
seed used = 141407505

K12                                  ATG GCA GTA AAG ATT TCA GGT GTA CTG AAA GAC GGC ACA GGA AAA CCG GTA CAG AAC TGC ACA ATC CAG CTG AAA GCA AAA CGT AAC AGC ACC ACG GTG GTG GTG AAC ACG CTG GCC TCA GAA AAT CCG GAT GAA GCC GGG CGT TAC AGC ATG GAC GTT GAG TAC GGT CAG TAC AGC GTT ATT CTG TTG GTG GAA GGA TTC CCG CCG TCA CAT GCC GGG ACC ATT ACC GTG TAT GAA GAT TCT CAA CCC GGT ACG CTG AAT GAT TTT CTC GGT GCC ATG ACG GAG GAT GAT GCC CGT CCG GAG GCA CTG CGC CGT TTT GAA CTG ATG GTG GAA GAG GTG GCG CGT AAC GCG TCC GCG GTG GCA CAG AAC ACG GCA GCC GCG AAG AAG TCA GCC AGT GAT GCC AGC ACA TCA GCC CGT GAG GCG GCA ACC CAT GCG GCT GAT GCT GCG GAC TCA GCA CGC GCA GCC AGC ACG TCA GCC GGA CAG GCC GCG TCG TCG GCT CAG TCA GCG TCT TCC AGC GCA GGA ACG GCA TCA ACA AAG GCC ACT GAA GCA TCA AAA AGT GCT GCC GCT GCA GAG TCC TCA AAA AGC GCG GCG GCC ACC AGT GCC GGT GCG GCG AAA ACG TCA GAA ACG AAT GCT TCA GCG TCA CTA CAA TCA GCA GCC ACA TCT GCA TCC ACC GCG ACC ACG AAG GCA TCA GAA GCT GCG ACC TCG GCC CGG GAT GCG GCG GCC TCA AAA GAA GCG GCA AAA TCA TCA GAA ACG AAC GCA TCA TCA AGC GCC AGT AGT GCA GCT TCC TCG GCA ACG GCG GCA GGA AAT TCC GCG AAG GCG GCA AAA ACG TCC GAG ACG AAC GCC AGG TCT TCT GAA ACG GCA GCG GGA CAG AGC GCC TCG GCT GCG GCA GGC TCA AAA ACA GCG GCT GCG TCG TCT GCC AGT GCA GCG TCA ACA AGT GCC GGG CAG GCC TCA GCC AGT GCC ACC GCC GCC GGA AAA TCG GCA GAA AGC GCC GCA TCG TCT GCT TCA ACA GCC ACA ACG AAG GCT GGC GAA GCC ACT GAA CAG GCC AGC GCA GCA GCG AGG TCT GCT TCC GCA GCG AAG ACA TCC GAA ACG AAC GCG AAA GCG TCG GAA ACA AGC GCA GAA TCC TCA AAA ACG GCT GCC GCA TCG TCA GCC AGT TCG GCG GCG TCA TCG GCA TCA TCG GCG TCT GCT TCA AAA GAT GAG GCG ACC AGA CAA GCG TCA GCA GCG AAG AGC AGC GCC ACG ACG GCA TCC ACG AAG GCG ACA GAG GCT GCT GGC AGT GCG ACG GCG GCA GCT CAG AGC AAA AGT ACG GCG GAA TCC GCG GCA ACG CGC GCC GAG ACA GCA GCT AAA CGG GCA GAG GAT ATT GCA TCC GCC GTG GCG CTT GAG GAT GCA AGT ACG ACG AAA AAG GGG ATA GTA CAG CTC AGC AGT GCG ACC AAC AGT ACG TCT GAA ACG CTG GCG GCA ACG CCA AAG GCA GTA AAA TCA GCC TAT GAC AAT GCA GAG AAA CGT CTG CAG AAA GAC CAG AAC GGC GCT GAT ATA CCC GAT AAG GGA TGC TTC CTG AAC AAC ATT AAC GCG GTC AGT AAA ACA GAC TTT GCT GAT AAG CGT GGT ATG CGT TAT GTG CGG GTT AAC GCT CCT GCA GGT GCA ACA TCT GGA AAA TAT TAC CCT GTT GTT GTT ATG CGT TCT GCT GGC TCA GTA AGC GAA CTG GCA TCA AGA GTC ATT ATC ACC ACG GCA ACG CGA ACC GCA GGC GAT CCG ATG AAT AAC TGC GAG TTT AAC --- --- GGA TTT GTT ATG CCT GGT GGC TGG ACT GAC AGG GGG CGT TAT GCT TAT GGC ATG TTC TGG CAA TAT CAA AAC AAT GAA CGA GCC ATT CAC TCA ATA ATG ATG AGT AAT AAG GGC GAT GAT TTG CGC TCT GTG TTC TAT GTT GAT GGC GCT GCT TTC CCT GTT TTT GCG TTT ATT GAA GAT GGC CTG TCA ATA TCC GCA CCT GGT GCT GAT CTC GTT GTT AAT GAT ACG ACC TAT AAG TTT GGG GCA ACA AAT CCG GCG ACT GAA TGT ATC GCG GCG GAC GTT ATC CTT GAT TTT AAG AGT GGG CGT GGT TTT TAT GAG TCT CAT TCG TTA ATC GTT AAC GAT AAC TTG TCG TGC AAA AAA CTT TTT GCC ACA GAC GAA ATT GTA GCG CGT GGT GGT AAT CAG ATT CGA ATG ATA GGT GGG GAG TAT GGT GCA TTA TGG CGT --- --- AAT GAT GGC GCT AAA ACT TAC CTG CTG CTT ACC AAT CAA GGT GAT GTT TAT GGT GGC TGG AAT ACA TTA AGA CCG TTT GCT ATT GAT AAC GCA ACC GGC GAA CTG GTT ATT GGA ACC AAA CTG TCC GCA AGT CTG AAC GGT AAT GCA TTA ACA GCA ACA AAG CTG CAA ACG CCA AGA CGG GTT TCT GGT GTT GAG TTT GAT GGT TCC AAA GAT ATT ACT TTA ACC GCC GCG CAT GTG GCT GCT TTT GCC AGA AGG GCA ACG GAT ACA TAT GCC GAT GCG GAT GGT GGC GTT CCA TGG AAT GCC GAA TCT GGC GCT TAC AAT GTC ACC CGC TCT GGC GAC AGC TAT ATT CTG GTT AAC TTC TAT ACC GGA GTC GGA AGT TGC CGG ACC CTG CAG ATG AAG GCG CAT TAC AGA AAT GGT GGT CTG TTC TAC CGT TCT TCA AGA GAC GGT TAT GGT TTT GAG GAA GAC TGG GCA GAA GTT TAT ACC TCG AAA AAT CTT CCA CCA GAA AGC TAC CCA GTC GGC GCA CCA ATC CCG TGG CCA TCA GAT ACC GTT CCG TCT GGT TAT GCC CTG ATG CAG GGG CAG GCT TTT GAC AAA TCT GCT TAC CCG AAA CTT GCA GCC GCT TAT CCG TCA GGC GTG ATC CCT GAT ATG CGT GGC TGG ACG ATT AAG GGC AAA CCT GCC AGT GGT CGG GCC GTA TTG TCT CAG GAA CAG GAC GGC ATT AAA TCG CAT ACC CAC AGC GCC AGC GCA TCC AGT ACA GAT TTG GGG ACG AAA ACC ACA TCG TCG TTT GAT TAC GGC ACT AAA TCC ACG AAT AAC ACC GGG GCA CAT ACA CAC AGT GTG AGC GGC TCT ACA AAC TCG GCT GGA GCA CAC ACA CAC TCA CTA GCC AAC GTG AAC ACG GCT AGT GCT AAC TCC GGT GCT GGT AGT GCA TCA ACA AGA TTG TCT GTT GTG CAT AAT CAA AAC TAT GCA ACA TCA TCT GCT GGC GCA CAT ACC CAC TCA CTG TCC GGC ACT GCT GCA AGC GCA GGT GCA CAC GCG CAT ACT GTC GGT ATT GGT GCT CAT ACG CAC TCC GTT GCG ATT GGT TCA CAT GGA CAC ACC ATC ACC GTT AAC GCT GCT GGT AAC GCG GAA AAC ACC GTC AAA AAC ATC GCA TTT AAC TAT ATT GTG AGG CTT GCA 
O157                                 ATG GCA GTA AAG ATT TCA GGT GTA CTG AAA GAC GGC ACA GGA AAA CCG GTA GAG AAC TGC ACC ATT CAA CTG AAA GCC AGA CGT AAC AGC GCC ACG GTG GTG GTG AAC ACG GTG GCC TCT GAA AAT CCG GAT GAA GCC GGT CGT TAC AGC ATG GAC GTT GAG TAC GGT CAG TAC AGC GTT ATT CTG TTG GTG GAA GGG TTC CCG CCG TCA CAT GCC GGG ACC ATC ACC GTG TAT GAA GAT TCT CAA CCC GGT ACG CTG AAT GAT TTT CTT GGT GCC ATG ACT GAG GAT GAT GTC CGT CCG GAG GCA CTG CGC CGT TTT GAG CTG ATG GTG GAA GAG GTG GCG CGT AAC GCG TCC GCG GTG GCA CAG AAC ACG GCA GCC GCG AAG AAG TCA GCC AGC GAT GCC AGC ACA TCA GCC CGT GAG GCG GCA ACC CAT GCG ACT GAT GCT GCG GAC TCA GCA CGC GCA GCC AGC ACG TCA GCC GGA CAG GCC GCG TCG TCG GCT CAG TCA GCG TCT TCC AGC GCA GGA ACG GCA TCA ACA AAG GCT ACT GAA GCA TCA AAA AGT GCT GCC GCT GCA GAG TCC TCA AAA AGC GCG GCG GCT ACC AGT GCC GGT GCG GCG AAA ACG TCA GAA ACG AAT GCG GCA GTG TCA CAA CAA TCA GCC GCC ACT TCT GCA TCC ACC GCG ACC ACG AAA GCG TCA GAA GCT GCC TCC TCA GCC AGG GAT GCG TCG GCT TCA AAA GAG GCG GCA AAA TCA TCA GAA ACG AGC GCA GCC TCG AGC GCC AGT AGT GCA GCC TCC TCG GCA ACG GCG GCA GGC AAT TCC GCG AAG GCG GCC AAA ACG TCT GAG ACA AAC GCT AAG TCC TCT GAA ACG GCA GCA GAA CAG AGT GCC TCC GCA GCA GCA GGC TCA AAA ACA GCG GCT GCA TTA TCT GCC AGT GCC GCG TCA ACA AGT GCC GGG CAG GCC TCA GCC AGT GCC ACC GCC GCC GGA AAA TCG GCA GAA AGT GCC GCA TCG TCT GCT TCA ACA GCC ACA ACG AAG GCT GGC GAA GCC ACT GAA CAG GCC AGC GCA GCA GCG AGT TCT GCT TCC GCA GCG AAG ACA TCC GAA ACG AAC GCG AAA GCG TCG GAA ACC AGC GCA GAA TCC TCA AAA ACG GCT GCC GCA TCG TCA GCC AGT TCG GCG GCG TCA TCG GCA TCA TCT GCG TCT GCT TCA AAA GAT GAG GCG ACC AGA CAA GCG TCA GCA GCG AAG AGC AGC GCC ACG ACG GCA TCC ACG AAG GCG ACA GAG GCA GCT GGT AGT GCG ACG GCA GCA GCT CAG AGC AAA AGT ACG GCG GAA TCT GCA GCA ACG CGC GCT GAG ACA GCG GCA AAA CGG GCA GAG GAT ATT GCA TCC GCC GTG GCG CTT GAG GAT GCG AGC ACG ACG AAA AAG GGG ATA GTA CAG CTC AGC AGT GCG ACT AAC AGC ACT TCC GAG TCA CTG GCG GCA ACG CCA AAA GCC GTT AAG GCC GCG TAT GAG CTG GCT AAC GGG AAA TAC ACC GCA CAG GAT GCA ACG ACA GCA CAG AAA GGG ATA GTT CAG CTT AGC AAC GCG ACC AAC AGC ACA TCT GAA ATG CTG GCG GCA ACG CCA AAG --- --- --- --- --- TCG GTA AAG GCA GCC TAT GAC CTT GCT AAC GGG AAA TAT ACT GCT CAG GAC GCT ACG ACA GCA CAA AAA GGA ATT GTC CAG CTC AGT AGT GCA ACC AAC AGC GCA TCT GAA ACG CTT GCC GCG ACA CCG AAA GCA GTG AAA GCA GCT AAT GAT AAT GCG AAT GGT CGG GTA CCT TCT GCC CGT AAG GTG AAT GGT AAG GCG CTT TCA TCG GAT ATA ACA CTG ACG CCG AAA GAT ATT GGT ACG CTT AAC TCA ACA ACA ATG TCA TTC AGC GGT --- --- --- --- --- --- --- --- --- --- GGT GCT GGT TGG TTC AAA TTA GCA --- --- --- --- --- --- ACG GTA ACC ATG CCA CAG GCG AGT TCT GTT GTT TCA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATT ACG TTG ATT GGT GGC GCG GGA TTT --- --- --- --- --- --- --- --- --- --- AAC GTG GGG TCA CCT CAA CAG GCA GGT ATA TCT GAA CTT GTT TTG CGT GCA GGT AAT --- --- GGT AAT CCG AAG GGG ATT ACT GGT GCT TTA TGG CAG CGC ACA TCG ACA GGG TTT ACA AAT TTT GCC TGG GTC AAT ACA TCT GGT GAT ACT TAC GAT ATT TAC GTT GCA ATC GGA AAT TAT GCG ACT GGT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GTA AAT ATT CAA TGG GAT TAT ACC AGT AAT GCC AGC GTG ACG ATT CAT ACG TCA CCA GCA TAT TCT GCT AAT AAG CCG GAA GGG TTA ACG GAC GGT ACA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GTT TAT TCA CTC TAT ACG CCA TCA GAG CAG TTT TAT CCG CCT GGC GCA CCA ATC CCG TGG CCA TCA GAT ACC GTT CCG TCT GGC TAT GCC CTG ATG CAG GGG CAG ACT TTT GAC AAA TCT GCA TAC CCG AAA CTT GCA GCC GCT TAT CCG TCA GGC GTG ATC CCT GAT ATG CGT GGC TGG ACG ATT AAG GGC AAA CCT GCC AGT GGT CGG GCC GTA TTG TCT CAG GAA CAG GAC GGC ATT AAA TCG CAC ACC CAC AGC GCC AGC GCA TCC AGT ACG GAT TTG GGG ACG AAA ACC ACA TCG TCG TTT GAT TAC GGC ACT AAA TCC ACG AAT AAC ACC GGG GCG CAC ACG CAC AGT GTG AGC GGT ACA GCC GCA AGT GCC GGA AAC CAT ACT CAT AGT GTC ACA GGC GCA TCA GCA GTC AGC CAG TGG TCA CAA AAT GGG TCA GTA CAT AAG --- --- --- GTA GTG TCT GCG GCC AGT GTG AAT ACA AGT GCT GCA GGA GCG CAC ACT CAT AGT GTC AGC GGC ACA GCT GCA TCT GCA GGT GCT CAC GCA CAT ACT GTC GGT ATT GGT GCT CAT ACG CAC TCT GTT GCG ATT GGC TCA CAT GGA CAC ACC ATC ACC GTT AAC GCT GCG GGT AAC GCG GAA AAC ACT GTC AAA AAC ATC GCA TTT AAC TAC ATT GTG AGG CTT GCA 
EDL933                               ATG GCA GTA AAG ATT TCA GGT GTA CTG AAA GAC GGC ACA GGA AAA CCG GTA GAG AAC TGC ACC ATT CAA CTG AAA GCC AGA CGT AAC AGC GCC ACG GTG GTG GTG AAC ACG GTG GCC TCT GAA AAT CCG GAT GAA GCC GGT CGT TAC AGC ATG GAC GTT GAG TAC GGT CAG TAC AGC GTT ATT CTG TTG GTG GAA GGG TTC CCG CCG TCA CAT GCC GGG ACC ATC ACC GTG TAT GAA GAT TCT CAA CCC GGT ACG CTG AAT GAT TTT CTT GGT GCC ATG ACT GAG GAT GAT GTC CGT CCG GAG GCA CTG CGC CGT TTT GAG CTG ATG GTG GAA GAA GTG GCG CGT AAC GCG TCC GCG GTG GCA CAG AAC ACG GCA GCC GCG AAG AAG TCA GCC AGC GAT GCC AGC ACA TCA GCC CGT GAG GCG GCA ACC CAT GCG ACT GAT GCT GCG GAC TCA GCA CGC GCA GCC AGC ACG TCA GCC GGA CAG GCC GCG TCG TCG GCT CAG TCA GCG TCT TCC AGC GCA GGA ACG GCA TCA ACA AAG GCT ACT GAA GCA TCA AAA AGT GCT GCC GCT GCA GAG TCC TCA AAA AGC GCG GCG GCT ACC AGT GCC GGT GCG GCG AAA ACG TCA GAA ACG AAT GCG GCA GTG TCA CAA CAA TCA GCC GCC ACT TCT GCA TCC ACC GCG ACC ACG AAA GCG TCA GAA GCT GCC TCC TCA GCC AGG GAT GCG TCG GCT TCA AAA GAG GCG GCA AAA TCA TCA GAA ACG AGC GCA GCC TCG AGC GCC AGT AGT GCA GCC TCC TCG GCA ACG GCG GCA GGC AAT TCC GCG AAG GCG GCC AAA ACG TCT GAG ACA AAC GCT AAG TCC TCT GAA ACG GCA GCA GAA CAG AGT GCC TCC GCA GCA GCA GGC TCA AAA ACA GCG GCT GCA TTA TCT GCC AGT GCC GCG TCA ACA AGT GCC GGG CAG GCC TCA GCC AGT GCC ACC GCC GCC GGA AAA TCG GCA GAA AGT GCC GCA TCG TCT GCT TCA ACA GCC ACA ACG AAG GCT GGC GAA GCC ACT GAA CAG GCC AGC GCA GCA GCG AGT TCT GCT TCC GCA GCG AAG ACA TCC GAA ACG AAC GCG AAA GCG TCG GAA ACC AGC GCA GAA TCC TCA AAA ACG GCT GCC GCA TCG TCA GCC AGT TCG GCG GCG TCA TCG GCA TCA TCT GCG TCT GCT TCA AAA GAT GAG GCG ACC AGA CAA GCG TCA GCA GCG AAG AGC AGC GCC ACG ACG GCA TCC ACG AAG GCG ACA GAG GCA GCT GGT AGT GCG ACG GCA GCA GCT CAG AGC AAA AGT ACG GCG GAA TCT GCA GCA ACG CGC GCT GAG ACA GCG GCA AAA CGG GCA GAG GAT ATT GCA TCC GCC GTG GCG CTT GAG GAT GCG AGC ACG ACG AAA AAG GGG ATA GTA CAG CTC AGC AGT GCG ACT AAC AGC ACT TCC GAG TCA CTG GCG GCA ACG CCA AAA GCC GTT AAG GCC GCG TAT GAG CTG GCT AAC GGG AAA TAC ACC GCA CAG GAT GCA ACG ACA GCA CAG AAA GGG ATA GTT CAG CTT AGC AAC GCG ACC AAC AGC ACA TCT GAA ATG CTG GCG GCA ACG CCA AAG --- --- --- --- --- TCG GTA AAG GCA GCC TAT GAC CTT GCT AAC GGG AAA TAT ACT GCT CAG GAC GCT ACG ACA GCA CAA AAA GGA ATT GTC CAG CTC AGT AGT GCA ACC AAC AGC GCA TCT GAA ACG CTT GCC GCG ACA CCG AAA GCA GTG AAA GCA GCT AAT GAT AAT GCG AAT GGT CGG GTA CCT TCT GCC CGT AAG GTG AAT GGT AAG GCG CTT TCA TCG GAT ATA ACA CTG ACG CCG AAA GAT ATT GGT ACG CTT AAC TCA ACA ACA ATG TCA TTC AGC GGT --- --- --- --- --- --- --- --- --- --- GGT GCT GGT TGG TTC AAA TTA GCA --- --- --- --- --- --- ACG GTA ACC ATG CCA CAG GCG AGT TCT GTT GTT TCA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATT ACG TTG ATT GGT GGC GCG GGA TTT --- --- --- --- --- --- --- --- --- --- AAC GTG GGG TCA CCT CAA CAG GCA GGT ATA TCT GAA CTT GTT TTG CGT GCA GGT AAT --- --- GGT AAT CCG AAG GGG ATT ACT GGT GCT TTA TGG CAG CGC ACA TCG ACA GGG TTT ACA AAT TTT GCC TGG GTC AAT ACA TCT GGT GAT ACT TAC GAT ATT TAC GTT GCA ATC GGA AAT TAT GCG ACT GGT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GTA AAT ATT CAA TGG GAT TAT ACC AGT AAT GCC AGC GTG ACG ATT CAT ACG TCA CCA GCA TAT TCT GCT AAT AAG CCG GAA GGG TTA ACG GAC GGT ACA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GTT TAT TCA CTC TAT ACG CCA TCA GAG CAG TTT TAT CCG CCT GGC GCA CCA ATC CCG TGG CCA TCA GAT ACC GTT CCG TCT GGC TAT GCC CTG ATG CAG GGG CAG ACT TTT GAC AAA TCT GCA TAC CCG AAA CTT GCA GCC GCT TAT CCG TCA GGC GTG ATC CCT GAT ATG CGT GGC TGG ACG ATT AAG GGC AAA CCT GCC AGT GGT CGG GCC GTA TTG TCT CAG GAA CAG GAC GGC ATT AAA TCG CAC ACC CAC AGC GCC AGC GCA TCC AGT ACG GAT TTG GGG ACG AAA ACC ACA TCG TCG TTT GAT TAC GGC ACT AAA TCC ACG AAT AAC ACC GGG GCG CAC ACG CAC AGT GTG AGC GGT ACA GCC GCA AGT GCC GGA AAC CAT ACT CAT AGT GTC ACA GGC GCA TCA GCA GTC AGC CAG TGG TCA CAA AAT GGG TCA GTA CAT AAG --- --- --- GTA GTG TCT GCG GCC AGT GTG AAT ACA AGT GCT GCA GGA GCG CAC ACT CAT AGT GTC AGC GGC ACA GCT GCA TCT GCA GGT GCT CAC GCA CAT ACT GTC GGT ATT GGT GCT CAT ACG CAC TCT GTT GCG ATT GGC TCA CAT GGA CAC ACC ATC ACC GTT AAC GCT GCG GGT AAC GCG GAA AAC ACT GTC AAA AAC ATC GCA TTT AAC TAC ATT GTG AGG CTT GCA 


CODONML (in paml 3.14, January 2004)    /home/melissa/melissashare/runpaml/NEWdna80/b1372.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 1124
# site patterns = 416
    7   41    5   11    8   31   13    8   25    5   10   12    6    9    1
   17    1    2    1    1    5    1    8   17    2   30   13    1   37    1
   20    6   17    2    5    8   11   13    3    2    1    5    7   14    1
    6   11    3    1    6    1    2    1    3    3    1   39   13    4    2
   18   12    5    4   14    4    1    1    1    2    2    6    1    1    1
    1    1    1    2    1    2    1    3    1    1    2    7    1    2    1
    8    1    1    1    1    4    2    3    1    1    3    1    3    2    1
    1    1    1    3    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    2    1    2    7    2    2    7    2    1    2    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    2    1    1    4    1    1    1    1    1    1    1    1
    1    1    1    1    1    2    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    2    2    2    1    1    1    2    1    1    6
    2    2    6    3    7    1    1    1    1    1    3    4    6    5    8
    1    1    2    1    1    1    1    1    1    2    6    3    1    6    3
    5    1    4    1    1    3    4    1    1    1    1    1    1    1    2
    2    1    2    4    1    1    1    1    1    1    1    1    1    1    1
    1    2    1    1    1    1    1    1    3    1    1    1    1    2    1
    1    1    1    1    1    1    1    1    1    1    1    2    1    1    1
    1    1    1    1    1    2    1    1    3    1    1    2    1    2    4
    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    2    1    1
    3    2    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    4    2    3    5    2    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    2    1

K12                                  ATG GCA GTA AAG ATT TCA GGT CTG AAA GAC GGC ACA GGA CCG CAG AAC TGC ACA ATC CAG GCA AAA CGT AGC ACC ACG GTG CTG GCC TCA GAA AAT GAT GGG TAC GTT GAG CAG TTG GGA TTC CAT GGG ACC ATT TAT TCT CAA CCC TTT CTC ACG GCC CGC GAA GAG GCG TCC AGT GCT GCT TCG GCC ACT AGT GCT TCA GCG CTA ACA AAG GCA GCG ACC TCG CGG GCG AAC TCA TCA GCT GGA TCC ACG AGG TCT GCG GGA AGC TCG GCT TCG AGG TCG AGA GGC CGG CTT ATA CTC ACC ACG CCA GTA AAA GCC GAC AAT GCA GAG AAA CGT CTG CAG AAA GAC CAG AAC GGC GCT GAT ATA CCC GAT AAG GGA TGC TTC CTG AAC ATT GCG GTC AGT AAA ACA GAC TTT GAT AAG CGT GGT ATG CGT TAT GTG CGG GTT AAC CCT GCA GGT GCA ACA TCT TAC CCT GTT GTT GTT ATG CGT TCT GCT GGC TCA GTA AGC GAA CTG GCA TCA AGA GTC ATT ATC ACC ACG GCA CGA GGC GAT CCG ATG AAT AAC TGC GAG TTT AAC --- --- GGA TTT GTT ATG CCT GGT GGC TGG ACT GAC AGG TAT GCT TAT GGC ATG TTC TGG CAA TAT CAA AAT GAA CGA GCC ATT CAC ATA ATG AGT AAT AAG GAT TTG CGC TCT TTC GTT GCT TTC CCT GTT TTT TTT ATT GAA GGC CTG TCA ATA TCC GCA CCT GGT GAT CTC AAT ACG ACC AAG GGG GCA ACA AAT CCG GCG ACT TGT ATC GAC CTT TTT AAG AGT GGG CGT GGT GAG CAT TCG TTA AAC TTG TCG TGC AAA AAA CTT TTT GCC ACA GAC GCG GGT CAG ATG ATA GGT GAG TAT TTA TGG CGT --- --- AAT GAT GGC GCT AAA ACT TAC CTG CTG CTT ACC AAT CAA GTT TAT GGT GGC TGG AAT ACA TTA AGA CCG TTT ATT GAT GGA AAA TCC AGT CAA CCA AGA CGG TCT GGT GTT GAG TTT GGT AAA GAT ATT ACT TTA ACC GCC GCG CAT GTG GCT GCC AGA GCA ACG GAT ACA TAT GAT GCG TGG GCC GCT TAC GTC AGC TGC TCA ACC TCG AAA AAT CTT CCA CCA AGC TAC CCA GTC ATC GGT CAT CAC ACA TCT ACA TCG GCA CAC CTA GCC AAC GTG AAC ACG GCT GCT AAC TCC GGT GCT GGT GCA TCA ACA CAT AAT CAA AAC TAT GCA TCT GGC CTG TCC ACT AGC GTC AGG 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ..C ..T ..A ..C .G. ... ... G.. ... ... G.. ... ..T ... ... ... ..T ... ... ... ... ... ..G ... ... ... ... ..C ... ... ... ... ... ..T ..T .T. ... ..G ... ... ... ..C A.. ... ... ..T ... ... ..G G.. .T. .A. ..T ..A ..G ..C T.. ..A A.. T.. .G. G.C ..G ..C ..C ..T ..A .A. ..C ..A .A. ..T ..C ..A .TA ..T ..T ... ..T ... ... ... ... ..T T.A ... ..T ..G ..G ..G CTG ..T A.C GGG AAA TAC ACC GC. C.G G.T GCA ACG A.A .CA CAG AAA .GG .TA .TT CAG C.T AGC GCG .CC AGC ACA TC. G.. .TG CTG GCG ACG CCA AAG --- --- --- --- --- TC. ..A ..G G.C TAT .AC CTT G.T AAC ACT G.. CAG .AC .C. .C. ACA G.A CAA AAA GG. A.T GT. C.G ..C AGT AGT GC. AC. .AC .G. G.A T.T .A. .TT ACA CCG AAA GCA GTG ..A GCA .CT AA. G.T AAT GCG AAT GG. CGG G.A ... TC. .C. C.T .AG .TG .AT GCG CT. .CA TCG GAT A.A ACA .TG ACG .CG G.. ATT G.T A.G C.. A.. .C. .CA TCA TTC .GC --- --- --- --- --- --- .G. .GG TTC AAA ..A --- --- --- --- --- A.G G.. A.. ATG ..A CAG AG. TCT TCA --- --- --- --- --- --- --- --- --- --- --- --- --- A.. ..G .TT G.. ..C GCG ..A --- --- --- --- --- G.. GG. .CA CCT C.. .AG GCA .GT .T. TCT TT. .CA --- .AT CCG AAG ATT AC. ... ... .AG CGC ACA TCG ACA ..G TT. .C. .A. .TT GCC TG. G.C .AT .CA TCT AC. ..C .A. ATT .AC GT. G.. A.C G.. AAT .A. .C. .G. --- --- --- --- --- --- --- --- GTA AA. A.. C.A .GG TA. .GT A.. GCC .GC G.G ..G ATT CAT ACG TCA C.A T.T GCT AAG C.. ..A GGG .TA ..C .GT --- --- --- --- --- --- --- --- T.A CTC T.T .CG .CA T.. GAG TTT ..T ..G CCT ... ..C ..C ... ..G A.A G.C AGT AAC ..T G.C A.A GG. .CA TCA G.A .TC CAG TGG ..A CAA AA. ..G .T. CAT .AG TC. GCG GCC .GT GTG AAT G.. ..A G.C AG. ..A TCT ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ..C ..T ..A ..C .G. ... ... G.. ... ... G.. ... ..T ... ... ... ..T ... ... ... ... ... ..G ... ... ... ... ..C ... ... ... ... ... ..T ..T .T. ... ..G ..A ... ... ..C A.. ... ... ..T ... ... ..G G.. .T. .A. ..T ..A ..G ..C T.. ..A A.. T.. .G. G.C ..G ..C ..C ..T ..A .A. ..C ..A .A. ..T ..C ..A .TA ..T ..T ... ..T ... ... ... ... ..T T.A ... ..T ..G ..G ..G CTG ..T A.C GGG AAA TAC ACC GC. C.G G.T GCA ACG A.A .CA CAG AAA .GG .TA .TT CAG C.T AGC GCG .CC AGC ACA TC. G.. .TG CTG GCG ACG CCA AAG --- --- --- --- --- TC. ..A ..G G.C TAT .AC CTT G.T AAC ACT G.. CAG .AC .C. .C. ACA G.A CAA AAA GG. A.T GT. C.G ..C AGT AGT GC. AC. .AC .G. G.A T.T .A. .TT ACA CCG AAA GCA GTG ..A GCA .CT AA. G.T AAT GCG AAT GG. CGG G.A ... TC. .C. C.T .AG .TG .AT GCG CT. .CA TCG GAT A.A ACA .TG ACG .CG G.. ATT G.T A.G C.. A.. .C. .CA TCA TTC .GC --- --- --- --- --- --- .G. .GG TTC AAA ..A --- --- --- --- --- A.G G.. A.. ATG ..A CAG AG. TCT TCA --- --- --- --- --- --- --- --- --- --- --- --- --- A.. ..G .TT G.. ..C GCG ..A --- --- --- --- --- G.. GG. .CA CCT C.. .AG GCA .GT .T. TCT TT. .CA --- .AT CCG AAG ATT AC. ... ... .AG CGC ACA TCG ACA ..G TT. .C. .A. .TT GCC TG. G.C .AT .CA TCT AC. ..C .A. ATT .AC GT. G.. A.C G.. AAT .A. .C. .G. --- --- --- --- --- --- --- --- GTA AA. A.. C.A .GG TA. .GT A.. GCC .GC G.G ..G ATT CAT ACG TCA C.A T.T GCT AAG C.. ..A GGG .TA ..C .GT --- --- --- --- --- --- --- --- T.A CTC T.T .CG .CA T.. GAG TTT ..T ..G CCT ... ..C ..C ... ..G A.A G.C AGT AAC ..T G.C A.A GG. .CA TCA G.A .TC CAG TGG ..A CAA AA. ..G .T. CAT .AG TC. GCG GCC .GT GTG AAT G.. ..A G.C AG. ..A TCT ... ... 



Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 18  9  9 | Ser TCT 24 25 25 | Tyr TAT 21 12 12 | Cys TGT  1  0  0
    TTC  7  3  3 |     TCC 21 17 17 |     TAC 11  9  9 |     TGC  5  1  1
Leu TTA  5  4  4 |     TCA 44 43 43 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  6  5  5 |     TCG 20 17 17 |     TAG  0  0  0 | Trp TGG  8  7  7
--------------------------------------------------------------------------
Leu CTT  7 10 10 | Pro CCT  7  5  5 | His CAT 12 10 10 | Arg CGT 16  9  9
    CTC  3  3  3 |     CCC  2  1  1 |     CAC  9  8  8 |     CGC  5  4  4
    CTA  2  0  0 |     CCA  8  7  7 | Gln CAA  8  9  9 |     CGA  3  0  0
    CTG 23 11 11 |     CCG 12 14 14 |     CAG 19 23 23 |     CGG  6  3  3
--------------------------------------------------------------------------
Ile ATT 19 17 17 | Thr ACT  9 17 17 | Asn AAT 21 19 19 | Ser AGT 24 26 26
    ATC  9  6  6 |     ACC 30 21 21 |     AAC 33 22 22 |     AGC 23 28 28
    ATA  5  4  4 |     ACA 28 28 28 | Lys AAA 36 34 34 | Arg AGA  8  2  2
Met ATG 15  9  9 |     ACG 39 43 43 |     AAG 20 20 20 |     AGG  5  2  2
--------------------------------------------------------------------------
Val GTT 24 12 12 | Ala GCT 44 32 32 | Asp GAT 35 22 22 | Gly GGT 33 27 27
    GTC  7  8  8 |     GCC 51 55 55 |     GAC 14  8  8 |     GGC 27 15 15
    GTA  8 11 11 |     GCA 70 71 71 | Glu GAA 32 24 25 |     GGA 15 10 10
    GTG 17 20 20 |     GCG 57 56 56 |     GAG 18 18 17 |     GGG 11 15 15
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.17054    C:0.12679    A:0.28929    G:0.41339
position  2:    T:0.15625    C:0.41607    A:0.25804    G:0.16964
position  3:    T:0.28125    C:0.22946    A:0.24286    G:0.24643

#2: O157           
position  1:    T:0.15654    C:0.12049    A:0.30690    G:0.41607
position  2:    T:0.13594    C:0.46550    A:0.24511    G:0.15345
position  3:    T:0.25953    C:0.21524    A:0.25438    G:0.27085

#3: EDL933         
position  1:    T:0.15654    C:0.12049    A:0.30690    G:0.41607
position  2:    T:0.13594    C:0.46550    A:0.24511    G:0.15345
position  3:    T:0.25953    C:0.21524    A:0.25541    G:0.26982

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      36 | Ser S TCT      74 | Tyr Y TAT      45 | Cys C TGT       1
      TTC      13 |       TCC      55 |       TAC      29 |       TGC       7
Leu L TTA      13 |       TCA     130 | *** * TAA       0 | *** * TGA       0
      TTG      16 |       TCG      54 |       TAG       0 | Trp W TGG      22
------------------------------------------------------------------------------
Leu L CTT      27 | Pro P CCT      17 | His H CAT      32 | Arg R CGT      34
      CTC       9 |       CCC       4 |       CAC      25 |       CGC      13
      CTA       2 |       CCA      22 | Gln Q CAA      26 |       CGA       3
      CTG      45 |       CCG      40 |       CAG      65 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      53 | Thr T ACT      43 | Asn N AAT      59 | Ser S AGT      76
      ATC      21 |       ACC      72 |       AAC      77 |       AGC      79
      ATA      13 |       ACA      84 | Lys K AAA     104 | Arg R AGA      12
Met M ATG      33 |       ACG     125 |       AAG      60 |       AGG       9
------------------------------------------------------------------------------
Val V GTT      48 | Ala A GCT     108 | Asp D GAT      79 | Gly G GGT      87
      GTC      23 |       GCC     161 |       GAC      30 |       GGC      57
      GTA      30 |       GCA     212 | Glu E GAA      81 |       GGA      35
      GTG      57 |       GCG     169 |       GAG      53 |       GGG      41
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.16166    C:0.12280    A:0.30046    G:0.41509
position  2:    T:0.14337    C:0.44742    A:0.24984    G:0.15937
position  3:    T:0.26747    C:0.22044    A:0.25049    G:0.26159

Codon frequencies under model, for use in evolver:
  0.00637215  0.00525177  0.00596757  0.00623210
  0.01988575  0.01638935  0.01862316  0.01944870
  0.01110409  0.00915172  0.00000000  0.00000000
  0.00708339  0.00583796  0.00000000  0.00692771
  0.00484026  0.00398922  0.00453294  0.00473388
  0.01510513  0.01244929  0.01414608  0.01477315
  0.00843462  0.00695161  0.00789909  0.00824924
  0.00538051  0.00443449  0.00503889  0.00526226
  0.01184318  0.00976087  0.01109124  0.01158289
  0.03695937  0.03046102  0.03461274  0.03614707
  0.02063790  0.01700925  0.01932755  0.02018432
  0.01316509  0.01085035  0.01232921  0.01287575
  0.01636162  0.01348485  0.01532278  0.01600202
  0.05106017  0.04208256  0.04781826  0.04993797
  0.02851170  0.02349865  0.02670143  0.02788507
  0.01818786  0.01498999  0.01703307  0.01778812



Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
O157                 0.5738 (0.2400 0.4183)
EDL933               0.5707 (0.2400 0.4206) 0.0000 (0.0000 0.0013)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -6472.135342     +0.000000
   4..1     4..5     5..2     5..3  
  5.23106 12.91371  0.00000  0.00107  2.78415  0.73533  0.00000  0.15592 222.67364
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =  18.14585

(1: 5.231059, (2: 0.000004, 3: 0.001070): 12.913714);

(K12: 5.231059, (O157: 0.000004, EDL933: 0.001070): 12.913714);

Detailed output identifying parameters

kappa (ts/tv) =  2.78415


dN/dS for site classes (K=3)

p:   0.73533  0.00000  0.26467
w:   0.15592  1.00000222.67364

dN & dS for each branch

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

   4..1       5.231   1195.4   2176.6  59.0489   2.6765   0.0453   54.2 5825.5
   4..5      12.914   1195.4   2176.6  59.0489   6.6073   0.1119  133.8 14381.2
   5..2       0.000   1195.4   2176.6  59.0489   0.0000   0.0000    0.0    0.0
   5..3       0.001   1195.4   2176.6  59.0489   0.0005   0.0000    0.0    1.2


Positively selected sites (*: P>95%; **: P>99%)

            Pr(w>1)     post mean +- SE for w

    18 Q      0.620         138.117
    38 L      0.624         139.112
   212 S      0.666         148.392
   215 L      0.618         137.632
   234 T      0.669         149.016
   240 A      0.660         147.098
   254 S      0.969*        215.858
   304 S      0.912         202.984
   353 R      0.602         134.212
   481 T      0.935         208.205
   491 S      0.969*        215.858
   494 D      0.603         134.326
   495 N      1.000**       222.672
   497 E      0.990**       220.467
   498 K      0.998**       222.212
   499 R      1.000**       222.659
   500 L      1.000**       222.671
   501 Q      1.000**       222.659
   502 K      0.989*        220.230
   503 D      0.997**       222.029
   504 Q      0.997**       222.004
   505 N      1.000**       222.582
   506 G      0.999**       222.552
   507 A      0.901         200.715
   508 D      0.974*        216.919
   509 I      1.000**       222.656
   510 P      1.000**       222.657
   511 D      0.969*        215.784
   512 K      0.971*        216.149
   513 G      0.983*        218.855
   514 C      1.000**       222.670
   515 F      0.956*        212.941
   516 L      1.000**       222.672
   518 N      1.000**       222.581
   519 I      0.852         189.836
   521 A      1.000**       222.588
   522 V      0.999**       222.353
   523 S      0.997**       221.983
   525 T      0.882         196.365
   526 D      1.000**       222.669
   527 F      1.000**       222.610
   529 D      0.999**       222.537
   530 K      1.000**       222.604
   531 R      1.000**       222.658
   537 R      0.996**       221.677
   539 N      0.602         134.049
   541 P      0.925         205.881
   542 A      1.000**       222.646
   543 G      0.858         191.107
   544 A      1.000**       222.617
   545 T      0.901         200.714
   546 S      1.000**       222.601
   550 Y      1.000**       222.618
   551 P      0.662         147.414
   552 V      1.000**       222.667
   553 V      0.944         210.272
   556 R      1.000**       222.657
   557 S      0.967*        215.401
   558 A      1.000**       222.652
   559 G      1.000**       222.608
   560 S      0.997**       221.977
   561 V      0.963*        214.370
   562 S      0.995**       221.577
   563 E      0.953*        212.129
   565 A      0.999**       222.562
   566 S      1.000**       222.653
   567 R      0.991**       220.604
   568 V      0.977*        217.473
   569 I      0.958*        213.254
   570 I      0.628         139.951
   571 T      0.908         202.254
   572 T      0.973*        216.628
   573 A      0.661         147.334
   575 R      0.995**       221.489
   578 G      0.999**       222.556
   579 D      1.000**       222.640
   580 P      1.000**       222.604
   581 M      0.997**       221.948
   582 N      1.000**       222.648
   583 N      0.601         133.873
   584 C      1.000**       222.656
   585 E      0.975*        217.007
   586 F      0.998**       222.278
   587 N      0.856         190.542
   590 G      1.000**       222.598
   591 F      0.998**       222.283
   592 V      1.000**       222.665
   593 M      0.936         208.418
   595 G      0.996**       221.816
   596 G      0.674         150.081
   597 W      0.991**       220.582
   598 T      0.981*        218.455
   599 D      0.991**       220.560
   600 R      0.992**       220.982
   602 R      1.000**       222.658
   603 Y      1.000**       222.646
   604 A      0.994**       221.377
   605 Y      0.990*        220.400
   606 G      1.000**       222.638
   607 M      1.000**       222.658
   608 F      0.994**       221.406
   609 W      1.000**       222.631
   610 Q      0.981*        218.511
   611 Y      1.000**       222.655
   612 Q      0.969*        215.754
   613 N      0.601         133.873
   615 E      1.000**       222.650
   616 R      0.988*        220.087
   617 A      0.905         201.624
   618 I      0.625         139.241
   619 H      0.624         138.935
   622 M      0.882         196.372
   624 S      1.000**       222.653
   625 N      1.000**       222.654
   626 K      0.993**       221.142
   640 A      0.663         147.609
   641 F      0.999**       222.438
   642 P      0.999**       222.513
   643 V      1.000**       222.647
   644 F      0.597         133.089
   652 S      0.935         208.177
   654 S      0.669         148.950
   655 A      0.997**       221.948
   657 G      1.000**       222.653
   659 D      0.978*        217.876
   660 L      0.999**       222.541
   663 N      1.000**       222.652
   685 L      0.625         139.128
   686 D      0.999**       222.537
   687 F      0.600         133.561
   688 K      0.997**       222.018
   691 R      1.000**       222.651
   705 L      0.623         138.765
   706 S      0.996**       221.816
   707 C      0.991**       220.759
   708 K      1.000**       222.654
   709 K      0.618         137.720
   710 L      0.997**       221.951
   711 F      1.000**       222.610
   712 A      0.924         205.683
   714 D      0.999**       222.556
   716 I      0.625         139.241
   718 A      0.993**       221.175
   720 G      0.968*        215.630
   725 R      0.988*        220.087
   726 M      0.997**       222.048
   727 I      0.999**       222.542
   728 G      1.000**       222.599
   730 E      1.000**       222.657
   731 Y      0.997**       222.040
   736 R      0.990**       220.524
   739 N      1.000**       222.651
   740 D      0.999**       222.539
   742 A      0.993**       221.177
   743 K      0.648         144.364
   744 T      0.648         144.368
   745 Y      0.975*        217.133
   746 L      1.000**       222.621
   747 L      0.990**       220.486
   748 L      0.970*        216.105
   749 T      0.934         207.981
   750 N      0.981*        218.379
   751 Q      1.000**       222.660
   754 V      0.970*        216.077
   757 G      1.000**       222.586
   758 W      0.999**       222.364
   759 N      0.992**       220.855
   761 L      0.994**       221.270
   763 P      1.000**       222.653
   764 F      0.617         137.557
   800 S      1.000**       222.563
   801 G      0.977*        217.604
   803 E      0.954*        212.355
   804 F      0.999**       222.414
   806 G      0.993**       221.074
   807 S      0.669         148.950
   808 K      0.992**       220.991
   810 I      0.996**       221.859
   811 T      0.945         210.415
   812 L      0.970*        216.061
   814 A      0.996**       221.858
   815 A      1.000**       222.650
   816 H      1.000**       222.658
   817 V      0.999**       222.392
   818 A      0.970*        216.049
   820 F      0.617         137.557
   821 A      0.921         205.108
   822 R      1.000**       222.570
   823 R      0.992**       220.982
   824 A      0.998**       222.275
   825 T      0.646         144.004
   826 D      0.604         134.459
   827 T      0.998**       222.309
   828 Y      0.999**       222.544
   829 A      0.905         201.624
   831 A      0.968*        215.610
   832 D      0.999**       222.539
   899 T      0.975*        217.065
   900 S      1.000**       222.618
   901 K      0.998**       222.288
   902 N      0.981*        218.385
   903 L      0.972*        216.480
   905 P      0.999**       222.560
   906 E      0.953*        212.129
   907 S      1.000**       222.660
   910 V      0.999**       222.422
  1018 S      0.973*        216.650
  1019 T      0.907         201.913
  1020 N      1.000**       222.582
  1021 S      1.000**       222.652
  1024 A      1.000**       222.582
  1028 S      1.000**       222.653
  1029 L      0.990*        220.437
  1030 A      0.907         201.898
  1031 N      0.982*        218.584
  1032 V      0.822         183.124
  1033 N      1.000**       222.656
  1034 T      0.790         175.906
  1035 A      0.830         184.955
  1037 A      1.000**       222.650
  1038 N      1.000**       222.671
  1040 G      1.000**       222.654
  1041 A      0.988*        220.058
  1043 S      1.000**       222.653
  1045 S      1.000**       222.653
  1046 T      0.934         208.069
  1052 H      0.995**       221.490
  1053 N      0.999**       222.550
  1054 Q      1.000**       222.652
  1055 N      0.889         197.915
  1056 Y      1.000**       222.667
  1057 A      0.999**       222.552
  1059 S      1.000**       222.653
  1060 S      0.665         148.187
  1067 S      1.000**       222.653
  1068 L      0.990*        220.388
  1069 S      0.998**       222.127
  1074 S      1.000**       222.613


Bayes Empirical Bayes (BEB) analysis
Positively selected sites (*: P>95%; **: P>99%)

            Pr(w>1)     post mean +- SE for w

    18 Q      0.914         9.636 +- 2.815
    27 K      0.857         9.068 +- 3.513
    31 T      0.883         9.324 +- 3.230
    38 L      0.922         9.724 +- 2.681
    98 A      0.881         9.303 +- 3.255
   146 A      0.859         9.081 +- 3.502
   212 S      0.939         9.895 +- 2.387
   213 A      0.857         9.068 +- 3.515
   215 L      0.953*        10.035 +- 2.107
   234 T      0.941         9.913 +- 2.353
   240 A      0.935         9.852 +- 2.464
   252 N      0.861         9.104 +- 3.474
   254 S      0.942         9.919 +- 2.341
   282 R      0.845         8.946 +- 3.634
   289 G      0.852         9.020 +- 3.561
   304 S      0.926         9.762 +- 2.619
   353 R      0.839         8.886 +- 3.690
   481 T      0.943         9.931 +- 2.319
   491 S      0.942         9.919 +- 2.341
   494 D      0.829         8.787 +- 3.782
   495 N      1.000**       10.497 +- 0.168
   497 E      0.989*        10.394 +- 0.999
   498 K      0.994**       10.443 +- 0.737
   499 R      0.999**       10.495 +- 0.215
   500 L      1.000**       10.496 +- 0.183
   501 Q      0.999**       10.493 +- 0.260
   502 K      0.993**       10.433 +- 0.797
   503 D      0.995**       10.449 +- 0.695
   504 Q      0.994**       10.446 +- 0.716
   505 N      0.998**       10.483 +- 0.404
   506 G      0.997**       10.472 +- 0.513
   507 A      0.873         9.230 +- 3.341
   508 D      0.975*        10.250 +- 1.556
   509 I      0.999**       10.493 +- 0.266
   510 P      0.999**       10.493 +- 0.263
   511 D      0.978*        10.279 +- 1.459
   512 K      0.977*        10.269 +- 1.496
   513 G      0.975*        10.250 +- 1.560
   514 C      1.000**       10.497 +- 0.164
   515 F      0.942         9.922 +- 2.335
   516 L      1.000**       10.497 +- 0.161
   518 N      0.998**       10.483 +- 0.403
   519 I      0.880         9.294 +- 3.266
   521 A      0.998**       10.483 +- 0.408
   522 V      0.993**       10.430 +- 0.814
   523 S      0.997**       10.470 +- 0.531
   524 K      0.831         8.803 +- 3.766
   525 T      0.941         9.911 +- 2.354
   526 D      1.000**       10.496 +- 0.191
   527 F      0.998**       10.479 +- 0.452
   529 D      0.998**       10.477 +- 0.465
   530 K      0.998**       10.478 +- 0.458
   531 R      0.999**       10.495 +- 0.216
   537 R      0.997**       10.467 +- 0.562
   539 N      0.848         8.979 +- 3.602
   541 P      0.933         9.833 +- 2.499
   542 A      0.999**       10.487 +- 0.345
   543 G      0.894         9.436 +- 3.093
   544 A      0.997**       10.469 +- 0.540
   545 T      0.873         9.230 +- 3.341
   546 S      0.997**       10.476 +- 0.478
   550 Y      0.998**       10.477 +- 0.466
   551 P      0.932         9.819 +- 2.522
   552 V      0.999**       10.495 +- 0.218
   553 V      0.943         9.926 +- 2.329
   554 V      0.855         9.042 +- 3.541
   555 M      0.831         8.799 +- 3.772
   556 R      0.999**       10.489 +- 0.326
   557 S      0.937         9.874 +- 2.426
   558 A      0.999**       10.491 +- 0.292
   559 G      0.999**       10.487 +- 0.347
   560 S      0.997**       10.473 +- 0.511
   561 V      0.939         9.885 +- 2.409
   562 S      0.997**       10.467 +- 0.562
   563 E      0.948         9.980 +- 2.225
   565 A      0.998**       10.478 +- 0.456
   566 S      0.999**       10.490 +- 0.305
   567 R      0.994**       10.445 +- 0.721
   568 V      0.991**       10.417 +- 0.886
   569 I      0.948         9.975 +- 2.232
   570 I      0.924         9.739 +- 2.655
   571 T      0.882         9.319 +- 3.237
   572 T      0.946         9.964 +- 2.255
   573 A      0.916         9.656 +- 2.786
   575 R      0.978*        10.278 +- 1.473
   576 T      0.883         9.324 +- 3.230
   578 G      0.997**       10.472 +- 0.515
   579 D      0.999**       10.489 +- 0.322
   580 P      0.998**       10.478 +- 0.457
   581 M      0.994**       10.445 +- 0.726
   582 N      0.999**       10.491 +- 0.295
   583 N      0.851         9.002 +- 3.580
   584 C      0.999**       10.486 +- 0.365
   585 E      0.976*        10.258 +- 1.533
   586 F      0.998**       10.477 +- 0.472
   587 N      0.904         9.534 +- 2.964
   590 G      0.999**       10.486 +- 0.368
   591 F      0.998**       10.479 +- 0.447
   592 V      0.999**       10.492 +- 0.271
   593 M      0.964*        10.142 +- 1.853
   595 G      0.997**       10.468 +- 0.551
   596 G      0.933         9.825 +- 2.512
   597 W      0.992**       10.424 +- 0.860
   598 T      0.980*        10.306 +- 1.377
   599 D      0.989*        10.390 +- 1.034
   600 R      0.990**       10.409 +- 0.928
   602 R      0.999**       10.495 +- 0.216
   603 Y      0.999**       10.488 +- 0.340
   604 A      0.996**       10.461 +- 0.609
   605 Y      0.963*        10.130 +- 1.891
   606 G      0.998**       10.483 +- 0.398
   607 M      0.999**       10.492 +- 0.269
   608 F      0.988*        10.382 +- 1.075
   609 W      0.998**       10.479 +- 0.446
   610 Q      0.964*        10.138 +- 1.867
   611 Y      0.999**       10.491 +- 0.294
   612 Q      0.941         9.910 +- 2.360
   613 N      0.851         9.002 +- 3.580
   614 N      0.809         8.584 +- 3.952
   615 E      0.999**       10.491 +- 0.284
   616 R      0.964*        10.143 +- 1.858
   617 A      0.883         9.327 +- 3.228
   618 I      0.924         9.740 +- 2.654
   619 H      0.926         9.760 +- 2.621
   621 I      0.850         8.999 +- 3.584
   622 M      0.941         9.911 +- 2.354
   624 S      0.999**       10.490 +- 0.305
   625 N      0.999**       10.487 +- 0.351
   626 K      0.992**       10.420 +- 0.873
   640 A      0.922         9.714 +- 2.696
   641 F      0.997**       10.472 +- 0.516
   642 P      0.996**       10.460 +- 0.616
   643 V      0.999**       10.491 +- 0.293
   644 F      0.916         9.662 +- 2.774
   652 S      0.943         9.931 +- 2.319
   653 I      0.846         8.951 +- 3.630
   654 S      0.941         9.913 +- 2.353
   655 A      0.994**       10.445 +- 0.726
   657 G      0.999**       10.492 +- 0.270
   659 D      0.989*        10.395 +- 0.998
   660 L      0.996**       10.463 +- 0.591
   663 N      0.999**       10.491 +- 0.286
   685 L      0.924         9.740 +- 2.654
   686 D      0.998**       10.477 +- 0.465
   687 F      0.911         9.606 +- 2.857
   688 K      0.994**       10.440 +- 0.756
   689 S      0.847         8.966 +- 3.614
   691 R      0.999**       10.486 +- 0.366
   705 L      0.917         9.670 +- 2.764
   706 S      0.997**       10.469 +- 0.545
   707 C      0.960*        10.103 +- 1.954
   708 K      0.999**       10.493 +- 0.263
   709 K      0.921         9.714 +- 2.694
   710 L      0.994**       10.438 +- 0.775
   711 F      0.998**       10.478 +- 0.462
   712 A      0.926         9.763 +- 2.617
   713 T      0.850         8.999 +- 3.584
   714 D      0.997**       10.469 +- 0.542
   716 I      0.924         9.740 +- 2.654
   718 A      0.996**       10.458 +- 0.630
   720 G      0.957*        10.065 +- 2.043
   725 R      0.964*        10.143 +- 1.858
   726 M      0.994**       10.439 +- 0.761
   727 I      0.998**       10.481 +- 0.422
   728 G      0.998**       10.485 +- 0.373
   730 E      0.999**       10.492 +- 0.267
   731 Y      0.997**       10.471 +- 0.524
   736 R      0.992**       10.421 +- 0.879
   739 N      0.999**       10.492 +- 0.281
   740 D      0.998**       10.477 +- 0.465
   742 A      0.995**       10.456 +- 0.648
   743 K      0.910         9.597 +- 2.872
   744 T      0.903         9.525 +- 2.975
   745 Y      0.953*        10.028 +- 2.121
   746 L      0.997**       10.471 +- 0.522
   747 L      0.995**       10.456 +- 0.660
   748 L      0.942         9.919 +- 2.343
   749 T      0.926         9.762 +- 2.620
   750 N      0.979*        10.293 +- 1.420
   751 Q      0.999**       10.493 +- 0.260
   754 V      0.988*        10.386 +- 1.036
   756 G      0.830         8.794 +- 3.774
   757 G      0.998**       10.477 +- 0.470
   758 W      0.997**       10.470 +- 0.536
   759 N      0.994**       10.445 +- 0.723
   760 T      0.868         9.179 +- 3.397
   761 L      0.987*        10.374 +- 1.113
   762 R      0.867         9.167 +- 3.408
   763 P      0.999**       10.492 +- 0.271
   764 F      0.937         9.871 +- 2.430
   766 I      0.850         8.999 +- 3.583
   767 D      0.830         8.794 +- 3.774
   800 S      0.996**       10.461 +- 0.612
   801 G      0.989*        10.395 +- 0.995
   802 V      0.846         8.958 +- 3.624
   803 E      0.948         9.984 +- 2.217
   804 F      0.997**       10.469 +- 0.540
   806 G      0.995**       10.453 +- 0.671
   807 S      0.941         9.913 +- 2.353
   808 K      0.991**       10.411 +- 0.917
   809 D      0.809         8.584 +- 3.951
   810 I      0.991**       10.410 +- 0.925
   811 T      0.932         9.821 +- 2.521
   812 L      0.955*        10.054 +- 2.068
   814 A      0.991**       10.410 +- 0.925
   815 A      0.999**       10.490 +- 0.305
   816 H      0.999**       10.493 +- 0.262
   817 V      0.995**       10.455 +- 0.654
   818 A      0.940         9.898 +- 2.383
   820 F      0.937         9.871 +- 2.430
   821 A      0.931         9.810 +- 2.537
   822 R      0.998**       10.480 +- 0.438
   823 R      0.990**       10.409 +- 0.928
   824 A      0.994**       10.444 +- 0.732
   825 T      0.933         9.828 +- 2.506
   826 D      0.822         8.712 +- 3.847
   827 T      0.994**       10.445 +- 0.720
   828 Y      0.997**       10.470 +- 0.535
   829 A      0.883         9.327 +- 3.228
   831 A      0.957*        10.069 +- 2.035
   832 D      0.998**       10.477 +- 0.465
   899 T      0.949         9.988 +- 2.206
   900 S      0.998**       10.476 +- 0.476
   901 K      0.996**       10.459 +- 0.623
   902 N      0.980*        10.299 +- 1.398
   903 L      0.927         9.774 +- 2.599
   904 P      0.901         9.505 +- 2.999
   905 P      0.997**       10.470 +- 0.535
   906 E      0.948         9.980 +- 2.225
   907 S      0.999**       10.489 +- 0.320
   910 V      0.995**       10.454 +- 0.661
   932 A      0.859         9.081 +- 3.502
  1018 S      0.945         9.946 +- 2.290
  1019 T      0.881         9.305 +- 3.253
  1020 N      0.998**       10.483 +- 0.404
  1021 S      0.999**       10.491 +- 0.296
  1024 A      0.998**       10.483 +- 0.404
  1028 S      0.999**       10.490 +- 0.305
  1029 L      0.955*        10.048 +- 2.080
  1030 A      0.881         9.305 +- 3.253
  1031 N      0.992**       10.421 +- 0.867
  1032 V      0.873         9.227 +- 3.344
  1033 N      0.999**       10.493 +- 0.262
  1034 T      0.860         9.099 +- 3.483
  1035 A      0.875         9.242 +- 3.327
  1037 A      0.999**       10.491 +- 0.298
  1038 N      1.000**       10.497 +- 0.180
  1040 G      0.999**       10.493 +- 0.266
  1041 A      0.992**       10.425 +- 0.845
  1043 S      0.999**       10.490 +- 0.305
  1044 A      0.865         9.143 +- 3.435
  1045 S      0.999**       10.489 +- 0.324
  1046 T      0.935         9.847 +- 2.476
  1052 H      0.996**       10.460 +- 0.618
  1053 N      0.998**       10.479 +- 0.448
  1054 Q      0.999**       10.491 +- 0.297
  1055 N      0.915         9.647 +- 2.801
  1056 Y      0.999**       10.494 +- 0.229
  1057 A      0.998**       10.479 +- 0.450
  1059 S      0.999**       10.490 +- 0.305
  1060 S      0.931         9.814 +- 2.531
  1067 S      0.999**       10.490 +- 0.305
  1068 L      0.963*        10.126 +- 1.900
  1069 S      0.997**       10.475 +- 0.489
  1074 S      0.998**       10.477 +- 0.466



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  1.000

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.994 0.005 0.000 0.000 0.000 0.000 0.000

sum of density on p0-p1 =   1.000000
