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jergosh/PAML_output

Created January 5, 2015 11:26
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PAML_output
seed used = 1386212133
4 1644
GLN_GLV_PISO0N06151G --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG GAG AAA GGC CCT TCA TCA CTT CAG GGT AAG AAA TAC CCT GCT AAG AAC CAT GCC CGC AGC GTA TAT AGG CAC TTT AAA GAC AAA AAG AAT CTG GTA CTG GAC GAA ACC GTT GCA TTT TTT GTT AGC GGT GAG GCA TTG GAA CTA TAT CAG TAC TGT GAT CAG ACG AAG CCC TTG CGA CAA AAT AGA TAC TTT TTT TAT TTA AGT GGA GTC GCT ATT CCT GGC TCA CAC GTT CTT TAT GAA CCT CTG AAG GAT AAG CTA ACG CTT TTC TTA CCT GAT GTT GAT GAG GAC GAT ATT ATG TGG TCG GGT CTT CCC CTC AGC GCT AAG GAG GCC GCC GCA AAA TAT GAC ATT GAC CAT GTC CTT TAT GCC TCA GAT ATT CCC CAG ACA TTA GAG GCT GTG AAT ACT AAG GCG AAA GTC TAC ACC ACC GAT GTG AAC AAA TTC AAT TCC AAT TAT GCT AAG TAT --- CTT GTT GAA GGT GAT GCT GAC TTT TTC TAT GCA TTG GAT GAA TCT CGT TTA TGT AAG GAC TCT TAC GAA ATC GAG CTC ATG CGC CAC GCT GCT CGT ATC ACG GAT AAC TGT CAC TTG GCA GTA ATG TCT GCC ACA CCT ATT GAG ACC AAC GAG ACA CAC ATA CAT GCA GAG TTC ATG TAT CAT GCC TTG AGA CAA GGC TCC AAA AAC CAG TCT TAT GAC CCC ATA TGC TGC AGC GGA CCC AAC TGC TCC ACT TTA CAC TAC GTC AAA AAT GAC GAT TCC ATC GAC CCA AGT AGG AGA TCC GTA TTA ATC GAT GCT GGT GCT GAA TGG GAG TGT TAT GCG AGT GAC GTG ACA AGA TGC TTC CCA ATT AAC GGT GAC TGG TCT AAA GAA CAT AGA GAA ATT TAT GAC ATC GTA TTG CGC ATG CAG CTG GAC ACC ATG GCT CTT ATC AAG CCA GGT GTA CTC TGG GAC GAC GTC CAT ATT CAT GCC CAC AAG GTA CTC ATT GAG AAT TTC TTG AGG CTT GGA ATC TTC AAA AAA GAG TAC CTG GCA GAG GAG ATA TTC GAA TCC AAA ATC AGT TCT GGC TTT TTC CCA CAC GGC TTA GGC CAT CTA CTT GGA ATG GAC ACG CAT GAT GTC GGG GGG AGA CCC AAC TAT GAC GAT CCT AAT CCT CTT CTT CGC TAC TTA AGA TTG AGG AGA CAT TTG CAG GTA GGA ATG GTA CTC ACC GAC GAG CCA GGC GTT TAT TTC TCA CCC TTT TTG TTG AAA GAA ATT TTA GAA GAC TCA TCG AAG TCA AAG TAC --- --- --- --- --- --- ATA GAC AGA GAT GTG TTG GAC AAA TAC TGG TAT ATC GGA GGT GTG AGA ATA GAA GAT GAT CTT GTT ATA ACA GAC TCT GGA TTT GAG AAC CTT ACT AAG ATC ACC TCT GAC CCA GAA GAA ATA TCA AAA ATC GTC AAG AAG GGT CTT TCT AAG GGA AAG TAT GGT TTT AAT GCT GGA CTT CAT GAT TAC CAG TAT
KPOL_1056_46 ATG GGA TTC CAT ATT ATA ACT GCT ATT GTT GTC ACC TCA TTG GTT TCG TTT GTT GCT TTG AAG AAG AGG AGT AGA AGA GTC GAG --- ATA GAT ATC AAT CAA GGA GAG AAG CAA CAG GAA CAA GAT CAG GAA AAA TTA TTC GTC GAA ATG AAC CAA AAG GAT AGC AAA AAG ATT TCA GAT CAA AAT TAC GTA CCT GGG ATA ATC AAA GGT AAG AAA TAC CCA GCT AAG AAT CAC AAC ATC AGG GTC AAG GAT ATT CTA TTG TCT AAA AAA GAT AAT TTA AAG GTT ACT GAA ACT GCT ATA TTA ATT GCA GGT GCA GAA CGT GAA CCT GTT AAA TAT TGT GAT CGT ACT AAA AAG TTT AGA CAG AAC CAA TAC TTT TAT TAT TTA ACT GGT GTT GAT ATT CCG GGA AGT GCA TTA TTA TTT AAC TTC AAA GAT GAT AAG TTA ACA CTG TTC TTG CCA AAT ATT GAT TAT GAC GAT ATC ATG TGG AGC GGT AAG CCA ATG AGC TTA GAA GAA GCT TTA AAA GAA TAT GAT GTA GAT GAA GTT TTA TAC TAT GAT GAT TTG AAA ATG AAA TTA GAC CAA --- TTG AAG GAT TTT ACT ATT TTT ACT ACC GAT AAT GAT AAT GTT CAT GAT GAT TCA ATT AAA GCT AGA TTG ACT CCC TCA GAC AGT GAT TTC TTT TTT GCT CTT GAT GAG GCT AGA GTC ATT AAA GAT TGG TAT GAA ATT GAA ATA ATA AGA AGA GCT TGT GAA ATC AGT GAT AAT TCG CAT TAC GCT GTT ATG TCA GCT TTA CCG ATT GAA ACT AAT GAA ATG CAC ATC GAA GCT GAA TTC AGT TAC CAT TCT ACC AGA CAA GGT GCT CGT ACT TTA GGT TAC GAC CCT GTT TGT TGC TCT GGC CCA GCT TGT GGA ACA TTA CAT TAC ATC ACC AAT GAT GAT GAT GTG GAT --- GGT AAG AGC TCT ATA TTG ATT GAT GCA GGC GCC GAA TGG AGA GGT TAT ACC AGT GAT GTA ACA AGA TGT TTC CCA ACT AGT GGT AAG TTT ACC AAG GAA CAT CGT GAA GTT TAC GAA ACC GTT CTG GAC ATG CAA ACA CAG GCA ATG AAT TGT ATC AAG CCA GGT TCT TCA TGG GAC GAT TTA CAT CTA TTG GCC CAC AAA GTT TTG ATT AAG CAT TTC TTG AAA TTG GGT ATC TTT AGA AAA GAA TTC TCT GAA GAT GAG ATT TTG AAA AGA AGA GTT TCC TGC GCT TTC TAC CCT CAT GGT TTG GGT CAT TTC ATA GGT ATT GAC GTT CAT GAT GTG GCC GGG AAT GCT AAC TAC GAA GAT CCA GAT CCA ATG TTC AGA TAC TTG AGA ATC CGT CGT ATA TTA AAA GAA GGT ATG GTG GTC ACT AAT GAA CCA GGT TGT TAC TTT AAC GAA TAC TTG TTG GAT GAA TTC TTG AGA --- --- --- --- --- AAA CAT CCT GAG AAA TTA GAA GTT GTT GAT GAG GCA ATT TTG GCC AAG TAC ATG TAT GTT GGT GGT GTT CGT ATT GAA GAT GAT GTT GTA GTT ACA AAA CAT GGT CAC GAA AAT TTA ACT AAA ATT ACC AGT GAT CCT GAT GAA ATT GAA AAG ATT GTT AGT GAT GGT TTA TCA AAG GGC CGT TCT CAC TTC CAT GTA GTT GTT --- --- --- --- ---
TBLA0C00520 ATG --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- TCT AAG AAA CTA GCT GAC GTT AAA GAG ATT CCA GCC TCA ATC TTG GGT AAA AAA TAC CCT GCT AAG GAA CAT AAT CTT AGA GTT AAA AAT CTG TTG TTA AAG ACT AAT ACT GAA TTA TCT TCA GAT ACT ACA GCT CTT TTT ATA ACC GGC GAA AGA ATA GAG CCT TTG AAA TAC TGT GAT GAA CAC AAG AAA TTT AGA CAA AAT AGA TAT TTT TAT TAT TTA TCG GGT GTA AAT ATT CCA AGA GCT TCT ATC TTA TAT GAT TTT AAG ACT GAA AAT TTA ACT CTA TTC TTA CCA AAT ATC GAT TGG GAT GAT GTT ATT TGG AGT GGT ATG CCA CAG AGT ATC GAA AAT GCT CAA AAA GAA TAC AAT GTC GAT GAA GTT GTC TAT TCT GAC AAG ATT ATC GAC AAA ATA AAC AAT --- TTA AAA GGT TAT AAG ATT TTC ACC ACT GAT CTG GAT GAA GTA ATT --- GAG CCA ATT AAA AAT CAA TTA ATC CCA TCA AAT AAA GAT TTT TTT TAT GCC ATG GAT GAA AGT AGA TTA ATC AAA GAT TGG TAT GAA ATT GAA ATT TTA AGG AAA GCT GCT GAA ATT ACT GAC AAT TCT CAT TTA GGT GTT ATG TCA GCT TTA CCA ATT GAA TTG AAT GAA TTG CAA ATT GAA GCT GAG TTT GCC TAT CAT GCT AAA CGT CAA GGT GCT CAC TCT ATG GGA TAC GAT CCA GTT TGT TGT GCC GGA CCA GCT TGT GGT ACT TTA CAT TAT GTT GAT AAT ACT AAA AAA ATT GAA --- AAT AAA GCT TCA ATC TTA ATC GAT GCT GGT GCT GAA TGG AGA AAC TAT ACT ACT GAT GTA ACG AGA TGT TTT CCA ACA TCG GGC AAG TTT ACT AAA GAA CAT CGT GAA ATT TAT GAA ACA GTG TTA GAC ATG CAA TCA CAA GCT ATG GAA AAG ATT AAA CCA GGT GCA TCT TGG GAA GAT TTA CAT GTT TTA GCT CAC AAA GTC TTA ATT AAA CAT TTT CTT GAA TTA GGA ATC TTT AAG AAG GAA TAT TCC GAA GAA GAA CTT TAT AAA AGA AAA GTT TCA TGT GGG TTT TAT CCT CAT GGT TTA GGC CAT CTG TTA GGT TTA GAT GTG CAT GAT GTT GCT GGT AAT GCT AAT TAC GAA GAT CCT GAT CCT ATT TTT GTC TTT TTG AGA TTA CGT CGT AAA TTA CAA GAA GGT ATG GTA GTT ACT AAT GAA CCT GGG TGC TAC TTT AAT GAA TAT TTA TTA AAA GAA TTT ATT GAA --- --- --- --- --- AAA CAT CCT GAA AGA AAA GAA GCT ATC GAT TAT GAT GTT TTA AAG AAA TAC ATG TAC GTT GGC GGT GTT AGA ATC GAA GAC AAT ATC TTG GTT ACC AAG GAT GGT TAT GAA AAT CTA ACA AAG ATT ACA AGT GAT CCA GAT GAA ATC GAA AAA ATA GTT TCA AAT GGA TTA AAG AAG AGT CGC TCC GAT TTC CAT GTG ATT GTT --- --- --- --- ---
NDAI0B02150 ATG AGA ACT TTT CTC TCG CTA GTT TTT ATC GCC ACA ATC CTA CTT CTA TTT GAT TAC ATT AGA AAG TAT AAT AGG AGG AAA GAA CCG ATA ACG AAA AAT TAC GAT CTG AAA ATG AGA ATG GAA GAT ACT TCA GAG ATC --- --- --- --- --- --- --- --- --- CAA AAC TTG GTT TCT GGT GAA AAT TTG CCG GCA AGC CTG GAA GGT AAG AAA TAT CCA AGC AAG GCT CAT AAT GAA AAA GTT AAG AAG ATT TTT CAA TCA GTC AAC CTA GAT CTG CCT GTT AAT --- AGT GCT GTT TTT ATC GCA GGC AAT GAA GTT GAG CCA ATT AAA TAT TGT GAC ATC TCT CAT CCA TTT AGA CAA GAA AGA TAC TTT TAC TAT TTG TCT GGT GTT GAT GTT CCA GGC TCA TCC ATC CTT TTC AAC ATG AAA TCA AAT AAG TTA ACA TTA TTC TTG CCG TTA GTT GAC GAT GAT GAT GTA ATG TGG AGT GGA ATG CCA ATG GGT ATC AAT GAA GCT TTG AAC ACC TTT GAT GTC GAT GAA GTC CTA TAT GCT GAC AAA ATT AAC GAA GTC TTT GAA AAG GAA TTA ACT GGA TTC AAA GTT TTC ACG ACC GAC TTG GAT AAT ATC CAT GAT AAT TCA ATA AAG GAA AAA TTA GTT TCC GGA GAT AAG CGT TTT TTT AAG GCC TTA GAT GAG GCA AGA CTA ACC AAG GAC TCC TAT GAG ATT GAA GTT TTA AGG CAT GCC GCT AAG ATT ACA GAT AAT TGT CAT TTA GCA GTA ATA TCG GCA TTA CCA ATT GAA TTA AAT GAA TAT CAA GTT CAA GCA GAA TTT GAA TAC CAT GCA GGG CGT CAA AAT GCT CAC GCC TTG GGA TAT GAT CCT ATT TGT TGT TCG GGC CCT GCC TGT GGA ACA TTA CAT TAT GTC AAG AAC TCT GAA GCT TTA CAT --- GGT AAA GTA AGT TTT TTG ATT GAT GCT GGT GCA GAA TGG AAA AAC TAT ACA ACT GAT GTT ACG AGA TGT TTC CCA ATC TCT GGG AAA TTT ACT AAG GAA CAT CGT GAA ATA TAT GAC GCA GTC TTA GAT ATG CAA ACT CAA ACT ATG CAA AAT ATA AGG CCA GGT GCC AGC TGG GAT GAG TTA CAT TTG CTA TCA CAT AAA GTT CTT ATT AAG CAC CTT TTA AAG ATC GGA ATC TTC AGG AAG GAA TTT TCA GCA GAA GAA ATT TTC AGA AGA AGG GTC ACT TGT GTA TTT TAT CCT CAT GGC TTA GGC CAC CTT ATG GGG CTT GAT GTT CAT GAT GTC GCC GGT AAT CCA AAT TAT GAG GAT CCT GAT CCT TAT TTC AAA TAT TTA CGT TTA CGC CGT ACT TTG GAG GAA AAT ATG GTT CTA ACT GAT GAA CCT GGA TGT TAT TTT AAT GAA TTC TTG ATT AAG GAA TTA CTT GAA --- --- --- --- --- AAA TAT CCT GAA AGA TTG GAA GTT GTT GAC AGA GAT ATC CTC AAT AAA TAT ATG TAT ATT GGA GGT GTC AGA ATT GAA GAT GAT ATT CTG GTG ACA AAG GCT GGA TTT GAA AAC TTG ACT GGA ATA ACT TCA GAT CCA GAT GAA ATC GAG ACA ATT GTT CAG AAA TCA TTG TCT AAG AGG CGT TCC GAT TTC CAT GTA ATT GTG --- --- --- --- ---
Printing out site pattern counts
4 1482 P
GLN_GLV_PISO0N06151G --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAA AAC AAC AAC AAC AAC AAC AAC AAC AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAT AAT AAT AAT AAT AAT AAT AAT AAT ACA ACA ACA ACA ACA ACC ACC ACC ACC ACC ACC ACC ACG ACG ACG ACG ACT ACT ACT AGA AGA AGA AGA AGA AGA AGA AGA AGA AGC AGC AGC AGC AGG AGG AGG AGG AGT AGT AGT AGT ATA ATA ATA ATA ATA ATA ATA ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATG ATG ATG ATG ATG ATG ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT CAA CAA CAC CAC CAC CAC CAC CAC CAG CAG CAG CAG CAG CAG CAG CAG CAT CAT CAT CAT CAT CAT CAT CAT CCA CCA CCA CCA CCA CCC CCC CCC CCC CCC CCC CCC CCT CCT CCT CCT CCT CCT CGA CGC CGC CGC CGC CGT CGT CTA CTA CTA CTC CTC CTC CTC CTC CTG CTG CTG CTG CTG CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GCA GCA GCA GCA GCA GCA GCA GCC GCC GCC GCC GCC GCC GCC GCG GCG GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GGA GGA GGA GGA GGA GGA GGA GGA GGA GGC GGC GGC GGC GGC GGC GGC GGG GGG GGT GGT GGT GGT GGT GGT GGT GGT GTA GTA GTA GTA GTA GTA GTA GTA GTA GTC GTC GTC GTC GTC GTC GTC GTG GTG GTG GTG GTG GTT GTT GTT GTT GTT GTT GTT TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCA TCA TCA TCA TCA TCA TCA TCC TCC TCC TCC TCC TCC TCG TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT TGC TGC TGG TGG TGG TGT TGT TGT TGT TTA TTA TTA TTA TTA TTA TTA TTA TTC TTC TTC TTC TTC TTC TTC TTC TTC TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTT TTT TTT TTT TTT TTT TTT TTT TTT
KPOL_1056_46 --- AAA AAA AAA AAC AAG AAG AAG AAG AAG AAT ACC ACT AGA AGA AGC AGG AGT ATA ATA ATC ATG ATG ATT ATT ATT CAA CAA CAA CAA CAG CAG CAT CCT GAA GAA GAA GAA GAG GAG GAG GAT GAT GAT GAT GCT GCT GGA GGA GTC GTC GTC GTT GTT GTT GTT TCA TCA TCG TTA TTA TTC TTC TTG TTG TTT AAA AAA AAA AAG AAG AAG AAT ACC ACT AGA AGA CGT GAA GAT TAC TTG AAC AAT AAT AAT ACT AGT GAT GCT --- AAA AAA AAA AAA AAA AAG AAG AAG AAG AGT CGT GAA GAT GAT GAT AAC AAT CAT CAT CAT GAT GAT GAT TTG AAA ACA ACA ATG TTA ACC ACC ACT ACT ACT GAA GCA ACA ACT AGT GTT AAG ACA ACT AAT AGA AGA AGA AGC CAA CGT CGT GAG AGC AGG GCA TCT AAA AAG CGT GAT ACT AGT GGT TCC ATC ATT ATT ATT GTT GTT GTT ACC ATC ATC ATC ATT ATT ATT ATT GTG GTT GTT AGT ATA ATG ATG ATG ATT CAA ACT ATC ATT ATT CTA GTA GTT TTC TTG CAA CAG AGA ATT CAC CAC CAT GCA --- AAA AAA AAA ATG CAA CGT TTA --- ATA CAC CAT CAT GAA GAA TTG --- CCA CCA CCT CCT AAA AAG CCA CCA CCT GAA GCT CCA CCA CCA CCG CCT TTC AGA AGA AGA ATC GAC AGA GAA CCT TTA TTC ATA ATG GTC TCA TTG AAA AAG AAT ACA TCT AAG ATA ATC ATG CTG GTT GTT TGT TTA TTA TTA TTA TTC TTG TTG AAA AAC ACT AGA CCC GAA GAA GAA GAG GAT --- AAA AAG AAT CAG GAA GAA GAC GAC GAT GAT GAT GAT GAT GAT GAT GCC GTT TCT AAG AAT AGA GAA GAA GAA GAC GAG GAT GCA TAT --- AAT GAC GAT GAT GAT GAT GAT GAT GAT GCA AAA GAA GAA GCT GCT GCT GCT AAC GCC GCT GCT TAT TCT TTA ACC TTT AAT AGT ATT CAA GAT GCA GCC GCT GCT GTA TGT TTA GGC GGC GGT GGT GGT GGT GGT GGT GTT GCT GGA GGT GGT GGT GGT GTA GCC GGG CAC GGC GGT GGT GGT GGT GGT TCA ATA GAA GTC GTG GTT GTT GTT TCT TTA ATC ATT GTG GTT GTT GTT TTA --- AAT ATT GTA GTT ACT ACT ATT ATT GTA TGT TTA --- CAT TAC TAC TAC TAC TAT TAT TTC TTT --- AAG GCT GTT TAC TAC TAC TAT TAT TAT TCA TCT TTT TTT --- AAC AGT ATA GAA GAT GGG AGA GAT GAT GCT GGA TCT --- AGC ACC AGT CAT GCT GGT TCA TCA TGC TGG TGC TGT ATG TGG TTT ATT GGT TCG TGT GTC TTA TTA TTA TTG TTG TTG TTG GTT TAC TTC TTC TTC TTC TTG TTT TTT ACC ATC CGT CTG CTT TAC TTA TTG TTG TTG TTG TTT ATA CAC CTA TAC TAT TTA TTC TTC TTT
TBLA0C00520 --- --- AAG AGA --- --- --- --- --- AAA --- --- --- --- CAA TCT --- --- --- --- --- --- ATG --- --- CTA --- --- --- --- --- --- --- CCT --- --- --- GAA --- --- GAA --- --- --- GAC --- --- --- --- --- --- --- --- --- --- GCT --- GCT --- --- AAA --- --- --- --- --- AAA AAG ACT AAA AAA AAA GAA GAT AAG AAA AAG CAC GAA AAA GAG TTA AAT AAT AAT GAA TCT TCG GAT GCT --- AAA AAA AAG AAG AAT AAA AAA AAG AAT TCA CGC GAA AAT ACT GGT AAT AAT ATT CAT CAT ACT GAG GAT TTA AAA ACC ACG TTG TTA ACA ACT ACC ACT TTG ACT GCT ACT CAC ACT GTG AAA ACT ACA AAT AGA AGA CGT GCT AGA AGA CGT TAT AGT AGA ACC GCC GAA AAA CGT AAT TCG ACT AAT TCA ATT ATC ATC CTT ATC GTT GTT ACA ATC ATT ATT ATA ATC ATT ATT ATT GTT GTT GCC TTA ATG ATG ATT TTA GTT ACA GTT ATT ATT GTT GTC ATT TTT ATT CAA CAA AAA CTG CAA CAC CAT TCT --- AAA CAA TTG GAC CAA GAA ATG --- AAA CAT CAT CAT GAA GAA TTA --- CCA CCT CCA CCT ATC AAA CCA CCA CCA GAA GCT CCA CCT CCT CCA CCA TTT AGA AGG GTC CTT GAC AGA GAA CCT TTA CTG ATT CAG GTT TCT TTA AAG TCT GAA TCA TCC ATG TTA ATC ATT CTA ATC GTT AAG CTA GTC TTA TTA TTT TTA TTA AAA GAT GAT GAA CCA GAA GAA GAG GAA GAT --- AAG AAG AAT CAA GAA GAA GAA GAT AAT ACT GAA GAT GAT GAT GAT AAG TCA AAG AAA AAA AGA AAT GAA GAG AAC GAA GAA GAA TGG --- AAT AAT AAA AAG AAT GAA GAC GAT GAT GAT AAA AGA GAA GCC GCT GCT GGT AAT GCT GCT GCT TCT GCT CAA ACT TAT GAA AAA ATT AAT AAT GCT GCT GCT GCT GTG GCT ATC AGT GGA GGA GGC GGT GGT GGT GGT ATT GGG AGA GGC GGG GGT GGT ATT GCT GGT GAT GGT GGA GGC GGC GGT GGT TCA ATC GAA GTT GTA GTC GTG GTT GCA TTA GTT ATT GTT GTA GTT GTT TTA --- CTG GTT GTA GTT ACA ATC ATA ATC TTG TGC ATC --- CAT TAC TAT TAT TTT TAC TAT TAT TTC --- AAA AAT TTG TAC TAT TAT TAC TAC TAT CCA TCC TAT TAT --- AAT GCT TCA GAA GAC GCC AGA --- AAA GCT GGT TCA --- AGT ACT AGT GAT AGT GGA AAG TCA TGT TGG TGT TGT ATG TGG TTT ATC AAC TCT TGT TTA ATA TTA TTA ATT TTA TTA TTG GTA TAT TTC TTT TTT TTT TAT TTT TTT AAA TTA ATA TTA ATG TTA TTA CTT TTA TTA TTA TTT CTT TAT TTG TAT TAT TTT TTC TTT TTT
NDAI0B02150 CCG GAG CAA AGA --- --- AAA AAG AGA AAC AAT ACA CTA AGG AAA --- TAT AAT ATA TCG AAA --- ATG CTC TTT TTG --- ATG GAA TAC ACT AGA TTT CCT --- ATG TCA GAA CTG GAA GAA --- ACG GAT TCT GTT TAC AGA GAT --- AAA GCC ATC CTT GAT GTT ATC GTT CTA ATC TTG --- ACT ATT CTA TTT AAA AAG GTC AAA AAG ACA AAT AAG AAA AGG AGG CAC ACC AAG AAT CAA AAT AAC AAT GCT GCC TCT GAT GCC --- AAA AAG CAT GGA AAC AAG AGG AAG AAG CAG CGT AAT AAA TCA GGA GAA AAC CAT CAC CAT CTA AAT GAT TTA GTC ACA ACG TAT TTA ACT ACC ACG ACT TTA --- ACT ACA TCT ACA GTT ACT ACA ACT AAT AGA CGT CGT GTA AGA AGA CGT AGA GGT AAA GCA TCG AAG AAA CGC AAG TCT ACT GGT ACT GTT ATC ATT ATT GTT ATT GTG GCA ATC ATA ATT ATT ATT ATA ATT TTA ATT GTC GAA TTA ATA ATG ATG CTT GGT ATC GTA ATT GTT TTG GTC ATA TTA ATT CAA CAA CAT ATT CAA CAT CAT TCC --- AAA GAG GAA GAA CAA ATC TTG --- ACT CAT CAC CAT CAA GAA CTA --- CCA CCT CCA CCT AAC CCA CCA CCT CCT GAA CCA CCG CCA CCT CCA CCG ATG AGA AGG AAA GAA GAT AGA AAG CCA TTA CTT GTT ATG CTA AGC CTT AAA CCT GAT ACT TCA ATG ATG CTG TAT TTA ATT GTG AAT TTG CTA CTT TTG TTC ATC TTA AGA AAC AAT GAA TCC GAA GAG GAG GAG GAT --- AAG AAA GAT CAA GAC GAG GAT GAT GAT TCT CAT CGT GAC GAG GAT AAT GTT TCA AAG GAA AAA GAA GAA GAA GAA GAA GAA AAT GAT --- TTA GAT GAA AAA GAT AAT GAT GAC GAT GAT AAC GAA GCA GCC GCA GCT GCA AAT TCA GCA GCT GCT GCA TTG ACA TTC CAA AAG ATA AAG GAT GCT GCA AGC GCC GTA GCT ATC AGG GGC GGA GGA AAT GGA GGG GGT ATT GTA GGC GGC GGA AAT GGC TTG GCC GGT GAT GGT TCA GGC GGG GGA GGT GGA TTT GAA GTT GTT GTT GTC GTA GCC CTG GTC GTT GTC GTT GTC GTT TTA GAA TTG ATC GTT GTC AGT GTT ATC GTT CTG TGT ATC --- TAT TAT TAC TAT TAT TAT TAT TTT TTC --- AAG GAA ATT TAT TAC TAT TAT TTT TAT TCA TCC AAG TTC --- AAT TCA AGC GAG GAC GCA AGA GAT GCT GCT GGA AGT --- AGT ACT TCA GCT GCA GGA TCT TCG TGT TCC TGT TGT ATG TGG TTT ACC AAC TGT TGT CTA TTT TTA TTG CTT TTA TTG TTA ATC TAT TTC CTT TTC TTT TTC TTC TTT GGG TTA GTT TTA TTA TTA TTG TTA ATT CTC TTG TTT GTT TTT TTT TTC TAC TTT TTC TTT TTT
1 1 1 1 1 1 1 1 1 1 1 1 1 2 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 2 1 1 1 1 1
1 2 2 1 1 1 1 1 2 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 2 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 3 1 1 1
1 1 2 1 1 1 1 1 1 1 1 1 1 1 1
3 1 1 1 1 1 1 1 1 1 1 1 1 1 4
1 1 1 1 2 1 1 1 1 1 1 1 1 1 1
1 1 2 2 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 6 1 1 1 1 1 1 1 1 1 1 1 1 3
1 1 1 1 2 1 3 1 1 1 1 1 1 1 6
1 1 1 1 1 1 1 1 1 1 1 1 1 2 3
5 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 3 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 2 1 1 1
1 1 1 1 1 1 1 1 3 1 2 1 1 2 1
1 1 1 2 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 3 1
3 1 1 1 1 1 1 1 1 1 1 1 2 1 1
1 1 1 1 1 1 1 2 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 2 1
CODONML (in paml version 4.4c, August 2010) OG7365.fa
Model: One dN/dS ratio for branches
Codon frequency model: F3x4
ns = 4 ls = 548
Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT 10 11 16 18 | Ser TCT 9 7 7 6 | Tyr TAT 18 9 18 19 | Cys TGT 4 7 6 8
TTC 10 14 3 10 | TCC 6 1 2 4 | TAC 11 15 8 5 | TGC 4 2 1 0
Leu TTA 9 19 28 19 | TCA 8 7 8 9 | *** TAA 0 0 0 0 | *** TGA 0 0 0 0
TTG 12 19 7 14 | TCG 2 2 2 3 | TAG 0 0 0 0 | Trp TGG 5 4 5 3
--------------------------------------------------------------------------------------
Leu CTT 15 1 4 7 | Pro CCT 8 6 7 8 | His CAT 11 14 12 14 | Arg CGT 2 8 4 6
CTC 5 0 0 2 | CCC 7 1 0 0 | CAC 8 5 3 3 | CGC 4 0 1 1
CTA 3 2 3 8 | CCA 6 9 12 10 | Gln CAA 2 9 8 9 | CGA 1 0 0 0
CTG 5 2 3 4 | CCG 0 2 0 3 | CAG 8 4 1 1 | CGG 0 0 0 0
--------------------------------------------------------------------------------------
Ile ATT 10 21 20 17 | Thr ACT 3 13 13 12 | Asn AAT 9 14 23 19 | Ser AGT 4 9 5 3
ATC 11 10 14 13 | ACC 7 8 3 3 | AAC 9 6 2 8 | AGC 4 4 0 3
ATA 7 9 4 6 | ACA 5 5 5 7 | Lys AAA 16 23 30 18 | Arg AGA 10 16 12 12
Met ATG 9 12 9 12 | ACG 4 0 1 3 | AAG 19 21 16 20 | AGG 4 2 1 7
--------------------------------------------------------------------------------------
Val GTT 7 24 17 20 | Ala GCT 12 16 20 9 | Asp GAT 18 43 27 31 | Gly GGT 10 20 15 9
GTC 7 6 4 9 | GCC 7 4 4 7 | GAC 24 7 6 7 | GGC 7 3 4 5
GTA 9 5 4 5 | GCA 7 6 1 10 | Glu GAA 15 33 40 35 | GGA 9 4 4 10
GTG 5 3 3 2 | GCG 2 0 0 0 | GAG 16 6 4 8 | GGG 2 2 2 3
--------------------------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: GLN_GLV_PISO0N06151G
position 1: T:0.22453 C:0.17672 A:0.27235 G:0.32640
position 2: T:0.27859 C:0.19335 A:0.38254 G:0.14553
position 3: T:0.31185 C:0.27235 A:0.22245 G:0.19335
Average T:0.27166 C:0.21414 A:0.29245 G:0.22176
#2: KPOL_1056_46
position 1: T:0.21869 C:0.11776 A:0.32336 G:0.34019
position 2: T:0.29533 C:0.16262 A:0.39065 G:0.15140
position 3: T:0.41682 C:0.16075 A:0.27477 G:0.14766
Average T:0.31028 C:0.14704 A:0.32960 G:0.21308
#3: TBLA0C00520
position 1: T:0.23029 C:0.12033 A:0.32780 G:0.32158
position 2: T:0.28838 C:0.17635 A:0.41079 G:0.12448
position 3: T:0.44398 C:0.11411 A:0.32988 G:0.11203
Average T:0.32089 C:0.13693 A:0.35615 G:0.18603
#4: NDAI0B02150
position 1: T:0.22391 C:0.14421 A:0.30930 G:0.32258
position 2: T:0.31499 C:0.17837 A:0.37381 G:0.13283
position 3: T:0.39089 C:0.15180 A:0.29981 G:0.15750
Average T:0.30993 C:0.15813 A:0.32764 G:0.20430
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 55 | Ser S TCT 29 | Tyr Y TAT 64 | Cys C TGT 25
TTC 37 | TCC 13 | TAC 39 | TGC 7
Leu L TTA 75 | TCA 32 | *** * TAA 0 | *** * TGA 0
TTG 52 | TCG 9 | TAG 0 | Trp W TGG 17
------------------------------------------------------------------------------
Leu L CTT 27 | Pro P CCT 29 | His H CAT 51 | Arg R CGT 20
CTC 7 | CCC 8 | CAC 19 | CGC 6
CTA 16 | CCA 37 | Gln Q CAA 28 | CGA 1
CTG 14 | CCG 5 | CAG 14 | CGG 0
------------------------------------------------------------------------------
Ile I ATT 68 | Thr T ACT 41 | Asn N AAT 65 | Ser S AGT 21
ATC 48 | ACC 21 | AAC 25 | AGC 11
ATA 26 | ACA 22 | Lys K AAA 87 | Arg R AGA 50
Met M ATG 42 | ACG 8 | AAG 76 | AGG 14
------------------------------------------------------------------------------
Val V GTT 68 | Ala A GCT 57 | Asp D GAT 119 | Gly G GGT 54
GTC 26 | GCC 22 | GAC 44 | GGC 19
GTA 23 | GCA 24 | Glu E GAA 123 | GGA 27
GTG 13 | GCG 2 | GAG 34 | GGG 9
------------------------------------------------------------------------------
(Ambiguity data are not used in the counts.)
Codon position x base (3x4) table, overall
position 1: T:0.22420 C:0.13926 A:0.30864 G:0.32790
position 2: T:0.29481 C:0.17728 A:0.38914 G:0.13877
position 3: T:0.39160 C:0.17383 A:0.28198 G:0.15259
Average T:0.30354 C:0.16346 A:0.32658 G:0.20642
Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
0.02715140 0.01205207 0.01955037 0.01057980
0.01632722 0.00724739 0.01175642 0.00636206
0.03583802 0.01590792 0.00000000 0.00000000
0.01277980 0.00567275 0.00000000 0.00497977
0.01686496 0.00748609 0.01214362 0.00657159
0.01014158 0.00450168 0.00730245 0.00395176
0.02226062 0.00988113 0.01602877 0.00867406
0.00793812 0.00352360 0.00571584 0.00309316
0.03737802 0.01659151 0.02691406 0.01456470
0.02247690 0.00997714 0.01618450 0.00875834
0.04933648 0.02189968 0.03552476 0.01922443
0.01759334 0.00780940 0.01266809 0.00685541
0.03971041 0.01762682 0.02859350 0.01547354
0.02387946 0.01059971 0.01719442 0.00930486
0.05241508 0.02326622 0.03774150 0.02042404
0.01869116 0.00829671 0.01345858 0.00728319
Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
GLN_GLV_PISO0N06151G
KPOL_1056_46 -1.0000 (0.4207 -1.0000)
TBLA0C00520 -1.0000 (0.4095 -1.0000) 0.1290 (0.2331 1.8074)
NDAI0B02150 -1.0000 (0.3952 -1.0000) 0.1106 (0.3243 2.9331) 0.1727 (0.2654 1.5362)
TREE # 1: (4, (2, 3), 1); MP score: -1
lnL(ntime: 5 np: 7): -6020.588433 +0.000000
5..4 5..6 6..2 6..3 5..1
2.002896 1.080898 2.261746 1.616762 4.719115 1.351302 0.040978
SEs for parameters:
0.330039 0.237796 0.370588 0.274877 0.699270 0.124780 0.006602
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 11.68142
(4: 2.002896, (2: 2.261746, 3: 1.616762): 1.080898, 1: 4.719115);
(NDAI0B02150: 2.002896, (KPOL_1056_46: 2.261746, TBLA0C00520: 1.616762): 1.080898, GLN_GLV_PISO0N06151G: 4.719115);
Detailed output identifying parameters
kappa (ts/tv) = 1.35130
omega (dN/dS) = 0.04098
dN & dS for each branch
branch t N S dN/dS dN dS N*dN S*dS
5..4 2.003 1308.9 335.1 0.0410 0.1157 2.8237 151.5 946.1
5..6 1.081 1308.9 335.1 0.0410 0.0624 1.5238 81.7 510.6
6..2 2.262 1308.9 335.1 0.0410 0.1307 3.1886 171.0 1068.4
6..3 1.617 1308.9 335.1 0.0410 0.0934 2.2793 122.3 763.7
5..1 4.719 1308.9 335.1 0.0410 0.2726 6.6530 356.8 2229.2
tree length for dN: 0.6748
tree length for dS: 16.4684
Time used: 0:03
chec
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