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m0f1x4.txt
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6 999
Human_Horai CTA CCC GCC GCA GTA CTG ATC ATT CTA TTT CCC CCT CTA TTG ATC CCC ACC TCC AAA TAT CTC ATC AAC AAC CGA CTA ATT ACC ACC CAA CAA TGA CTA ATC AAA CTA ACC TCA AAA CAA ATG ATA GCC ATA CAC AAC ACT AAA GGA CGA ACC TGA TCT CTT ATA CTA GTA TCC TTA ATC ATT TTT ATT GCC ACA ACT AAC CTC CTC GGA CTC CTG CCT CAC TCA TTT ACA CCA ACC ACC CAA CTA TCT ATA AAC CTA GCC ATG GCC ATC CCC TTA TGA GCG GGC GCA GTG ATT ATA GGC TTT CGC TCT AAG ATT AAA AAT GCC CTA GCC CAC TTC TTA CCA CAA GGC ACA CCT ACA CCC CTT ATC CCC ATA CTA GTT ATT ATC GAA ACC ATC AGC CTA CTC ATT CAA CCA ATA GCC CTG GCC GTA CGC CTA ACC GCT AAC ATT ACT GCA GGC CAC CTA CTC ATG CAT CTA ATT GGA AGC GCC ACC CTA GCA ATA TCA ACC ATT AAC CTT CCC TCT ACA CTT ATC ATC TTC ACA ATT CTA ATT CTA CTG ACT ATC CTA GAA ATC GCT GTC GCC TTA ATC CAA GCC TAC GTT TTC ACA CTT CTA GTA AGC CTC TAC CTG CAC GAC AAC ACA CCC CAA CTA AAT ACT ACC GTA TGG CCC ACC ATA ATT ACC CCC ATA CTC CTT ACA CTA TTT CTC ATC ACC CAA CTA AAA ATA TTA AAC ACA AGC TAC CAC TTA CCT CCC TCA CCA AAG CCC ATA AAA ATA AAA AAT TAT AAC AAA CCC TGA GAA CCA ACC CCA ATA CGC AAA ATT AAC CCC CTA ATA AAA TTA ATT AAC CAC TCA TTC ATC GAC CTC CCC ACC CCA TCC AAC ATC TCC GCA TGA TGA AAC TTC GGC TCA CTC CTT GGC GCC TGC CTG ATC CTC CAA ATC ACC ACA GGA CTA TTC CTA GCC ATG CAC TAC TCA CCA GAC GCC TCA ACC GCC TTT TCA TCA ATC GCC CAC ATC ACT CGA GAC
Human_Arnason CTA CCC GCC GCA GTA CTG ATC ATT CTA TTT CCC CCT CTA TTG ATC CCC ACC TCC AAA TAT CTC ATC AAC AAC CGA CTA ATC ACC ACC CAA CAA TGA CTA ATC AAA CTA ACC TCA AAA CAA ATG ATA ACC ATA CAC AAC ACT AAA GGA CGA ACC TGA TCT CTT ATA CTA GTA TCC TTA ATC ATT TTT ATT GCC ACA ACT AAC CTC CTC GGA CTC CTG CCT CAC TCA TTT ACA CCA ACC ACC CAA CTA TCT ATA AAC CTA GCC ATG GCC ATC CCC TTA TGA GCG GGC GCA GTG ATT ATA GGC TTT CGC TCT AAG ATT AAA AAT GCC CTA GCC CAC TTC TTA CCA CAA GGC ACA CCT ACA CCC CTT ATC CCC ATA CTA GTT ATT ATC GAA ACC ATC AGC CTA CTC ATT CAA CCA ATA GCC CTG GCC GTA CGC CTA ACC GCT AAC ATT ACT GCA GGC CAC CTA CTC ATG CAC CTA ATT GGA AGC GCC ACC CTA GCA ATA TCA ACC ATT AAC CTT CCC TCT ACA CTT ATC ATC TTC ACA ATT CTA ATT CTA CTG ACT ATC CTA GAA ATC GCT GTC GCC TTA ATC CAA GCC TAC GTT TTC ACA CTT CTA GTA AGC CTC TAC CTG CAC GAC AAC ACA CCC CAA CTA AAT ACT ACC GTA TGG CCC ACC ATA ATT ACC CCC ATA CTC CTT ACA CTA TTC CTC ATC ACC CAA CTA AAA ATA TTA AAC ACA AAC TAC CAC CTA CCT CCC TCA CCA AAG CCC ATA AAA ATA AAA AAT TAT AAC AAA CCC TGA GAA CCA ACC CCA ATA CGC AAA ATT AAC CCC CTA ATA AAA TTA ATT AAC CGC TCA TTC ATC GAC CTC CCC ACC CCA TCC AAC ATC TCC GCA TGA TGA AAC TTC GGC TCA CTC CTT GGC ACC TGC CTG ATC CTC CAA ATC ACC ACA GGA CTA TTC CTA GCC ATG CAC TAC TCA CCA GAC GCC TCA ACC GCC TTT TCA TCA ATC GCC CAC ATC ACT CGA GAC
Chimp_Horai TTA CCC GCC GCA GTA CTA ATC ATT CTA TTC CCC CCT CTA CTG GTC CCC ACT TCT AAA CAT CTC ATC AAC AAC CGA CTA ATT ACC ACC CAA CAA TGA CTA ATT CAA CTG ACC TCA AAA CAA ATA ATA ACT ATA CAC AGC ACT AAA GGA CGA ACC TGA TCT CTC ATA CTA GTA TCC TTA ATC ATT TTT ATT ACC ACA ACC AAT CTT CTT GGG CTT CTA CCC CAC TCA TTC ACA CCA ACC ACC CAA CTA TCT ATA AAC CTA GCC ATG GCT ATC CCC CTA TGA GCA GGC GCA GTA GTC ATA GGC TTT CGC TTT AAG ACT AAA AAT GCC CTA GCC CAC TTC TTA CCG CAA GGC ACA CCT ACA CCC CTT ATC CCC ATA CTA GTT ATC ATC GAA ACT ATT AGC CTA CTC ATT CAA CCA ATA GCC TTA GCC GTA CGT CTA ACC GCT AAC ATT ACT GCA GGC CAC CTA CTC ATG CAC CTA ATT GGA AGC GCC ACA CTA GCA TTA TCA ACT ATC AAT CTA CCC TAT GCA CTC ATT ATC TTC ACA ATT CTA ATC CTA CTG ACT ATT CTA GAG ATC GCC GTC GCC TTA ATC CAA GCC TAC GTT TTT ACA CTT CTA GTG AGC CTC TAC CTG CAC GAC AAC ACA CCC CAA CTA AAT ACC GCC GTA TGA CCC ACC ATA ATT ACC CCC ATA CTC CTG ACA CTA TTT CTC GTC ACC CAA CTA AAA ATA TTA AAT TCA AAT TAC CAT CTA CCC CCC TCA CCA AAA CCC ATA AAA ATA AAA AAC TAC AAT AAA CCC TGA GAA CCA ACC CCG ACA CGC AAA ATT AAC CCA CTA ATA AAA TTA ATT AAT CAC TCA TTT ATC GAC CTC CCC ACC CCA TCC AAC ATT TCC GCA TGA TGG AAC TTC GGC TCA CTT CTC GGC GCC TGC CTA ATC CTT CAA ATT ACC ACA GGA TTA TTC CTA GCT ATA CAC TAC TCA CCA GAC GCC TCA ACC GCC TTC TCG TCG ATC GCC CAC ATC ACC CGA GAC
Chimp_Arnason TTA CCC GCC GCA GTA CTA ATC ATT CTA TTC CCC CCT CTA CTG GTC CCC ACT TCT AAA CAT CTC ATC AAC AAC CGA CTA ATT ACC ACC CAA CAA TGA CTA ATT CAA CTG ACC TCA AAA CAA ATA ATA ACT ATA CAC AGC ACT AAA GGA CGA ACC TGA TCT CTC ATA CTA GTA TCC TTA ATC ATT TTT ATT ACC ACA ACC AAT CTT CTT GGA CTT CTA CCC CAC TCA TTC ACA CCA ACC ACC CAA CTA TCT ATA AAC CTA GCC ATG GCT ATC CCC CTA TGA GCA GGC GCA GTA GTC ATA GGC TTT CGC TTT AAG ACT AAA AAT GCC CTA GCC CAC TTC TTA CCG CAA GGC ACA CCT ACA CCC CTT ATC CCC ATA CTA GTT ATC ATC GAA ACT ATT AGC CTA CTC ATT CAA CCA ATA GCC TTA GCC GTA CGT CTA ACC GCT AAC ATT ACT GCA GGC CAC CTA CTC ATG CAC CTA ATT GGA AGC GCC ACA CTA GCA TTA TCA ACT ATC AAT CTA CCC TCT GCA CTC ATT ATC TTC ACA ATT CTA ATC CTA CTG ACT ATT CTA GAG ATC GCC GTC GCC TTA ATC CAA GCC TAC GTT TTT ACA CTT CTA GTG AGC CTC TAC CTG CAC GAC AAC ACA CCC CAA CTA AAT ACC GCC GTA TGA CCC ACC ATA ATT ACC CCC ATA CTC CTG ACA CTA TTT CTC GTC ACC CAA CTA AAA ATA TTA AAT TCA AAT TAC CAT CTA CCC CCC TCA CCA AAA CCC ATA AAA ATA AAA AAC TAC AAT AAA CCC TGA GAA CCA ACC CCG ACA CGC AAA ATT AAC CCA CTA ATA AAA TTA ATT AAT CAC TCA TTT ATC GAC CTC CCC ACC CCA TCC AAC ATT TCC GCA TGA TGG AAC TTC GGC TCA CTT CTC GGC GCC TGC CTA ATC CTT CAA ATT ACC ACA GGA TTA TTC CTA GCT ATA CAC TAC TCA CCA GAC GCC TCA ACC GCC TTC TCG TCG ATC GCC CAC ATC ACC CGA GAC
Gorilla_Horai TTA CCC GCC GCA GTA TTA ATT ATC CTA CTT CCC CCT CTA CTG ATC CCC ACC TCC AAA TAT CTC ATC AAC AAC CGA CTG ATT GCC ACC CAA CAG TGA CTA ATC CAA CTA ACC TCA AAA CAA ATA ATA ACT ATA CAT AAC GCC AAG GGA CGA ACC TGA TCC CTT ATG TTA ATA TGA TTA ATT ATT TTT ATT GCC ACA ACC AAC CTC CTC GGA CTC TTG CCC CAC TCA TTC ACA CCA ACT ACC CAG CTA TCT ATA AAC CTG GCC ATA GCC ATC CCC CTG TGA GCA GGC GCA GTA ACT ACA GGC TTT CGC TCC AAG ACT AAA AAT GCC CTA GCC CAC CTA CTA CCA CAA GGC ACC CCT ACA CCC CTT ATC CCT ATA CTA GTC ATC ATT GAA ACC ATC AGC CTA TTC ATC CAA CCA ATA GCC CTA GCT GTA CGC CTA ACC GCT AAC ATC ACT GCA GGT CAC CTA CTT ATG CAC CTA ATC GGA AGC GCC ACA CTA GCA ATA TCA ACT ACC AAT CTT CCC TCA ACA CTC ATT ATC TTT ACA GTC CTA ATT TTA TTA ACT ATA CTA GAA ATC GCT GTC GCC CTC ATC CAA GCC TAC GTT TTC ACA CTT TTA GTG AGC CTC TAC CTG CAC GAG AAC ACA CCC CAG CTA AAT ACC ACC GTA TGG CCC ACC ATA ATT GCC CCA ATA CTC CTC ACA CTA TTT CTC ATT ACC CAA CTA AAA GTT TTA AAC ACA AAT TAC CAC CTA CCC CCC TTA CCA AAA ACT ATA AAA ATA AAA AAC TTC TGT AAA CCC TGA GAA CCA ACC CCT ATA CGC AAA ACT AAC CCA CTA GCA AAA CTA ATT AAC CAC TCA TTC ATT GAC CTC CCT ACC CCG TCC AAC ATC TCC ACA TGA TGA AAC TTC GGC TCA CTC CTT GGT GCC TGC TTA ATC CTT CAA ATC ACC ACA GGG CTA TTC CTA GCC ATA CAC TAC TCA CCT GAT GCC TCA ACC GCC TTC TCA TCA ATT GCC CAC ATC ACC CGA GAT
Gorilla_Arnason TTA CCC GCC GCA GTA TTA ATT ATC CTA CTT CCC CCT CTA CTG ATC CCC ACC TCC AAA TAT CTC ATC AAC AAC CGA CTG ATT GCC ACC CAA CAG TGA CTA ATC CAA CTA ACC TCA AAA CAA ATA ATA ACT ATA CAT AAC GCC AAG GGA CGA ACC TGA TCC CTT ATG TTA ATA TCA TTA ATT ATT TTT ATT GCC ACA ACC AAC CTC CTC GGA CTC TTG CCC CAC TCA TTC ACA CCA ACT ACC CAG CTA TCT ATA AAC CTG GCC ATA GCC ATC CCC CTG TGA GCA GGC GCA GTA ACT ACA GGC TTT CGC TCC AAG ACT AAA AAT GCC CTA GCC CAC CTA CTA CCA CAA GGC ACC CCT ACA CCC CTT ATC CCT ATA CTA GTC ATC ATT GAA ACC ATC AGC CTA TTC ATC CAA CCA ATA GCC CTA GCT GTA CGC CTA ACC GCT AAC ATC ACT GCA GGT CAC CTA CTT ATG CAC CTA ATC GGA AGC GCC ACA CTA GCA ATA TCA ACT ACC AAT CTT CCC TCA ACA CTC ATT ATC TTT ACA GTC CTA ATT TTA TTA ACT ATA CTA GAA ATC GCT GTC GCC CTC ATC CAA GCC TAC GTT TTC ACA CTT TTA GTG AGC CTC TAC CTG CAC GAG AAC ACA CCC CAG CTA AAT ACC ACC GTA TGG CCC ACC ATA ATT GCC CCA ATA CTC CTC ACA CTA TTT CTC ATT ACC CAA CTA AAA GTT TTA AAC ACA AAT TAC CAC CTA CCC CCC TTA CCA AAA ACT ATA AAA ATA AAA AAC TTC TGT AAA CCC TGA GAA TCA ACC CCT ATA CGC AAA ACT AAC CCA CTA GCA AAA CTA ATT AAC CAC TCA TTC ATT GAC CTC CCT ACC CCG TCC AAC ATC TCC ACA TGA TGA AAC TTC GGC TCA CTC CTT GGT GCC TGC TTA ATC CTT CAA ATC ACC ACA GGG CTA TTC CTA GCC ATA CAC TAC TCA CCT GAT GCC TCA ACC GCC TTC TCA TCA ATC GCC CAC ATC ACC CGA GAT
Printing out site pattern counts
6 477 P
Human_Horai AAA AAA AAA AAC AAC AAC AAC AAC AAG AAG AAT AAT ACA ACA ACA ACA ACC ACC ACC ACC ACC ACC ACC ACT ACT ACT AGC AGC ATA ATA ATA ATA ATA ATA ATA ATC ATC ATC ATC ATC ATC ATC ATC ATG ATG ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT CAA CAA CAC CAC CAC CAC CAT CCA CCA CCA CCA CCA CCA CCC CCC CCC CCC CCC CCT CCT CGA CGC CGC CTA CTA CTA CTA CTA CTA CTC CTC CTC CTC CTC CTG CTG CTG CTG CTG CTT CTT CTT CTT CTT GAA GAA GAC GAC GAC GCA GCA GCC GCC GCC GCC GCC GCC GCG GCT GCT GGA GGA GGA GGC GGC GTA GTA GTA GTC GTG GTT GTT TAC TAT TAT TCA TCA TCA TCC TCC TCC TCT TCT TCT TCT TGA TGA TGC TGG TTA TTA TTA TTA TTA TTC TTC TTC TTC TTG TTT TTT TTT TTT
Human_Arnason ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ..C ... ... ...
Chimp_Horai ... ... C.. ... ..T ..T ..T .G. ..A ... ..C ... ... ... G.. T.. ..A ... ... ... ..T ..T G.. ..C ... ... .AT ... .C. ... ... ... ... ... T.. ... ... ... ..T ..T ..T G.. G.. ..A ... ... ... .C. ..C ..C ..C ... ... ... ... G.C ... ... ... ... ..T ... ..C ... ... ... ... ..G ..G ..A ... ... ... ... ..C ... ... ... ..T ... ... ... ..G T.. T.. ... ... ... ..T ..T ..A ..A ... ... T.A ..A ..C ..C ..G ... ... ..G ... ... ... ... ... A.T ... A.. ... ... ..T ..A ..C ... ... ... ..G ... ... ... ... ..G ... ..A ... ... ... C.. ..C ... ... ..G ... ... ..T .A. ... ... .T. ... ..G ... ..A C.. C.. ... ... ... ... ... ... ..T C.. ... ..C ..C ...
Chimp_Arnason ... ... C.. ... ..T ..T ..T .G. ..A ... ..C ... ... ... G.. T.. ..A ... ... ... ..T ..T G.. ..C ... ... .AT ... .C. ... ... ... ... ... T.. ... ... ... ..T ..T ..T G.. G.. ..A ... ... ... .C. ..C ..C ..C ... ... ... ... G.C ... ... ... ... ..T ... ..C ... ... ... ... ..G ..G ..A ... ... ... ... ..C ... ... ... ..T ... ... ... ..G T.. T.. ... ... ... ..T ..T ..A ..A ... ... T.A ..A ..C ..C ..G ... ... ..G ... ... ... ... ... A.T ... A.. ... ... ..T ..A ..C ... ... ... ... ... ... ... ... ..G ... ..A ... ... ... C.. ..C ... ... ..G ... ... ..T ... ... ... .T. ... ..G ... ..A C.. C.. ... ... ... ... ... ... ..T C.. ... ..C ..C ...
Gorilla_Horai ... ..G C.. ... ... ..T TGT ... ..A ... ..C ... ... ..C ... ... ..A ... ..T G.. ... ..T ... ..C ... G.C .AT ... ... .C. ... ..G GC. G.T ... ... ..T ..T ..A ... ..T ... ..T ..A ..A ... ... .C. .CC ..C ... .C. ..C ... G.C .C. ... ..G ... ..T ... ... ..C ... ... ..G ..T ... ..T ..A A.T ..A ... ..T ..C ... ... ... ... ... ..G T.. ... ... T.. ... ..T T.. ... ..T T.A T.. ... T.A ..A ... ..C ... ..C ... ... ... ... ..G ..T A.. ... A.T ... ... ... ..T ... ..A ... ... ... ..G ... ... ..T A.. ... ..G ... ..A ..C ... ... ... .TC ... .T. ... ... .GA ... ..A ..C ... ..C ... ... ... ... C.. C.G C.. C.C ... C.A ... ..T ... C.. ... C.. ..C ...
Gorilla_Arnason ... ..G C.. ... ... ..T TGT ... ..A ... ..C ... ... ..C ... ... ..A ... ..T G.. ... ..T ... ..C ... G.C .AT ... ... .C. ... ..G GC. G.T ... ... ... ..T ..A ... ..T ... ..T ..A ..A ... ... .C. .CC ..C ... .C. ..C ... G.C .C. ... ..G ... ..T ... ... ..C ... T.. ..G ..T ... ..T ..A A.T ..A ... ..T ..C ... ... ... ... ... ..G T.. ... ... T.. ... ..T T.. ... ..T T.A T.. ... T.A ..A ... ..C ... ..C ... ... ... ... ..G ..T A.. ... A.T ... ... ... ..T ... ..A ... ... ... ..G ... ... ..T A.. ... ..G ... ..A ..C ... ... ... .TC ... .T. ... ... ..A ... ..A ..C ... ..C ... ... ... ... C.. C.G C.. C.C ... C.A ... ..T ... C.. ... C.. ..C ...
9 1 1 8 3 1 1 1 1 1 1 2 8 1 1
1 1 11 1 2 2 1 1 3 2 1 1 3 1 1
9 1 1 1 1 8 1 4 1 4 1 1 1 2 1
1 1 1 1 1 1 1 4 4 1 1 7 3 6 1
1 1 1 3 1 1 1 1 1 1 1 1 10 2 2
2 3 2 1 18 2 3 1 1 1 5 1 1 4 1
2 1 1 1 1 1 1 2 1 2 2 1 1 1 2
1 4 1 1 1 11 1 2 1 1 1 2 1 1 4
2 1 3 1 1 1 1 1 4 1 1 7 1 2 2
1 1 1 1 1 1 5 1 1 1 1 1 2 1 2
1 2 1 2 1 1 1 2 2
CODONML (in paml version 4.8a, August 2014) codon.txt
Model: One dN/dS ratio for branches, Global clock
Codon frequency model: F1x4
ns = 6 ls = 333
Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT 6 5 6 6 4 4 | Ser TCT 4 4 3 4 1 1 | Tyr TAT 2 2 1 0 1 1 | Cys TGT 0 0 0 0 1 1
TTC 6 7 7 7 8 8 | TCC 4 4 3 3 5 5 | TAC 4 4 5 5 4 4 | TGC 1 1 1 1 1 1
Leu TTA 7 6 9 9 10 10 | TCA 10 10 9 9 10 12 | *** TAA 0 0 0 0 0 0 | Trp TGA 6 6 6 6 7 6
TTG 1 1 0 0 1 1 | TCG 0 0 2 2 0 0 | TAG 0 0 0 0 0 0 | TGG 1 1 1 1 1 1
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT 7 7 7 7 8 8 | Pro CCT 4 4 2 2 6 6 | His CAT 1 0 2 2 1 1 | Arg CGT 0 0 1 1 0 0
CTC 12 12 10 10 12 12 | CCC 15 15 16 16 12 12 | CAC 9 9 9 9 9 9 | CGC 3 4 2 2 3 3
CTA 26 27 29 29 25 25 | CCA 8 8 7 7 7 6 | Gln CAA 10 10 11 11 8 8 | CGA 3 3 3 3 3 3
CTG 6 6 5 5 5 5 | CCG 0 0 2 2 1 1 | CAG 0 0 0 0 3 3 | CGG 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT 16 15 17 17 13 12 | Thr ACT 6 6 8 8 9 9 | Asn AAT 3 3 8 8 4 4 | Ser AGT 0 0 0 0 0 0
ATC 21 22 16 16 18 19 | ACC 19 21 18 18 19 19 | AAC 14 15 9 9 13 13 | AGC 4 3 4 4 3 3
Met ATA 15 15 15 15 16 16 | ACA 11 11 11 11 13 13 | Lys AAA 11 11 11 11 10 10 | *** AGA 0 0 0 0 0 0
ATG 4 4 2 2 2 2 | ACG 0 0 0 0 0 0 | AAG 2 2 1 1 2 2 | AGG 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT 2 2 2 2 2 2 | Ala GCT 2 2 3 3 3 3 | Asp GAT 0 0 0 0 2 2 | Gly GGT 0 0 0 0 2 2
GTC 1 1 4 4 3 3 | GCC 17 15 15 15 18 18 | GAC 4 4 4 4 1 1 | GGC 6 6 6 6 4 4
GTA 5 5 5 5 4 4 | GCA 5 5 7 7 6 6 | Glu GAA 3 3 2 2 3 3 | GGA 4 4 3 4 3 3
GTG 1 1 1 1 1 1 | GCG 1 1 0 0 0 0 | GAG 0 0 1 1 1 1 | GGG 0 0 1 0 1 1
--------------------------------------------------------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: Human_Horai
position 1: T:0.15616 C:0.31231 A:0.37838 G:0.15315
position 2: T:0.40841 C:0.31832 A:0.18919 G:0.08408
position 3: T:0.15916 C:0.42042 A:0.37237 G:0.04805
Average T:0.24124 C:0.35035 A:0.31331 G:0.09510
#2: Human_Arnason
position 1: T:0.15315 C:0.31532 A:0.38438 G:0.14715
position 2: T:0.40841 C:0.31832 A:0.18919 G:0.08408
position 3: T:0.15015 C:0.42943 A:0.37237 G:0.04805
Average T:0.23724 C:0.35435 A:0.31532 G:0.09309
#3: Chimp_Horai
position 1: T:0.15916 C:0.31832 A:0.36036 G:0.16216
position 2: T:0.40541 C:0.31832 A:0.19219 G:0.08408
position 3: T:0.18018 C:0.38739 A:0.38438 G:0.04805
Average T:0.24825 C:0.34134 A:0.31231 G:0.09810
#4: Chimp_Arnason
position 1: T:0.15916 C:0.31832 A:0.36036 G:0.16216
position 2: T:0.40541 C:0.32132 A:0.18919 G:0.08408
position 3: T:0.18018 C:0.38739 A:0.38739 G:0.04505
Average T:0.24825 C:0.34234 A:0.31231 G:0.09710
#5: Gorilla_Horai
position 1: T:0.16216 C:0.30931 A:0.36637 G:0.16216
position 2: T:0.39640 C:0.33033 A:0.18619 G:0.08709
position 3: T:0.17117 C:0.39940 A:0.37538 G:0.05405
Average T:0.24324 C:0.34635 A:0.30931 G:0.10110
#6: Gorilla_Arnason
position 1: T:0.16517 C:0.30631 A:0.36637 G:0.16216
position 2: T:0.39640 C:0.33333 A:0.18619 G:0.08408
position 3: T:0.16817 C:0.40240 A:0.37538 G:0.05405
Average T:0.24324 C:0.34735 A:0.30931 G:0.10010
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 31 | Ser S TCT 17 | Tyr Y TAT 7 | Cys C TGT 2
TTC 43 | TCC 24 | TAC 26 | TGC 6
Leu L TTA 51 | TCA 60 | *** * TAA 0 | Trp W TGA 37
TTG 4 | TCG 4 | TAG 0 | TGG 6
------------------------------------------------------------------------------
Leu L CTT 44 | Pro P CCT 24 | His H CAT 7 | Arg R CGT 2
CTC 68 | CCC 86 | CAC 54 | CGC 17
CTA 161 | CCA 43 | Gln Q CAA 58 | CGA 18
CTG 32 | CCG 6 | CAG 6 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 90 | Thr T ACT 46 | Asn N AAT 30 | Ser S AGT 0
ATC 112 | ACC 114 | AAC 73 | AGC 21
Met M ATA 92 | ACA 70 | Lys K AAA 64 | *** * AGA 0
ATG 16 | ACG 0 | AAG 10 | AGG 0
------------------------------------------------------------------------------
Val V GTT 12 | Ala A GCT 16 | Asp D GAT 4 | Gly G GGT 4
GTC 16 | GCC 98 | GAC 18 | GGC 32
GTA 28 | GCA 36 | Glu E GAA 16 | GGA 21
GTG 6 | GCG 2 | GAG 4 | GGG 3
------------------------------------------------------------------------------
Codon position x base (3x4) table, overall
position 1: T:0.15916 C:0.31331 A:0.36937 G:0.15816
position 2: T:0.40340 C:0.32332 A:0.18869 G:0.08458
position 3: T:0.16817 C:0.40440 A:0.37788 G:0.04955
Average T:0.24358 C:0.34701 A:0.31198 G:0.09743
Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
0.01510945 0.02152580 0.01935252 0.00604378
0.02152580 0.03066689 0.02757071 0.00861032
0.01935252 0.02757071 0.00000000 0.00000000
0.00604378 0.00861032 0.00774101 0.00241751
0.02152580 0.03066689 0.02757071 0.00861032
0.03066689 0.04368981 0.03927882 0.01226676
0.02757071 0.03927882 0.03531317 0.01102828
0.00861032 0.01226676 0.01102828 0.00344413
0.01935252 0.02757071 0.02478713 0.00774101
0.02757071 0.03927882 0.03531317 0.01102828
0.02478713 0.03531317 0.03174790 0.00991485
0.00774101 0.01102828 0.00000000 0.00000000
0.00604378 0.00861032 0.00774101 0.00241751
0.00861032 0.01226676 0.01102828 0.00344413
0.00774101 0.01102828 0.00991485 0.00309640
0.00241751 0.00344413 0.00309640 0.00096701
Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
Human_Horai
Human_Arnason 0.3443 (0.0054 0.0157)
Chimp_Horai 0.0623 (0.0233 0.3738) 0.0626 (0.0233 0.3728)
Chimp_Arnason 0.0597 (0.0219 0.3670) 0.0599 (0.0219 0.3660) 0.3511 (0.0014 0.0039)
Gorilla_Horai 0.0862 (0.0416 0.4832) 0.0865 (0.0417 0.4817) 0.1091 (0.0547 0.5014) 0.1080 (0.0533 0.4932)
Gorilla_Arnason 0.0855 (0.0409 0.4786) 0.0859 (0.0410 0.4771) 0.1087 (0.0540 0.4967) 0.1076 (0.0526 0.4886) 0.7042 (0.0027 0.0039)
TREE # 1: ((1, 2), (3, 4), (5, 6)); MP score: 171
lnL(ntime: 4 np: 6): -2009.834314 +0.000000
7..8 8..1 8..2 7..9 9..3 9..4 7..10 10..5 10..6
0.266662 0.014702 0.003339 0.004302 13.498110 0.101951
tree length = 0.82233
((1: 0.014702, 2: 0.014702): 0.251960, (3: 0.003339, 4: 0.003339): 0.263323, (5: 0.004302, 6: 0.004302): 0.262361);
((Human_Horai: 0.014702, Human_Arnason: 0.014702): 0.251960, (Chimp_Horai: 0.003339, Chimp_Arnason: 0.003339): 0.263323, (Gorilla_Horai: 0.004302, Gorilla_Arnason: 0.004302): 0.262361);
((1_Human_Horai, 2_Human_Arnason) 8 , (3_Chimp_Horai, 4_Chimp_Arnason) 9 , (5_Gorilla_Horai, 6_Gorilla_Arnason) 10 ) 7 ;
Detailed output identifying parameters
kappa (ts/tv) = 13.49811
omega (dN/dS) = 0.10195
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
7..8 0.252 656.5 342.5 0.1020 0.0209 0.2049 13.7 70.2
8..1 0.015 656.5 342.5 0.1020 0.0012 0.0120 0.8 4.1
8..2 0.015 656.5 342.5 0.1020 0.0012 0.0120 0.8 4.1
7..9 0.263 656.5 342.5 0.1020 0.0218 0.2141 14.3 73.4
9..3 0.003 656.5 342.5 0.1020 0.0003 0.0027 0.2 0.9
9..4 0.003 656.5 342.5 0.1020 0.0003 0.0027 0.2 0.9
7..10 0.262 656.5 342.5 0.1020 0.0218 0.2134 14.3 73.1
10..5 0.004 656.5 342.5 0.1020 0.0004 0.0035 0.2 1.2
10..6 0.004 656.5 342.5 0.1020 0.0004 0.0035 0.2 1.2
tree length for dN: 0.0682
tree length for dS: 0.6688
Time used: 0:04