     11   1014

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



Printing out site pattern counts


        11        669  P

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

    1    6    1    1    1    1    1    1    2    1    1    1    1    1    5
    1    1    1    1    1    1    1    1    2    1    2    1    1    1    1
    1    4    1    1    3    1    1    1    2    1    1    1    1    6    1
    1    4    1    1    1    1    1   12    1    1    1    1    1    1    1
    1    1    1    4    1    1    1    1    1    1    2    1    1    1    1
    1    1    1    1    1    5    1    1    1    1    1    1    1    1    2
    1    1    1    1    1    1    1    1    2    1    1    1    1    2    1
    1    1    1    1    1    3    1    1    1    1    1    1    9    1    1
    1    1    1    4    1    1    3    1    1    1    1    1    1    9    1
    1    1    1    2    2    1    3    1    1    1    2    1    1    1    1
    1    1    2    1    5    1    1    1    1    6    1    1    1    1    2
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1   10    1    1    3    1    6    1    1    1    3    1    1    2    1
    1    1    1    1    2    1    1    1    1    2    1    1    1    1    1
    5    1    2    1    1    1    1    3    1    1    1    1    1

CODONML (in paml version 4.9h, March 2018)  CEACAM18seq.fasta
Model: One dN/dS ratio, 
Codon frequency model: F3x4
Site-class models: 
ns =  11  ls = 338

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   1   1   1   1   1   1 | Ser TCT   3   3   3   3   3   3 | Tyr TAT   6   6   6   5   6   8 | Cys TGT   3   3   3   3   4   3
    TTC   7   7   7   7   8   8 |     TCC   8   8   8   7   7   7 |     TAC   8   8   8   9   9   8 |     TGC   4   5   5   4   3   3
Leu TTA   2   2   2   2   2   2 |     TCA   4   4   4   4   3   3 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   2   2   2   1   2   2 |     TCG   1   1   1   1   1   1 |     TAG   0   0   0   0   0   0 | Trp TGG   6   6   6   6   5   5
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   2   2   2   2   3   3 | Pro CCT   7   8   8   7   6   6 | His CAT   2   3   2   2   1   0 | Arg CGT   1   0   1   2   2   2
    CTC   7   7   7   7   5   6 |     CCC   5   4   4   4   5   6 |     CAC   4   5   5   5   5   5 |     CGC   2   1   1   3   2   4
    CTA   1   1   1   1   1   1 |     CCA   3   2   2   2   3   3 | Gln CAA   4   5   5   4   4   5 |     CGA   1   0   0   1   1   1
    CTG  16  16  16  17  16  15 |     CCG   2   4   4   4   4   5 |     CAG   7   7   7   7   6   6 |     CGG   4   4   4   4   5   5
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   4   4   4   5   4   3 | Thr ACT   6   6   6   6   6   7 | Asn AAT   9   8   8   9   8  10 | Ser AGT   6   6   6   6   4   5
    ATC  22  21  22  20  22  21 |     ACC   7   7   6   7   7   8 |     AAC  11  12  12  13  14  13 |     AGC   8   9   9   7   9   7
    ATA   1   2   1   1   1   1 |     ACA   7   6   7   7   8   4 | Lys AAA   1   1   1   1   1   2 | Arg AGA   5   5   5   5   6   4
Met ATG  13  13  12  13  10  10 |     ACG   2   2   2   2   3   2 |     AAG   5   4   4   4   4   4 |     AGG   6   6   6   6   7   7
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   5   4   4   4   4   4 | Ala GCT   5   4   5   4   4   4 | Asp GAT   9   8   8   9   8   7 | Gly GGT   2   3   3   2   3   2
    GTC   8   9   8   9   8   8 |     GCC   6   7   7   7   8   6 |     GAC   8   9   9   8   9   9 |     GGC  11  10  10  11   8  11
    GTA   1   1   1   2   1   2 |     GCA   6   6   6   6   5   7 | Glu GAA   4   4   4   4   4   5 |     GGA   6   6   6   5   6   7
    GTG  15  14  15  14  16  16 |     GCG   0   0   0   0   0   0 |     GAG  12  12  12  12  13  12 |     GGG   4   4   4   4   4   3
--------------------------------------------------------------------------------------------------------------------------------------

----------------------------------------------------------------------------------------------------------------------
Phe TTT   1   1   1   1   1 | Ser TCT   3   3   4   5   4 | Tyr TAT   8   8   8   8   6 | Cys TGT   3   3   5   4   3
    TTC   8   7   5   5   6 |     TCC   6   8   7   7   7 |     TAC   8   8   8   8   9 |     TGC   4   4   3   2   3
Leu TTA   2   2   2   2   2 |     TCA   3   3   4   4   4 | *** TAA   0   0   0   0   0 | *** TGA   0   0   0   0   0
    TTG   2   2   3   3   3 |     TCG   2   1   1   1   0 |     TAG   0   0   0   0   0 | Trp TGG   5   6   6   6   6
----------------------------------------------------------------------------------------------------------------------
Leu CTT   3   3   3   2   3 | Pro CCT   6   6   5   4   5 | His CAT   0   0   1   1   1 | Arg CGT   2   2   1   2   2
    CTC   6   6   9   9   9 |     CCC   6   6   7   7   6 |     CAC   4   4   4   4   4 |     CGC   4   4   1   1   1
    CTA   1   1   1   0   0 |     CCA   4   3   4   5   4 | Gln CAA   5   5   2   2   1 |     CGA   1   1   1   1   1
    CTG  15  15  11  14  13 |     CCG   4   5   3   2   3 |     CAG   6   6   7   8   9 |     CGG   5   4   4   4   4
----------------------------------------------------------------------------------------------------------------------
Ile ATT   3   2   3   4   3 | Thr ACT   7   7   6   6   7 | Asn AAT  10  10  11  10   9 | Ser AGT   5   5   6   6   7
    ATC  22  20  19  20  19 |     ACC   8   8   9  10  10 |     AAC  13  12  11  13  12 |     AGC   7   8   8   7   6
    ATA   1   2   4   5   5 |     ACA   4   4   6   4   5 | Lys AAA   2   2   2   2   2 | Arg AGA   4   4   4   4   5
Met ATG  10  10   9   8   8 |     ACG   2   2   2   2   1 |     AAG   4   4   2   3   4 |     AGG   7   7  10   9   9
----------------------------------------------------------------------------------------------------------------------
Val GTT   4   4   3   4   3 | Ala GCT   4   4   7   6   9 | Asp GAT   7   7   4   4   5 | Gly GGT   2   2   1   1   1
    GTC   7   9  10   8   9 |     GCC   6   6   8   9   7 |     GAC   9   9   9   8   7 |     GGC  11  11  10  10  10
    GTA   2   2   2   3   3 |     GCA   7   7   4   4   4 | Glu GAA   5   5   6   5   7 |     GGA   7   7   6   6   6
    GTG  16  16  15  14  15 |     GCG   0   0   3   3   4 |     GAG  12  12  12  14  13 |     GGG   3   3   5   4   3
----------------------------------------------------------------------------------------------------------------------

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

#1: human          
position  1:    T:0.16272    C:0.20118    A:0.33432    G:0.30178
position  2:    T:0.31657    C:0.21302    A:0.26627    G:0.20414
position  3:    T:0.21006    C:0.37278    A:0.13609    G:0.28107
Average         T:0.22978    C:0.26233    A:0.24556    G:0.26233

#2: chimpanzee     
position  1:    T:0.16568    C:0.20414    A:0.33136    G:0.29882
position  2:    T:0.31361    C:0.21302    A:0.27219    G:0.20118
position  3:    T:0.20414    C:0.38166    A:0.13314    G:0.28107
Average         T:0.22781    C:0.26627    A:0.24556    G:0.26036

#3: bonobo         
position  1:    T:0.16568    C:0.20414    A:0.32840    G:0.30178
position  2:    T:0.31065    C:0.21598    A:0.26923    G:0.20414
position  3:    T:0.20710    C:0.37870    A:0.13314    G:0.28107
Average         T:0.22781    C:0.26627    A:0.24359    G:0.26233

#4: gorilla        
position  1:    T:0.15680    C:0.21302    A:0.33136    G:0.29882
position  2:    T:0.31361    C:0.21006    A:0.27219    G:0.20414
position  3:    T:0.20710    C:0.37870    A:0.13314    G:0.28107
Average         T:0.22584    C:0.26726    A:0.24556    G:0.26134

#5: orangutan      
position  1:    T:0.15976    C:0.20414    A:0.33728    G:0.29882
position  2:    T:0.30769    C:0.21598    A:0.27219    G:0.20414
position  3:    T:0.19822    C:0.38166    A:0.13609    G:0.28402
Average         T:0.22189    C:0.26726    A:0.24852    G:0.26233

#6: rhesus         
position  1:    T:0.15976    C:0.21598    A:0.31953    G:0.30473
position  2:    T:0.30473    C:0.21302    A:0.27811    G:0.20414
position  3:    T:0.20118    C:0.38462    A:0.13905    G:0.27515
Average         T:0.22189    C:0.27120    A:0.24556    G:0.26134

#7: CEmac          
position  1:    T:0.16272    C:0.21302    A:0.32249    G:0.30178
position  2:    T:0.30473    C:0.21302    A:0.27515    G:0.20710
position  3:    T:0.20118    C:0.38166    A:0.14201    G:0.27515
Average         T:0.22288    C:0.26923    A:0.24655    G:0.26134

#8: PTmac          
position  1:    T:0.16568    C:0.21006    A:0.31657    G:0.30769
position  2:    T:0.30178    C:0.21598    A:0.27219    G:0.21006
position  3:    T:0.19822    C:0.38462    A:0.14201    G:0.27515
Average         T:0.22189    C:0.27022    A:0.24359    G:0.26430

#9: capuchin       
position  1:    T:0.16864    C:0.18935    A:0.33136    G:0.31065
position  2:    T:0.29586    C:0.23669    A:0.25740    G:0.21006
position  3:    T:0.20414    C:0.37870    A:0.14201    G:0.27515
Average         T:0.22288    C:0.26824    A:0.24359    G:0.26529

#10: nightM         
position  1:    T:0.16568    C:0.19527    A:0.33432    G:0.30473
position  2:    T:0.30178    C:0.23373    A:0.26627    G:0.19822
position  3:    T:0.20118    C:0.37870    A:0.13905    G:0.28107
Average         T:0.22288    C:0.26923    A:0.24655    G:0.26134

#11: marmoset       
position  1:    T:0.15976    C:0.19527    A:0.33136    G:0.31361
position  2:    T:0.30178    C:0.23669    A:0.26331    G:0.19822
position  3:    T:0.20414    C:0.36982    A:0.14497    G:0.28107
Average         T:0.22189    C:0.26726    A:0.24655    G:0.26430

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      11 | Ser S TCT      37 | Tyr Y TAT      75 | Cys C TGT      37
      TTC      75 |       TCC      80 |       TAC      91 |       TGC      40
Leu L TTA      22 |       TCA      40 | *** * TAA       0 | *** * TGA       0
      TTG      24 |       TCG      11 |       TAG       0 | Trp W TGG      63
------------------------------------------------------------------------------
Leu L CTT      28 | Pro P CCT      68 | His H CAT      13 | Arg R CGT      17
      CTC      78 |       CCC      60 |       CAC      49 |       CGC      24
      CTA       9 |       CCA      35 | Gln Q CAA      42 |       CGA       9
      CTG     164 |       CCG      40 |       CAG      76 |       CGG      47
------------------------------------------------------------------------------
Ile I ATT      39 | Thr T ACT      70 | Asn N AAT     102 | Ser S AGT      62
      ATC     228 |       ACC      87 |       AAC     136 |       AGC      85
      ATA      24 |       ACA      62 | Lys K AAA      17 | Arg R AGA      51
Met M ATG     116 |       ACG      22 |       AAG      42 |       AGG      80
------------------------------------------------------------------------------
Val V GTT      43 | Ala A GCT      56 | Asp D GAT      76 | Gly G GGT      22
      GTC      93 |       GCC      77 |       GAC      94 |       GGC     113
      GTA      20 |       GCA      62 | Glu E GAA      53 |       GGA      68
      GTG     166 |       GCG      10 |       GAG     136 |       GGG      41
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16299    C:0.20414    A:0.32894    G:0.30393
position  2:    T:0.30662    C:0.21974    A:0.26950    G:0.20414
position  3:    T:0.20334    C:0.37924    A:0.13825    G:0.27918
Average         T:0.22431    C:0.26771    A:0.24556    G:0.26242

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.01040035  0.01939748  0.00707114  0.01427985
  0.00745359  0.01390153  0.00506765  0.01023389
  0.00914136  0.01704937  0.00000000  0.00000000
  0.00692445  0.01291464  0.00000000  0.00950737
  0.01302618  0.02429487  0.00885643  0.01788516
  0.00933543  0.01741132  0.00634711  0.01281770
  0.01144933  0.02135391  0.00778433  0.01572011
  0.00867270  0.01617527  0.00589652  0.01190775
  0.02098949  0.03914706  0.01427063  0.02881890
  0.01504247  0.02805540  0.01022729  0.02065355
  0.01844866  0.03440821  0.01254313  0.02533030
  0.01397458  0.02606370  0.00950124  0.01918732
  0.01939340  0.03617022  0.01318546  0.02662744
  0.01389860  0.02592199  0.00944958  0.01908300
  0.01704577  0.03179172  0.01158932  0.02340412
  0.01291192  0.02408175  0.00877874  0.01772827


Model 1: NearlyNeutral (2 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), ((6, 7), 8)), (9, (11, 10)));   MP score: 254
This is a rooted tree.  Please check!
lnL(ntime: 20  np: 23):  -2834.685760      +0.000000
  12..13   13..14   14..15   15..16   16..1    16..17   17..2    17..3    15..4    14..5    13..18   18..19   19..6    19..7    18..8    12..20   20..9    20..21   21..11   21..10 
 0.206902 0.023612 0.042376 0.003474 0.031872 0.016757 0.009854 0.008470 0.029710 0.056955 0.126264 0.002901 0.006114 0.009180 0.012438 0.164163 0.067853 0.005598 0.076860 0.038512 3.975683 0.653098 0.220768

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

tree length =  0.939865

(((((1: 0.031872, (2: 0.009854, 3: 0.008470): 0.016757): 0.003474, 4: 0.029710): 0.042376, 5: 0.056955): 0.023612, ((6: 0.006114, 7: 0.009180): 0.002901, 8: 0.012438): 0.126264): 0.206902, (9: 0.067853, (11: 0.076860, 10: 0.038512): 0.005598): 0.164163);

(((((human: 0.031872, (chimpanzee: 0.009854, bonobo: 0.008470): 0.016757): 0.003474, gorilla: 0.029710): 0.042376, orangutan: 0.056955): 0.023612, ((rhesus: 0.006114, CEmac: 0.009180): 0.002901, PTmac: 0.012438): 0.126264): 0.206902, (capuchin: 0.067853, (marmoset: 0.076860, nightM: 0.038512): 0.005598): 0.164163);

Detailed output identifying parameters

kappa (ts/tv) =  3.97568


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

p:   0.65310  0.34690
w:   0.22077  1.00000

dN & dS for each branch

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

  12..13      0.207    756.2    257.8   0.4911   0.0546   0.1112   41.3   28.7
  13..14      0.024    756.2    257.8   0.4911   0.0062   0.0127    4.7    3.3
  14..15      0.042    756.2    257.8   0.4911   0.0112   0.0228    8.5    5.9
  15..16      0.003    756.2    257.8   0.4911   0.0009   0.0019    0.7    0.5
  16..1       0.032    756.2    257.8   0.4911   0.0084   0.0171    6.4    4.4
  16..17      0.017    756.2    257.8   0.4911   0.0044   0.0090    3.3    2.3
  17..2       0.010    756.2    257.8   0.4911   0.0026   0.0053    2.0    1.4
  17..3       0.008    756.2    257.8   0.4911   0.0022   0.0046    1.7    1.2
  15..4       0.030    756.2    257.8   0.4911   0.0078   0.0160    5.9    4.1
  14..5       0.057    756.2    257.8   0.4911   0.0150   0.0306   11.4    7.9
  13..18      0.126    756.2    257.8   0.4911   0.0333   0.0678   25.2   17.5
  18..19      0.003    756.2    257.8   0.4911   0.0008   0.0016    0.6    0.4
  19..6       0.006    756.2    257.8   0.4911   0.0016   0.0033    1.2    0.8
  19..7       0.009    756.2    257.8   0.4911   0.0024   0.0049    1.8    1.3
  18..8       0.012    756.2    257.8   0.4911   0.0033   0.0067    2.5    1.7
  12..20      0.164    756.2    257.8   0.4911   0.0433   0.0882   32.7   22.7
  20..9       0.068    756.2    257.8   0.4911   0.0179   0.0365   13.5    9.4
  20..21      0.006    756.2    257.8   0.4911   0.0015   0.0030    1.1    0.8
  21..11      0.077    756.2    257.8   0.4911   0.0203   0.0413   15.3   10.6
  21..10      0.039    756.2    257.8   0.4911   0.0102   0.0207    7.7    5.3


Time used:  1:05


Model 2: PositiveSelection (3 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), ((6, 7), 8)), (9, (11, 10)));   MP score: 254
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 20  np: 25):  -2832.579077      +0.000000
  12..13   13..14   14..15   15..16   16..1    16..17   17..2    17..3    15..4    14..5    13..18   18..19   19..6    19..7    18..8    12..20   20..9    20..21   21..11   21..10 
 0.223318 0.026261 0.043721 0.003316 0.032465 0.017097 0.009931 0.008686 0.030266 0.057834 0.127320 0.002988 0.006197 0.009328 0.012604 0.159956 0.068924 0.005894 0.078594 0.038871 4.070188 0.912909 0.000001 0.365179 2.509524

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

tree length =  0.963572

(((((1: 0.032465, (2: 0.009931, 3: 0.008686): 0.017097): 0.003316, 4: 0.030266): 0.043721, 5: 0.057834): 0.026261, ((6: 0.006197, 7: 0.009328): 0.002988, 8: 0.012604): 0.127320): 0.223318, (9: 0.068924, (11: 0.078594, 10: 0.038871): 0.005894): 0.159956);

(((((human: 0.032465, (chimpanzee: 0.009931, bonobo: 0.008686): 0.017097): 0.003316, gorilla: 0.030266): 0.043721, orangutan: 0.057834): 0.026261, ((rhesus: 0.006197, CEmac: 0.009328): 0.002988, PTmac: 0.012604): 0.127320): 0.223318, (capuchin: 0.068924, (marmoset: 0.078594, nightM: 0.038871): 0.005894): 0.159956);

Detailed output identifying parameters

kappa (ts/tv) =  4.07019


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

p:   0.91291  0.00000  0.08709
w:   0.36518  1.00000  2.50952

dN & dS for each branch

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

  12..13      0.223    755.5    258.5   0.5519   0.0617   0.1117   46.6   28.9
  13..14      0.026    755.5    258.5   0.5519   0.0073   0.0131    5.5    3.4
  14..15      0.044    755.5    258.5   0.5519   0.0121   0.0219    9.1    5.7
  15..16      0.003    755.5    258.5   0.5519   0.0009   0.0017    0.7    0.4
  16..1       0.032    755.5    258.5   0.5519   0.0090   0.0162    6.8    4.2
  16..17      0.017    755.5    258.5   0.5519   0.0047   0.0086    3.6    2.2
  17..2       0.010    755.5    258.5   0.5519   0.0027   0.0050    2.1    1.3
  17..3       0.009    755.5    258.5   0.5519   0.0024   0.0043    1.8    1.1
  15..4       0.030    755.5    258.5   0.5519   0.0084   0.0151    6.3    3.9
  14..5       0.058    755.5    258.5   0.5519   0.0160   0.0289   12.1    7.5
  13..18      0.127    755.5    258.5   0.5519   0.0352   0.0637   26.6   16.5
  18..19      0.003    755.5    258.5   0.5519   0.0008   0.0015    0.6    0.4
  19..6       0.006    755.5    258.5   0.5519   0.0017   0.0031    1.3    0.8
  19..7       0.009    755.5    258.5   0.5519   0.0026   0.0047    1.9    1.2
  18..8       0.013    755.5    258.5   0.5519   0.0035   0.0063    2.6    1.6
  12..20      0.160    755.5    258.5   0.5519   0.0442   0.0800   33.4   20.7
  20..9       0.069    755.5    258.5   0.5519   0.0190   0.0345   14.4    8.9
  20..21      0.006    755.5    258.5   0.5519   0.0016   0.0029    1.2    0.8
  21..11      0.079    755.5    258.5   0.5519   0.0217   0.0393   16.4   10.2
  21..10      0.039    755.5    258.5   0.5519   0.0107   0.0195    8.1    5.0


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

    14 R      0.763         2.002
    51 Q      0.788         2.054
   142 V      0.548         1.541
   151 T      0.612         1.679
   156 G      0.688         1.841
   167 Y      0.918         2.333
   174 M      0.821         2.126
   187 R      0.971*        2.448
   213 T      0.728         1.926
   261 R      0.560         1.566
   276 M      0.997**       2.503
   283 P      0.630         1.716
   284 H      0.637         1.732
   295 V      0.588         1.626
   301 G      0.575         1.599
   313 L      0.505         1.447
   334 T      0.592         1.636


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

    14 R      0.529         2.048 +- 1.552
    51 Q      0.514         1.980 +- 1.479
   167 Y      0.690         2.512 +- 1.564
   174 M      0.504         1.940 +- 1.416
   187 R      0.759         2.671 +- 1.505
   276 M      0.899         3.027 +- 1.433



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:   0.003  0.078  0.411  0.442  0.066  0.000  0.000  0.000  0.000  0.000
w2:   0.203  0.297  0.267  0.143  0.058  0.020  0.007  0.002  0.001  0.000

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

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.028
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.015 0.106
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.012 0.055 0.177
 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 0.014 0.031 0.096 0.160
 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 0.019 0.029 0.039 0.121 0.080

sum of density on p0-p1 =   1.000000

Time used:  4:01


Model 7: beta (10 categories)


TREE #  1:  (((((1, (2, 3)), 4), 5), ((6, 7), 8)), (9, (11, 10)));   MP score: 254
This is a rooted tree.  Please check!
lnL(ntime: 20  np: 23):  -2835.537951      +0.000000
  12..13   13..14   14..15   15..16   16..1    16..17   17..2    17..3    15..4    14..5    13..18   18..19   19..6    19..7    18..8    12..20   20..9    20..21   21..11   21..10 
 0.193248 0.023027 0.042054 0.003496 0.031763 0.016697 0.009839 0.008428 0.029606 0.056872 0.126247 0.002881 0.006095 0.009153 0.012405 0.175804 0.067699 0.005522 0.076587 0.038465 3.985549 0.499773 0.499201

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

tree length =  0.935890

(((((1: 0.031763, (2: 0.009839, 3: 0.008428): 0.016697): 0.003496, 4: 0.029606): 0.042054, 5: 0.056872): 0.023027, ((6: 0.006095, 7: 0.009153): 0.002881, 8: 0.012405): 0.126247): 0.193248, (9: 0.067699, (11: 0.076587, 10: 0.038465): 0.005522): 0.175804);

(((((human: 0.031763, (chimpanzee: 0.009839, bonobo: 0.008428): 0.016697): 0.003496, gorilla: 0.029606): 0.042054, orangutan: 0.056872): 0.023027, ((rhesus: 0.006095, CEmac: 0.009153): 0.002881, PTmac: 0.012405): 0.126247): 0.193248, (capuchin: 0.067699, (marmoset: 0.076587, nightM: 0.038465): 0.005522): 0.175804);

Detailed output identifying parameters

kappa (ts/tv) =  3.98555

Parameters in M7 (beta):
 p =   0.49977  q =   0.49920


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:   0.00615  0.05453  0.14659  0.27330  0.42224  0.57879  0.72758  0.85402  0.94577  0.99390

dN & dS for each branch

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

  12..13      0.193    756.1    257.9   0.5003   0.0514   0.1027   38.8   26.5
  13..14      0.023    756.1    257.9   0.5003   0.0061   0.0122    4.6    3.2
  14..15      0.042    756.1    257.9   0.5003   0.0112   0.0223    8.5    5.8
  15..16      0.003    756.1    257.9   0.5003   0.0009   0.0019    0.7    0.5
  16..1       0.032    756.1    257.9   0.5003   0.0084   0.0169    6.4    4.4
  16..17      0.017    756.1    257.9   0.5003   0.0044   0.0089    3.4    2.3
  17..2       0.010    756.1    257.9   0.5003   0.0026   0.0052    2.0    1.3
  17..3       0.008    756.1    257.9   0.5003   0.0022   0.0045    1.7    1.2
  15..4       0.030    756.1    257.9   0.5003   0.0079   0.0157    6.0    4.1
  14..5       0.057    756.1    257.9   0.5003   0.0151   0.0302   11.4    7.8
  13..18      0.126    756.1    257.9   0.5003   0.0336   0.0671   25.4   17.3
  18..19      0.003    756.1    257.9   0.5003   0.0008   0.0015    0.6    0.4
  19..6       0.006    756.1    257.9   0.5003   0.0016   0.0032    1.2    0.8
  19..7       0.009    756.1    257.9   0.5003   0.0024   0.0049    1.8    1.3
  18..8       0.012    756.1    257.9   0.5003   0.0033   0.0066    2.5    1.7
  12..20      0.176    756.1    257.9   0.5003   0.0467   0.0934   35.3   24.1
  20..9       0.068    756.1    257.9   0.5003   0.0180   0.0360   13.6    9.3
  20..21      0.006    756.1    257.9   0.5003   0.0015   0.0029    1.1    0.8
  21..11      0.077    756.1    257.9   0.5003   0.0204   0.0407   15.4   10.5
  21..10      0.038    756.1    257.9   0.5003   0.0102   0.0204    7.7    5.3


Time used:  8:53


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


TREE #  1:  (((((1, (2, 3)), 4), 5), ((6, 7), 8)), (9, (11, 10)));   MP score: 254
This is a rooted tree.  Please check!
lnL(ntime: 20  np: 25):  -2832.579113      +0.000000
  12..13   13..14   14..15   15..16   16..1    16..17   17..2    17..3    15..4    14..5    13..18   18..19   19..6    19..7    18..8    12..20   20..9    20..21   21..11   21..10 
 0.204977 0.026248 0.043709 0.003317 0.032463 0.017096 0.009932 0.008685 0.030265 0.057841 0.127333 0.002988 0.006197 0.009328 0.012604 0.178289 0.068925 0.005892 0.078593 0.038870 4.070140 0.914283 57.278555 98.786303 2.524735

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

tree length =  0.963550

(((((1: 0.032463, (2: 0.009932, 3: 0.008685): 0.017096): 0.003317, 4: 0.030265): 0.043709, 5: 0.057841): 0.026248, ((6: 0.006197, 7: 0.009328): 0.002988, 8: 0.012604): 0.127333): 0.204977, (9: 0.068925, (11: 0.078593, 10: 0.038870): 0.005892): 0.178289);

(((((human: 0.032463, (chimpanzee: 0.009932, bonobo: 0.008685): 0.017096): 0.003317, gorilla: 0.030265): 0.043709, orangutan: 0.057841): 0.026248, ((rhesus: 0.006197, CEmac: 0.009328): 0.002988, PTmac: 0.012604): 0.127333): 0.204977, (capuchin: 0.068925, (marmoset: 0.078593, nightM: 0.038870): 0.005892): 0.178289);

Detailed output identifying parameters

kappa (ts/tv) =  4.07014

Parameters in M8 (beta&w>1):
  p0 =   0.91428  p =  57.27855 q =  98.78630
 (p1 =   0.08572) w =   2.52473


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

p:   0.09143  0.09143  0.09143  0.09143  0.09143  0.09143  0.09143  0.09143  0.09143  0.09143  0.08572
w:   0.30472  0.32709  0.34067  0.35165  0.36160  0.37131  0.38141  0.39275  0.40703  0.43126  2.52473

dN & dS for each branch

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

  12..13      0.205    755.5    258.5   0.5519   0.0566   0.1026   42.8   26.5
  13..14      0.026    755.5    258.5   0.5519   0.0072   0.0131    5.5    3.4
  14..15      0.044    755.5    258.5   0.5519   0.0121   0.0219    9.1    5.7
  15..16      0.003    755.5    258.5   0.5519   0.0009   0.0017    0.7    0.4
  16..1       0.032    755.5    258.5   0.5519   0.0090   0.0162    6.8    4.2
  16..17      0.017    755.5    258.5   0.5519   0.0047   0.0086    3.6    2.2
  17..2       0.010    755.5    258.5   0.5519   0.0027   0.0050    2.1    1.3
  17..3       0.009    755.5    258.5   0.5519   0.0024   0.0043    1.8    1.1
  15..4       0.030    755.5    258.5   0.5519   0.0084   0.0151    6.3    3.9
  14..5       0.058    755.5    258.5   0.5519   0.0160   0.0289   12.1    7.5
  13..18      0.127    755.5    258.5   0.5519   0.0352   0.0637   26.6   16.5
  18..19      0.003    755.5    258.5   0.5519   0.0008   0.0015    0.6    0.4
  19..6       0.006    755.5    258.5   0.5519   0.0017   0.0031    1.3    0.8
  19..7       0.009    755.5    258.5   0.5519   0.0026   0.0047    1.9    1.2
  18..8       0.013    755.5    258.5   0.5519   0.0035   0.0063    2.6    1.6
  12..20      0.178    755.5    258.5   0.5519   0.0492   0.0892   37.2   23.1
  20..9       0.069    755.5    258.5   0.5519   0.0190   0.0345   14.4    8.9
  20..21      0.006    755.5    258.5   0.5519   0.0016   0.0029    1.2    0.8
  21..11      0.079    755.5    258.5   0.5519   0.0217   0.0393   16.4   10.2
  21..10      0.039    755.5    258.5   0.5519   0.0107   0.0195    8.1    5.0


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

    14 R      0.758         2.005
    51 Q      0.782         2.056
   142 V      0.541         1.538
   151 T      0.606         1.677
   156 G      0.681         1.838
   167 Y      0.914         2.341
   174 M      0.814         2.126
   187 R      0.969*        2.459
   213 T      0.722         1.927
   261 R      0.553         1.563
   276 M      0.996**       2.517
   283 P      0.623         1.714
   284 H      0.631         1.731
   295 V      0.581         1.624
   301 G      0.568         1.596
   334 T      0.586         1.633


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

    14 R      0.545         2.014 +- 1.458
    51 Q      0.535         1.969 +- 1.423
   167 Y      0.717         2.451 +- 1.412
   174 M      0.524         1.929 +- 1.389
   187 R      0.805         2.643 +- 1.327
   276 M      0.935         2.930 +- 1.166



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  0.016  0.102  0.882
p :   0.004  0.018  0.058  0.117  0.177  0.217  0.203  0.130  0.058  0.019
q :   0.004  0.011  0.022  0.048  0.076  0.106  0.138  0.169  0.200  0.226
ws:   0.171  0.341  0.327  0.122  0.030  0.006  0.001  0.000  0.000  0.000

Time used: 21:52
