T.. G.C TC. ... A.C ... ..T ... ... ... ... ..C ... ... ..G A.A AAC ... ..C .A. ... ... ... AAA ... T.. ... ... ... ... ... ..T CAT ... ... ..A ... ..T ... ... ... ... ... ... ..T A.. A.T ..G AT. ... .G. ..C ... C.G ..G ... ... ... ..C TGT .CA ... ... .TC ... ..A .G. ..T ... ..C ...
27 marsupial ... ..C ..G GA. ..T ... ... ..T C.. ..G ..A ... AT. ... ..T ... ..G ..A .GC ... ..C ..T .CC ..C .CA ..T ..A ..T ..T .CC ..A .CC ... ..C ... ... ..T ... ... ..C ... ... ... ... TC. .C. ... ..C ... ... A.C C.. ..T ..T ..T ... ..A ... ..T ..C ..T T.. C.G ..T ..T ..C C.. ... C.. ... GGA A.C A.. ... AAA ..A ... ... ... ..C ..G A.A ..T ..C ..G ... ... ... ..C TCT ... A.C ... ... ... ..G AG. AAG ..T ..G ..T ..C .AA ... ... ... ... T.T ..C ... GCT ... ..G ..G ... ... T.. ... T.. ... ... AAC TG. A.C ... A.. A.C TCT C.G ..T ..C C.G AC. ... ... ..T ... ..C ..T ... ..C ... ACC ..T ... .G. AG. ... ..T ... ... ... T.. ... .GC ... ..C ... TCA ..T T.. ..T C.A ..C ... GCT ..G T.G ACC T.. ..C G.. ..A .CA G.C AAG ..T T.. ... ... ..G ... .A. ... .AG T.. ... ... ... ..T ..C ... ... .A. A.G ..G ..T A.C A.T ..G ATC TGC ..T G.G ... ... ..G ..T ..T ..T ..T GA. TGT .T. ..T .GG C.C ..A C.. ... ... ..C ...
29 Codon usage in sequences
30 --------------------------------------------------------------------------------------------------
31 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
32 TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3
33 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
34 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
35 --------------------------------------------------------------------------------------------------
36 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
37 CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0
38 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
39 CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0
40 --------------------------------------------------------------------------------------------------
41 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
42 ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3
43 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
44 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
45 --------------------------------------------------------------------------------------------------
46 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
47 GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5
48 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
49 GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2
50 --------------------------------------------------------------------------------------------------
52 Codon position x base (3x4) table for each sequence.
54 #1: human
55 position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649
56 position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333
57 position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140
59 #2: goat-cow
60 position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000
61 position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035
62 position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088
64 #3: rabbit
65 position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140
66 position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684
67 position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439
69 #4: rat
70 position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895
71 position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439
72 position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421
74 #5: marsupial
75 position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439
76 position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333
77 position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123
79 Sums of codon usage counts
80 ------------------------------------------------------------------------------
81 Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8
82 TTC 51 | TCC 31 | TAC 19 | TGC 9
83 Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0
84 TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16
85 ------------------------------------------------------------------------------
86 Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7
87 CTC 24 | CCC 25 | CAC 68 | CGC 1
88 CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0
89 CTG 123 | CCG 5 | CAG 25 | CGG 2
90 ------------------------------------------------------------------------------
91 Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13
92 ATC 12 | ACC 53 | AAC 35 | AGC 19
93 ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3
94 Met M ATG 17 | ACG 0 | AAG 98 | AGG 17
95 ------------------------------------------------------------------------------
96 Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30
97 GTC 19 | GCC 92 | GAC 48 | GGC 60
98 GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7
99 GTG 89 | GCG 14 | GAG 40 | GGG 7
100 ------------------------------------------------------------------------------
103 Codon position x base (3x4) table, overall
105 position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825
106 position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965
107 position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842
110 Nei & Gojobori 1986. dN/dS (dN, dS)
111 (Note: This matrix is not used in later m.l. analysis.
112 Use runmode = -2 for ML pairwise comparison.)
114 human
115 goat-cow 0.2507 (0.0863 0.3443)
116 rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581)
117 rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187)
118 marsupial 0.1902 (0.1931 1.0148) 0.1891 (0.1910 1.0099) 0.2184 (0.2111 0.9668) 0.2716 (0.2404 0.8852)
120 pairwise comparison, codon frequencies: F3x4.
123 2 (goat-cow) ... 1 (human)
124 lnL =-1508.607268
125 0.47825 2.29137 0.19479
127 t= 0.4783 S= 186.0 N= 669.0 dN/dS= 0.1948 dN= 0.0839 dS= 0.4309
130 3 (rabbit) ... 1 (human)
131 lnL =-1512.583367
132 0.46755 2.19039 0.19819
134 t= 0.4676 S= 179.9 N= 675.1 dN/dS= 0.1982 dN= 0.0842 dS= 0.4247
137 3 (rabbit) ... 2 (goat-cow)
138 lnL =-1557.337680
139 0.53837 2.26427 0.22670
141 t= 0.5384 S= 183.5 N= 671.5 dN/dS= 0.2267 dN= 0.1036 dS= 0.4570
144 4 (rat) ... 1 (human)
145 lnL =-1649.727994
146 0.82576 1.78920 0.15108
148 t= 0.8258 S= 190.2 N= 664.8 dN/dS= 0.1511 dN= 0.1223 dS= 0.8097
151 4 (rat) ... 2 (goat-cow)
152 lnL =-1677.101606
153 0.88091 2.40576 0.18757
155 t= 0.8809 S= 200.2 N= 654.8 dN/dS= 0.1876 dN= 0.1458 dS= 0.7773
158 4 (rat) ... 3 (rabbit)
159 lnL =-1666.440696
160 0.85281 2.21652 0.16114
162 t= 0.8528 S= 193.2 N= 661.8 dN/dS= 0.1611 dN= 0.1306 dS= 0.8105
165 5 (marsupial) ... 1 (human)
166 lnL =-1769.079306
167 2.29076 0.98664 0.05689
169 t= 2.2908 S= 176.2 N= 678.8 dN/dS= 0.0569 dN= 0.1729 dS= 3.0396
172 5 (marsupial) ... 2 (goat-cow)
173 lnL =-1774.766235
174 1.80490 1.19637 0.08052
176 t= 1.8049 S= 180.8 N= 674.2 dN/dS= 0.0805 dN= 0.1762 dS= 2.1879
179 5 (marsupial) ... 3 (rabbit)
180 lnL =-1794.595175
181 2.09985 1.06589 0.06930
183 t= 2.0998 S= 173.1 N= 681.9 dN/dS= 0.0693 dN= 0.1882 dS= 2.7162
186 5 (marsupial) ... 4 (rat)
187 lnL =-1842.638722
188 1.66307 1.02118 0.12318
190 t= 1.6631 S= 180.6 N= 674.4 dN/dS= 0.1232 dN= 0.2214 dS= 1.7973