     16    801

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



Printing out site pattern counts


        16        420  P

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

    5    1    1    1    1    1    1    4    1    2    4    1    1    1    6
    1    1    1    1    1    2    1    3    1    1    1    1    1    1    1
    1    2    1    1    7    1    1    1    5    3    1    2    1    2    1
    1    2    1   10    1    1    1    1    7    1    1    1    7    1    1
    1    1    1    1    5    1    1    2    1    1    2    3    1    1    1
    1    1    8    1    1    1    1    3    3    1    9    1    1    1    4
    1    2    1    1    7    1    1    1    1    1    1    1    1    4    3
    1    1    6    3    1    1    2    2    1    1    3    1    1    5    4
    1    1    1    2    1    1    1    4    1    1    1    3    3    4    1
    1    1    1    1    1

CODONML (in paml version 4.9h, March 2018)  CEACAM19seq.fasta
Model: One dN/dS ratio, 
Codon frequency model: F3x4
Site-class models: 
ns =  16  ls = 267

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   1   1   1   1   1   1 | Ser TCT   4   4   4   4   4   6 | Tyr TAT   2   3   3   3   4   3 | Cys TGT   0   0   0   0   0   0
    TTC   3   3   3   3   3   3 |     TCC   6   6   6   6   6   5 |     TAC   7   6   6   6   5   5 |     TGC   3   3   3   3   3   3
Leu TTA   0   0   0   0   0   0 |     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   0 |     TAG   0   0   0   0   0   0 | Trp TGG   4   4   4   4   4   4
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   3   3   3   3   3   3 | Pro CCT   8   8   8   8   9   7 | His CAT   1   1   1   1   1   1 | Arg CGT   0   0   0   0   0   0
    CTC   5   5   5   5   5   7 |     CCC  11  11  11  11  11  12 |     CAC   4   4   4   4   3   4 |     CGC   2   2   2   2   3   2
    CTA   2   2   2   2   2   3 |     CCA   9   8   8   8   8   9 | Gln CAA   3   3   3   3   3   3 |     CGA   1   1   1   1   1   1
    CTG  15  15  15  15  15  13 |     CCG   1   2   2   2   4   1 |     CAG  16  16  16  16  15  17 |     CGG   2   2   2   2   1   1
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   4   4   4   4   4   3 | Thr ACT   3   3   3   3   2   2 | Asn AAT   2   2   2   2   2   3 | Ser AGT   4   4   4   4   4   4
    ATC  10  10  10  10  10  10 |     ACC   7   7   7   7   8   8 |     AAC   9   9   9   9   9   7 |     AGC   3   3   3   3   3   3
    ATA   2   2   2   2   2   2 |     ACA   7   7   7   6   5   5 | Lys AAA   0   0   0   0   0   1 | Arg AGA   1   1   1   1   1   1
Met ATG   5   5   5   5   5   7 |     ACG   3   3   3   4   4   3 |     AAG   7   7   7   8   7   8 |     AGG   6   5   5   4   5   3
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   0   0   0   0   0   1 | Ala GCT   8   8   8   8   7   8 | Asp GAT   2   2   2   2   2   2 | Gly GGT   3   3   3   3   3   3
    GTC   4   4   4   4   4   4 |     GCC  10  10  10  10  10  10 |     GAC   9   9   9   9   9  10 |     GGC   7   7   7   7   7   7
    GTA   3   4   4   3   2   2 |     GCA   0   0   0   0   1   1 | Glu GAA   4   4   4   4   4   6 |     GGA   4   4   4   4   4   4
    GTG   7   6   6   7   8   8 |     GCG   3   3   3   3   3   2 |     GAG   8   7   7   7   7   5 |     GGG   4   6   6   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   1   1   2   2   2   1 | Ser TCT   6   6   6   6   6   5 | Tyr TAT   3   3   3   3   3   3 | Cys TGT   0   0   0   0   0   0
    TTC   3   3   2   2   2   4 |     TCC   6   5   5   5   5   6 |     TAC   5   5   5   5   5   5 |     TGC   3   3   3   3   3   3
Leu TTA   0   0   0   0   0   0 |     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   0   0   0   0   0   0 |     TAG   0   0   0   0   0   0 | Trp TGG   4   4   4   4   4   4
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   3   3   3   3   3   4 | Pro CCT   7   7   7   7   7   7 | His CAT   1   2   1   1   1   2 | Arg CGT   0   0   0   0   0   0
    CTC   6   6   6   6   6   4 |     CCC  11  12  12  12  11  13 |     CAC   4   4   4   4   4   3 |     CGC   2   2   2   2   2   2
    CTA   3   3   4   4   4   3 |     CCA   9   9   9   9  10   9 | Gln CAA   3   3   3   3   3   4 |     CGA   1   1   1   1   1   1
    CTG  14  14  13  13  13  12 |     CCG   1   1   1   1   1   1 |     CAG  17  16  17  16  16  16 |     CGG   1   1   1   1   1   1
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   3   4   3   3   3   4 | Thr ACT   2   2   2   2   2   2 | Asn AAT   3   3   3   3   3   3 | Ser AGT   4   4   4   4   4   4
    ATC  10   9  10  10  10  10 |     ACC   8   8   8   8   8   8 |     AAC   8   8   8   8   8   8 |     AGC   3   4   4   4   4   3
    ATA   2   2   2   2   2   2 |     ACA   5   5   5   5   5   6 | Lys AAA   0   0   1   1   1   0 | Arg AGA   1   1   1   1   1   1
Met ATG   7   7   7   7   7   6 |     ACG   3   3   3   3   3   3 |     AAG   9   9   8   8   8   8 |     AGG   3   3   3   3   3   4
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   1   1   1   1   1   0 | Ala GCT   8   8   8   8   8   8 | Asp GAT   2   2   2   2   2   2 | Gly GGT   3   3   3   3   3   3
    GTC   4   4   4   4   4   4 |     GCC  10  10  10  10  10  10 |     GAC   9   9   9   9   9   9 |     GGC   7   6   6   6   6   7
    GTA   2   2   2   2   2   2 |     GCA   1   1   1   1   1   2 | Glu GAA   6   6   6   6   6   5 |     GGA   4   4   4   4   4   4
    GTG   8   8   8   8   8   9 |     GCG   2   2   2   2   2   1 |     GAG   5   5   5   6   6   6 |     GGG   6   6   6   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------------------------
Phe TTT   1   1   1   1 | Ser TCT   5   6   4   5 | Tyr TAT   3   3   4   3 | Cys TGT   0   0   0   0
    TTC   3   3   3   3 |     TCC   6   5   6   6 |     TAC   6   5   4   5 |     TGC   3   3   3   3
Leu TTA   0   0   0   0 |     TCA   2   2   2   2 | *** TAA   0   0   0   0 | *** TGA   0   0   0   0
    TTG   2   2   2   2 |     TCG   0   0   1   1 |     TAG   0   0   0   0 | Trp TGG   4   4   4   4
------------------------------------------------------------------------------------------------------
Leu CTT   3   3   4   4 | Pro CCT   7   8   8   6 | His CAT   0   1   1   1 | Arg CGT   0   0   0   0
    CTC   5   6   4   4 |     CCC  13  11  12  13 |     CAC   3   4   4   4 |     CGC   2   2   2   2
    CTA   3   3   2   2 |     CCA   8  10   9  10 | Gln CAA   3   3   5   6 |     CGA   1   1   1   1
    CTG  14  14  14  14 |     CCG   2   0   2   1 |     CAG  17  17  12  13 |     CGG   1   1   2   1
------------------------------------------------------------------------------------------------------
Ile ATT   3   3   4   4 | Thr ACT   2   3   3   3 | Asn AAT   4   3   3   3 | Ser AGT   4   4   3   2
    ATC  10  10  11  11 |     ACC   8   8   9   9 |     AAC   7   8   8   8 |     AGC   3   4   4   5
    ATA   2   2   1   1 |     ACA   6   5   6   6 | Lys AAA   0   0   1   1 | Arg AGA   1   1   1   0
Met ATG   7   8   5   5 |     ACG   2   3   2   2 |     AAG   9   8   6   5 |     AGG   4   5   5   6
------------------------------------------------------------------------------------------------------
Val GTT   1   1   0   0 | Ala GCT   8   7   6   6 | Asp GAT   2   2   3   2 | Gly GGT   3   4   3   3
    GTC   4   4   5   5 |     GCC  10  10   9   8 |     GAC   9   9  10  11 |     GGC   7   6   7   7
    GTA   2   2   4   2 |     GCA   1   1   3   5 | Glu GAA   5   6   3   3 |     GGA   4   4   4   4
    GTG   8   8   7   8 |     GCG   2   1   1   1 |     GAG   6   5   7   7 |     GGG   6   4   7   7
------------------------------------------------------------------------------------------------------

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

#1: human          
position  1:    T:0.13109    C:0.31086    A:0.27341    G:0.28464
position  2:    T:0.24719    C:0.31086    A:0.27715    G:0.16479
position  3:    T:0.16854    C:0.37453    A:0.14232    G:0.31461
Average         T:0.18227    C:0.33208    A:0.23096    G:0.25468

#2: chimpanzee     
position  1:    T:0.13109    C:0.31086    A:0.26966    G:0.28839
position  2:    T:0.24719    C:0.31086    A:0.27341    G:0.16854
position  3:    T:0.17228    C:0.37079    A:0.14232    G:0.31461
Average         T:0.18352    C:0.33084    A:0.22846    G:0.25718

#3: bonobo         
position  1:    T:0.13109    C:0.31086    A:0.26966    G:0.28839
position  2:    T:0.24719    C:0.31086    A:0.27341    G:0.16854
position  3:    T:0.17228    C:0.37079    A:0.14232    G:0.31461
Average         T:0.18352    C:0.33084    A:0.22846    G:0.25718

#4: gorilla        
position  1:    T:0.13109    C:0.31086    A:0.26966    G:0.28839
position  2:    T:0.24719    C:0.31086    A:0.27715    G:0.16479
position  3:    T:0.17228    C:0.37079    A:0.13483    G:0.32210
Average         T:0.18352    C:0.33084    A:0.22722    G:0.25843

#5: orangutan      
position  1:    T:0.13109    C:0.31461    A:0.26592    G:0.28839
position  2:    T:0.24719    C:0.31835    A:0.26592    G:0.16854
position  3:    T:0.17228    C:0.37079    A:0.13109    G:0.32584
Average         T:0.18352    C:0.33458    A:0.22097    G:0.26092

#6: drill          
position  1:    T:0.12734    C:0.31461    A:0.26217    G:0.29588
position  2:    T:0.25843    C:0.30337    A:0.28090    G:0.15730
position  3:    T:0.17603    C:0.37453    A:0.14981    G:0.29963
Average         T:0.18727    C:0.33084    A:0.23096    G:0.25094

#7: sootyM         
position  1:    T:0.13109    C:0.31086    A:0.26592    G:0.29213
position  2:    T:0.25843    C:0.30337    A:0.28090    G:0.15730
position  3:    T:0.17603    C:0.37079    A:0.14607    G:0.30712
Average         T:0.18851    C:0.32834    A:0.23096    G:0.25218

#8: baboon         
position  1:    T:0.12734    C:0.31461    A:0.26966    G:0.28839
position  2:    T:0.25843    C:0.30337    A:0.28090    G:0.15730
position  3:    T:0.18352    C:0.36704    A:0.14607    G:0.30337
Average         T:0.18976    C:0.32834    A:0.23221    G:0.24969

#9: PTmac          
position  1:    T:0.12734    C:0.31461    A:0.26966    G:0.28839
position  2:    T:0.25843    C:0.30337    A:0.28090    G:0.15730
position  3:    T:0.17978    C:0.36704    A:0.15356    G:0.29963
Average         T:0.18851    C:0.32834    A:0.23471    G:0.24844

#10: rhesus         
position  1:    T:0.12734    C:0.31086    A:0.26966    G:0.29213
position  2:    T:0.25843    C:0.30337    A:0.28090    G:0.15730
position  3:    T:0.17978    C:0.36704    A:0.15356    G:0.29963
Average         T:0.18851    C:0.32709    A:0.23471    G:0.24969

#11: CEmac          
position  1:    T:0.12734    C:0.31086    A:0.26966    G:0.29213
position  2:    T:0.25843    C:0.30337    A:0.28090    G:0.15730
position  3:    T:0.17978    C:0.36330    A:0.15730    G:0.29963
Average         T:0.18851    C:0.32584    A:0.23596    G:0.24969

#12: GSNM           
position  1:    T:0.13109    C:0.30712    A:0.26966    G:0.29213
position  2:    T:0.25094    C:0.31086    A:0.27715    G:0.16105
position  3:    T:0.17978    C:0.37079    A:0.15356    G:0.29588
Average         T:0.18727    C:0.32959    A:0.23346    G:0.24969

#13: colobus        
position  1:    T:0.13109    C:0.30712    A:0.26966    G:0.29213
position  2:    T:0.25468    C:0.30712    A:0.27715    G:0.16105
position  3:    T:0.17228    C:0.37079    A:0.14232    G:0.31461
Average         T:0.18602    C:0.32834    A:0.22971    G:0.25593

#14: AGM            
position  1:    T:0.12734    C:0.31461    A:0.28090    G:0.27715
position  2:    T:0.26217    C:0.29963    A:0.27715    G:0.16105
position  3:    T:0.18352    C:0.36704    A:0.14981    G:0.29963
Average         T:0.19101    C:0.32709    A:0.23596    G:0.24594

#15: squirrelM      
position  1:    T:0.12734    C:0.30712    A:0.26966    G:0.29588
position  2:    T:0.25094    C:0.31086    A:0.26592    G:0.17228
position  3:    T:0.17603    C:0.37828    A:0.15730    G:0.28839
Average         T:0.18477    C:0.33208    A:0.23096    G:0.25218

#16: nightM         
position  1:    T:0.13109    C:0.30712    A:0.26592    G:0.29588
position  2:    T:0.24719    C:0.31461    A:0.26966    G:0.16854
position  3:    T:0.16105    C:0.38951    A:0.16105    G:0.28839
Average         T:0.17978    C:0.33708    A:0.23221    G:0.25094

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      19 | Ser S TCT      81 | Tyr Y TAT      49 | Cys C TGT       0
      TTC      46 |       TCC      90 |       TAC      85 |       TGC      48
Leu L TTA       0 |       TCA      32 | *** * TAA       0 | *** * TGA       0
      TTG      32 |       TCG       7 |       TAG       0 | Trp W TGG      64
------------------------------------------------------------------------------
Leu L CTT      51 | Pro P CCT     119 | His H CAT      17 | Arg R CGT       0
      CTC      85 |       CCC     187 |       CAC      61 |       CGC      33
      CTA      44 |       CCA     142 | Gln Q CAA      54 |       CGA      16
      CTG     223 |       CCG      23 |       CAG     253 |       CGG      21
------------------------------------------------------------------------------
Ile I ATT      57 | Thr T ACT      39 | Asn N AAT      44 | Ser S AGT      61
      ATC     161 |       ACC     126 |       AAC     131 |       AGC      56
      ATA      30 |       ACA      91 | Lys K AAA       6 | Arg R AGA      15
Met M ATG      98 |       ACG      47 |       AAG     122 |       AGG      67
------------------------------------------------------------------------------
Val V GTT       8 | Ala A GCT     122 | Asp D GAT      33 | Gly G GGT      49
      GTC      66 |       GCC     157 |       GAC     148 |       GGC     107
      GTA      40 |       GCA      19 | Glu E GAA      78 |       GGA      64
      GTG     122 |       GCG      33 |       GAG      99 |       GGG      94
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12945    C:0.31110    A:0.26943    G:0.29003
position  2:    T:0.25328    C:0.30782    A:0.27622    G:0.16269
position  3:    T:0.17533    C:0.37149    A:0.14771    G:0.30548
Average         T:0.18602    C:0.33013    A:0.23112    G:0.25273

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.00586153  0.01241955  0.00493808  0.01021267
  0.00712376  0.01509400  0.00600146  0.01241189
  0.00639242  0.01354442  0.00000000  0.00000000
  0.00376503  0.00797744  0.00000000  0.00655990
  0.01408674  0.02984734  0.01186747  0.02454366
  0.01712021  0.03627473  0.01442303  0.02982894
  0.01536262  0.03255071  0.01294234  0.02676665
  0.00904832  0.01917181  0.00762282  0.01576510
  0.01220003  0.02584973  0.01027800  0.02125639
  0.01482721  0.03141626  0.01249128  0.02583379
  0.01330502  0.02819102  0.01120891  0.02318165
  0.00783643  0.01660403  0.00660186  0.01365360
  0.01313279  0.02782608  0.01106380  0.02288156
  0.01596083  0.03381820  0.01344630  0.02780892
  0.01432226  0.03034637  0.01206588  0.02495401
  0.00843557  0.01787350  0.00710660  0.01469749


Model 1: NearlyNeutral (2 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((10, 11), 9), (8, (7, 6))), 14), (13, 12))), (15, 16));   MP score: 133
This is a rooted tree.  Please check!
lnL(ntime: 30  np: 33):  -1860.748452      +0.000000
  17..18   18..19   19..20   20..21   21..1    21..22   22..2    22..3    20..4    19..5    18..23   23..24   24..25   25..26   26..27   27..10   27..11   26..9    25..28   28..8    28..29   29..7    29..6    24..14   23..30   30..13   30..12   17..31   31..15   31..16 
 0.114542 0.028288 0.010129 0.003900 0.015679 0.003874 0.000004 0.000004 0.003899 0.022229 0.030678 0.025526 0.007460 0.011664 0.003854 0.000004 0.003854 0.000004 0.000004 0.007814 0.003828 0.003854 0.011683 0.040089 0.003839 0.021356 0.026084 0.065635 0.072099 0.032873 7.004717 0.690938 0.000001

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

tree length =  0.574750

(((((1: 0.015679, (2: 0.000004, 3: 0.000004): 0.003874): 0.003900, 4: 0.003899): 0.010129, 5: 0.022229): 0.028288, (((((10: 0.000004, 11: 0.003854): 0.003854, 9: 0.000004): 0.011664, (8: 0.007814, (7: 0.003854, 6: 0.011683): 0.003828): 0.000004): 0.007460, 14: 0.040089): 0.025526, (13: 0.021356, 12: 0.026084): 0.003839): 0.030678): 0.114542, (15: 0.072099, 16: 0.032873): 0.065635);

(((((human: 0.015679, (chimpanzee: 0.000004, bonobo: 0.000004): 0.003874): 0.003900, gorilla: 0.003899): 0.010129, orangutan: 0.022229): 0.028288, (((((rhesus: 0.000004, CEmac: 0.003854): 0.003854, PTmac: 0.000004): 0.011664, (baboon: 0.007814, (sootyM: 0.003854, drill: 0.011683): 0.003828): 0.000004): 0.007460, AGM: 0.040089): 0.025526, (colobus: 0.021356, GSNM: 0.026084): 0.003839): 0.030678): 0.114542, (squirrelM: 0.072099, nightM: 0.032873): 0.065635);

Detailed output identifying parameters

kappa (ts/tv) =  7.00472


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

p:   0.69094  0.30906
w:   0.00000  1.00000

dN & dS for each branch

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

  17..18      0.115    573.9    227.1   0.3091   0.0234   0.0756   13.4   17.2
  18..19      0.028    573.9    227.1   0.3091   0.0058   0.0187    3.3    4.2
  19..20      0.010    573.9    227.1   0.3091   0.0021   0.0067    1.2    1.5
  20..21      0.004    573.9    227.1   0.3091   0.0008   0.0026    0.5    0.6
  21..1       0.016    573.9    227.1   0.3091   0.0032   0.0104    1.8    2.4
  21..22      0.004    573.9    227.1   0.3091   0.0008   0.0026    0.5    0.6
  22..2       0.000    573.9    227.1   0.3091   0.0000   0.0000    0.0    0.0
  22..3       0.000    573.9    227.1   0.3091   0.0000   0.0000    0.0    0.0
  20..4       0.004    573.9    227.1   0.3091   0.0008   0.0026    0.5    0.6
  19..5       0.022    573.9    227.1   0.3091   0.0045   0.0147    2.6    3.3
  18..23      0.031    573.9    227.1   0.3091   0.0063   0.0203    3.6    4.6
  23..24      0.026    573.9    227.1   0.3091   0.0052   0.0169    3.0    3.8
  24..25      0.007    573.9    227.1   0.3091   0.0015   0.0049    0.9    1.1
  25..26      0.012    573.9    227.1   0.3091   0.0024   0.0077    1.4    1.7
  26..27      0.004    573.9    227.1   0.3091   0.0008   0.0025    0.5    0.6
  27..10      0.000    573.9    227.1   0.3091   0.0000   0.0000    0.0    0.0
  27..11      0.004    573.9    227.1   0.3091   0.0008   0.0025    0.5    0.6
  26..9       0.000    573.9    227.1   0.3091   0.0000   0.0000    0.0    0.0
  25..28      0.000    573.9    227.1   0.3091   0.0000   0.0000    0.0    0.0
  28..8       0.008    573.9    227.1   0.3091   0.0016   0.0052    0.9    1.2
  28..29      0.004    573.9    227.1   0.3091   0.0008   0.0025    0.4    0.6
  29..7       0.004    573.9    227.1   0.3091   0.0008   0.0025    0.5    0.6
  29..6       0.012    573.9    227.1   0.3091   0.0024   0.0077    1.4    1.8
  24..14      0.040    573.9    227.1   0.3091   0.0082   0.0265    4.7    6.0
  23..30      0.004    573.9    227.1   0.3091   0.0008   0.0025    0.4    0.6
  30..13      0.021    573.9    227.1   0.3091   0.0044   0.0141    2.5    3.2
  30..12      0.026    573.9    227.1   0.3091   0.0053   0.0172    3.1    3.9
  17..31      0.066    573.9    227.1   0.3091   0.0134   0.0433    7.7    9.8
  31..15      0.072    573.9    227.1   0.3091   0.0147   0.0476    8.4   10.8
  31..16      0.033    573.9    227.1   0.3091   0.0067   0.0217    3.8    4.9


Time used:  2:04


Model 2: PositiveSelection (3 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((10, 11), 9), (8, (7, 6))), 14), (13, 12))), (15, 16));   MP score: 133
This is a rooted tree.  Please check!
lnL(ntime: 30  np: 35):  -1860.041005      +0.000000
  17..18   18..19   19..20   20..21   21..1    21..22   22..2    22..3    20..4    19..5    18..23   23..24   24..25   25..26   26..27   27..10   27..11   26..9    25..28   28..8    28..29   29..7    29..6    24..14   23..30   30..13   30..12   17..31   31..15   31..16 
 0.094999 0.028725 0.010195 0.003929 0.015778 0.003899 0.000004 0.000004 0.003913 0.022400 0.030691 0.025717 0.007369 0.011729 0.003868 0.000004 0.003865 0.000004 0.000004 0.007860 0.003832 0.003862 0.011749 0.040463 0.003953 0.021414 0.026275 0.088925 0.073412 0.032567 7.245796 0.730413 0.000000 0.000001 1.350157

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

tree length =  0.581410

(((((1: 0.015778, (2: 0.000004, 3: 0.000004): 0.003899): 0.003929, 4: 0.003913): 0.010195, 5: 0.022400): 0.028725, (((((10: 0.000004, 11: 0.003865): 0.003868, 9: 0.000004): 0.011729, (8: 0.007860, (7: 0.003862, 6: 0.011749): 0.003832): 0.000004): 0.007369, 14: 0.040463): 0.025717, (13: 0.021414, 12: 0.026275): 0.003953): 0.030691): 0.094999, (15: 0.073412, 16: 0.032567): 0.088925);

(((((human: 0.015778, (chimpanzee: 0.000004, bonobo: 0.000004): 0.003899): 0.003929, gorilla: 0.003913): 0.010195, orangutan: 0.022400): 0.028725, (((((rhesus: 0.000004, CEmac: 0.003865): 0.003868, PTmac: 0.000004): 0.011729, (baboon: 0.007860, (sootyM: 0.003862, drill: 0.011749): 0.003832): 0.000004): 0.007369, AGM: 0.040463): 0.025717, (colobus: 0.021414, GSNM: 0.026275): 0.003953): 0.030691): 0.094999, (squirrelM: 0.073412, nightM: 0.032567): 0.088925);

Detailed output identifying parameters

kappa (ts/tv) =  7.24580


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

p:   0.73041  0.00000  0.26959
w:   0.00000  1.00000  1.35016

dN & dS for each branch

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

  17..18      0.095    573.5    227.5   0.3640   0.0212   0.0581   12.1   13.2
  18..19      0.029    573.5    227.5   0.3640   0.0064   0.0176    3.7    4.0
  19..20      0.010    573.5    227.5   0.3640   0.0023   0.0062    1.3    1.4
  20..21      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  21..1       0.016    573.5    227.5   0.3640   0.0035   0.0097    2.0    2.2
  21..22      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  22..2       0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  22..3       0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  20..4       0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  19..5       0.022    573.5    227.5   0.3640   0.0050   0.0137    2.9    3.1
  18..23      0.031    573.5    227.5   0.3640   0.0068   0.0188    3.9    4.3
  23..24      0.026    573.5    227.5   0.3640   0.0057   0.0157    3.3    3.6
  24..25      0.007    573.5    227.5   0.3640   0.0016   0.0045    0.9    1.0
  25..26      0.012    573.5    227.5   0.3640   0.0026   0.0072    1.5    1.6
  26..27      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  27..10      0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  27..11      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  26..9       0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  25..28      0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  28..8       0.008    573.5    227.5   0.3640   0.0018   0.0048    1.0    1.1
  28..29      0.004    573.5    227.5   0.3640   0.0009   0.0023    0.5    0.5
  29..7       0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  29..6       0.012    573.5    227.5   0.3640   0.0026   0.0072    1.5    1.6
  24..14      0.040    573.5    227.5   0.3640   0.0090   0.0248    5.2    5.6
  23..30      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.6
  30..13      0.021    573.5    227.5   0.3640   0.0048   0.0131    2.7    3.0
  30..12      0.026    573.5    227.5   0.3640   0.0059   0.0161    3.4    3.7
  17..31      0.089    573.5    227.5   0.3640   0.0198   0.0544   11.4   12.4
  31..15      0.073    573.5    227.5   0.3640   0.0164   0.0449    9.4   10.2
  31..16      0.033    573.5    227.5   0.3640   0.0073   0.0199    4.2    4.5


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

     3 Y      1.000**       1.350
    15 Q      1.000**       1.350
    31 F      1.000**       1.350
    39 T      1.000**       1.350
    76 L      1.000**       1.350
    80 A      1.000**       1.350
    83 T      1.000**       1.350
    92 I      1.000**       1.350
    97 E      1.000**       1.350
   111 K      1.000**       1.350
   119 H      1.000**       1.350
   136 A      1.000**       1.350
   152 R      1.000**       1.350
   155 R      1.000**       1.350
   161 L      1.000**       1.350
   162 P      1.000**       1.350
   165 R      1.000**       1.350
   166 G      1.000**       1.350
   169 S      1.000**       1.350
   172 I      1.000**       1.350
   173 L      1.000**       1.350
   175 S      1.000**       1.350
   184 T      1.000**       1.350
   193 E      1.000**       1.350
   197 L      1.000**       1.350
   200 A      1.000**       1.350
   201 H      1.000**       1.350
   203 A      1.000**       1.350
   204 G      1.000**       1.350
   215 V      1.000**       1.350
   216 L      1.000**       1.350
   224 T      1.000**       1.350
   225 R      1.000**       1.350
   227 I      1.000**       1.350
   231 R      1.000**       1.350
   234 P      1.000**       1.350
   235 T      1.000**       1.350
   236 P      1.000**       1.350
   238 H      1.000**       1.350
   240 Q      1.000**       1.350
   241 A      1.000**       1.350
   242 E      1.000**       1.350
   245 N      1.000**       1.350
   249 Q      1.000**       1.350


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

    31 F      0.514         1.443 +- 0.689
    39 T      0.585         1.563 +- 0.766
    92 I      0.549         1.512 +- 0.765
   161 L      0.620         1.656 +- 0.896
   165 R      0.558         1.528 +- 0.773
   166 G      0.504         1.426 +- 0.674
   184 T      0.533         1.481 +- 0.732
   200 A      0.602         1.621 +- 0.867
   224 T      0.552         1.515 +- 0.759
   225 R      0.539         1.491 +- 0.735
   231 R      0.725         1.846 +- 0.997
   235 T      0.570         1.552 +- 0.797
   238 H      0.522         1.463 +- 0.723
   240 Q      0.718         1.831 +- 0.988
   241 A      0.531         1.476 +- 0.724



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:   0.958  0.041  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.570  0.283  0.095  0.032  0.012  0.004  0.002  0.001  0.000  0.000

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 0.000
 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 0.000 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 0.000 0.000 0.000 0.025
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.005 0.042 0.216
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.016 0.123 0.185 0.030
 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 0.006 0.089 0.164 0.077 0.019 0.001

sum of density on p0-p1 =   1.000000

Time used:  7:21


Model 7: beta (10 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((10, 11), 9), (8, (7, 6))), 14), (13, 12))), (15, 16));   MP score: 133
This is a rooted tree.  Please check!
lnL(ntime: 30  np: 33):  -1860.767581      +0.000000
  17..18   18..19   19..20   20..21   21..1    21..22   22..2    22..3    20..4    19..5    18..23   23..24   24..25   25..26   26..27   27..10   27..11   26..9    25..28   28..8    28..29   29..7    29..6    24..14   23..30   30..13   30..12   17..31   31..15   31..16 
 0.077844 0.028150 0.010076 0.003881 0.015602 0.003854 0.000004 0.000004 0.003879 0.022127 0.030545 0.025406 0.007419 0.011604 0.003834 0.000004 0.003833 0.000004 0.000004 0.007774 0.003808 0.003835 0.011624 0.039894 0.003813 0.021250 0.025956 0.101685 0.071783 0.032688 6.988676 0.005000 0.011754

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

tree length =  0.572186

(((((1: 0.015602, (2: 0.000004, 3: 0.000004): 0.003854): 0.003881, 4: 0.003879): 0.010076, 5: 0.022127): 0.028150, (((((10: 0.000004, 11: 0.003833): 0.003834, 9: 0.000004): 0.011604, (8: 0.007774, (7: 0.003835, 6: 0.011624): 0.003808): 0.000004): 0.007419, 14: 0.039894): 0.025406, (13: 0.021250, 12: 0.025956): 0.003813): 0.030545): 0.077844, (15: 0.071783, 16: 0.032688): 0.101685);

(((((human: 0.015602, (chimpanzee: 0.000004, bonobo: 0.000004): 0.003854): 0.003881, gorilla: 0.003879): 0.010076, orangutan: 0.022127): 0.028150, (((((rhesus: 0.000004, CEmac: 0.003833): 0.003834, PTmac: 0.000004): 0.011604, (baboon: 0.007774, (sootyM: 0.003835, drill: 0.011624): 0.003808): 0.000004): 0.007419, AGM: 0.039894): 0.025406, (colobus: 0.021250, GSNM: 0.025956): 0.003813): 0.030545): 0.077844, (squirrelM: 0.071783, nightM: 0.032688): 0.101685);

Detailed output identifying parameters

kappa (ts/tv) =  6.98868

Parameters in M7 (beta):
 p =   0.00500  q =   0.01175


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  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  1.00000  1.00000  1.00000

dN & dS for each branch

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

  17..18      0.078    574.0    227.0   0.3000   0.0156   0.0521    9.0   11.8
  18..19      0.028    574.0    227.0   0.3000   0.0056   0.0188    3.2    4.3
  19..20      0.010    574.0    227.0   0.3000   0.0020   0.0067    1.2    1.5
  20..21      0.004    574.0    227.0   0.3000   0.0008   0.0026    0.4    0.6
  21..1       0.016    574.0    227.0   0.3000   0.0031   0.0104    1.8    2.4
  21..22      0.004    574.0    227.0   0.3000   0.0008   0.0026    0.4    0.6
  22..2       0.000    574.0    227.0   0.3000   0.0000   0.0000    0.0    0.0
  22..3       0.000    574.0    227.0   0.3000   0.0000   0.0000    0.0    0.0
  20..4       0.004    574.0    227.0   0.3000   0.0008   0.0026    0.4    0.6
  19..5       0.022    574.0    227.0   0.3000   0.0044   0.0148    2.5    3.4
  18..23      0.031    574.0    227.0   0.3000   0.0061   0.0204    3.5    4.6
  23..24      0.025    574.0    227.0   0.3000   0.0051   0.0170    2.9    3.9
  24..25      0.007    574.0    227.0   0.3000   0.0015   0.0050    0.9    1.1
  25..26      0.012    574.0    227.0   0.3000   0.0023   0.0078    1.3    1.8
  26..27      0.004    574.0    227.0   0.3000   0.0008   0.0026    0.4    0.6
  27..10      0.000    574.0    227.0   0.3000   0.0000   0.0000    0.0    0.0
  27..11      0.004    574.0    227.0   0.3000   0.0008   0.0026    0.4    0.6
  26..9       0.000    574.0    227.0   0.3000   0.0000   0.0000    0.0    0.0
  25..28      0.000    574.0    227.0   0.3000   0.0000   0.0000    0.0    0.0
  28..8       0.008    574.0    227.0   0.3000   0.0016   0.0052    0.9    1.2
  28..29      0.004    574.0    227.0   0.3000   0.0008   0.0025    0.4    0.6
  29..7       0.004    574.0    227.0   0.3000   0.0008   0.0026    0.4    0.6
  29..6       0.012    574.0    227.0   0.3000   0.0023   0.0078    1.3    1.8
  24..14      0.040    574.0    227.0   0.3000   0.0080   0.0267    4.6    6.1
  23..30      0.004    574.0    227.0   0.3000   0.0008   0.0026    0.4    0.6
  30..13      0.021    574.0    227.0   0.3000   0.0043   0.0142    2.4    3.2
  30..12      0.026    574.0    227.0   0.3000   0.0052   0.0174    3.0    3.9
  17..31      0.102    574.0    227.0   0.3000   0.0204   0.0680   11.7   15.4
  31..15      0.072    574.0    227.0   0.3000   0.0144   0.0480    8.3   10.9
  31..16      0.033    574.0    227.0   0.3000   0.0066   0.0219    3.8    5.0


Time used: 16:11


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


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((10, 11), 9), (8, (7, 6))), 14), (13, 12))), (15, 16));   MP score: 133
This is a rooted tree.  Please check!
lnL(ntime: 30  np: 35):  -1860.041004      +0.000000
  17..18   18..19   19..20   20..21   21..1    21..22   22..2    22..3    20..4    19..5    18..23   23..24   24..25   25..26   26..27   27..10   27..11   26..9    25..28   28..8    28..29   29..7    29..6    24..14   23..30   30..13   30..12   17..31   31..15   31..16 
 0.094441 0.028725 0.010195 0.003929 0.015778 0.003899 0.000004 0.000004 0.003913 0.022400 0.030690 0.025717 0.007369 0.011729 0.003868 0.000004 0.003865 0.000004 0.000004 0.007860 0.003832 0.003862 0.011749 0.040464 0.003953 0.021414 0.026275 0.089483 0.073412 0.032567 7.245786 0.730413 0.005001 2.597248 1.350158

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

tree length =  0.581411

(((((1: 0.015778, (2: 0.000004, 3: 0.000004): 0.003899): 0.003929, 4: 0.003913): 0.010195, 5: 0.022400): 0.028725, (((((10: 0.000004, 11: 0.003865): 0.003868, 9: 0.000004): 0.011729, (8: 0.007860, (7: 0.003862, 6: 0.011749): 0.003832): 0.000004): 0.007369, 14: 0.040464): 0.025717, (13: 0.021414, 12: 0.026275): 0.003953): 0.030690): 0.094441, (15: 0.073412, 16: 0.032567): 0.089483);

(((((human: 0.015778, (chimpanzee: 0.000004, bonobo: 0.000004): 0.003899): 0.003929, gorilla: 0.003913): 0.010195, orangutan: 0.022400): 0.028725, (((((rhesus: 0.000004, CEmac: 0.003865): 0.003868, PTmac: 0.000004): 0.011729, (baboon: 0.007860, (sootyM: 0.003862, drill: 0.011749): 0.003832): 0.000004): 0.007369, AGM: 0.040464): 0.025717, (colobus: 0.021414, GSNM: 0.026275): 0.003953): 0.030690): 0.094441, (squirrelM: 0.073412, nightM: 0.032567): 0.089483);

Detailed output identifying parameters

kappa (ts/tv) =  7.24579

Parameters in M8 (beta&w>1):
  p0 =   0.73041  p =   0.00500 q =   2.59725
 (p1 =   0.26959) w =   1.35016


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

p:   0.07304  0.07304  0.07304  0.07304  0.07304  0.07304  0.07304  0.07304  0.07304  0.07304  0.26959
w:   0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00001  1.35016

dN & dS for each branch

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

  17..18      0.094    573.5    227.5   0.3640   0.0210   0.0578   12.1   13.2
  18..19      0.029    573.5    227.5   0.3640   0.0064   0.0176    3.7    4.0
  19..20      0.010    573.5    227.5   0.3640   0.0023   0.0062    1.3    1.4
  20..21      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  21..1       0.016    573.5    227.5   0.3640   0.0035   0.0097    2.0    2.2
  21..22      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  22..2       0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  22..3       0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  20..4       0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  19..5       0.022    573.5    227.5   0.3640   0.0050   0.0137    2.9    3.1
  18..23      0.031    573.5    227.5   0.3640   0.0068   0.0188    3.9    4.3
  23..24      0.026    573.5    227.5   0.3640   0.0057   0.0157    3.3    3.6
  24..25      0.007    573.5    227.5   0.3640   0.0016   0.0045    0.9    1.0
  25..26      0.012    573.5    227.5   0.3640   0.0026   0.0072    1.5    1.6
  26..27      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  27..10      0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  27..11      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  26..9       0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  25..28      0.000    573.5    227.5   0.3640   0.0000   0.0000    0.0    0.0
  28..8       0.008    573.5    227.5   0.3640   0.0018   0.0048    1.0    1.1
  28..29      0.004    573.5    227.5   0.3640   0.0009   0.0023    0.5    0.5
  29..7       0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.5
  29..6       0.012    573.5    227.5   0.3640   0.0026   0.0072    1.5    1.6
  24..14      0.040    573.5    227.5   0.3640   0.0090   0.0248    5.2    5.6
  23..30      0.004    573.5    227.5   0.3640   0.0009   0.0024    0.5    0.6
  30..13      0.021    573.5    227.5   0.3640   0.0048   0.0131    2.7    3.0
  30..12      0.026    573.5    227.5   0.3640   0.0059   0.0161    3.4    3.7
  17..31      0.089    573.5    227.5   0.3640   0.0199   0.0548   11.4   12.5
  31..15      0.073    573.5    227.5   0.3640   0.0164   0.0449    9.4   10.2
  31..16      0.033    573.5    227.5   0.3640   0.0073   0.0199    4.2    4.5


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

     3 Y      1.000**       1.350
    15 Q      1.000**       1.350
    31 F      1.000**       1.350
    39 T      1.000**       1.350
    76 L      1.000**       1.350
    80 A      1.000**       1.350
    83 T      1.000**       1.350
    92 I      1.000**       1.350
    97 E      1.000**       1.350
   111 K      1.000**       1.350
   119 H      1.000**       1.350
   136 A      1.000**       1.350
   152 R      1.000**       1.350
   155 R      1.000**       1.350
   161 L      1.000**       1.350
   162 P      1.000**       1.350
   165 R      1.000**       1.350
   166 G      1.000**       1.350
   169 S      1.000**       1.350
   172 I      1.000**       1.350
   173 L      1.000**       1.350
   175 S      1.000**       1.350
   184 T      1.000**       1.350
   193 E      1.000**       1.350
   197 L      1.000**       1.350
   200 A      1.000**       1.350
   201 H      1.000**       1.350
   203 A      1.000**       1.350
   204 G      1.000**       1.350
   215 V      1.000**       1.350
   216 L      1.000**       1.350
   224 T      1.000**       1.350
   225 R      1.000**       1.350
   227 I      1.000**       1.350
   231 R      1.000**       1.350
   234 P      1.000**       1.350
   235 T      1.000**       1.350
   236 P      1.000**       1.350
   238 H      1.000**       1.350
   240 Q      1.000**       1.350
   241 A      1.000**       1.350
   242 E      1.000**       1.350
   245 N      1.000**       1.350
   249 Q      1.000**       1.350


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

    31 F      0.731         1.513 +- 0.748
    39 T      0.817         1.667 +- 0.747
    83 T      0.513         1.116 +- 0.836
    92 I      0.765         1.580 +- 0.768
   161 L      0.827         1.699 +- 0.785
   162 P      0.513         1.116 +- 0.836
   165 R      0.776         1.599 +- 0.768
   166 G      0.720         1.493 +- 0.745
   169 S      0.514         1.119 +- 0.836
   173 L      0.535         1.158 +- 0.846
   184 T      0.749         1.550 +- 0.761
   197 L      0.545         1.177 +- 0.849
   200 A      0.813         1.672 +- 0.783
   201 H      0.512         1.115 +- 0.836
   224 T      0.770         1.588 +- 0.765
   225 R      0.757         1.564 +- 0.760
   227 I      0.601         1.272 +- 0.811
   231 R      0.914         1.846 +- 0.756
   235 T      0.786         1.619 +- 0.773
   238 H      0.736         1.526 +- 0.761
   240 Q      0.911         1.839 +- 0.757
   241 A      0.748         1.547 +- 0.758
   245 N      0.698         1.452 +- 0.739



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  0.000  0.000  0.123  0.660  0.217
p :   0.781  0.175  0.038  0.005  0.000  0.000  0.000  0.000  0.000  0.000
q :   0.000  0.048  0.066  0.078  0.102  0.119  0.131  0.141  0.152  0.164
ws:   0.648  0.273  0.061  0.014  0.003  0.001  0.000  0.000  0.000  0.000

Time used: 25:06
