CODONML (in paml 3.12 February 2002) abglobin.nuc Model: several dN/dS ratios for branches
Codon frequencies: F3x4
ns = 5 ls = 285
# site patterns = 223
9 2 1 1 1 4 3 1 1 1 2 1 1 3 1
7 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 5 1 1 1 4 2 2 1 6 1 1 1 1
1 3 1 1 3 1 1 1 2 3 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 3 1 1
1 1 6 1 1 1 1 1 1 1 1 1 1 1 1
1 1 2 1 1 1 1 1 1 1 1 1 1 1 1
3 1 1 2 1 1 1 1 1 1 1 1 1 1 1
3 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 2 1 1 1 1 1 2 1 1 1
1 2 1 1 1 1 1 1 1 1 1 1 1 2 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1
1
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
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
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 ...
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 ...
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 ...
Codon usage in sequences
--------------------------------------------------------------------------------------------------
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
TTC 10 9 13 11 8 | TCC 6 7 7 3 8 | TAC 3 3 3 5 5 | TGC 1 1 1 3 3
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
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
--------------------------------------------------------------------------------------------------
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
CTC 5 4 4 4 7 | CCC 3 6 5 4 7 | CAC 16 11 15 14 12 | CGC 0 1 0 0 0
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
CTG 29 28 30 21 15 | CCG 2 2 1 0 0 | CAG 4 4 5 5 7 | CGG 1 0 1 0 0
--------------------------------------------------------------------------------------------------
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
ATC 0 0 3 2 7 | ACC 12 11 12 9 9 | AAC 9 7 7 8 4 | AGC 4 4 3 5 3
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
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
--------------------------------------------------------------------------------------------------
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
GTC 4 6 2 4 3 | GCC 21 18 16 18 19 | GAC 10 10 10 8 10 | GGC 14 15 14 12 5
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
GTG 21 19 21 14 14 | GCG 7 4 3 0 0 | GAG 10 9 10 5 6 | GGG 1 1 1 2 2
--------------------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: human
position 1: T:0.12982 C:0.25965 A:0.21404 G:0.39649
position 2: T:0.29474 C:0.26667 A:0.30526 G:0.13333
position 3: T:0.18947 C:0.41404 A:0.03509 G:0.36140
#2: goat-cow
position 1: T:0.13684 C:0.23509 A:0.22807 G:0.40000
position 2: T:0.30526 C:0.24211 A:0.31228 G:0.14035
position 3: T:0.21754 C:0.39649 A:0.03509 G:0.35088
#3: rabbit
position 1: T:0.14386 C:0.24912 A:0.24561 G:0.36140
position 2: T:0.29474 C:0.23860 A:0.32982 G:0.13684
position 3: T:0.19298 C:0.40351 A:0.04912 G:0.35439
#4: rat
position 1: T:0.14737 C:0.22807 A:0.24561 G:0.37895
position 2: T:0.28070 C:0.23860 A:0.32632 G:0.15439
position 3: T:0.25965 C:0.38596 A:0.07018 G:0.28421
#5: marsupial
position 1: T:0.17895 C:0.22105 A:0.24561 G:0.35439
position 2: T:0.28772 C:0.27018 A:0.30877 G:0.13333
position 3: T:0.25965 C:0.38596 A:0.06316 G:0.29123
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 25 | Ser S TCT 25 | Tyr Y TAT 10 | Cys C TGT 8
TTC 51 | TCC 31 | TAC 19 | TGC 9
Leu L TTA 0 | TCA 1 | *** * TAA 0 | *** * TGA 0
TTG 12 | TCG 3 | TAG 0 | Trp W TGG 16
------------------------------------------------------------------------------
Leu L CTT 6 | Pro P CCT 23 | His H CAT 21 | Arg R CGT 7
CTC 24 | CCC 25 | CAC 68 | CGC 1
CTA 6 | CCA 3 | Gln Q CAA 1 | CGA 0
CTG 123 | CCG 5 | CAG 25 | CGG 2
------------------------------------------------------------------------------
Ile I ATT 6 | Thr T ACT 24 | Asn N AAT 16 | Ser S AGT 13
ATC 12 | ACC 53 | AAC 35 | AGC 19
ATA 1 | ACA 2 | Lys K AAA 20 | Arg R AGA 3
Met M ATG 17 | ACG 0 | AAG 98 | AGG 17
------------------------------------------------------------------------------
Val V GTT 24 | Ala A GCT 50 | Asp D GAT 31 | Gly G GGT 30
GTC 19 | GCC 92 | GAC 48 | GGC 60
GTA 2 | GCA 7 | Glu E GAA 19 | GGA 7
GTG 89 | GCG 14 | GAG 40 | GGG 7
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.14737 C:0.23860 A:0.23579 G:0.37825
position 2: T:0.29263 C:0.25123 A:0.31649 G:0.13965
position 3: T:0.22386 C:0.39719 A:0.05053 G:0.32842
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)
human
goat-cow 0.2507 (0.0863 0.3443)
rabbit 0.2627 (0.0867 0.3301) 0.2943 (0.1054 0.3581)
rat 0.2045 (0.1261 0.6164) 0.2462 (0.1493 0.6065) 0.2178 (0.1348 0.6187)
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)
pairwise comparison, codon frequencies: F3x4.
2 (goat-cow) ... 1 (human)
lnL =-1508.607268
0.47825 2.29137 0.19479
t= 0.4783 S= 186.0 N= 669.0 dN/dS= 0.1948 dN= 0.0839 dS= 0.4309
3 (rabbit) ... 1 (human)
lnL =-1512.583367
0.46755 2.19039 0.19819
t= 0.4676 S= 179.9 N= 675.1 dN/dS= 0.1982 dN= 0.0842 dS= 0.4247
3 (rabbit) ... 2 (goat-cow)
lnL =-1557.337680
0.53837 2.26427 0.22670
t= 0.5384 S= 183.5 N= 671.5 dN/dS= 0.2267 dN= 0.1036 dS= 0.4570
4 (rat) ... 1 (human)
lnL =-1649.727994
0.82576 1.78920 0.15108
t= 0.8258 S= 190.2 N= 664.8 dN/dS= 0.1511 dN= 0.1223 dS= 0.8097
4 (rat) ... 2 (goat-cow)
lnL =-1677.101606
0.88091 2.40576 0.18757
t= 0.8809 S= 200.2 N= 654.8 dN/dS= 0.1876 dN= 0.1458 dS= 0.7773
4 (rat) ... 3 (rabbit)
lnL =-1666.440696
0.85281 2.21652 0.16114
t= 0.8528 S= 193.2 N= 661.8 dN/dS= 0.1611 dN= 0.1306 dS= 0.8105
5 (marsupial) ... 1 (human)
lnL =-1769.079306
2.29076 0.98664 0.05689
t= 2.2908 S= 176.2 N= 678.8 dN/dS= 0.0569 dN= 0.1729 dS= 3.0396
5 (marsupial) ... 2 (goat-cow)
lnL =-1774.766235
1.80490 1.19637 0.08052
t= 1.8049 S= 180.8 N= 674.2 dN/dS= 0.0805 dN= 0.1762 dS= 2.1879
5 (marsupial) ... 3 (rabbit)
lnL =-1794.595175
2.09985 1.06589 0.06930
t= 2.0998 S= 173.1 N= 681.9 dN/dS= 0.0693 dN= 0.1882 dS= 2.7162
5 (marsupial) ... 4 (rat)
lnL =-1842.638722
1.66307 1.02118 0.12318
t= 1.6631 S= 180.6 N= 674.4 dN/dS= 0.1232 dN= 0.2214 dS= 1.7973