     18    936

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



Printing out site pattern counts


        18        687  P

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

    1    1    1    6    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    3    1    1    1    1    1    1    1    1    1
    4    1    1    4    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    2    1    1    1    2    1    1    1    1    1    2    1
    4    1    2    1    1    1    5    1    1    1    1    1    3    1    1
    1    2    1    1    1    1    1    1    1    1    5    1    1    1    1
    2    1    1    1    1    1    5    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    3
    1    1    1    1    9    1    2    1    1    4    1    1    1    1    1
    1    1    1    1    2    1    1    2    2    1    1    3    1    1    1
    1    3    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    3    1    1    1    1    1    1    1    4    1    1    1    1    1
    1    1    1    1    1    1    6    1    1    1    1    1    3    1    1
    1    1    1    1    3    1    1    1    1    1    2    1    2    1    1
    1    1    1    5    1    1    1    2    2    3    1    1    2    1    1
    2    1    1    1

CODONML (in paml version 4.9h, March 2018)  CEACAM6seq.txt
Model: One dN/dS ratio, 
Codon frequency model: F3x4
Site-class models: 
ns =  18  ls = 312

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   2   2   3   2   2   2 | Ser TCT   3   3   3   3   3   3 | Tyr TAT   5   5   5   5   4   3 | Cys TGT   2   2   2   2   2   2
    TTC   5   5   4   5   5   5 |     TCC  11  11  11  11  10  11 |     TAC   8   8   8   8  10   9 |     TGC   2   2   2   2   2   2
Leu TTA   0   0   0   0   0   1 |     TCA   4   3   3   3   3   3 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   0   0   0   1   0   0 |     TCG   0   1   1   1   1   0 |     TAG   0   0   0   0   0   0 | Trp TGG   5   5   5   5   5   7
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   2   2   2   2   4   3 | Pro CCT   3   3   3   3   4   2 | His CAT   2   2   2   2   2   2 | Arg CGT   2   3   3   2   3   2
    CTC   9   9   9   9   7   9 |     CCC  11  11  11  11   9   9 |     CAC   2   2   2   2   2   3 |     CGC   1   1   1   1   1   0
    CTA   4   4   4   4   4   4 |     CCA   6   6   6   6   6   6 | Gln CAA   6   6   6   6   8   6 |     CGA   1   1   1   1   1   1
    CTG  11  11  11  10  11  11 |     CCG   3   3   3   3   3   3 |     CAG  10  10  10  10   9  10 |     CGG   0   0   0   0   0   0
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   5   5   5   5   6   5 | Thr ACT   5   6   6   5   8  10 | Asn AAT  14  14  14  15  14  17 | Ser AGT   6   5   5   6   6   4
    ATC   7   7   7   7   9   7 |     ACC  12  11  11  12  11  10 |     AAC  15  15  15  13  14  13 |     AGC   5   5   5   5   3   8
    ATA   5   5   5   5   5   3 |     ACA   6   6   6   7   6   5 | Lys AAA   2   2   2   3   3   4 | Arg AGA   2   2   2   2   3   1
Met ATG   3   4   4   4   4   6 |     ACG   4   3   3   3   3   0 |     AAG   6   6   6   6   5   3 |     AGG   4   4   4   4   3   6
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   2   2   2   2   2   1 | Ala GCT   5   5   5   5   3   7 | Asp GAT   5   5   5   5   5   5 | Gly GGT   3   3   3   3   2   1
    GTC  11  11  10  11  10  11 |     GCC   9   9   9   9  10   9 |     GAC   3   3   3   3   3   4 |     GGC   6   6   7   6   5   5
    GTA   4   3   3   4   5   7 |     GCA   7   7   7   6   8   8 | Glu GAA   8   9   9  10   9   8 |     GGA   8   8   8   7   6   7
    GTG   8   9   9   8   6   7 |     GCG   1   1   1   1   2   0 |     GAG   7   6   6   6   7   6 |     GGG   4   4   4   4   5   5
--------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   2   2   2   2   2   2 | Ser TCT   3   3   3   3   3   3 | Tyr TAT   3   3   3   5   4   4 | Cys TGT   2   2   2   2   2   2
    TTC   6   6   6   5   5   5 |     TCC  11  11  11  11  11  11 |     TAC   8   9   8   8   9   9 |     TGC   2   2   2   2   2   2
Leu TTA   1   1   1   1   1   1 |     TCA   3   3   3   3   3   3 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   0   0   0   0   0   0 |     TCG   0   0   0   0   0   0 |     TAG   0   0   0   0   0   0 | Trp TGG   6   6   6   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   3   3   3   2   2   2 | Pro CCT   3   2   2   2   2   3 | His CAT   2   2   2   1   1   1 | Arg CGT   2   2   2   2   2   2
    CTC   9   9   9  10  10  10 |     CCC   9  10  10  10  10   9 |     CAC   3   4   3   3   3   3 |     CGC   0   0   0   0   0   0
    CTA   4   5   5   5   5   5 |     CCA   7   7   7   7   7   7 | Gln CAA   5   6   7   6   6   5 |     CGA   1   1   1   1   1   1
    CTG  10  10  10  10  10  10 |     CCG   2   2   2   2   2   2 |     CAG   9   8   8   9   9   9 |     CGG   1   1   1   1   1   1
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   4   4   4   5   5   5 | Thr ACT  12  11  12  11  11  12 | Asn AAT  18  15  16  16  16  14 | Ser AGT   4   4   4   4   4   5
    ATC   7   7   7   7   7   7 |     ACC   9   9   8   9   9   9 |     AAC  12  13  12  13  13  13 |     AGC   6   6   6   6   6   6
    ATA   4   4   4   4   4   5 |     ACA   6   7   7   6   6   6 | Lys AAA   4   4   3   3   3   4 | Arg AGA   1   2   2   1   1   2
Met ATG   4   4   4   4   4   4 |     ACG   1   1   1   1   1   1 |     AAG   4   4   4   4   4   4 |     AGG   6   6   6   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   2   2   2   1   1   1 | Ala GCT   4   4   4   4   4   4 | Asp GAT   4   5   5   6   6   6 | Gly GGT   3   3   3   2   3   2
    GTC  11  10  10  12  12  11 |     GCC  10  10  11   9   9  10 |     GAC   5   5   5   5   5   5 |     GGC   5   5   5   5   4   5
    GTA   6   6   6   6   6   5 |     GCA   8   8   8   8   8   8 | Glu GAA   7   8   9   8   9   9 |     GGA   8   6   6   8   7   6
    GTG   9   8   8   8   8   8 |     GCG   0   0   0   0   0   0 |     GAG   6   6   6   6   6   6 |     GGG   5   5   5   5   5   5
--------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   2   3   1   1   1   2 | Ser TCT   3   3   3   4   4   4 | Tyr TAT   4   2   4   4   4   4 | Cys TGT   2   2   4   4   4   4
    TTC   6   4   4   4   5   6 |     TCC  10  12  11  10  11  11 |     TAC   8  10   7   8   8   8 |     TGC   3   2   2   3   2   2
Leu TTA   1   0   1   1   1   1 |     TCA   3   4   2   2   2   2 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   0   1   0   0   0   0 |     TCG   0   0   1   1   1   1 |     TAG   0   0   0   0   0   0 | Trp TGG   6   4   4   4   4   4
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   3   4   3   3   3   2 | Pro CCT   3   3   3   3   2   1 | His CAT   3   4   1   2   1   1 | Arg CGT   1   2   3   3   5   2
    CTC   8   9   7   6   6   7 |     CCC  11   9  10  10  11  10 |     CAC   3   2   7   4   5   5 |     CGC   0   0   2   3   2   2
    CTA   5   4   4   4   4   4 |     CCA   6   6   5   4   9   7 | Gln CAA   6   5   5   5   6   5 |     CGA   2   2   2   2   2   2
    CTG  11  10  13  13  13  13 |     CCG   3   3   1   3   1   1 |     CAG   9  10  11  10   9  10 |     CGG   1   2   0   0   0   0
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   5   5   5   5   6   4 | Thr ACT  10  10   9   8   8   8 | Asn AAT  16  15  10  10  12  13 | Ser AGT   4   4   6   6   7   7
    ATC   7   9   9  10  10   8 |     ACC   7   9  12  12  11  14 |     AAC  12  14  16  15  15  12 |     AGC   8   4  11  10   6  10
    ATA   4   5   4   3   5   6 |     ACA   5   6   9  11   7   9 | Lys AAA   2   2   1   2   2   2 | Arg AGA   2   2   0   0   0   1
Met ATG   5   4   3   2   1   2 |     ACG   2   1   2   2   1   2 |     AAG   4   5   2   2   3   2 |     AGG   6   5   5   4   4   4
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   1   2   3   2   2   3 | Ala GCT   4   3   2   4   3   4 | Asp GAT   5   5   7   6   5   6 | Gly GGT   3   3   1   2   1   1
    GTC  11  12   8   9  10  10 |     GCC  11   8   6   7   6   5 |     GAC   5   5   7   4   7   5 |     GGC   4   6   5   5   7   6
    GTA   5   4   3   3   3   2 |     GCA   8   6   9  11   9   7 | Glu GAA   9   8   7   4   6   9 |     GGA   6   8   5   6   5   4
    GTG   6   9   9  12  10  10 |     GCG   0   1   1   0   2   1 |     GAG   7   6   8   8   6   8 |     GGG   5   4   6   6   6   6
--------------------------------------------------------------------------------------------------------------------------------------

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

#1: human          
position  1:    T:0.15064    C:0.23397    A:0.32372    G:0.29167
position  2:    T:0.25000    C:0.28846    A:0.29808    G:0.16346
position  3:    T:0.21154    C:0.37500    A:0.20192    G:0.21154
Average         T:0.20406    C:0.29915    A:0.27457    G:0.22222

#2: chimpanzee     
position  1:    T:0.15064    C:0.23718    A:0.32051    G:0.29167
position  2:    T:0.25321    C:0.28526    A:0.29808    G:0.16346
position  3:    T:0.21474    C:0.37179    A:0.19872    G:0.21474
Average         T:0.20620    C:0.29808    A:0.27244    G:0.22329

#3: bonobo         
position  1:    T:0.15064    C:0.23718    A:0.32051    G:0.29167
position  2:    T:0.25000    C:0.28526    A:0.29808    G:0.16667
position  3:    T:0.21795    C:0.36859    A:0.19872    G:0.21474
Average         T:0.20620    C:0.29701    A:0.27244    G:0.22436

#4: gorilla        
position  1:    T:0.15385    C:0.23077    A:0.32692    G:0.28846
position  2:    T:0.25321    C:0.28526    A:0.30128    G:0.16026
position  3:    T:0.21474    C:0.36859    A:0.20513    G:0.21154
Average         T:0.20726    C:0.29487    A:0.27778    G:0.22009

#5: orangutan      
position  1:    T:0.15064    C:0.23718    A:0.33013    G:0.28205
position  2:    T:0.25641    C:0.28846    A:0.30449    G:0.15064
position  3:    T:0.22436    C:0.35577    A:0.21474    G:0.20513
Average         T:0.21047    C:0.29380    A:0.28312    G:0.21261

#6: colobus        
position  1:    T:0.15385    C:0.22756    A:0.32692    G:0.29167
position  2:    T:0.26282    C:0.27564    A:0.29808    G:0.16346
position  3:    T:0.22115    C:0.36859    A:0.20513    G:0.20513
Average         T:0.21261    C:0.29060    A:0.27671    G:0.22009

#7: baboon         
position  1:    T:0.15064    C:0.22436    A:0.32692    G:0.29808
position  2:    T:0.26282    C:0.28205    A:0.28846    G:0.16667
position  3:    T:0.22756    C:0.36218    A:0.20833    G:0.20192
Average         T:0.21368    C:0.28953    A:0.27457    G:0.22222

#8: drill          
position  1:    T:0.15385    C:0.23077    A:0.32372    G:0.29167
position  2:    T:0.25962    C:0.28205    A:0.29487    G:0.16346
position  3:    T:0.21474    C:0.37179    A:0.21795    G:0.19551
Average         T:0.20940    C:0.29487    A:0.27885    G:0.21688

#9: sootyM         
position  1:    T:0.15064    C:0.23077    A:0.32051    G:0.29808
position  2:    T:0.25962    C:0.28526    A:0.29167    G:0.16346
position  3:    T:0.22115    C:0.36218    A:0.22115    G:0.19551
Average         T:0.21047    C:0.29274    A:0.27778    G:0.21902

#10: CEmac          
position  1:    T:0.15385    C:0.22756    A:0.32051    G:0.29808
position  2:    T:0.26282    C:0.27564    A:0.29808    G:0.16346
position  3:    T:0.21795    C:0.36859    A:0.21474    G:0.19872
Average         T:0.21154    C:0.29060    A:0.27778    G:0.22009

#11: rhesus         
position  1:    T:0.15385    C:0.22756    A:0.32051    G:0.29808
position  2:    T:0.26282    C:0.27564    A:0.30128    G:0.16026
position  3:    T:0.21795    C:0.36859    A:0.21474    G:0.19872
Average         T:0.21154    C:0.29060    A:0.27885    G:0.21902

#12: PTmac          
position  1:    T:0.15385    C:0.22436    A:0.33013    G:0.29167
position  2:    T:0.25962    C:0.28205    A:0.29487    G:0.16346
position  3:    T:0.21795    C:0.36859    A:0.21474    G:0.19872
Average         T:0.21047    C:0.29167    A:0.27991    G:0.21795

#13: GSNM           
position  1:    T:0.15385    C:0.24038    A:0.31731    G:0.28846
position  2:    T:0.25641    C:0.27564    A:0.29808    G:0.16987
position  3:    T:0.22115    C:0.36538    A:0.20513    G:0.20833
Average         T:0.21047    C:0.29380    A:0.27350    G:0.22222

#14: AGM            
position  1:    T:0.15064    C:0.24038    A:0.32051    G:0.28846
position  2:    T:0.27244    C:0.26923    A:0.29808    G:0.16026
position  3:    T:0.22436    C:0.36859    A:0.19872    G:0.20833
Average         T:0.21581    C:0.29274    A:0.27244    G:0.21902

#15: nightM         
position  1:    T:0.14103    C:0.24679    A:0.33333    G:0.27885
position  2:    T:0.24679    C:0.27564    A:0.29808    G:0.17949
position  3:    T:0.20833    C:0.39744    A:0.18269    G:0.21154
Average         T:0.19872    C:0.30662    A:0.27137    G:0.22329

#16: squirrelM      
position  1:    T:0.14744    C:0.24038    A:0.32692    G:0.28526
position  2:    T:0.25000    C:0.29487    A:0.26923    G:0.18590
position  3:    T:0.21474    C:0.38462    A:0.18590    G:0.21474
Average         T:0.20406    C:0.30662    A:0.26068    G:0.22863

#17: capuchin       
position  1:    T:0.15064    C:0.25321    A:0.31410    G:0.28205
position  2:    T:0.25641    C:0.28205    A:0.28526    G:0.17628
position  3:    T:0.21795    C:0.39103    A:0.19551    G:0.19551
Average         T:0.20833    C:0.30876    A:0.26496    G:0.21795

#18: marmoset       
position  1:    T:0.15705    C:0.23077    A:0.33333    G:0.27885
position  2:    T:0.25641    C:0.27885    A:0.28846    G:0.17628
position  3:    T:0.21154    C:0.38782    A:0.19551    G:0.20513
Average         T:0.20833    C:0.29915    A:0.27244    G:0.22009

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      35 | Ser S TCT      57 | Tyr Y TAT      71 | Cys C TGT      44
      TTC      91 |       TCC     196 |       TAC     151 |       TGC      38
Leu L TTA      12 |       TCA      52 | *** * TAA       0 | *** * TGA       0
      TTG       2 |       TCG       8 |       TAG       0 | Trp W TGG      94
------------------------------------------------------------------------------
Leu L CTT      48 | Pro P CCT      47 | His H CAT      33 | Arg R CGT      43
      CTC     152 |       CCC     181 |       CAC      58 |       CGC      14
      CTA      78 |       CCA     115 | Gln Q CAA     105 |       CGA      24
      CTG     198 |       CCG      42 |       CAG     170 |       CGG       9
------------------------------------------------------------------------------
Ile I ATT      88 | Thr T ACT     162 | Asn N AAT     259 | Ser S AGT      91
      ATC     139 |       ACC     185 |       AAC     245 |       AGC     116
      ATA      80 |       ACA     121 | Lys K AAA      48 | Arg R AGA      26
Met M ATG      66 |       ACG      32 |       AAG      74 |       AGG      89
------------------------------------------------------------------------------
Val V GTT      33 | Ala A GCT      74 | Asp D GAT      96 | Gly G GGT      42
      GTC     190 |       GCC     157 |       GAC      82 |       GGC      97
      GTA      81 |       GCA     141 | Glu E GAA     146 |       GGA     119
      GTG     152 |       GCG      11 |       GAG     117 |       GGG      89
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15153    C:0.23451    A:0.32425    G:0.28971
position  2:    T:0.25730    C:0.28152    A:0.29469    G:0.16649
position  3:    T:0.21777    C:0.37251    A:0.20442    G:0.20531
Average         T:0.20887    C:0.29618    A:0.27445    G:0.22050

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.00869460  0.01487253  0.00816141  0.00819695
  0.00951291  0.01627230  0.00892954  0.00896843
  0.00995817  0.01703393  0.00000000  0.00000000
  0.00562592  0.00962340  0.00000000  0.00530391
  0.01345568  0.02301659  0.01263052  0.01268553
  0.01472210  0.02518286  0.01381927  0.01387946
  0.01541118  0.02636156  0.01446610  0.01452910
  0.00870662  0.01489309  0.00817269  0.00820828
  0.01860501  0.03182476  0.01746407  0.01754013
  0.02035607  0.03482003  0.01910774  0.01919097
  0.02130885  0.03644981  0.02000210  0.02008921
  0.01203854  0.02059249  0.01130028  0.01134950
  0.01662293  0.02843432  0.01560353  0.01567149
  0.01818744  0.03111049  0.01707210  0.01714646
  0.01903872  0.03256664  0.01787118  0.01794901
  0.01075601  0.01839867  0.01009640  0.01014038


Model 1: NearlyNeutral (2 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (7, (9, 8))), 14), (6, 13))), ((16, 17), (18, 15)));   MP score: 365
This is a rooted tree.  Please check!
lnL(ntime: 34  np: 37):  -3472.908591      +0.000000
  19..20   20..21   21..22   22..23   23..1    23..24   24..2    24..3    22..4    21..5    20..25   25..26   26..27   27..28   28..29   29..11   29..10   28..12   27..30   30..7    30..31   31..9    31..8    26..14   25..32   32..6    32..13   19..33   33..34   34..16   34..17   33..35   35..18   35..15 
 0.139271 0.047768 0.041246 0.003726 0.012941 0.013628 0.000004 0.006606 0.017738 0.068446 0.092612 0.007791 0.014386 0.009933 0.010328 0.006592 0.003281 0.016129 0.004537 0.035740 0.010007 0.017424 0.005750 0.103164 0.020402 0.047204 0.044614 0.092159 0.024750 0.096185 0.093540 0.004925 0.169603 0.091207 2.884821 0.412676 0.037687

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

tree length =  1.373636

(((((1: 0.012941, (2: 0.000004, 3: 0.006606): 0.013628): 0.003726, 4: 0.017738): 0.041246, 5: 0.068446): 0.047768, (((((11: 0.006592, 10: 0.003281): 0.010328, 12: 0.016129): 0.009933, (7: 0.035740, (9: 0.017424, 8: 0.005750): 0.010007): 0.004537): 0.014386, 14: 0.103164): 0.007791, (6: 0.047204, 13: 0.044614): 0.020402): 0.092612): 0.139271, ((16: 0.096185, 17: 0.093540): 0.024750, (18: 0.169603, 15: 0.091207): 0.004925): 0.092159);

(((((human: 0.012941, (chimpanzee: 0.000004, bonobo: 0.006606): 0.013628): 0.003726, gorilla: 0.017738): 0.041246, orangutan: 0.068446): 0.047768, (((((rhesus: 0.006592, CEmac: 0.003281): 0.010328, PTmac: 0.016129): 0.009933, (baboon: 0.035740, (sootyM: 0.017424, drill: 0.005750): 0.010007): 0.004537): 0.014386, AGM: 0.103164): 0.007791, (colobus: 0.047204, GSNM: 0.044614): 0.020402): 0.092612): 0.139271, ((squirrelM: 0.096185, capuchin: 0.093540): 0.024750, (marmoset: 0.169603, nightM: 0.091207): 0.004925): 0.092159);

Detailed output identifying parameters

kappa (ts/tv) =  2.88482


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

p:   0.41268  0.58732
w:   0.03769  1.00000

dN & dS for each branch

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

  19..20      0.139    684.9    251.1   0.6029   0.0395   0.0654   27.0   16.4
  20..21      0.048    684.9    251.1   0.6029   0.0135   0.0224    9.3    5.6
  21..22      0.041    684.9    251.1   0.6029   0.0117   0.0194    8.0    4.9
  22..23      0.004    684.9    251.1   0.6029   0.0011   0.0018    0.7    0.4
  23..1       0.013    684.9    251.1   0.6029   0.0037   0.0061    2.5    1.5
  23..24      0.014    684.9    251.1   0.6029   0.0039   0.0064    2.6    1.6
  24..2       0.000    684.9    251.1   0.6029   0.0000   0.0000    0.0    0.0
  24..3       0.007    684.9    251.1   0.6029   0.0019   0.0031    1.3    0.8
  22..4       0.018    684.9    251.1   0.6029   0.0050   0.0083    3.4    2.1
  21..5       0.068    684.9    251.1   0.6029   0.0194   0.0322   13.3    8.1
  20..25      0.093    684.9    251.1   0.6029   0.0262   0.0435   18.0   10.9
  25..26      0.008    684.9    251.1   0.6029   0.0022   0.0037    1.5    0.9
  26..27      0.014    684.9    251.1   0.6029   0.0041   0.0068    2.8    1.7
  27..28      0.010    684.9    251.1   0.6029   0.0028   0.0047    1.9    1.2
  28..29      0.010    684.9    251.1   0.6029   0.0029   0.0049    2.0    1.2
  29..11      0.007    684.9    251.1   0.6029   0.0019   0.0031    1.3    0.8
  29..10      0.003    684.9    251.1   0.6029   0.0009   0.0015    0.6    0.4
  28..12      0.016    684.9    251.1   0.6029   0.0046   0.0076    3.1    1.9
  27..30      0.005    684.9    251.1   0.6029   0.0013   0.0021    0.9    0.5
  30..7       0.036    684.9    251.1   0.6029   0.0101   0.0168    6.9    4.2
  30..31      0.010    684.9    251.1   0.6029   0.0028   0.0047    1.9    1.2
  31..9       0.017    684.9    251.1   0.6029   0.0049   0.0082    3.4    2.1
  31..8       0.006    684.9    251.1   0.6029   0.0016   0.0027    1.1    0.7
  26..14      0.103    684.9    251.1   0.6029   0.0292   0.0485   20.0   12.2
  25..32      0.020    684.9    251.1   0.6029   0.0058   0.0096    4.0    2.4
  32..6       0.047    684.9    251.1   0.6029   0.0134   0.0222    9.2    5.6
  32..13      0.045    684.9    251.1   0.6029   0.0126   0.0210    8.7    5.3
  19..33      0.092    684.9    251.1   0.6029   0.0261   0.0433   17.9   10.9
  33..34      0.025    684.9    251.1   0.6029   0.0070   0.0116    4.8    2.9
  34..16      0.096    684.9    251.1   0.6029   0.0272   0.0452   18.7   11.3
  34..17      0.094    684.9    251.1   0.6029   0.0265   0.0440   18.1   11.0
  33..35      0.005    684.9    251.1   0.6029   0.0014   0.0023    1.0    0.6
  35..18      0.170    684.9    251.1   0.6029   0.0480   0.0797   32.9   20.0
  35..15      0.091    684.9    251.1   0.6029   0.0258   0.0429   17.7   10.8


Time used:  4:39


Model 2: PositiveSelection (3 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (7, (9, 8))), 14), (6, 13))), ((16, 17), (18, 15)));   MP score: 365
This is a rooted tree.  Please check!
lnL(ntime: 34  np: 39):  -3446.065445      +0.000000
  19..20   20..21   21..22   22..23   23..1    23..24   24..2    24..3    22..4    21..5    20..25   25..26   26..27   27..28   28..29   29..11   29..10   28..12   27..30   30..7    30..31   31..9    31..8    26..14   25..32   32..6    32..13   19..33   33..34   34..16   34..17   33..35   35..18   35..15 
 0.253813 0.049033 0.042914 0.003769 0.013346 0.014064 0.000004 0.006817 0.018351 0.072417 0.101728 0.008225 0.013866 0.010298 0.010572 0.006809 0.003413 0.016865 0.004603 0.037309 0.010356 0.018139 0.005919 0.110475 0.021700 0.048103 0.047449 0.000004 0.023864 0.101881 0.097887 0.005060 0.179527 0.097410 3.216687 0.324969 0.603460 0.000001 5.678206

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

tree length =  1.455989

(((((1: 0.013346, (2: 0.000004, 3: 0.006817): 0.014064): 0.003769, 4: 0.018351): 0.042914, 5: 0.072417): 0.049033, (((((11: 0.006809, 10: 0.003413): 0.010572, 12: 0.016865): 0.010298, (7: 0.037309, (9: 0.018139, 8: 0.005919): 0.010356): 0.004603): 0.013866, 14: 0.110475): 0.008225, (6: 0.048103, 13: 0.047449): 0.021700): 0.101728): 0.253813, ((16: 0.101881, 17: 0.097887): 0.023864, (18: 0.179527, 15: 0.097410): 0.005060): 0.000004);

(((((human: 0.013346, (chimpanzee: 0.000004, bonobo: 0.006817): 0.014064): 0.003769, gorilla: 0.018351): 0.042914, orangutan: 0.072417): 0.049033, (((((rhesus: 0.006809, CEmac: 0.003413): 0.010572, PTmac: 0.016865): 0.010298, (baboon: 0.037309, (sootyM: 0.018139, drill: 0.005919): 0.010356): 0.004603): 0.013866, AGM: 0.110475): 0.008225, (colobus: 0.048103, GSNM: 0.047449): 0.021700): 0.101728): 0.253813, ((squirrelM: 0.101881, capuchin: 0.097887): 0.023864, (marmoset: 0.179527, nightM: 0.097410): 0.005060): 0.000004);

Detailed output identifying parameters

kappa (ts/tv) =  3.21669


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

p:   0.32497  0.60346  0.07157
w:   0.00000  1.00000  5.67821

dN & dS for each branch

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

  19..20      0.254    681.7    254.3   1.0099   0.0848   0.0840   57.8   21.4
  20..21      0.049    681.7    254.3   1.0099   0.0164   0.0162   11.2    4.1
  21..22      0.043    681.7    254.3   1.0099   0.0143   0.0142    9.8    3.6
  22..23      0.004    681.7    254.3   1.0099   0.0013   0.0012    0.9    0.3
  23..1       0.013    681.7    254.3   1.0099   0.0045   0.0044    3.0    1.1
  23..24      0.014    681.7    254.3   1.0099   0.0047   0.0047    3.2    1.2
  24..2       0.000    681.7    254.3   1.0099   0.0000   0.0000    0.0    0.0
  24..3       0.007    681.7    254.3   1.0099   0.0023   0.0023    1.6    0.6
  22..4       0.018    681.7    254.3   1.0099   0.0061   0.0061    4.2    1.5
  21..5       0.072    681.7    254.3   1.0099   0.0242   0.0240   16.5    6.1
  20..25      0.102    681.7    254.3   1.0099   0.0340   0.0337   23.2    8.6
  25..26      0.008    681.7    254.3   1.0099   0.0027   0.0027    1.9    0.7
  26..27      0.014    681.7    254.3   1.0099   0.0046   0.0046    3.2    1.2
  27..28      0.010    681.7    254.3   1.0099   0.0034   0.0034    2.3    0.9
  28..29      0.011    681.7    254.3   1.0099   0.0035   0.0035    2.4    0.9
  29..11      0.007    681.7    254.3   1.0099   0.0023   0.0023    1.6    0.6
  29..10      0.003    681.7    254.3   1.0099   0.0011   0.0011    0.8    0.3
  28..12      0.017    681.7    254.3   1.0099   0.0056   0.0056    3.8    1.4
  27..30      0.005    681.7    254.3   1.0099   0.0015   0.0015    1.0    0.4
  30..7       0.037    681.7    254.3   1.0099   0.0125   0.0123    8.5    3.1
  30..31      0.010    681.7    254.3   1.0099   0.0035   0.0034    2.4    0.9
  31..9       0.018    681.7    254.3   1.0099   0.0061   0.0060    4.1    1.5
  31..8       0.006    681.7    254.3   1.0099   0.0020   0.0020    1.3    0.5
  26..14      0.110    681.7    254.3   1.0099   0.0369   0.0366   25.2    9.3
  25..32      0.022    681.7    254.3   1.0099   0.0073   0.0072    4.9    1.8
  32..6       0.048    681.7    254.3   1.0099   0.0161   0.0159   11.0    4.0
  32..13      0.047    681.7    254.3   1.0099   0.0159   0.0157   10.8    4.0
  19..33      0.000    681.7    254.3   1.0099   0.0000   0.0000    0.0    0.0
  33..34      0.024    681.7    254.3   1.0099   0.0080   0.0079    5.4    2.0
  34..16      0.102    681.7    254.3   1.0099   0.0341   0.0337   23.2    8.6
  34..17      0.098    681.7    254.3   1.0099   0.0327   0.0324   22.3    8.2
  33..35      0.005    681.7    254.3   1.0099   0.0017   0.0017    1.2    0.4
  35..18      0.180    681.7    254.3   1.0099   0.0600   0.0594   40.9   15.1
  35..15      0.097    681.7    254.3   1.0099   0.0326   0.0322   22.2    8.2


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

    28 R      0.973*        5.550
    29 I      0.986*        5.614
    41 G      0.931         5.354
    43 S      0.900         5.210
    44 L      0.756         4.535
    47 G      0.509         3.380
    51 G      1.000**       5.677
    53 Q      0.842         4.938
    67 I      0.685         4.207
    80 Q      0.901         5.216
    93 S      0.994**       5.648
   103 Q      0.571         3.670
   105 H      0.867         5.054
   114 S      0.991**       5.637
   139 N      0.866         5.051
   148 G      0.998**       5.670
   311 R      0.903         5.222


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

    28 R      0.974*        5.474 +- 1.380
    29 I      0.987*        5.532 +- 1.292
    41 G      0.931         5.240 +- 1.618
    43 S      0.907         5.147 +- 1.745
    44 L      0.776         4.518 +- 2.163
    47 G      0.549         3.386 +- 2.330
    51 G      1.000**       5.590 +- 1.191
    53 Q      0.852         4.869 +- 1.945
    67 I      0.708         4.140 +- 2.240
    80 Q      0.908         5.153 +- 1.739
    93 S      0.994**       5.563 +- 1.239
   103 Q      0.606         3.666 +- 2.339
   105 H      0.877         5.008 +- 1.872
   114 S      0.991**       5.551 +- 1.257
   139 N      0.867         4.911 +- 1.872
   148 G      0.998**       5.583 +- 1.204
   200 L      0.540         3.303 +- 2.283
   232 P      0.542         3.351 +- 2.330
   311 R      0.908         5.136 +- 1.735



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:   0.509  0.301  0.128  0.047  0.013  0.002  0.000  0.000  0.000  0.000
w2:   0.000  0.001  0.088  0.218  0.342  0.243  0.083  0.020  0.004  0.001

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 0.002
 0.000 0.000 0.000 0.000 0.001 0.071 0.042
 0.000 0.000 0.000 0.000 0.000 0.000 0.040 0.453 0.017
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.009 0.072 0.149 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.017 0.043 0.023 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.014 0.017 0.003 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 0.001 0.008 0.006 0.001 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 0.001 0.004 0.002 0.000 0.000

sum of density on p0-p1 =   1.000000

Time used: 13:07


Model 7: beta (10 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (7, (9, 8))), 14), (6, 13))), ((16, 17), (18, 15)));   MP score: 365
This is a rooted tree.  Please check!
lnL(ntime: 34  np: 37):  -3472.978789      +0.000000
  19..20   20..21   21..22   22..23   23..1    23..24   24..2    24..3    22..4    21..5    20..25   25..26   26..27   27..28   28..29   29..11   29..10   28..12   27..30   30..7    30..31   31..9    31..8    26..14   25..32   32..6    32..13   19..33   33..34   34..16   34..17   33..35   35..18   35..15 
 0.088931 0.047762 0.041226 0.003729 0.012929 0.013624 0.000004 0.006605 0.017729 0.068419 0.092583 0.007766 0.014385 0.009929 0.010332 0.006565 0.003286 0.016120 0.004540 0.035706 0.010011 0.017427 0.005738 0.103150 0.020400 0.047186 0.044585 0.142343 0.024670 0.096152 0.093524 0.004984 0.169517 0.091170 2.892409 0.026923 0.015859

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

tree length =  1.373026

(((((1: 0.012929, (2: 0.000004, 3: 0.006605): 0.013624): 0.003729, 4: 0.017729): 0.041226, 5: 0.068419): 0.047762, (((((11: 0.006565, 10: 0.003286): 0.010332, 12: 0.016120): 0.009929, (7: 0.035706, (9: 0.017427, 8: 0.005738): 0.010011): 0.004540): 0.014385, 14: 0.103150): 0.007766, (6: 0.047186, 13: 0.044585): 0.020400): 0.092583): 0.088931, ((16: 0.096152, 17: 0.093524): 0.024670, (18: 0.169517, 15: 0.091170): 0.004984): 0.142343);

(((((human: 0.012929, (chimpanzee: 0.000004, bonobo: 0.006605): 0.013624): 0.003729, gorilla: 0.017729): 0.041226, orangutan: 0.068419): 0.047762, (((((rhesus: 0.006565, CEmac: 0.003286): 0.010332, PTmac: 0.016120): 0.009929, (baboon: 0.035706, (sootyM: 0.017427, drill: 0.005738): 0.010011): 0.004540): 0.014385, AGM: 0.103150): 0.007766, (colobus: 0.047186, GSNM: 0.044585): 0.020400): 0.092583): 0.088931, ((squirrelM: 0.096152, capuchin: 0.093524): 0.024670, (marmoset: 0.169517, nightM: 0.091170): 0.004984): 0.142343);

Detailed output identifying parameters

kappa (ts/tv) =  2.89241

Parameters in M7 (beta):
 p =   0.02692  q =   0.01586


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  0.10394  0.99980  1.00000  1.00000  1.00000  1.00000  1.00000

dN & dS for each branch

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

  19..20      0.089    684.8    251.2   0.6104   0.0253   0.0415   17.3   10.4
  20..21      0.048    684.8    251.2   0.6104   0.0136   0.0223    9.3    5.6
  21..22      0.041    684.8    251.2   0.6104   0.0117   0.0192    8.0    4.8
  22..23      0.004    684.8    251.2   0.6104   0.0011   0.0017    0.7    0.4
  23..1       0.013    684.8    251.2   0.6104   0.0037   0.0060    2.5    1.5
  23..24      0.014    684.8    251.2   0.6104   0.0039   0.0064    2.7    1.6
  24..2       0.000    684.8    251.2   0.6104   0.0000   0.0000    0.0    0.0
  24..3       0.007    684.8    251.2   0.6104   0.0019   0.0031    1.3    0.8
  22..4       0.018    684.8    251.2   0.6104   0.0050   0.0083    3.5    2.1
  21..5       0.068    684.8    251.2   0.6104   0.0195   0.0319   13.3    8.0
  20..25      0.093    684.8    251.2   0.6104   0.0263   0.0432   18.0   10.8
  25..26      0.008    684.8    251.2   0.6104   0.0022   0.0036    1.5    0.9
  26..27      0.014    684.8    251.2   0.6104   0.0041   0.0067    2.8    1.7
  27..28      0.010    684.8    251.2   0.6104   0.0028   0.0046    1.9    1.2
  28..29      0.010    684.8    251.2   0.6104   0.0029   0.0048    2.0    1.2
  29..11      0.007    684.8    251.2   0.6104   0.0019   0.0031    1.3    0.8
  29..10      0.003    684.8    251.2   0.6104   0.0009   0.0015    0.6    0.4
  28..12      0.016    684.8    251.2   0.6104   0.0046   0.0075    3.1    1.9
  27..30      0.005    684.8    251.2   0.6104   0.0013   0.0021    0.9    0.5
  30..7       0.036    684.8    251.2   0.6104   0.0102   0.0166    7.0    4.2
  30..31      0.010    684.8    251.2   0.6104   0.0028   0.0047    2.0    1.2
  31..9       0.017    684.8    251.2   0.6104   0.0050   0.0081    3.4    2.0
  31..8       0.006    684.8    251.2   0.6104   0.0016   0.0027    1.1    0.7
  26..14      0.103    684.8    251.2   0.6104   0.0294   0.0481   20.1   12.1
  25..32      0.020    684.8    251.2   0.6104   0.0058   0.0095    4.0    2.4
  32..6       0.047    684.8    251.2   0.6104   0.0134   0.0220    9.2    5.5
  32..13      0.045    684.8    251.2   0.6104   0.0127   0.0208    8.7    5.2
  19..33      0.142    684.8    251.2   0.6104   0.0405   0.0664   27.7   16.7
  33..34      0.025    684.8    251.2   0.6104   0.0070   0.0115    4.8    2.9
  34..16      0.096    684.8    251.2   0.6104   0.0274   0.0448   18.7   11.3
  34..17      0.094    684.8    251.2   0.6104   0.0266   0.0436   18.2   11.0
  33..35      0.005    684.8    251.2   0.6104   0.0014   0.0023    1.0    0.6
  35..18      0.170    684.8    251.2   0.6104   0.0482   0.0790   33.0   19.9
  35..15      0.091    684.8    251.2   0.6104   0.0259   0.0425   17.8   10.7


Time used: 27:38


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


TREE #  1:  (((((1, (2, 3)), 4), 5), (((((11, 10), 12), (7, (9, 8))), 14), (6, 13))), ((16, 17), (18, 15)));   MP score: 365
This is a rooted tree.  Please check!
lnL(ntime: 34  np: 39):  -3446.130357      +0.000000
  19..20   20..21   21..22   22..23   23..1    23..24   24..2    24..3    22..4    21..5    20..25   25..26   26..27   27..28   28..29   29..11   29..10   28..12   27..30   30..7    30..31   31..9    31..8    26..14   25..32   32..6    32..13   19..33   33..34   34..16   34..17   33..35   35..18   35..15 
 0.126739 0.048947 0.042867 0.003768 0.013319 0.014048 0.000004 0.006810 0.018325 0.072282 0.101606 0.008203 0.013800 0.010285 0.010552 0.006798 0.003406 0.016839 0.004593 0.037247 0.010344 0.018108 0.005911 0.110373 0.021661 0.048055 0.047358 0.126609 0.023895 0.101742 0.097717 0.005010 0.179266 0.097256 3.202437 0.925610 0.033296 0.018853 5.471868

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

tree length =  1.453745

(((((1: 0.013319, (2: 0.000004, 3: 0.006810): 0.014048): 0.003768, 4: 0.018325): 0.042867, 5: 0.072282): 0.048947, (((((11: 0.006798, 10: 0.003406): 0.010552, 12: 0.016839): 0.010285, (7: 0.037247, (9: 0.018108, 8: 0.005911): 0.010344): 0.004593): 0.013800, 14: 0.110373): 0.008203, (6: 0.048055, 13: 0.047358): 0.021661): 0.101606): 0.126739, ((16: 0.101742, 17: 0.097717): 0.023895, (18: 0.179266, 15: 0.097256): 0.005010): 0.126609);

(((((human: 0.013319, (chimpanzee: 0.000004, bonobo: 0.006810): 0.014048): 0.003768, gorilla: 0.018325): 0.042867, orangutan: 0.072282): 0.048947, (((((rhesus: 0.006798, CEmac: 0.003406): 0.010552, PTmac: 0.016839): 0.010285, (baboon: 0.037247, (sootyM: 0.018108, drill: 0.005911): 0.010344): 0.004593): 0.013800, AGM: 0.110373): 0.008203, (colobus: 0.048055, GSNM: 0.047358): 0.021661): 0.101606): 0.126739, ((squirrelM: 0.101742, capuchin: 0.097717): 0.023895, (marmoset: 0.179266, nightM: 0.097256): 0.005010): 0.126609);

Detailed output identifying parameters

kappa (ts/tv) =  3.20244

Parameters in M8 (beta&w>1):
  p0 =   0.92561  p =   0.03330 q =   0.01885
 (p1 =   0.07439) w =   5.47187


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

p:   0.09256  0.09256  0.09256  0.09256  0.09256  0.09256  0.09256  0.09256  0.09256  0.09256  0.07439
w:   0.00000  0.00000  0.00001  0.27173  0.99965  1.00000  1.00000  1.00000  1.00000  1.00000  5.47187

dN & dS for each branch

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

  19..20      0.127    681.8    254.2   0.9875   0.0421   0.0426   28.7   10.8
  20..21      0.049    681.8    254.2   0.9875   0.0163   0.0165   11.1    4.2
  21..22      0.043    681.8    254.2   0.9875   0.0142   0.0144    9.7    3.7
  22..23      0.004    681.8    254.2   0.9875   0.0013   0.0013    0.9    0.3
  23..1       0.013    681.8    254.2   0.9875   0.0044   0.0045    3.0    1.1
  23..24      0.014    681.8    254.2   0.9875   0.0047   0.0047    3.2    1.2
  24..2       0.000    681.8    254.2   0.9875   0.0000   0.0000    0.0    0.0
  24..3       0.007    681.8    254.2   0.9875   0.0023   0.0023    1.5    0.6
  22..4       0.018    681.8    254.2   0.9875   0.0061   0.0062    4.2    1.6
  21..5       0.072    681.8    254.2   0.9875   0.0240   0.0243   16.4    6.2
  20..25      0.102    681.8    254.2   0.9875   0.0338   0.0342   23.0    8.7
  25..26      0.008    681.8    254.2   0.9875   0.0027   0.0028    1.9    0.7
  26..27      0.014    681.8    254.2   0.9875   0.0046   0.0046    3.1    1.2
  27..28      0.010    681.8    254.2   0.9875   0.0034   0.0035    2.3    0.9
  28..29      0.011    681.8    254.2   0.9875   0.0035   0.0035    2.4    0.9
  29..11      0.007    681.8    254.2   0.9875   0.0023   0.0023    1.5    0.6
  29..10      0.003    681.8    254.2   0.9875   0.0011   0.0011    0.8    0.3
  28..12      0.017    681.8    254.2   0.9875   0.0056   0.0057    3.8    1.4
  27..30      0.005    681.8    254.2   0.9875   0.0015   0.0015    1.0    0.4
  30..7       0.037    681.8    254.2   0.9875   0.0124   0.0125    8.4    3.2
  30..31      0.010    681.8    254.2   0.9875   0.0034   0.0035    2.3    0.9
  31..9       0.018    681.8    254.2   0.9875   0.0060   0.0061    4.1    1.5
  31..8       0.006    681.8    254.2   0.9875   0.0020   0.0020    1.3    0.5
  26..14      0.110    681.8    254.2   0.9875   0.0367   0.0371   25.0    9.4
  25..32      0.022    681.8    254.2   0.9875   0.0072   0.0073    4.9    1.9
  32..6       0.048    681.8    254.2   0.9875   0.0160   0.0162   10.9    4.1
  32..13      0.047    681.8    254.2   0.9875   0.0157   0.0159   10.7    4.0
  19..33      0.127    681.8    254.2   0.9875   0.0421   0.0426   28.7   10.8
  33..34      0.024    681.8    254.2   0.9875   0.0079   0.0080    5.4    2.0
  34..16      0.102    681.8    254.2   0.9875   0.0338   0.0342   23.0    8.7
  34..17      0.098    681.8    254.2   0.9875   0.0325   0.0329   22.1    8.4
  33..35      0.005    681.8    254.2   0.9875   0.0017   0.0017    1.1    0.4
  35..18      0.179    681.8    254.2   0.9875   0.0596   0.0603   40.6   15.3
  35..15      0.097    681.8    254.2   0.9875   0.0323   0.0327   22.0    8.3


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

    28 R      0.973*        5.352
    29 I      0.986*        5.411
    41 G      0.934         5.179
    43 S      0.904         5.043
    44 L      0.767         4.429
    47 G      0.532         3.379
    51 G      1.000**       5.471
    53 Q      0.850         4.799
    67 I      0.704         4.149
    80 Q      0.905         5.047
    93 S      0.994**       5.443
   103 Q      0.591         3.641
   105 H      0.872         4.897
   114 S      0.991**       5.432
   139 N      0.875         4.911
   148 G      0.998**       5.464
   200 L      0.526         3.349
   232 P      0.523         3.338
   311 R      0.907         5.057


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

     7 T      0.682         2.953 +- 1.579
    28 R      0.990*        4.086 +- 0.959
    29 I      0.994**       4.103 +- 0.936
    32 S      0.660         2.854 +- 1.542
    38 R      0.566         2.548 +- 1.609
    41 G      0.983*        4.054 +- 0.978
    43 S      0.964*        3.993 +- 1.068
    44 L      0.898         3.756 +- 1.287
    46 V      0.649         2.831 +- 1.592
    47 G      0.798         3.374 +- 1.465
    50 I      0.537         2.448 +- 1.607
    51 G      1.000**       4.121 +- 0.908
    53 Q      0.947         3.925 +- 1.124
    54 Q      0.525         2.424 +- 1.667
    61 Y      0.522         2.398 +- 1.602
    67 I      0.899         3.736 +- 1.248
    80 Q      0.964*        3.994 +- 1.067
    87 T      0.604         2.677 +- 1.601
    93 S      0.997**       4.113 +- 0.921
    97 N      0.634         2.783 +- 1.599
   103 Q      0.825         3.475 +- 1.428
   105 H      0.944         3.925 +- 1.147
   114 S      0.997**       4.111 +- 0.922
   130 A      0.718         3.058 +- 1.507
   139 N      0.966*        3.986 +- 1.036
   148 G      0.999**       4.119 +- 0.911
   178 S      0.781         3.282 +- 1.442
   180 E      0.630         2.768 +- 1.602
   200 L      0.827         3.455 +- 1.384
   232 P      0.793         3.356 +- 1.474
   306 A      0.687         2.965 +- 1.571
   311 R      0.970*        4.010 +- 1.037



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  0.001  0.020  0.871  0.108
p :   0.049  0.075  0.124  0.127  0.131  0.130  0.124  0.107  0.081  0.053
q :   0.055  0.117  0.112  0.111  0.112  0.111  0.109  0.103  0.093  0.077
ws:   0.000  0.013  0.538  0.337  0.058  0.039  0.013  0.002  0.000  0.000

Time used: 47:58
