     14    663

human                           TCA CTT TTA ACC TTC TGG CAC CCG CCC ACC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC TGC AAT ATT TCA GAA ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT ATA ACA GAC ATT CAA GCA AAT ATC CCA GGG GCC GCA TAC AGT GGT GAG ACA GTA TAC CCC AAT GGA TCC CTG CTG TTC CAA AAC ATC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAC GAC TCT GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCC GTC GCT GGC ATC GTG ACT GGG GTC CTG GTT GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTT CTG CTT CTC TCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG CAG CCG CCC CCA GCC TCC ACC CCT GGC CAT GGT CCC TCT CAC AGA TCC ACC TTC TCG GCC CCT CTA CCC AGC CCC AGA ACA GCC ACT CCC ATC TAT GAG GAA TTG CTA TAC TCT GAT GCA AAC ATT TAC TGC CAG ATC GAC CAC AAA GCA GAT GTG GTC TCT 
chimpanzee                      TCA CTT TTA ACC TTC TGG GAC CCG CCC ACC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC TGC AAT ATT TCA GAA ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT ATA ACA GAC ATT CAA GCA AAT ATC CCA GGG GCC GCA TAC AGT GGT GAG ACA GTA TAC CCC AAT GGA TCC CTG CTG TTC CAA AAC ATC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAC GAC TCT GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCC GTC GCT GGC ATC GTG ACT GGG GTC CTG GTT GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTT CTG CTC CTC TCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG CAG CCG CCC CCA GCC TCC ACC CCC GGC CAT GGT CCC TCT CAC AGA TCC ACC TTC TCG GCC CCT CTA CCC AGC CCC AGA ACA GCC ACT CCC ATC TAT GAG GAA TTG CTA TAC TCT GAC GCA AAC GTT TAC TGC CGG ATC GAC CAC AAA GCA GAT GTG GTC TCT 
bonobo                          TCA CTT TTA ACC TTC TGG GAC CCA CCC ACC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC TGC AAT ATT TCA GAA ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT ATA ACA GAC ATT CAA GCA AAT ATC CCA GGG GCC GCA TAC AGT GGT GAG ACA GTA TAC CCC AAT GGA TCC CTG CTG TTC CAA AAC ATC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAC GAC TCT GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCC GTC GCT GGC ATC GTG ACT GGG GTC CTG GTT GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTT CTG CTC CTC TCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG CAG CCG CCC CCA GCC TCC ACC CCC GGC CAT GGT CCC TCT CAC AGA TCC ACC TTC TCG GCC CCT CTA CCC AGC CCC AGA ACA GCC ACT CCC ATC TAT GAG GAA TTG CTA TAC TCT GAC GCA AAC GTT TAC TGC CGG ATC GAC CAC AAA GCA GAT GTG GTC TCT 
gorilla                         TCA CTT TTA ACC TTC TGG GAC CCG CCC ACC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT ATT CTA CTG GCC TGC AAT ATT TCA GAA ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT ATA ACA GAT ATT CAA GCA AAT ATC CCA GGG GCC GCA TAC AGT GGT GAG ACA GTA TAC CCC AAT GGA TCA CTG CTG TTC CAA AAC ATC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAC GAC TCT GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GCG GGG GCC GTC GCT GGC ATC GTG ACT GGG GTC CTG GTT GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTT CTG CTC CTC TCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG CAG CCA CCC CCA GCC TCC ACC CCA GGC CAT GGT CCC TCT CAC AGA TCC ACC TTC TCG GCC CCT CTA CCC AGC CCC AGA ACA GCC ACT CCC ATC TAT GAG GAA TTG CTA TAC TCT GAC GCA AAC ATT TAC TGC CAG ATC GAC CAC AAA GCA GAT GTG GTC TCT 
orangutan                       TCA CTT TTA ACC TTC TGG GAC CCG CCC AGC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCA TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC TGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT ATA ACA GAC ATT CAA GCA AAT ATC CCA GGG GCC GCA TAC AGT GGT GAG ACA GTA TAC CCC AAT GGA TCC CTG CTG TTC CAA AAC ATC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAC GAC TCT GAC CAA GCA ACT GGC CAG CTC CAT GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCC GTC GCT GGC ATC GTG ACT GGG GTC CTG GTT GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTG CTG CTC CTC TCC AGG ACT GGA AGG ACC AGC ATC CAG CGT GAC CTC AGG GAG CAG CCG CCC CCA GCC TCC ACC CCT GGC CAT GGT CCC TCT CAC AGA TCC ACC TTC TCG GCC CCC CTA CCA AGC ACC AGA ACA GCC AGT CGT ATC TAT GAG GAA TTG CTA TAC TCT GAC GCA AAC ATT TAC TGC CAG ATC GAC CAC AAA GCA GAT GTG GTC TCT 
colobus                         TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CCG GCC CGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG CAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ACA GAC GTT CAA GTA AAT ATC CCG GGG ACT GCA TAC AGC GGT GAG ACA ATA TAC CCC AAT GGA TCC TTG CTG TTT CAA AAC GTC ACC CTG GAG GAC ACA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCT GTC GCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GCG GCT CTG GTG GCC GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG GAG AGG CCC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCC ACC TTC TCG GCT CCC CTA CCT GGC CCC AGG ACA GCC ACT CCC ATG TAT GAG GAA TTG CTA CAC TCT GAC GCA AAC ATT TAC TGC CGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
baboon                          TCA CTT TTA ACC TTC TGG GAC CTG CCC CCC ACT GTC CAG TTC ACT ATC GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CGG GCC TGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCG GGG ACT GCA TAC AGC GGT GAG ACA ATA TAC TCC AAC GGA TCC CTG CTG TTC CAA AAC GTC ACG CTG GAG GAC GCA GGA TCC TAC ACC CTC CGA ACC ATA AAC GCC AAG TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCT GTC GCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT GGA AGG GCC AGC ATC CGG CGT GAC CTC AGG GAG CAG AGG CCC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCT GCC TTC TCG GCT CCT CTA CCT GGT CCC AGG ACA GCC ACT CCC CTG TAT GAG GAA TTG CTA CAC TCT GAC GCA AAC ATT TAC TGC CGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
drill                           TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATC GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CGG GCC TGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCG GGG ACT GCA TAC AGC GGT GAG ACA ATA TAC TCC AAC GGA TCC CTG CTG TTC CAA AAC GTC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAC GCC AAT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCT GTC GCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT GGA AGG GCC AGC ATC CGG CGT GAC CTC AGG GAG CAG AGG CCC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TAT GCC TTC TCG GCT CCC CTA CCT GGC CCC AGG ACA GCC ACT CCC CTG TAT GAG GAA TTG CTA CAC TCT GAC GCA AAC ATT TAC TGC TGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
sootyM                          TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATC GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CGG GCC TGC AAT ATT TCA GAA ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCG GGG ACT GCA TAC AGC GGT GAG AAA ATA TAC TCC AAC GGA TCC CTG CTG TTC CAA AAC GTC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAC GCC AAT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT ATG GGG GCT GTC TCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GCG GCC GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT GGA AGG GCC AGC ATC CGG CGT GAC CTC AGG GAG CAG AGG CCC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCT GCC TTC TCG TCT CCT CTA CCT GGC CCC AGG ACA GCC ACT CCC CTG TAT GAG GAA TTG CTA CAC TCT GAC GCA AAC ATT TAC TGC TGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
CEmac                           TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATC GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC TGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCA GGG ACT GCA TAC AGC AGT GAG ACA ATA TAC TCC AAC GGA TCC CTG CTG TTC CAA AAC GTC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAC GCC AAT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC ATC CCA GGC CTT CCT GTG GGG GCT GTC GCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG ACG CAG AGG CCC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCC GCC TTC TCG GCC CCC CTA CCT GGC CCC AGG ACA ACC ACT CCC CTG TAT GAG GAA TTG CTA CAC TCT GAC GCA AAC ATT TAC TGC CGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
rhesus                          TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATC GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC TGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCA GGG ACT GCA TAC AGC GGT GAG ACA ATA TAC TCC AAC GGA TCC CTG CTG TTC CAA AAC GTC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAC GCC AAT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCT GTC ACT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTC CTG CTT CTC GCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG ACG CAG AGG CCC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCC GCC TTC TCG GCC CCC CTA CCT GGC CCC AGG ACA ACC ACT CCC CTG TAT GAG GAA TTG CTA CAC TCT GAC CCA AAC ATT TAC TGC CGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
PTmac                           TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATC GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC TGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCA GGG ACT GCA TAC AGC GGT GAG ACA ATA TAC TCC AAC GGA TCC CTG CTG TTC CAA AAC GTC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAC GCC AAT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTA CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GAT GTC GCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GTG GCC GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT GGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG CAG AGG CCC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCC GCC TTC TCG GCC CCC CTA CCT GGC CCC AGG ACA ACC ACT CCC CTG TAT GAG GAA TTG CTA CAT TCT GAC GCA AAC ATT TAC TGC CGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
BSNM                            TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC CGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCG GGG ACT GCA TAC AGC GGT GAG ACA ATA TAC CCC AAT GGA TCC CTG CTG TTC CAA AAC GTC ACC CTG GAG GAT GCA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTG CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCT GTC GCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GTG GCT GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT AGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG CAG AGG CTC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCC ACC TTC TCG GCC CCC CTA CCT GGC CCC AGG ACA GCC ACT CCC ATG TAT GAG GAA TTG CTA CAC TCT GAC GCA AAC ATT TAC TGC CGG ATT GAC CAC AAA GCA GAT GTG GTC TCT 
GSNM                            TCA CTT TTA ACC TTC TGG GAC CTG CCC ACC ACT GTC CAG TTC ACT ATT GAA GCC CTG CCG TCC AGT GCT GCA GAG GGA AAG GAT GTT CTT CTA CTG GCC CGC AAT ATT TCA GAG ACT ATT CAA GCC TAT TAT TGG CAC AAG GGG AAA ACG GCA GAA GGG AGC CCT CTC ATT GCT GGT TAT TTG ATA GAC GTT CAA GTA AAT ATC CCG GGG ACT GCA TAC AGC GGT GAG ACA ATA TAC CCC AAT GGA TCC CTG CTG TTC CAA AAC GTC ACC CTG GAG GAC GCA GGA TCC TAC ACC CTA CGA ACC ATA AAT GCC AGT TAT GAC TCC GAC CAA GCA ACT GGC CAG CTC CAC GTG CAC CAA AAC AAC GTC CCA GGC CTT CCT GTG GGG GCT GTC GCT GGC ATC GTG ACT GGG GTC CTG GTC GGG GTG GCT CTG GTG GCT GCC CTG GTG TGT TTC CTG CTC CTC GCC AGG ACT AGA AGG GCC AGC ATC CAG CGT GAC CTC AGG GAG CAG AGG CTC CCA GCC TCC ACC CCC GGC CAC GGT CCC TCT CAC AGA TCC ACC TTC TCG GCC CCC CTA CCT GGC CCC AGG ACA GCC ACT CCC ATG TAT GAG GAA TTG CTA CAC TCT GAC GCA AAC ATT TAC TGC CGG ATT GAC CAC AAA GCA GAT GGG GTC TCT 



Printing out site pattern counts


        14        384  P

human                           AAA AAA AAC AAG AAT AAT ACA ACA ACA ACC ACC ACC ACC ACG ACT ACT AGA AGA AGC AGC AGG AGT AGT AGT ATA ATA ATC ATC ATC ATC ATT ATT ATT ATT CAA CAC CAC CAC CAG CAG CAG CAG CAT CCA CCA CCC CCC CCC CCC CCC CCC CCG CCG CCG CCT CCT CCT CGA CGT CTA CTA CTC CTG CTG CTG CTT CTT CTT GAA GAA GAC GAC GAC GAG GAG GAT GAT GCA GCA GCA GCA GCC GCC GCC GCC GCC GCC GCC GCT GCT GGA GGA GGC GGG GGT GGT GTA GTA GTC GTC GTG GTG GTG GTG GTG GTT GTT TAC TAC TAC TAT TCA TCC TCC TCC TCC TCG TCT TCT TGC TGC TGG TGT TTA TTC TTC TTG TTT 
chimpanzee                      ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
bonobo                          ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... G.. ... ... ... .G. ... ... ... ... ... ... ... ... ... ..A ... ... ..C ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
gorilla                         ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ..A ... ... ... ... ... ... ... ... ... ... ..C A.. ... ... ... ... ... ..T ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
orangutan                       ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T G.. ... ... ... ... ... ... ... A.. ..A ... ... ... .GT ... ... ..A ... ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ..G ... ... ... ... ... ..C ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G 
colobus                         ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... G.. ... ..C ... ... ... T.G ... ..G ..T G.. ... ... G.. ... ... ... ... G.. ... ... G.. .G. ..C ... ..G ... ..T ... ... ... ... .T. AG. ... ..C ..C ... ... ... ... ... ... .C. ... T.. ..C ... ... ... ..G ... ... ... ... ... ..C ... A.. ... ... .T. ... A.T ... ... ... ..T ..T ... ... ... ... ... ... ... ... A.. ... ... ... ... .C. ... ... ... ..C ... C.. ... ..T ... ... ... G.. ... ... ... ..C ... C.. ... ... ... ... ... ..T ... ..C 
baboon                          ... ... ... ... ..C ... ... ... .T. ... ..G G.. C.. ... ... ... ... ..G ... G.T ... ..C .AG ... ... T.G ... C.G ..T G.. ..C ... G.. ... ... ... ... G.. ... .G. ... .G. ..C ... ..G ... ..T ... ... T.. ... .T. AG. ... ..C ... ... ... ... ... ..C ... .G. ... ... ..C ... ... ... ..G ... ... ... ... ... ..C ... ... ... ... .T. ... A.T ... ... ... ..T ..T ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ..C ... C.. ... ..T ... ... ... G.. ... ..T ... ..C ... ... ... ... ... ... ... ... ... ..C 
drill                           ... ... ... ... ..C ... ... ... .T. ... ... G.. ... ... ... ... ... ..G ... G.. ... ..C .A. ... ... T.G ... C.G ..T G.. ..C ... G.. ... ... ... ... G.. ... .G. ... TG. ..C ... ..G ... ..T ... ... T.. ... .T. AG. ... ..C ..C ... ... ... ... ... ... .G. ... ... ..C ... ... ... ..G ... ... ... ... ... ..C ... ... ... ... .T. ... A.T ... ... ... ..T ..T ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ..C ... C.. ... ..T ... ... ... G.. ... .AT ... ..C ... ... ... ... ... ... ... ... ... ..C 
sootyM                          ... ... ... ... ..C ... .A. ... .T. ... ... G.. ... ... ... ... ... ..G ... G.. ... ..C .A. ... ... T.G ... C.G ..T G.. ..C ... G.. ... ... ... ... G.. ... .G. ... TG. ..C ... ..G ... ..T ... ... T.. ... .T. AG. ... ..C ... ... ... ... ... ... ... .G. ... ... ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ... .T. ... A.T ... ... ... ..T T.T ... T.. ... ... ... ... ... ... A.. ... ... ... A.. ... .C. ... ... ..C ... C.. ... ..T ... ... ... G.. ... ..T ... ..C ... ... ... ... ... ... ... ... ... ..C 
CEmac                           ... ... ... ... ..C ... ... ... .T. ... ... G.. ... ... ... ... ... ..G ... G.. ... ..C .A. ... ... T.G ... C.G ..T G.. ..C ... G.. ... ... ... ... G.. ... ... ... .G. ..C ... ... ... ..T ... ... T.. ... .T. AG. ... ..C ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ..G ... ... ... AC. ... ..C ... ... ... ... .T. ... A.T A.. ... ... ..T ... ... ... ... ... ... ... A.. ... A.. ... A.. ... ... ... ... ... ... ..C ... C.. ... ..T ... ... ... G.. ... ... ... ..C ... ... ... ... ... ... ... ... ... ..C 
rhesus                          ... ... ... ... ..C ... ... ... .T. ... ... G.. ... ... ... ... ... ..G ... G.. ... ..C .A. ... ... T.G ... C.G ..T G.. ..C ... G.. ... ... ... ... G.. ... ... ... .G. ..C ... ... ... ..T ... ... T.. ... .T. AG. ... ..C ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... AC. ... ..C ... ... C.. ... .T. ... A.T A.. ... ... ..T ... ... A.. ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ..C ... C.. ... ..T ... ... ... G.. ... ... ... ..C ... ... ... ... ... ... ... ... ... ..C 
PTmac                           ... ... ... ... ..C ... ... ... .T. ... ... G.. ... ... ... ... ... ..G ... G.. ... ..C .A. ... ... T.G ... C.G ..T G.. ..C ... G.. ... ... ... ... G.. ... ... ... .G. ..C ... ... ... ..T ... ... T.. ... .T. AG. ... ..C ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ..G ... ... ... ... ... ..C ... ... ... ... .T. ... A.T A.. ... ... .AT ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ..C ... C.T ... ..T ... ... ... G.. ... ... ... ..C ... ... ... ... ... ... ... ... ... ..C 
BSNM                            ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ..G ... G.. ... ..C ... ... ... T.G ... ..G ..T G.. ... ... G.. ... ... ... ... G.. ... ... ... .G. ..C ... ..G ... ..T ... .T. ... ... .T. AG. ... ..C ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ..G ... ..T ... ... ... ..C ... ... ... ... .T. ... A.T ... ... ..T ..T ... ... ... A.. ... ... ... ... ... A.. ..G ... ... ... ... ... ... ... ..C ... C.. ... ..T ... ... ... G.. ... ... ... ..C ... C.. ... ... ... ... ... ... ... ..C 
GSNM                            ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ..G ... G.. ... ..C ... ... ... T.G ... ..G ..T G.. ... ... G.. ... ... ... ... G.. ... ... ... .G. ..C ... ..G ... ..T ... .T. ... ... .T. AG. ... ..C ..C ... ... ... ... ... ... ... ... ... ..C ... ... ... ..G ... ... ... ... ... ..C ... ... ... ... .T. ... A.T ... ... ..T ..T ... ... ... A.. ... ... ... ... ... A.. ..G ... ... ... ... ... .G. ... ..C ... C.. ... ..T ... ... ... G.. ... ... ... ..C ... C.. ... ... ... ... ... ... ... ..C 

    1    1    4    2    2    2    1    1    1    4    1    1    1    1    6
    1    1    1    2    1    3    1    1    1    1    1    3    1    1    1
    1    3    1    1    5    4    1    1    2    1    1    1    1    2    1
    1    1    2    1    1    1    1    1    1    1    1    2    1    1    3
    1    4    1    7    1    1    1    2    3    1    4    1    1    1    4
    1    2    1    1    5    1    1    1    1    6    1    1    1    3    1
    1    3    4    6    1    2    1    1    1    4    1    1    1    1    2
    1    1    1    4    1    4    2    1    1    3    1    1    1    3    1
    1    2    1    1    3    1    1    1

CODONML (in paml version 4.9h, March 2018)  CEACAM4seq.txt
Model: One dN/dS ratio, 
Codon frequency model: F3x4
Site-class models: 
ns =  14  ls = 221

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   1   1   1   1   0   1 | Ser TCT   4   4   4   4   4   3 | Tyr TAT   4   4   4   4   4   5 | Cys TGT   1   1   1   1   1   1
    TTC   4   4   4   4   4   4 |     TCC   6   6   6   5   6   6 |     TAC   6   6   6   6   6   4 |     TGC   2   2   2   2   2   1
Leu TTA   1   1   1   1   1   1 |     TCA   2   2   2   3   2   2 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   1   1   1   1   2   3 |     TCG   1   1   1   1   1   1 |     TAG   0   0   0   0   0   0 | Trp TGG   2   2   2   2   2   2
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   4   3   3   2   3   3 | Pro CCT   4   3   3   3   3   3 | His CAT   1   1   1   1   2   0 | Arg CGT   1   1   1   1   2   1
    CTC   4   5   5   5   5   5 |     CCC   7   8   8   7   5   8 |     CAC   6   5   5   5   4   7 |     CGC   0   0   0   0   0   1
    CTA   4   4   4   4   4   4 |     CCA   3   3   4   5   5   2 | Gln CAA   5   5   5   5   5   6 |     CGA   1   1   1   1   1   1
    CTG   9   9   9   9   9   8 |     CCG   3   3   2   2   2   3 |     CAG   5   4   4   5   5   3 |     CGG   0   1   1   0   0   1
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   6   5   5   7   6   6 | Thr ACT   7   7   7   7   6   8 | Asn AAT   4   4   4   4   4   4 | Ser AGT   3   3   3   3   4   2
    ATC   6   6   6   6   6   3 |     ACC   7   7   7   7   8   7 |     AAC   4   4   4   4   4   4 |     AGC   3   3   3   3   4   3
    ATA   2   2   2   2   2   2 |     ACA   3   3   3   3   3   4 | Lys AAA   2   2   2   2   2   1 | Arg AGA   2   2   2   2   2   1
Met ATG   0   0   0   0   0   1 |     ACG   1   1   1   1   1   1 |     AAG   2   2   2   2   2   2 |     AGG   3   3   3   3   3   5
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   2   3   3   2   2   2 | Ala GCT   4   4   4   4   4   6 | Asp GAT   3   2   2   3   2   2 | Gly GGT   3   3   3   3   3   3
    GTC   5   5   5   5   5   7 |     GCC  12  12  12  12  11  10 |     GAC   6   8   8   7   8   8 |     GGC   4   4   4   4   4   5
    GTA   2   2   2   2   2   2 |     GCA   8   8   8   8   8   6 | Glu GAA   4   4   4   4   3   3 |     GGA   4   4   4   4   4   4
    GTG   6   6   6   5   6   5 |     GCG   0   0   0   1   0   1 |     GAG   5   5   5   5   6   7 |     GGG   6   6   6   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   0   0   0   0   0   0 | Ser TCT   4   3   6   3   3   3 | Tyr TAT   5   6   5   5   5   5 | Cys TGT   1   1   1   1   1   1
    TTC   5   5   5   5   5   5 |     TCC   6   6   6   7   7   7 |     TAC   4   4   4   4   4   4 |     TGC   2   2   2   2   2   2
Leu TTA   1   1   1   1   1   1 |     TCA   2   2   2   2   2   2 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   2   2   2   2   2   2 |     TCG   1   1   1   1   1   1 |     TAG   0   0   0   0   0   0 | Trp TGG   2   3   3   2   2   2
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   3   3   3   3   4   3 | Pro CCT   4   3   4   3   3   3 | His CAT   0   0   0   0   0   1 | Arg CGT   1   1   1   1   1   1
    CTC   6   5   5   5   4   5 |     CCC   7   7   6   7   7   7 |     CAC   7   7   7   7   7   6 |     CGC   0   0   0   0   0   0
    CTA   3   4   4   4   4   4 |     CCA   2   2   2   3   4   3 | Gln CAA   5   5   5   5   5   5 |     CGA   1   1   1   1   1   1
    CTG  10  10  10  11  11  11 |     CCG   2   2   2   1   1   1 |     CAG   3   3   3   4   4   4 |     CGG   3   2   2   1   1   1
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   5   5   5   5   5   5 | Thr ACT   8   8   8   8   9   8 | Asn AAT   2   3   3   3   3   3 | Ser AGT   1   1   1   2   1   1
    ATC   4   4   4   5   4   4 |     ACC   4   6   6   7   7   7 |     AAC   6   6   6   6   6   6 |     AGC   3   3   3   3   3   3
    ATA   3   3   3   3   3   3 |     ACA   2   2   1   2   2   2 | Lys AAA   2   2   3   2   2   2 | Arg AGA   1   1   1   1   1   1
Met ATG   0   0   1   0   0   0 |     ACG   2   1   1   2   2   1 |     AAG   3   2   2   2   2   2 |     AGG   5   5   5   5   5   5
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   2   2   2   2   2   2 | Ala GCT   6   6   4   5   4   4 | Asp GAT   2   2   2   2   2   3 | Gly GGT   4   3   3   2   3   3
    GTC   7   7   7   6   7   7 |     GCC  11  11  11  11  11  11 |     GAC   8   8   8   8   8   8 |     GGC   4   5   5   5   5   5
    GTA   2   2   2   2   2   2 |     GCA   7   7   7   7   6   7 | Glu GAA   3   3   4   3   3   3 |     GGA   4   4   4   4   4   4
    GTG   6   6   4   6   6   6 |     GCG   0   0   1   0   0   0 |     GAG   6   6   5   5   5   6 |     GGG   6   6   6   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------

----------------------------------------------------------------------
Phe TTT   0   0 | Ser TCT   3   3 | Tyr TAT   5   5 | Cys TGT   1   1
    TTC   5   5 |     TCC   6   6 |     TAC   4   4 |     TGC   1   1
Leu TTA   1   1 |     TCA   2   2 | *** TAA   0   0 | *** TGA   0   0
    TTG   2   2 |     TCG   1   1 |     TAG   0   0 | Trp TGG   2   2
----------------------------------------------------------------------
Leu CTT   3   3 | Pro CCT   3   3 | His CAT   0   0 | Arg CGT   1   1
    CTC   6   6 |     CCC   7   7 |     CAC   7   7 |     CGC   1   1
    CTA   4   4 |     CCA   2   2 | Gln CAA   5   5 |     CGA   1   1
    CTG  10  10 |     CCG   2   2 |     CAG   4   4 |     CGG   1   1
----------------------------------------------------------------------
Ile ATT   6   6 | Thr ACT   8   8 | Asn AAT   4   4 | Ser AGT   2   2
    ATC   3   3 |     ACC   7   7 |     AAC   4   4 |     AGC   3   3
    ATA   3   3 |     ACA   2   2 | Lys AAA   2   2 | Arg AGA   2   2
Met ATG   1   1 |     ACG   1   1 |     AAG   2   2 |     AGG   5   5
----------------------------------------------------------------------
Val GTT   2   2 | Ala GCT   6   6 | Asp GAT   3   2 | Gly GGT   3   3
    GTC   7   7 |     GCC  10  10 |     GAC   7   8 |     GGC   5   5
    GTA   1   1 |     GCA   7   7 | Glu GAA   3   3 |     GGA   3   3
    GTG   7   6 |     GCG   0   0 |     GAG   6   6 |     GGG   6   7
----------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: human          
position  1:    T:0.15837    C:0.25792    A:0.24887    G:0.33484
position  2:    T:0.25792    C:0.32579    A:0.25792    G:0.15837
position  3:    T:0.23529    C:0.37104    A:0.19457    G:0.19910
Average         T:0.21719    C:0.31825    A:0.23379    G:0.23077

#2: chimpanzee     
position  1:    T:0.15837    C:0.25339    A:0.24434    G:0.34389
position  2:    T:0.25792    C:0.32579    A:0.25339    G:0.16290
position  3:    T:0.22172    C:0.38462    A:0.19457    G:0.19910
Average         T:0.21267    C:0.32127    A:0.23077    G:0.23529

#3: bonobo         
position  1:    T:0.15837    C:0.25339    A:0.24434    G:0.34389
position  2:    T:0.25792    C:0.32579    A:0.25339    G:0.16290
position  3:    T:0.22172    C:0.38462    A:0.19910    G:0.19457
Average         T:0.21267    C:0.32127    A:0.23228    G:0.23379

#4: gorilla        
position  1:    T:0.15837    C:0.24887    A:0.25339    G:0.33937
position  2:    T:0.25339    C:0.33032    A:0.25792    G:0.15837
position  3:    T:0.22624    C:0.37104    A:0.20814    G:0.19457
Average         T:0.21267    C:0.31674    A:0.23982    G:0.23077

#5: orangutan      
position  1:    T:0.15837    C:0.24887    A:0.25792    G:0.33484
position  2:    T:0.25792    C:0.31222    A:0.25792    G:0.17195
position  3:    T:0.22624    C:0.37104    A:0.19910    G:0.20362
Average         T:0.21418    C:0.31071    A:0.23831    G:0.23680

#6: colobus        
position  1:    T:0.15385    C:0.25339    A:0.24434    G:0.34842
position  2:    T:0.25792    C:0.32127    A:0.25339    G:0.16742
position  3:    T:0.22624    C:0.37557    A:0.17647    G:0.22172
Average         T:0.21267    C:0.31674    A:0.22474    G:0.24585

#7: baboon         
position  1:    T:0.15837    C:0.25792    A:0.23077    G:0.35294
position  2:    T:0.26697    C:0.30769    A:0.25339    G:0.17195
position  3:    T:0.21719    C:0.38009    A:0.17195    G:0.23077
Average         T:0.21418    C:0.31523    A:0.21870    G:0.25189

#8: drill          
position  1:    T:0.16290    C:0.24887    A:0.23529    G:0.35294
position  2:    T:0.26697    C:0.30317    A:0.25792    G:0.17195
position  3:    T:0.21267    C:0.38914    A:0.17647    G:0.22172
Average         T:0.21418    C:0.31373    A:0.22323    G:0.24887

#9: sootyM         
position  1:    T:0.17195    C:0.24887    A:0.23982    G:0.33937
position  2:    T:0.26244    C:0.30769    A:0.25792    G:0.17195
position  3:    T:0.21719    C:0.38462    A:0.18100    G:0.21719
Average         T:0.21719    C:0.31373    A:0.22624    G:0.24284

#10: CEmac          
position  1:    T:0.15837    C:0.25339    A:0.25339    G:0.33484
position  2:    T:0.27149    C:0.31222    A:0.25339    G:0.16290
position  3:    T:0.20362    C:0.39819    A:0.18100    G:0.21719
Average         T:0.21116    C:0.32127    A:0.22926    G:0.23831

#11: rhesus         
position  1:    T:0.15837    C:0.25792    A:0.24887    G:0.33484
position  2:    T:0.27149    C:0.31222    A:0.25339    G:0.16290
position  3:    T:0.20814    C:0.39367    A:0.18100    G:0.21719
Average         T:0.21267    C:0.32127    A:0.22775    G:0.23831

#12: PTmac          
position  1:    T:0.15837    C:0.25339    A:0.23982    G:0.34842
position  2:    T:0.27149    C:0.30317    A:0.26244    G:0.16290
position  3:    T:0.20814    C:0.39367    A:0.18100    G:0.21719
Average         T:0.21267    C:0.31674    A:0.22775    G:0.24284

#13: BSNM           
position  1:    T:0.14932    C:0.25792    A:0.24887    G:0.34389
position  2:    T:0.27602    C:0.30317    A:0.25339    G:0.16742
position  3:    T:0.22624    C:0.37557    A:0.17195    G:0.22624
Average         T:0.21719    C:0.31222    A:0.22474    G:0.24585

#14: GSNM           
position  1:    T:0.14932    C:0.25792    A:0.24887    G:0.34389
position  2:    T:0.27149    C:0.30317    A:0.25339    G:0.17195
position  3:    T:0.22172    C:0.38009    A:0.17195    G:0.22624
Average         T:0.21418    C:0.31373    A:0.22474    G:0.24736

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       5 | Ser S TCT      51 | Tyr Y TAT      66 | Cys C TGT      14
      TTC      64 |       TCC      86 |       TAC      66 |       TGC      25
Leu L TTA      14 |       TCA      29 | *** * TAA       0 | *** * TGA       0
      TTG      25 |       TCG      14 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT      43 | Pro P CCT      45 | His H CAT       7 | Arg R CGT      15
      CTC      71 |       CCC      98 |       CAC      87 |       CGC       3
      CTA      55 |       CCA      42 | Gln Q CAA      71 |       CGA      14
      CTG     136 |       CCG      28 |       CAG      55 |       CGG      15
------------------------------------------------------------------------------
Ile I ATT      77 | Thr T ACT     107 | Asn N AAT      49 | Ser S AGT      29
      ATC      64 |       ACC      94 |       AAC      68 |       AGC      43
      ATA      36 |       ACA      34 | Lys K AAA      28 | Arg R AGA      21
Met M ATG       4 |       ACG      17 |       AAG      29 |       AGG      60
------------------------------------------------------------------------------
Val V GTT      30 | Ala A GCT      67 | Asp D GAT      32 | Gly G GGT      42
      GTC      87 |       GCC     155 |       GAC     108 |       GGC      64
      GTA      26 |       GCA     101 | Glu E GAA      47 |       GGA      54
      GTG      81 |       GCG       3 |       GAG      78 |       GGG      85
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15805    C:0.25372    A:0.24564    G:0.34260
position  2:    T:0.26438    C:0.31383    A:0.25566    G:0.16613
position  3:    T:0.21946    C:0.38235    A:0.18487    G:0.21332
Average         T:0.21396    C:0.31663    A:0.22872    G:0.24068

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.00936619  0.01631842  0.00789023  0.00910411
  0.01111806  0.01937064  0.00936603  0.01080695
  0.00905704  0.01577979  0.00000000  0.00000000
  0.00588536  0.01025387  0.00000000  0.00572067
  0.01503571  0.02619624  0.01266631  0.01461498
  0.01784801  0.03109602  0.01503544  0.01734858
  0.01453942  0.02533157  0.01224823  0.01413258
  0.00944787  0.01646072  0.00795903  0.00918349
  0.01455687  0.02536196  0.01226293  0.01414953
  0.01727961  0.03010570  0.01455660  0.01679608
  0.01407638  0.02452483  0.01185816  0.01368249
  0.00914698  0.01593649  0.00770556  0.00889103
  0.02030300  0.03537326  0.01710356  0.01973487
  0.02410050  0.04198954  0.02030263  0.02342611
  0.01963285  0.03420569  0.01653901  0.01908348
  0.01275763  0.02222721  0.01074722  0.01240064


Model 1: NearlyNeutral (2 categories)


TREE #  1:  ((((1, (2, 3)), 4), 5), ((((11, 10), 12), (7, (9, 8))), (6, (14, 13))));   MP score: 102
This is a rooted tree.  Please check!
lnL(ntime: 26  np: 29):  -1560.328739      +0.000000
  15..16   16..17   17..18   18..1    18..19   19..2    19..3    17..4    16..5    15..20   20..21   21..22   22..23   23..11   23..10   22..12   21..24   24..7    24..25   25..9    25..8    20..26   26..6    26..27   27..14   27..13 
 0.034369 0.007332 0.000004 0.014770 0.012917 0.000004 0.004591 0.027938 0.050867 0.108429 0.034003 0.008924 0.009334 0.013944 0.009243 0.009280 0.019950 0.027453 0.004572 0.032142 0.005497 0.004377 0.041763 0.019289 0.004681 0.004563 4.478277 0.520458 0.086002

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  0.510235

((((1: 0.014770, (2: 0.000004, 3: 0.004591): 0.012917): 0.000004, 4: 0.027938): 0.007332, 5: 0.050867): 0.034369, ((((11: 0.013944, 10: 0.009243): 0.009334, 12: 0.009280): 0.008924, (7: 0.027453, (9: 0.032142, 8: 0.005497): 0.004572): 0.019950): 0.034003, (6: 0.041763, (14: 0.004681, 13: 0.004563): 0.019289): 0.004377): 0.108429);

((((human: 0.014770, (chimpanzee: 0.000004, bonobo: 0.004591): 0.012917): 0.000004, gorilla: 0.027938): 0.007332, orangutan: 0.050867): 0.034369, ((((rhesus: 0.013944, CEmac: 0.009243): 0.009334, PTmac: 0.009280): 0.008924, (baboon: 0.027453, (sootyM: 0.032142, drill: 0.005497): 0.004572): 0.019950): 0.034003, (colobus: 0.041763, (GSNM: 0.004681, BSNM: 0.004563): 0.019289): 0.004377): 0.108429);

Detailed output identifying parameters

kappa (ts/tv) =  4.47828


MLEs of dN/dS (w) for site classes (K=2)

p:   0.52046  0.47954
w:   0.08600  1.00000

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  15..16      0.034    467.6    195.4   0.5243   0.0090   0.0172    4.2    3.4
  16..17      0.007    467.6    195.4   0.5243   0.0019   0.0037    0.9    0.7
  17..18      0.000    467.6    195.4   0.5243   0.0000   0.0000    0.0    0.0
  18..1       0.015    467.6    195.4   0.5243   0.0039   0.0074    1.8    1.4
  18..19      0.013    467.6    195.4   0.5243   0.0034   0.0065    1.6    1.3
  19..2       0.000    467.6    195.4   0.5243   0.0000   0.0000    0.0    0.0
  19..3       0.005    467.6    195.4   0.5243   0.0012   0.0023    0.6    0.5
  17..4       0.028    467.6    195.4   0.5243   0.0073   0.0140    3.4    2.7
  16..5       0.051    467.6    195.4   0.5243   0.0134   0.0255    6.3    5.0
  15..20      0.108    467.6    195.4   0.5243   0.0285   0.0544   13.3   10.6
  20..21      0.034    467.6    195.4   0.5243   0.0089   0.0171    4.2    3.3
  21..22      0.009    467.6    195.4   0.5243   0.0023   0.0045    1.1    0.9
  22..23      0.009    467.6    195.4   0.5243   0.0025   0.0047    1.1    0.9
  23..11      0.014    467.6    195.4   0.5243   0.0037   0.0070    1.7    1.4
  23..10      0.009    467.6    195.4   0.5243   0.0024   0.0046    1.1    0.9
  22..12      0.009    467.6    195.4   0.5243   0.0024   0.0047    1.1    0.9
  21..24      0.020    467.6    195.4   0.5243   0.0052   0.0100    2.5    2.0
  24..7       0.027    467.6    195.4   0.5243   0.0072   0.0138    3.4    2.7
  24..25      0.005    467.6    195.4   0.5243   0.0012   0.0023    0.6    0.4
  25..9       0.032    467.6    195.4   0.5243   0.0085   0.0161    4.0    3.2
  25..8       0.005    467.6    195.4   0.5243   0.0014   0.0028    0.7    0.5
  20..26      0.004    467.6    195.4   0.5243   0.0012   0.0022    0.5    0.4
  26..6       0.042    467.6    195.4   0.5243   0.0110   0.0209    5.1    4.1
  26..27      0.019    467.6    195.4   0.5243   0.0051   0.0097    2.4    1.9
  27..14      0.005    467.6    195.4   0.5243   0.0012   0.0023    0.6    0.5
  27..13      0.005    467.6    195.4   0.5243   0.0012   0.0023    0.6    0.4


Time used:  1:21


Model 2: PositiveSelection (3 categories)


TREE #  1:  ((((1, (2, 3)), 4), 5), ((((11, 10), 12), (7, (9, 8))), (6, (14, 13))));   MP score: 102
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 26  np: 31):  -1560.221766      +0.000000
  15..16   16..17   17..18   18..1    18..19   19..2    19..3    17..4    16..5    15..20   20..21   21..22   22..23   23..11   23..10   22..12   21..24   24..7    24..25   25..9    25..8    20..26   26..6    26..27   27..14   27..13 
 0.045781 0.007394 0.000004 0.014936 0.012963 0.000004 0.004627 0.028210 0.051339 0.098348 0.034268 0.009021 0.009404 0.014064 0.009336 0.009361 0.020352 0.027903 0.004355 0.032496 0.005598 0.004467 0.042112 0.019450 0.004720 0.004601 4.521794 0.563702 0.430416 0.135592 5.968392

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  0.515114

((((1: 0.014936, (2: 0.000004, 3: 0.004627): 0.012963): 0.000004, 4: 0.028210): 0.007394, 5: 0.051339): 0.045781, ((((11: 0.014064, 10: 0.009336): 0.009404, 12: 0.009361): 0.009021, (7: 0.027903, (9: 0.032496, 8: 0.005598): 0.004355): 0.020352): 0.034268, (6: 0.042112, (14: 0.004720, 13: 0.004601): 0.019450): 0.004467): 0.098348);

((((human: 0.014936, (chimpanzee: 0.000004, bonobo: 0.004627): 0.012963): 0.000004, gorilla: 0.028210): 0.007394, orangutan: 0.051339): 0.045781, ((((rhesus: 0.014064, CEmac: 0.009336): 0.009404, PTmac: 0.009361): 0.009021, (baboon: 0.027903, (sootyM: 0.032496, drill: 0.005598): 0.004355): 0.020352): 0.034268, (colobus: 0.042112, (GSNM: 0.004720, BSNM: 0.004601): 0.019450): 0.004467): 0.098348);

Detailed output identifying parameters

kappa (ts/tv) =  4.52179


MLEs of dN/dS (w) for site classes (K=3)

p:   0.56370  0.43042  0.00588
w:   0.13559  1.00000  5.96839

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  15..16      0.046    467.4    195.6   0.5420   0.0122   0.0225    5.7    4.4
  16..17      0.007    467.4    195.6   0.5420   0.0020   0.0036    0.9    0.7
  17..18      0.000    467.4    195.6   0.5420   0.0000   0.0000    0.0    0.0
  18..1       0.015    467.4    195.6   0.5420   0.0040   0.0074    1.9    1.4
  18..19      0.013    467.4    195.6   0.5420   0.0035   0.0064    1.6    1.2
  19..2       0.000    467.4    195.6   0.5420   0.0000   0.0000    0.0    0.0
  19..3       0.005    467.4    195.6   0.5420   0.0012   0.0023    0.6    0.4
  17..4       0.028    467.4    195.6   0.5420   0.0075   0.0139    3.5    2.7
  16..5       0.051    467.4    195.6   0.5420   0.0137   0.0253    6.4    4.9
  15..20      0.098    467.4    195.6   0.5420   0.0262   0.0484   12.3    9.5
  20..21      0.034    467.4    195.6   0.5420   0.0091   0.0169    4.3    3.3
  21..22      0.009    467.4    195.6   0.5420   0.0024   0.0044    1.1    0.9
  22..23      0.009    467.4    195.6   0.5420   0.0025   0.0046    1.2    0.9
  23..11      0.014    467.4    195.6   0.5420   0.0038   0.0069    1.8    1.4
  23..10      0.009    467.4    195.6   0.5420   0.0025   0.0046    1.2    0.9
  22..12      0.009    467.4    195.6   0.5420   0.0025   0.0046    1.2    0.9
  21..24      0.020    467.4    195.6   0.5420   0.0054   0.0100    2.5    2.0
  24..7       0.028    467.4    195.6   0.5420   0.0074   0.0137    3.5    2.7
  24..25      0.004    467.4    195.6   0.5420   0.0012   0.0021    0.5    0.4
  25..9       0.032    467.4    195.6   0.5420   0.0087   0.0160    4.1    3.1
  25..8       0.006    467.4    195.6   0.5420   0.0015   0.0028    0.7    0.5
  20..26      0.004    467.4    195.6   0.5420   0.0012   0.0022    0.6    0.4
  26..6       0.042    467.4    195.6   0.5420   0.0112   0.0207    5.3    4.1
  26..27      0.019    467.4    195.6   0.5420   0.0052   0.0096    2.4    1.9
  27..14      0.005    467.4    195.6   0.5420   0.0013   0.0023    0.6    0.5
  27..13      0.005    467.4    195.6   0.5420   0.0012   0.0023    0.6    0.4


Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w



Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w

   212 Q      0.705         2.594 +- 1.986



The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.174  0.249  0.270  0.205  0.086  0.015  0.001  0.000  0.000  0.000
w2:   0.410  0.219  0.142  0.091  0.056  0.034  0.021  0.013  0.009  0.006

Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.032
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.022 0.090
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.007 0.019 0.049 0.108
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.010 0.019 0.029 0.056 0.099
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.011 0.018 0.025 0.030 0.054 0.081
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.005 0.011 0.017 0.021 0.025 0.029 0.047 0.062

sum of density on p0-p1 =   1.000000

Time used:  5:12


Model 7: beta (10 categories)


TREE #  1:  ((((1, (2, 3)), 4), 5), ((((11, 10), 12), (7, (9, 8))), (6, (14, 13))));   MP score: 102
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 26  np: 29):  -1560.346253      +0.000000
  15..16   16..17   17..18   18..1    18..19   19..2    19..3    17..4    16..5    15..20   20..21   21..22   22..23   23..11   23..10   22..12   21..24   24..7    24..25   25..9    25..8    20..26   26..6    26..27   27..14   27..13 
 0.095819 0.007349 0.000004 0.014763 0.012911 0.000004 0.004589 0.027923 0.050822 0.046907 0.034003 0.008907 0.009332 0.013936 0.009234 0.009275 0.019946 0.027433 0.004573 0.032126 0.005493 0.004358 0.041747 0.019280 0.004679 0.004560 4.479810 0.103706 0.093150

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  0.509974

((((1: 0.014763, (2: 0.000004, 3: 0.004589): 0.012911): 0.000004, 4: 0.027923): 0.007349, 5: 0.050822): 0.095819, ((((11: 0.013936, 10: 0.009234): 0.009332, 12: 0.009275): 0.008907, (7: 0.027433, (9: 0.032126, 8: 0.005493): 0.004573): 0.019946): 0.034003, (6: 0.041747, (14: 0.004679, 13: 0.004560): 0.019280): 0.004358): 0.046907);

((((human: 0.014763, (chimpanzee: 0.000004, bonobo: 0.004589): 0.012911): 0.000004, gorilla: 0.027923): 0.007349, orangutan: 0.050822): 0.095819, ((((rhesus: 0.013936, CEmac: 0.009234): 0.009332, PTmac: 0.009275): 0.008907, (baboon: 0.027433, (sootyM: 0.032126, drill: 0.005493): 0.004573): 0.019946): 0.034003, (colobus: 0.041747, (GSNM: 0.004679, BSNM: 0.004560): 0.019280): 0.004358): 0.046907);

Detailed output identifying parameters

kappa (ts/tv) =  4.47981

Parameters in M7 (beta):
 p =   0.10371  q =   0.09315


MLEs of dN/dS (w) for site classes (K=10)

p:   0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000  0.10000
w:   0.00000  0.00001  0.00186  0.04593  0.37091  0.85974  0.98941  0.99971  1.00000  1.00000

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  15..16      0.096    467.6    195.4   0.5268   0.0253   0.0479   11.8    9.4
  16..17      0.007    467.6    195.4   0.5268   0.0019   0.0037    0.9    0.7
  17..18      0.000    467.6    195.4   0.5268   0.0000   0.0000    0.0    0.0
  18..1       0.015    467.6    195.4   0.5268   0.0039   0.0074    1.8    1.4
  18..19      0.013    467.6    195.4   0.5268   0.0034   0.0065    1.6    1.3
  19..2       0.000    467.6    195.4   0.5268   0.0000   0.0000    0.0    0.0
  19..3       0.005    467.6    195.4   0.5268   0.0012   0.0023    0.6    0.4
  17..4       0.028    467.6    195.4   0.5268   0.0074   0.0140    3.4    2.7
  16..5       0.051    467.6    195.4   0.5268   0.0134   0.0254    6.3    5.0
  15..20      0.047    467.6    195.4   0.5268   0.0124   0.0235    5.8    4.6
  20..21      0.034    467.6    195.4   0.5268   0.0090   0.0170    4.2    3.3
  21..22      0.009    467.6    195.4   0.5268   0.0023   0.0045    1.1    0.9
  22..23      0.009    467.6    195.4   0.5268   0.0025   0.0047    1.1    0.9
  23..11      0.014    467.6    195.4   0.5268   0.0037   0.0070    1.7    1.4
  23..10      0.009    467.6    195.4   0.5268   0.0024   0.0046    1.1    0.9
  22..12      0.009    467.6    195.4   0.5268   0.0024   0.0046    1.1    0.9
  21..24      0.020    467.6    195.4   0.5268   0.0053   0.0100    2.5    2.0
  24..7       0.027    467.6    195.4   0.5268   0.0072   0.0137    3.4    2.7
  24..25      0.005    467.6    195.4   0.5268   0.0012   0.0023    0.6    0.4
  25..9       0.032    467.6    195.4   0.5268   0.0085   0.0161    4.0    3.1
  25..8       0.005    467.6    195.4   0.5268   0.0014   0.0027    0.7    0.5
  20..26      0.004    467.6    195.4   0.5268   0.0011   0.0022    0.5    0.4
  26..6       0.042    467.6    195.4   0.5268   0.0110   0.0209    5.1    4.1
  26..27      0.019    467.6    195.4   0.5268   0.0051   0.0096    2.4    1.9
  27..14      0.005    467.6    195.4   0.5268   0.0012   0.0023    0.6    0.5
  27..13      0.005    467.6    195.4   0.5268   0.0012   0.0023    0.6    0.4


Time used: 14:38


Model 8: beta&w>1 (11 categories)


TREE #  1:  ((((1, (2, 3)), 4), 5), ((((11, 10), 12), (7, (9, 8))), (6, (14, 13))));   MP score: 102
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 26  np: 31):  -1560.213655      +0.000000
  15..16   16..17   17..18   18..1    18..19   19..2    19..3    17..4    16..5    15..20   20..21   21..22   22..23   23..11   23..10   22..12   21..24   24..7    24..25   25..9    25..8    20..26   26..6    26..27   27..14   27..13 
 0.089356 0.007394 0.000004 0.014947 0.012961 0.000004 0.004629 0.028223 0.051353 0.054781 0.034273 0.009016 0.009406 0.014065 0.009334 0.009362 0.020386 0.027923 0.004327 0.032507 0.005605 0.004476 0.042120 0.019454 0.004721 0.004602 4.523918 0.993053 0.253627 0.249453 5.852833

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  0.515229

((((1: 0.014947, (2: 0.000004, 3: 0.004629): 0.012961): 0.000004, 4: 0.028223): 0.007394, 5: 0.051353): 0.089356, ((((11: 0.014065, 10: 0.009334): 0.009406, 12: 0.009362): 0.009016, (7: 0.027923, (9: 0.032507, 8: 0.005605): 0.004327): 0.020386): 0.034273, (6: 0.042120, (14: 0.004721, 13: 0.004602): 0.019454): 0.004476): 0.054781);

((((human: 0.014947, (chimpanzee: 0.000004, bonobo: 0.004629): 0.012961): 0.000004, gorilla: 0.028223): 0.007394, orangutan: 0.051353): 0.089356, ((((rhesus: 0.014065, CEmac: 0.009334): 0.009406, PTmac: 0.009362): 0.009016, (baboon: 0.027923, (sootyM: 0.032507, drill: 0.005605): 0.004327): 0.020386): 0.034273, (colobus: 0.042120, (GSNM: 0.004721, BSNM: 0.004602): 0.019454): 0.004476): 0.054781);

Detailed output identifying parameters

kappa (ts/tv) =  4.52392

Parameters in M8 (beta&w>1):
  p0 =   0.99305  p =   0.25363 q =   0.24945
 (p1 =   0.00695) w =   5.85283


MLEs of dN/dS (w) for site classes (K=11)

p:   0.09931  0.09931  0.09931  0.09931  0.09931  0.09931  0.09931  0.09931  0.09931  0.09931  0.00695
w:   0.00009  0.00660  0.04825  0.16802  0.38261  0.63909  0.84565  0.95693  0.99432  0.99993  5.85283

dN & dS for each branch

 branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

  15..16      0.089    467.4    195.6   0.5413   0.0238   0.0440   11.1    8.6
  16..17      0.007    467.4    195.6   0.5413   0.0020   0.0036    0.9    0.7
  17..18      0.000    467.4    195.6   0.5413   0.0000   0.0000    0.0    0.0
  18..1       0.015    467.4    195.6   0.5413   0.0040   0.0074    1.9    1.4
  18..19      0.013    467.4    195.6   0.5413   0.0035   0.0064    1.6    1.2
  19..2       0.000    467.4    195.6   0.5413   0.0000   0.0000    0.0    0.0
  19..3       0.005    467.4    195.6   0.5413   0.0012   0.0023    0.6    0.4
  17..4       0.028    467.4    195.6   0.5413   0.0075   0.0139    3.5    2.7
  16..5       0.051    467.4    195.6   0.5413   0.0137   0.0253    6.4    4.9
  15..20      0.055    467.4    195.6   0.5413   0.0146   0.0270    6.8    5.3
  20..21      0.034    467.4    195.6   0.5413   0.0091   0.0169    4.3    3.3
  21..22      0.009    467.4    195.6   0.5413   0.0024   0.0044    1.1    0.9
  22..23      0.009    467.4    195.6   0.5413   0.0025   0.0046    1.2    0.9
  23..11      0.014    467.4    195.6   0.5413   0.0038   0.0069    1.8    1.4
  23..10      0.009    467.4    195.6   0.5413   0.0025   0.0046    1.2    0.9
  22..12      0.009    467.4    195.6   0.5413   0.0025   0.0046    1.2    0.9
  21..24      0.020    467.4    195.6   0.5413   0.0054   0.0100    2.5    2.0
  24..7       0.028    467.4    195.6   0.5413   0.0074   0.0138    3.5    2.7
  24..25      0.004    467.4    195.6   0.5413   0.0012   0.0021    0.5    0.4
  25..9       0.033    467.4    195.6   0.5413   0.0087   0.0160    4.1    3.1
  25..8       0.006    467.4    195.6   0.5413   0.0015   0.0028    0.7    0.5
  20..26      0.004    467.4    195.6   0.5413   0.0012   0.0022    0.6    0.4
  26..6       0.042    467.4    195.6   0.5413   0.0112   0.0208    5.3    4.1
  26..27      0.019    467.4    195.6   0.5413   0.0052   0.0096    2.4    1.9
  27..14      0.005    467.4    195.6   0.5413   0.0013   0.0023    0.6    0.5
  27..13      0.005    467.4    195.6   0.5413   0.0012   0.0023    0.6    0.4


Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w

   212 Q      0.516         3.467


Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: human)

            Pr(w>1)     post mean +- SE for w

    32 L      0.557         1.791 +- 1.496
   105 S      0.501         1.612 +- 1.359
   212 Q      0.782         2.346 +- 1.598



The grid 

p0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
p :   0.100  0.300  0.500  0.700  0.900  1.100  1.300  1.500  1.700  1.900
q :   0.100  0.300  0.500  0.700  0.900  1.100  1.300  1.500  1.700  1.900
ws:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

p0:   0.000  0.000  0.000  0.000  0.000  0.005  0.047  0.118  0.209  0.620
p :   0.067  0.109  0.137  0.150  0.148  0.131  0.104  0.074  0.049  0.031
q :   0.020  0.031  0.055  0.076  0.096  0.115  0.133  0.148  0.159  0.166
ws:   0.462  0.228  0.150  0.084  0.041  0.019  0.009  0.004  0.002  0.001

Time used: 26:30
