     15   1176

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



Printing out site pattern counts


        15        660  P

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

    3    1    1    6    1    1    1    1    1    5    1    1    1    1    1
    1    7    1    1    1    1    5    1    1    1    1    1    1    7    1
    1    1    1    4    1    1    1    1    1    1    4    1    1    3    1
    1    1    3    1    1    1    1    1    1    1    1    7    1    1    1
    2    1    1    1    2    1    1    1    1    3    1    3    1    1    1
   11    1    1    2    1    1    1    6    1    5    1    1    1    1    1
    1    1    1    1    1    1    1    1    2    1    1    1    1    1    1
    1    1    1    3   13    1    1    1    1    8    2    1    1    1    3
    1    1    1    6    1    1    6    1    1    1    1    1    1    4    1
    1    1    2    1    1    1    1    3    1    1    1    1    1   11    1
    1    1    1    1    2    1    1    1    2    1    5    1    1    1    1
    4    1    1    4    1    1    2    1    1    2    1    1    1    1    9
    1    1    1    1    1    7    1    1    1    1    1    1    1    1    1
    1    1    5    1    1    1    1    1    2   11    1    1    3    1    2
    1    3    1    2    1    4    1    1    1    1

CODONML (in paml version 4.9h, March 2018)  CEACAM3seq.txt
Model: One dN/dS ratio, 
Codon frequency model: F3x4
Site-class models: 
ns =  15  ls = 392

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   3   3   3   2   3   1 | Ser TCT   4   4   4   4   5   6 | Tyr TAT   6   6   6   6   8   7 | Cys TGT   3   3   3   3   5   4
    TTC   5   6   6   6   5   6 |     TCC  16  16  16  16  14  15 |     TAC   9   9   9   8   9   8 |     TGC   4   4   4   4   4   3
Leu TTA   0   0   0   0   1   0 |     TCA   2   2   2   2   2   2 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   1   1   1   1   1   1 |     TCG   1   1   1   1   1   0 |     TAG   0   0   0   0   0   0 | Trp TGG   3   3   3   3   3   3
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   7   7   7   5   4   7 | Pro CCT   5   5   5   5   4   4 | His CAT   5   5   5   4   3   4 | Arg CGT   2   2   2   3   3   1
    CTC  15  15  15  15  14  16 |     CCC  13  14  14  15  15  14 |     CAC   6   6   6   6   8   6 |     CGC   0   0   0   0   0   0
    CTA   6   6   6   6   6   3 |     CCA   7   8   8   8   7  10 | Gln CAA   5   5   6   5   5   5 |     CGA   1   1   0   0   1   4
    CTG  12  11  11  12  12  11 |     CCG   5   4   4   4   4   3 |     CAG  12  13  13  13  14  15 |     CGG   1   1   1   2   1   2
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   6   7   7   8   7   4 | Thr ACT   7   6   6   5   7   7 | Asn AAT  11  12  12  13  13  11 | Ser AGT   8   8   7   9   6   8
    ATC   9  10  10   9  11  10 |     ACC  10  10  10  12  10   9 |     AAC  11  11  11  12  12  13 |     AGC   8   6   7   6   9   6
    ATA   5   5   5   3   3   5 |     ACA  11  10  10  13  15  13 | Lys AAA   4   4   4   4   7   3 | Arg AGA   2   2   2   2   2   3
Met ATG   5   4   4   5   3   6 |     ACG   1   2   2   1   2   0 |     AAG  11   9  10   9   8   7 |     AGG   4   4   4   4   5   5
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   0   0   0   2   2   4 | Ala GCT   5   5   5   5   3   6 | Asp GAT   4   3   4   4   3   6 | Gly GGT   4   4   4   4   4   3
    GTC  14  13  13  12  12  13 |     GCC  16  17  17  16  17  17 |     GAC   9   8   8   9   9   9 |     GGC   7   8   8   7   5  10
    GTA   4   4   4   4   3   4 |     GCA   9  11  10   9   7   3 | Glu GAA  10  10  11  11  11   8 |     GGA  10   9   9  11   7  11
    GTG  12  13  12  11  12  10 |     GCG   2   1   1   1   1   3 |     GAG   8   9   8   7   8   9 |     GGG   6   6   6   5   6   5
--------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   1   1   1   1   1   1 | Ser TCT   5   5   5   5   5   5 | Tyr TAT   9   9   8   8   8   8 | Cys TGT   3   3   3   3   4   5
    TTC   6   7   6   6   6   6 |     TCC  16  16  17  17  18  17 |     TAC   4   4   5   5   3   3 |     TGC   3   3   3   3   3   3
Leu TTA   0   1   0   0   0   0 |     TCA   1   1   1   1   2   2 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   3   3   3   3   3   3 |     TCG   0   0   0   0   0   0 |     TAG   0   0   0   0   0   0 | Trp TGG   3   4   3   3   3   3
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   7   6   7   7   8   8 | Pro CCT   2   5   5   5   3   3 | His CAT   3   2   2   2   5   4 | Arg CGT   2   2   2   2   1   1
    CTC  16  16  16  16  15  15 |     CCC  16  13  12  12  13  14 |     CAC   7   7   8   8   7   7 |     CGC   1   1   1   1   1   1
    CTA   5   5   5   5   4   4 |     CCA   9   9   9   9   9   9 | Gln CAA   5   5   4   4   4   4 |     CGA   2   2   2   2   3   3
    CTG   9   9   9   9   9   9 |     CCG   3   3   3   3   3   3 |     CAG  14  14  15  15  15  15 |     CGG   3   2   2   2   2   2
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   5   4   5   5   3   4 | Thr ACT   8   8   7   7   8   8 | Asn AAT  12  14  14  14  13  14 | Ser AGT   7   7   7   7   7   6
    ATC   8   9   8   8   9   9 |     ACC  11  11  11  11  11  11 |     AAC  13  12  12  12  12  12 |     AGC   5   6   6   6   5   5
    ATA   6   4   4   4   4   3 |     ACA  11  12  13  12  13  13 | Lys AAA   5   5   6   6   4   5 | Arg AGA   3   3   3   3   3   3
Met ATG   6   5   5   6   5   5 |     ACG   0   0   0   0   0   0 |     AAG   6   6   6   6   6   6 |     AGG   5   5   5   5   5   5
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   2   2   2   2   4   3 | Ala GCT   6   7   7   7   7   7 | Asp GAT   6   6   6   6   6   5 | Gly GGT   3   3   3   3   3   3
    GTC  14  13  14  14  14  14 |     GCC  18  17  17  17  17  17 |     GAC   9   9   9   9  10  11 |     GGC   9   8   8   8   9   9
    GTA   4   5   5   5   4   5 |     GCA   6   7   7   6   5   5 | Glu GAA   8   8   9   8   9   8 |     GGA  11  10   9  10  11  11
    GTG  12  13  11  11  12  12 |     GCG   2   1   1   2   2   2 |     GAG   8   8   9   9   8   8 |     GGG   5   6   6   6   5   5
--------------------------------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------
Phe TTT   1   1   1 | Ser TCT   4   4   4 | Tyr TAT   8   8   9 | Cys TGT   2   2   2
    TTC   5   5   5 |     TCC  16  16  16 |     TAC   7   7   7 |     TGC   4   4   4
Leu TTA   0   0   0 |     TCA   2   2   1 | *** TAA   0   0   0 | *** TGA   0   0   0
    TTG   2   2   2 |     TCG   0   0   0 |     TAG   0   0   0 | Trp TGG   3   3   3
--------------------------------------------------------------------------------------
Leu CTT   8   8   9 | Pro CCT   5   5   4 | His CAT   4   4   4 | Arg CGT   2   2   1
    CTC  14  14  14 |     CCC  13  13  15 |     CAC   6   6   6 |     CGC   1   1   1
    CTA   3   3   4 |     CCA   9  10   9 | Gln CAA   6   6   5 |     CGA   2   2   3
    CTG  11  11  11 |     CCG   2   1   1 |     CAG  14  14  15 |     CGG   2   2   2
--------------------------------------------------------------------------------------
Ile ATT   7   7   4 | Thr ACT   8   8   8 | Asn AAT  12  12  12 | Ser AGT   6   6   6
    ATC   9   9   9 |     ACC  11  11  12 |     AAC  11  11  11 |     AGC   8   8   7
    ATA   5   5   3 |     ACA  12  12  14 | Lys AAA   6   6   4 | Arg AGA   3   3   3
Met ATG   5   5   6 |     ACG   0   0   0 |     AAG   7   7   6 |     AGG   5   5   4
--------------------------------------------------------------------------------------
Val GTT   3   3   2 | Ala GCT   4   4   7 | Asp GAT   6   6   6 | Gly GGT   5   5   3
    GTC  11  11  12 |     GCC  20  20  18 |     GAC  10  10   9 |     GGC   8   8  10
    GTA   4   4   6 |     GCA   6   6   6 | Glu GAA   8   8   8 |     GGA  11  11  11
    GTG  13  13  13 |     GCG   0   0   1 |     GAG   7   7   7 |     GGG   5   5   6
--------------------------------------------------------------------------------------

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

#1: human          
position  1:    T:0.14541    C:0.26020    A:0.28827    G:0.30612
position  2:    T:0.26531    C:0.29082    A:0.28316    G:0.16071
position  3:    T:0.20408    C:0.38776    A:0.19388    G:0.21429
Average         T:0.20493    C:0.31293    A:0.25510    G:0.22704

#2: chimpanzee     
position  1:    T:0.14796    C:0.26276    A:0.28061    G:0.30867
position  2:    T:0.26786    C:0.29592    A:0.28061    G:0.15561
position  3:    T:0.20408    C:0.39031    A:0.19643    G:0.20918
Average         T:0.20663    C:0.31633    A:0.25255    G:0.22449

#3: bonobo         
position  1:    T:0.14796    C:0.26276    A:0.28316    G:0.30612
position  2:    T:0.26531    C:0.29337    A:0.28827    G:0.15306
position  3:    T:0.20408    C:0.39286    A:0.19643    G:0.20663
Average         T:0.20578    C:0.31633    A:0.25595    G:0.22194

#4: gorilla        
position  1:    T:0.14286    C:0.26276    A:0.29337    G:0.30102
position  2:    T:0.25765    C:0.29847    A:0.28316    G:0.16071
position  3:    T:0.20918    C:0.39031    A:0.19898    G:0.20153
Average         T:0.20323    C:0.31718    A:0.25850    G:0.22109

#5: orangutan      
position  1:    T:0.15561    C:0.25765    A:0.30612    G:0.28061
position  2:    T:0.25255    C:0.29082    A:0.30102    G:0.15561
position  3:    T:0.20408    C:0.39286    A:0.19643    G:0.20663
Average         T:0.20408    C:0.31378    A:0.26786    G:0.21429

#6: AGM            
position  1:    T:0.14286    C:0.26786    A:0.28061    G:0.30867
position  2:    T:0.25765    C:0.28571    A:0.28316    G:0.17347
position  3:    T:0.21173    C:0.39541    A:0.18878    G:0.20408
Average         T:0.20408    C:0.31633    A:0.25085    G:0.22874

#7: baboon         
position  1:    T:0.13776    C:0.26531    A:0.28316    G:0.31378
position  2:    T:0.26531    C:0.29082    A:0.27806    G:0.16582
position  3:    T:0.20663    C:0.39796    A:0.19388    G:0.20153
Average         T:0.20323    C:0.31803    A:0.25170    G:0.22704

#8: CEmac          
position  1:    T:0.14541    C:0.25765    A:0.28316    G:0.31378
position  2:    T:0.26276    C:0.29337    A:0.27806    G:0.16582
position  3:    T:0.21429    C:0.38776    A:0.19643    G:0.20153
Average         T:0.20748    C:0.31293    A:0.25255    G:0.22704

#9: rhesus         
position  1:    T:0.14031    C:0.26020    A:0.28571    G:0.31378
position  2:    T:0.25765    C:0.29337    A:0.28827    G:0.16071
position  3:    T:0.21429    C:0.39031    A:0.19643    G:0.19898
Average         T:0.20408    C:0.31463    A:0.25680    G:0.22449

#10: PTmac          
position  1:    T:0.14031    C:0.26020    A:0.28571    G:0.31378
position  2:    T:0.26020    C:0.29082    A:0.28571    G:0.16327
position  3:    T:0.21429    C:0.39031    A:0.19133    G:0.20408
Average         T:0.20493    C:0.31378    A:0.25425    G:0.22704

#11: sootyM         
position  1:    T:0.14286    C:0.26020    A:0.27551    G:0.32143
position  2:    T:0.25765    C:0.29592    A:0.28061    G:0.16582
position  3:    T:0.21939    C:0.39031    A:0.19133    G:0.19898
Average         T:0.20663    C:0.31548    A:0.24915    G:0.22874

#12: drill          
position  1:    T:0.14286    C:0.26020    A:0.27806    G:0.31888
position  2:    T:0.25765    C:0.29592    A:0.28061    G:0.16582
position  3:    T:0.21684    C:0.39286    A:0.19133    G:0.19898
Average         T:0.20578    C:0.31633    A:0.25000    G:0.22789

#13: BSNM           
position  1:    T:0.13776    C:0.26020    A:0.29337    G:0.30867
position  2:    T:0.25765    C:0.28571    A:0.28571    G:0.17092
position  3:    T:0.21684    C:0.39286    A:0.19643    G:0.19388
Average         T:0.20408    C:0.31293    A:0.25850    G:0.22449

#14: GSNM           
position  1:    T:0.13776    C:0.26020    A:0.29337    G:0.30867
position  2:    T:0.25765    C:0.28571    A:0.28571    G:0.17092
position  3:    T:0.21684    C:0.39286    A:0.19898    G:0.19133
Average         T:0.20408    C:0.31293    A:0.25935    G:0.22364

#15: colobus        
position  1:    T:0.13776    C:0.26531    A:0.27806    G:0.31888
position  2:    T:0.25765    C:0.29592    A:0.27806    G:0.16837
position  3:    T:0.20918    C:0.39796    A:0.19643    G:0.19643
Average         T:0.20153    C:0.31973    A:0.25085    G:0.22789

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      24 | Ser S TCT      69 | Tyr Y TAT     114 | Cys C TGT      48
      TTC      86 |       TCC     242 |       TAC      97 |       TGC      53
Leu L TTA       2 |       TCA      25 | *** * TAA       0 | *** * TGA       0
      TTG      30 |       TCG       5 |       TAG       0 | Trp W TGG      46
------------------------------------------------------------------------------
Leu L CTT     105 | Pro P CCT      65 | His H CAT      56 | Arg R CGT      28
      CTC     226 |       CCC     206 |       CAC     100 |       CGC       9
      CTA      71 |       CCA     130 | Gln Q CAA      74 |       CGA      28
      CTG     156 |       CCG      46 |       CAG     211 |       CGG      27
------------------------------------------------------------------------------
Ile I ATT      83 | Thr T ACT     108 | Asn N AAT     189 | Ser S AGT     105
      ATC     137 |       ACC     161 |       AAC     176 |       AGC      98
      ATA      64 |       ACA     184 | Lys K AAA      73 | Arg R AGA      40
Met M ATG      75 |       ACG       8 |       AAG     110 |       AGG      70
------------------------------------------------------------------------------
Val V GTT      31 | Ala A GCT      85 | Asp D GAT      77 | Gly G GGT      54
      GTC     194 |       GCC     261 |       GAC     138 |       GGC     122
      GTA      65 |       GCA     103 | Glu E GAA     135 |       GGA     152
      GTG     180 |       GCG      20 |       GAG     120 |       GGG      83
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14303    C:0.26156    A:0.28588    G:0.30952
position  2:    T:0.26003    C:0.29218    A:0.28401    G:0.16378
position  3:    T:0.21105    C:0.39218    A:0.19490    G:0.20187
Average         T:0.20471    C:0.31531    A:0.25493    G:0.22506

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.00801530  0.01489386  0.00740172  0.00766653
  0.00900608  0.01673490  0.00831665  0.00861419
  0.00875445  0.01626733  0.00000000  0.00000000
  0.00504822  0.00938050  0.00000000  0.00482856
  0.01465819  0.02723753  0.01353608  0.01402036
  0.01647009  0.03060437  0.01520928  0.01575342
  0.01600992  0.02974930  0.01478434  0.01531328
  0.00923207  0.01715484  0.00852534  0.00883035
  0.01602107  0.02977002  0.01479464  0.01532394
  0.01800144  0.03344990  0.01662341  0.01721814
  0.01749849  0.03251533  0.01615896  0.01673707
  0.01009045  0.01874986  0.00931801  0.00965138
  0.01734584  0.03223167  0.01601799  0.01659106
  0.01948996  0.03621583  0.01799798  0.01864189
  0.01894542  0.03520398  0.01749513  0.01812104
  0.01092481  0.02030026  0.01008851  0.01044944


Model 1: NearlyNeutral (2 categories)


TREE #  1:  ((((1, (2, 3)), 4), 5), (((((9, 8), 10), (7, (11, 12))), 6), (15, (14, 13))));   MP score: 302
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 28  np: 31):  -3484.590823      +0.000000
  16..17   17..18   18..19   19..1    19..20   20..2    20..3    18..4    17..5    16..21   21..22   22..23   23..24   24..25   25..9    25..8    24..10   23..26   26..7    26..27   27..11   27..12   22..6    21..28   28..15   28..29   29..14   29..13 
 0.071182 0.037912 0.026373 0.031058 0.013348 0.009359 0.006640 0.035280 0.116650 0.067838 0.042760 0.026949 0.035839 0.002517 0.013388 0.037756 0.000004 0.002775 0.029462 0.027064 0.005258 0.015946 0.080517 0.017673 0.059534 0.074125 0.002638 0.000004 3.593377 0.436702 0.000001

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

tree length =  0.889849

((((1: 0.031058, (2: 0.009359, 3: 0.006640): 0.013348): 0.026373, 4: 0.035280): 0.037912, 5: 0.116650): 0.071182, (((((9: 0.013388, 8: 0.037756): 0.002517, 10: 0.000004): 0.035839, (7: 0.029462, (11: 0.005258, 12: 0.015946): 0.027064): 0.002775): 0.026949, 6: 0.080517): 0.042760, (15: 0.059534, (14: 0.002638, 13: 0.000004): 0.074125): 0.017673): 0.067838);

((((human: 0.031058, (chimpanzee: 0.009359, bonobo: 0.006640): 0.013348): 0.026373, gorilla: 0.035280): 0.037912, orangutan: 0.116650): 0.071182, (((((rhesus: 0.013388, CEmac: 0.037756): 0.002517, PTmac: 0.000004): 0.035839, (baboon: 0.029462, (sootyM: 0.005258, drill: 0.015946): 0.027064): 0.002775): 0.026949, AGM: 0.080517): 0.042760, (colobus: 0.059534, (GSNM: 0.002638, BSNM: 0.000004): 0.074125): 0.017673): 0.067838);

Detailed output identifying parameters

kappa (ts/tv) =  3.59338


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

p:   0.43670  0.56330
w:   0.00000  1.00000

dN & dS for each branch

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

  16..17      0.071    851.0    325.0   0.5633   0.0195   0.0347   16.6   11.3
  17..18      0.038    851.0    325.0   0.5633   0.0104   0.0185    8.9    6.0
  18..19      0.026    851.0    325.0   0.5633   0.0072   0.0129    6.2    4.2
  19..1       0.031    851.0    325.0   0.5633   0.0085   0.0151    7.3    4.9
  19..20      0.013    851.0    325.0   0.5633   0.0037   0.0065    3.1    2.1
  20..2       0.009    851.0    325.0   0.5633   0.0026   0.0046    2.2    1.5
  20..3       0.007    851.0    325.0   0.5633   0.0018   0.0032    1.6    1.1
  18..4       0.035    851.0    325.0   0.5633   0.0097   0.0172    8.2    5.6
  17..5       0.117    851.0    325.0   0.5633   0.0320   0.0568   27.3   18.5
  16..21      0.068    851.0    325.0   0.5633   0.0186   0.0331   15.8   10.7
  21..22      0.043    851.0    325.0   0.5633   0.0117   0.0208   10.0    6.8
  22..23      0.027    851.0    325.0   0.5633   0.0074   0.0131    6.3    4.3
  23..24      0.036    851.0    325.0   0.5633   0.0098   0.0175    8.4    5.7
  24..25      0.003    851.0    325.0   0.5633   0.0007   0.0012    0.6    0.4
  25..9       0.013    851.0    325.0   0.5633   0.0037   0.0065    3.1    2.1
  25..8       0.038    851.0    325.0   0.5633   0.0104   0.0184    8.8    6.0
  24..10      0.000    851.0    325.0   0.5633   0.0000   0.0000    0.0    0.0
  23..26      0.003    851.0    325.0   0.5633   0.0008   0.0014    0.6    0.4
  26..7       0.029    851.0    325.0   0.5633   0.0081   0.0144    6.9    4.7
  26..27      0.027    851.0    325.0   0.5633   0.0074   0.0132    6.3    4.3
  27..11      0.005    851.0    325.0   0.5633   0.0014   0.0026    1.2    0.8
  27..12      0.016    851.0    325.0   0.5633   0.0044   0.0078    3.7    2.5
  22..6       0.081    851.0    325.0   0.5633   0.0221   0.0392   18.8   12.8
  21..28      0.018    851.0    325.0   0.5633   0.0049   0.0086    4.1    2.8
  28..15      0.060    851.0    325.0   0.5633   0.0163   0.0290   13.9    9.4
  28..29      0.074    851.0    325.0   0.5633   0.0203   0.0361   17.3   11.7
  29..14      0.003    851.0    325.0   0.5633   0.0007   0.0013    0.6    0.4
  29..13      0.000    851.0    325.0   0.5633   0.0000   0.0000    0.0    0.0


Time used:  3:12


Model 2: PositiveSelection (3 categories)


TREE #  1:  ((((1, (2, 3)), 4), 5), (((((9, 8), 10), (7, (11, 12))), 6), (15, (14, 13))));   MP score: 302
This is a rooted tree.  Please check!
lnL(ntime: 28  np: 33):  -3445.214786      +0.000000
  16..17   17..18   18..19   19..1    19..20   20..2    20..3    18..4    17..5    16..21   21..22   22..23   23..24   24..25   25..9    25..8    24..10   23..26   26..7    26..27   27..11   27..12   22..6    21..28   28..15   28..29   29..14   29..13 
 0.051104 0.041703 0.028476 0.032888 0.013898 0.009733 0.006985 0.036805 0.128493 0.105121 0.048328 0.030253 0.037166 0.002793 0.013836 0.040183 0.000004 0.002905 0.030120 0.029989 0.005633 0.016701 0.087635 0.016265 0.066204 0.080325 0.002760 0.000004 4.041510 0.351466 0.579373 0.000001 8.084374

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

tree length =  0.966309

((((1: 0.032888, (2: 0.009733, 3: 0.006985): 0.013898): 0.028476, 4: 0.036805): 0.041703, 5: 0.128493): 0.051104, (((((9: 0.013836, 8: 0.040183): 0.002793, 10: 0.000004): 0.037166, (7: 0.030120, (11: 0.005633, 12: 0.016701): 0.029989): 0.002905): 0.030253, 6: 0.087635): 0.048328, (15: 0.066204, (14: 0.002760, 13: 0.000004): 0.080325): 0.016265): 0.105121);

((((human: 0.032888, (chimpanzee: 0.009733, bonobo: 0.006985): 0.013898): 0.028476, gorilla: 0.036805): 0.041703, orangutan: 0.128493): 0.051104, (((((rhesus: 0.013836, CEmac: 0.040183): 0.002793, PTmac: 0.000004): 0.037166, (baboon: 0.030120, (sootyM: 0.005633, drill: 0.016701): 0.029989): 0.002905): 0.030253, AGM: 0.087635): 0.048328, (colobus: 0.066204, (GSNM: 0.002760, BSNM: 0.000004): 0.080325): 0.016265): 0.105121);

Detailed output identifying parameters

kappa (ts/tv) =  4.04151


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

p:   0.35147  0.57937  0.06916
w:   0.00000  1.00000  8.08437

dN & dS for each branch

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

  16..17      0.051    847.1    328.9   1.1385   0.0176   0.0155   14.9    5.1
  17..18      0.042    847.1    328.9   1.1385   0.0144   0.0126   12.2    4.2
  18..19      0.028    847.1    328.9   1.1385   0.0098   0.0086    8.3    2.8
  19..1       0.033    847.1    328.9   1.1385   0.0113   0.0100    9.6    3.3
  19..20      0.014    847.1    328.9   1.1385   0.0048   0.0042    4.1    1.4
  20..2       0.010    847.1    328.9   1.1385   0.0034   0.0030    2.8    1.0
  20..3       0.007    847.1    328.9   1.1385   0.0024   0.0021    2.0    0.7
  18..4       0.037    847.1    328.9   1.1385   0.0127   0.0112   10.8    3.7
  17..5       0.128    847.1    328.9   1.1385   0.0443   0.0389   37.6   12.8
  16..21      0.105    847.1    328.9   1.1385   0.0363   0.0319   30.7   10.5
  21..22      0.048    847.1    328.9   1.1385   0.0167   0.0146   14.1    4.8
  22..23      0.030    847.1    328.9   1.1385   0.0104   0.0092    8.8    3.0
  23..24      0.037    847.1    328.9   1.1385   0.0128   0.0113   10.9    3.7
  24..25      0.003    847.1    328.9   1.1385   0.0010   0.0008    0.8    0.3
  25..9       0.014    847.1    328.9   1.1385   0.0048   0.0042    4.0    1.4
  25..8       0.040    847.1    328.9   1.1385   0.0139   0.0122   11.7    4.0
  24..10      0.000    847.1    328.9   1.1385   0.0000   0.0000    0.0    0.0
  23..26      0.003    847.1    328.9   1.1385   0.0010   0.0009    0.8    0.3
  26..7       0.030    847.1    328.9   1.1385   0.0104   0.0091    8.8    3.0
  26..27      0.030    847.1    328.9   1.1385   0.0103   0.0091    8.8    3.0
  27..11      0.006    847.1    328.9   1.1385   0.0019   0.0017    1.6    0.6
  27..12      0.017    847.1    328.9   1.1385   0.0058   0.0051    4.9    1.7
  22..6       0.088    847.1    328.9   1.1385   0.0302   0.0266   25.6    8.7
  21..28      0.016    847.1    328.9   1.1385   0.0056   0.0049    4.8    1.6
  28..15      0.066    847.1    328.9   1.1385   0.0228   0.0201   19.4    6.6
  28..29      0.080    847.1    328.9   1.1385   0.0277   0.0243   23.5    8.0
  29..14      0.003    847.1    328.9   1.1385   0.0010   0.0008    0.8    0.3
  29..13      0.000    847.1    328.9   1.1385   0.0000   0.0000    0.0    0.0


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 L      0.978*        7.930
    29 F      1.000**       8.084
    32 S      0.676         5.787
    43 S      0.986*        7.983
    44 L      0.919         7.508
    46 V      0.973*        7.892
    47 G      0.997**       8.065
    49 V      0.995**       8.046
    50 I      0.584         5.137
    53 Q      0.972*        7.885
    66 T      0.983*        7.963
    68 Y      0.870         7.162
    92 S      1.000**       8.084
   104 H      0.767         6.434
   121 K      0.993**       8.034
   132 E      0.733         6.191
   135 I      0.938         7.648
   137 S      0.593         5.203
   360 L      0.910         7.449
   388 A      0.803         6.689


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 L      0.980*        7.824 +- 1.730
    29 F      1.000**       7.961 +- 1.448
    32 S      0.706         5.770 +- 3.319
    43 S      0.987*        7.871 +- 1.641
    44 L      0.927         7.445 +- 2.289
    46 V      0.976*        7.789 +- 1.790
    47 G      0.997**       7.945 +- 1.487
    49 V      0.995**       7.927 +- 1.525
    50 I      0.621         5.166 +- 3.466
    53 Q      0.975*        7.781 +- 1.801
    66 T      0.984*        7.852 +- 1.676
    67 I      0.529         4.490 +- 3.477
    68 Y      0.880         7.072 +- 2.623
    87 L      0.501         4.346 +- 3.538
    92 S      1.000**       7.961 +- 1.448
   104 H      0.787         6.420 +- 3.112
   121 K      0.994**       7.917 +- 1.546
   132 E      0.757         6.179 +- 3.205
   135 I      0.944         7.555 +- 2.129
   137 S      0.627         5.159 +- 3.412
   359 P      0.521         4.437 +- 3.487
   360 L      0.919         7.389 +- 2.352
   388 A      0.822         6.667 +- 2.956



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:   0.434  0.277  0.157  0.084  0.038  0.009  0.001  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.022  0.082  0.136  0.253  0.262  0.165  0.080

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 0.000 0.045 0.023
 0.000 0.000 0.000 0.000 0.000 0.000 0.007 0.397 0.016
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.034 0.257 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.033 0.077 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 0.024 0.024 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 0.005 0.016 0.009 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 0.004 0.011 0.004 0.000

sum of density on p0-p1 =   1.000000

Time used:  8:04


Model 7: beta (10 categories)


TREE #  1:  ((((1, (2, 3)), 4), 5), (((((9, 8), 10), (7, (11, 12))), 6), (15, (14, 13))));   MP score: 302
This is a rooted tree.  Please check!
lnL(ntime: 28  np: 31):  -3484.904774      +0.000000
  16..17   17..18   18..19   19..1    19..20   20..2    20..3    18..4    17..5    16..21   21..22   22..23   23..24   24..25   25..9    25..8    24..10   23..26   26..7    26..27   27..11   27..12   22..6    21..28   28..15   28..29   29..14   29..13 
 0.080609 0.038300 0.026616 0.031346 0.013495 0.009453 0.006709 0.035626 0.117573 0.059408 0.043098 0.027204 0.036190 0.002547 0.013519 0.038121 0.000004 0.002810 0.029748 0.027327 0.005318 0.016104 0.081222 0.017911 0.060056 0.074793 0.002665 0.000004 3.619490 0.007363 0.005000

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

tree length =  0.897774

((((1: 0.031346, (2: 0.009453, 3: 0.006709): 0.013495): 0.026616, 4: 0.035626): 0.038300, 5: 0.117573): 0.080609, (((((9: 0.013519, 8: 0.038121): 0.002547, 10: 0.000004): 0.036190, (7: 0.029748, (11: 0.005318, 12: 0.016104): 0.027327): 0.002810): 0.027204, 6: 0.081222): 0.043098, (15: 0.060056, (14: 0.002665, 13: 0.000004): 0.074793): 0.017911): 0.059408);

((((human: 0.031346, (chimpanzee: 0.009453, bonobo: 0.006709): 0.013495): 0.026616, gorilla: 0.035626): 0.038300, orangutan: 0.117573): 0.080609, (((((rhesus: 0.013519, CEmac: 0.038121): 0.002547, PTmac: 0.000004): 0.036190, (baboon: 0.029748, (sootyM: 0.005318, drill: 0.016104): 0.027327): 0.002810): 0.027204, AGM: 0.081222): 0.043098, (colobus: 0.060056, (GSNM: 0.002665, BSNM: 0.000004): 0.074793): 0.017911): 0.059408);

Detailed output identifying parameters

kappa (ts/tv) =  3.61949

Parameters in M7 (beta):
 p =   0.00736  q =   0.00500


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  1.00000  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

  16..17      0.081    850.7    325.3   0.6000   0.0227   0.0378   19.3   12.3
  17..18      0.038    850.7    325.3   0.6000   0.0108   0.0180    9.2    5.8
  18..19      0.027    850.7    325.3   0.6000   0.0075   0.0125    6.4    4.1
  19..1       0.031    850.7    325.3   0.6000   0.0088   0.0147    7.5    4.8
  19..20      0.013    850.7    325.3   0.6000   0.0038   0.0063    3.2    2.1
  20..2       0.009    850.7    325.3   0.6000   0.0027   0.0044    2.3    1.4
  20..3       0.007    850.7    325.3   0.6000   0.0019   0.0031    1.6    1.0
  18..4       0.036    850.7    325.3   0.6000   0.0100   0.0167    8.5    5.4
  17..5       0.118    850.7    325.3   0.6000   0.0331   0.0551   28.2   17.9
  16..21      0.059    850.7    325.3   0.6000   0.0167   0.0279   14.2    9.1
  21..22      0.043    850.7    325.3   0.6000   0.0121   0.0202   10.3    6.6
  22..23      0.027    850.7    325.3   0.6000   0.0077   0.0128    6.5    4.2
  23..24      0.036    850.7    325.3   0.6000   0.0102   0.0170    8.7    5.5
  24..25      0.003    850.7    325.3   0.6000   0.0007   0.0012    0.6    0.4
  25..9       0.014    850.7    325.3   0.6000   0.0038   0.0063    3.2    2.1
  25..8       0.038    850.7    325.3   0.6000   0.0107   0.0179    9.1    5.8
  24..10      0.000    850.7    325.3   0.6000   0.0000   0.0000    0.0    0.0
  23..26      0.003    850.7    325.3   0.6000   0.0008   0.0013    0.7    0.4
  26..7       0.030    850.7    325.3   0.6000   0.0084   0.0140    7.1    4.5
  26..27      0.027    850.7    325.3   0.6000   0.0077   0.0128    6.5    4.2
  27..11      0.005    850.7    325.3   0.6000   0.0015   0.0025    1.3    0.8
  27..12      0.016    850.7    325.3   0.6000   0.0045   0.0076    3.9    2.5
  22..6       0.081    850.7    325.3   0.6000   0.0229   0.0381   19.4   12.4
  21..28      0.018    850.7    325.3   0.6000   0.0050   0.0084    4.3    2.7
  28..15      0.060    850.7    325.3   0.6000   0.0169   0.0282   14.4    9.2
  28..29      0.075    850.7    325.3   0.6000   0.0210   0.0351   17.9   11.4
  29..14      0.003    850.7    325.3   0.6000   0.0008   0.0013    0.6    0.4
  29..13      0.000    850.7    325.3   0.6000   0.0000   0.0000    0.0    0.0


Time used: 25:21


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


TREE #  1:  ((((1, (2, 3)), 4), 5), (((((9, 8), 10), (7, (11, 12))), 6), (15, (14, 13))));   MP score: 302
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 28  np: 33):  -3445.277991      +0.000000
  16..17   17..18   18..19   19..1    19..20   20..2    20..3    18..4    17..5    16..21   21..22   22..23   23..24   24..25   25..9    25..8    24..10   23..26   26..7    26..27   27..11   27..12   22..6    21..28   28..15   28..29   29..14   29..13 
 0.049466 0.041553 0.028406 0.032828 0.013847 0.009712 0.006967 0.036726 0.128273 0.106530 0.048255 0.030189 0.037080 0.002783 0.013808 0.040087 0.000004 0.002890 0.030051 0.029917 0.005616 0.016663 0.087441 0.016152 0.066049 0.080164 0.002753 0.000004 4.029514 0.929999 0.007861 0.005001 7.871171

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

tree length =  0.964214

((((1: 0.032828, (2: 0.009712, 3: 0.006967): 0.013847): 0.028406, 4: 0.036726): 0.041553, 5: 0.128273): 0.049466, (((((9: 0.013808, 8: 0.040087): 0.002783, 10: 0.000004): 0.037080, (7: 0.030051, (11: 0.005616, 12: 0.016663): 0.029917): 0.002890): 0.030189, 6: 0.087441): 0.048255, (15: 0.066049, (14: 0.002753, 13: 0.000004): 0.080164): 0.016152): 0.106530);

((((human: 0.032828, (chimpanzee: 0.009712, bonobo: 0.006967): 0.013847): 0.028406, gorilla: 0.036726): 0.041553, orangutan: 0.128273): 0.049466, (((((rhesus: 0.013808, CEmac: 0.040087): 0.002783, PTmac: 0.000004): 0.037080, (baboon: 0.030051, (sootyM: 0.005616, drill: 0.016663): 0.029917): 0.002890): 0.030189, AGM: 0.087441): 0.048255, (colobus: 0.066049, (GSNM: 0.002753, BSNM: 0.000004): 0.080164): 0.016152): 0.106530);

Detailed output identifying parameters

kappa (ts/tv) =  4.02951

Parameters in M8 (beta&w>1):
  p0 =   0.93000  p =   0.00786 q =   0.00500
 (p1 =   0.07000) w =   7.87117


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

p:   0.09300  0.09300  0.09300  0.09300  0.09300  0.09300  0.09300  0.09300  0.09300  0.09300  0.07000
w:   0.00000  0.00000  0.00000  0.00000  1.00000  1.00000  1.00000  1.00000  1.00000  1.00000  7.87117

dN & dS for each branch

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

  16..17      0.049    847.2    328.8   1.1090   0.0170   0.0153   14.4    5.0
  17..18      0.042    847.2    328.8   1.1090   0.0142   0.0128   12.1    4.2
  18..19      0.028    847.2    328.8   1.1090   0.0097   0.0088    8.2    2.9
  19..1       0.033    847.2    328.8   1.1090   0.0113   0.0101    9.5    3.3
  19..20      0.014    847.2    328.8   1.1090   0.0047   0.0043    4.0    1.4
  20..2       0.010    847.2    328.8   1.1090   0.0033   0.0030    2.8    1.0
  20..3       0.007    847.2    328.8   1.1090   0.0024   0.0022    2.0    0.7
  18..4       0.037    847.2    328.8   1.1090   0.0126   0.0114   10.7    3.7
  17..5       0.128    847.2    328.8   1.1090   0.0440   0.0396   37.2   13.0
  16..21      0.107    847.2    328.8   1.1090   0.0365   0.0329   30.9   10.8
  21..22      0.048    847.2    328.8   1.1090   0.0165   0.0149   14.0    4.9
  22..23      0.030    847.2    328.8   1.1090   0.0103   0.0093    8.8    3.1
  23..24      0.037    847.2    328.8   1.1090   0.0127   0.0115   10.8    3.8
  24..25      0.003    847.2    328.8   1.1090   0.0010   0.0009    0.8    0.3
  25..9       0.014    847.2    328.8   1.1090   0.0047   0.0043    4.0    1.4
  25..8       0.040    847.2    328.8   1.1090   0.0137   0.0124   11.6    4.1
  24..10      0.000    847.2    328.8   1.1090   0.0000   0.0000    0.0    0.0
  23..26      0.003    847.2    328.8   1.1090   0.0010   0.0009    0.8    0.3
  26..7       0.030    847.2    328.8   1.1090   0.0103   0.0093    8.7    3.1
  26..27      0.030    847.2    328.8   1.1090   0.0103   0.0092    8.7    3.0
  27..11      0.006    847.2    328.8   1.1090   0.0019   0.0017    1.6    0.6
  27..12      0.017    847.2    328.8   1.1090   0.0057   0.0051    4.8    1.7
  22..6       0.087    847.2    328.8   1.1090   0.0300   0.0270   25.4    8.9
  21..28      0.016    847.2    328.8   1.1090   0.0055   0.0050    4.7    1.6
  28..15      0.066    847.2    328.8   1.1090   0.0226   0.0204   19.2    6.7
  28..29      0.080    847.2    328.8   1.1090   0.0275   0.0248   23.3    8.1
  29..14      0.003    847.2    328.8   1.1090   0.0009   0.0009    0.8    0.3
  29..13      0.000    847.2    328.8   1.1090   0.0000   0.0000    0.0    0.0


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 L      0.978*        7.717
    29 F      1.000**       7.871
    32 S      0.677         5.649
    43 S      0.985*        7.770
    44 L      0.918         7.308
    46 V      0.972*        7.680
    47 G      0.997**       7.852
    49 V      0.994**       7.832
    50 I      0.589         5.045
    53 Q      0.971*        7.673
    66 T      0.982*        7.749
    68 Y      0.869         6.974
    92 S      1.000**       7.871
   104 H      0.768         6.274
   121 K      0.993**       7.821
   132 E      0.735         6.047
   135 I      0.938         7.443
   137 S      0.597         5.102
   360 L      0.910         7.251
   388 A      0.804         6.523


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

    25 P      0.633         4.074 +- 2.744
    28 L      0.989*        6.563 +- 1.906
    29 F      1.000**       6.631 +- 1.824
    32 S      0.840         5.469 +- 2.550
    42 N      0.639         4.104 +- 2.727
    43 S      0.993**       6.586 +- 1.880
    44 L      0.955*        6.341 +- 2.137
    46 V      0.987*        6.546 +- 1.924
    47 G      0.999**       6.623 +- 1.835
    48 Y      0.576         3.803 +- 2.845
    49 V      0.998**       6.615 +- 1.843
    50 I      0.769         5.003 +- 2.713
    53 Q      0.986*        6.542 +- 1.927
    66 T      0.991**       6.576 +- 1.890
    67 I      0.709         4.584 +- 2.751
    68 Y      0.938         6.187 +- 2.209
    87 L      0.642         4.241 +- 2.894
    92 S      1.000**       6.631 +- 1.824
   102 Q      0.560         3.701 +- 2.829
   104 H      0.862         5.694 +- 2.555
   112 S      0.648         4.164 +- 2.740
   121 K      0.997**       6.611 +- 1.848
   132 E      0.854         5.614 +- 2.554
   133 P      0.547         3.619 +- 2.814
   135 I      0.971*        6.432 +- 2.029
   137 S      0.796         5.128 +- 2.601
   293 V      0.616         3.957 +- 2.717
   359 P      0.689         4.467 +- 2.786
   360 L      0.951*        6.310 +- 2.162
   388 A      0.893         5.900 +- 2.429



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  0.002  0.599  0.399
p :   0.044  0.056  0.122  0.123  0.132  0.137  0.131  0.110  0.084  0.060
q :   0.056  0.122  0.114  0.113  0.111  0.107  0.102  0.097  0.092  0.086
ws:   0.000  0.000  0.004  0.184  0.332  0.104  0.103  0.131  0.096  0.047

Time used: 51:40
