
seed used = 139980929

K12                                  ATG GCG CGT TCC AAA ACT GCT CAG CCA AAA CAC TCA CTG CGT AAA ATC GCA GTT GTA GTA GCC ACA GCG GTT AGC GGC ATG TCT GTT TAT GCA CAG GCA GCG GTT GAA CCG AAA GAA GAC ACT ATC ACC GTT ACC GCT GCA CCT GCG CCG CAA GAA AGC GCA TGG GGG CCT GCT GCA ACT ATT GCG GCG CGA CAG TCT GCT ACC GGC ACT AAA ACC GAT ACG CCG ATT CAA AAA GTG CCA CAG TCT ATT TCT GTT GTG ACC GCC GAA GAG ATG GCG CTG CAT CAG CCG AAG TCG GTA AAA GAA GCG CTT AGC TAC ACG CCG GGT GTC TCT GTT GGT ACG CGT GGC GCA TCC AAC ACC TAT GAC CAC CTG ATC ATT CGC GGC TTT GCG GCA GAA GGC CAA AGC CAG AAT AAC TAT CTG AAT GGC CTG AAG TTG CAG GGC AAC TTC TAT AAC GAT GCG GTC ATT GAC CCG TAT ATG CTG GAA CGC GCT GAA ATT ATG CGT GGC CCG GTT TCC GTG CTT TAC GGT AAA AGC AGT CCT GGC GGC CTG TTG AAT ATG GTC AGC AAG CGT CCG ACC ACC GAA CCG CTG AAA GAA GTT CAG TTT AAA GCC GGT ACT GAC AGC CTG TTC CAG ACT GGT TTT GAC TTT AGC GAT TCG TTG GAT GAT GAC GGT GTT TAC TCT TAT CGC CTG ACC GGT CTT GCG CGT TCT GCC AAT GCC CAG CAG AAA GGG TCA GAA GAG CAG CGT TAT GCT ATT GCA CCG GCG TTC ACC TGG CGT CCG GAT GAT AAA ACC AAT TTT ACC TTC CTT TCT TAC TTC CAG AAC GAG CCG GAA ACC GGT TAT TAC GGC TGG TTG CCG AAA GAG GGA ACC GTT GAG CCG CTG CCG AAC GGT AAG CGT CTG CCG ACA GAC TTT AAT GAA GGG GCG AAG AAC AAC ACC TAT TCT CGT AAT GAG AAG ATG GTC GGC TAC AGC TTC GAT CAC GAA TTT AAC GAC ACC TTT ACT GTG CGT CAG AAC CTG CGC TTT GCT GAA AAC AAA ACC TCG CAA AAC AGC GTT TAT GGT TAC GGC GTC TGC TCC GAT CCG GCG AAT GCT TAC AGC AAA --- --- --- --- --- --- CAG TGT GCG GCA TTA GCG CCA GCG GAT AAA GGC CAT TAT CTG GCA CGT AAA TAC GTC GTT GAT GAT GAG AAG CTG CAA AAC TTC TCC GTT GAT ACC CAG TTG CAG AGC AAG TTT GCC ACT GGC GAT ATC GAC CAC ACC CTG CTG ACC GGT GTC GAC TTT ATG CGT ATG CGT AAT GAC ATC AAC GCC TGG TTT GGT TAC GAC GAC TCT GTG CCA CTG CTC AAT CTG TAC AAT CCG GTG AAT ACC GAT TTC GAC TTC AAT GCC AAA GAT CCG GCA AAC TCC GGC CCT TAC CGC ATT CTG AAT AAA CAG AAA CAA ACG GGC GTT TAT GTT CAG GAT CAG GCG CAG TGG GAT AAA GTG CTG GTC ACC CTA GGC GGT CGT TAT GAC TGG GCA GAT CAA GAA TCT CTT AAC CGC GTT GCC GGG ACG ACC GAT AAA CGT GAT GAC AAA CAG TTT ACC TGG CGT GGT GGT GTT AAC TAC CTG TTT GAT AAT GGT GTA ACA CCT TAC TTC AGC TAT AGC GAA TCG TTT GAA CCT TCT TCG CAA GTT GGG AAG GAT GGT AAT ATT TTC GCA CCG TCT AAA GGT AAG CAG TAT GAA GTC GGC GTG AAA TAT GTA CCG GAA GAT CGT CCG ATT GTA GTT ACT GGT GCC GTG TAT AAT CTC ACT AAA ACC AAC AAC CTG ATG GCG GAC CCT GAG GGT TCC TTC TTC TCG GTT GAA GGT GGC GAG ATC CGC GCA CGT GGC GTA GAA ATC GAA GCG AAA GCG GCG CTG TCG GCG AGT GTT AAC GTA GTC GGT TCT TAT ACT TAC ACC GAT GCG GAA TAC ACC ACC GAT ACT ACC TAT AAA GGC AAT ACG CCT GCA CAG GTG CCA AAA CAC ATG GCT TCG TTG TGG GCT GAC TAC ACC TTC TTT GAC GGT CCG CTT TCA GGT CTG ACG CTG GGC ACC GGT GGT CGT TAT ACT GGC TCC AGT TAT GGT GAT CCG GCT AAC TCC TTT AAA GTG GGA AGT TAT ACG GTC GTG GAT GCG TTA GTA CGT TAT GAT CTG GCG CGA GTC GGC ATG GCT GGC TCC AAC GTG GCG CTG CAT GTT AAC AAC CTG TTC GAT CGT GAA TAC GTC GCC AGC TGC TTT AAC ACT TAT GGC TGC TTC TGG GGC GCA GAA CGT CAG GTC GTT GCA ACC GCA ACC TTC CGT TTC 
S2457T                               ATG GCG CGT TCC AAA ACT GCT CAG CCA AAA CAC TCA CTG CGT AAA ATC GCA GTT GTA GTA GCC ACA GCG GTT AGC GGC ATG TCT GTT TAT GCA CAG GCA GCG GTT GAA CCG AAA GAA GAC ACT ATC ACC GTT ACC GCT GCA CCT GCG CCG CAA GAA AGC GCA TGG GGG CCT GCT GCA ACT ATT GCG GCG CGG CAG TCA GCT ACC GGC ACT AAA ACC GAT ACG CCG ATT CAA AAA GTG CCA CAG TCT ATT TCT GTT GTG ACC GCC GAA GAG ATG GCG CTG CAT CAG CCG AAG TCG GTA AAA GAA GCG CTT AGC TAC ACG CCG GGT GTC TCT GTT GGT ACG CGT GGC GCA TCC AAC ACC TAT GAC CAC CTG ATC ATT CGC GGT TTT GCG GCA GAA GGC CAA AGC CAA AAT AAC TAT CTG AAT GGC CTG AAG TTG CAG GGC AAC TTC TAT AAC GAT GCG GTC ATT GAC CCG TAT ATG CTG GAA CGC GCT GAA ATT ATG CGT GGC CCG GTT TCC GTG CTT TAC GGT AAA AGC AGT CCT GGC GGT CTG TTG AAT ATG GTC AGC AAG CGT CCG ACC ACC GAA CCG CTG AAA GAA GTT CAG TTT AAA GCC GGT ACT GAC AGC CTG TTC CAG ACT GGT TTT GAC TTT AGC GAT GCG TTG GAT GAT GAC GGT GTT TAC TCT TAT CGC CTG ACC GGT CTT GCG CGT TCT GCC AAT GCC CAG CAG AAA GGG TCA GAA GAG CAG CGT TAT GCT ATT GCA CCG GCG TTC ACC TGG CGT CCG GAT GAT AAA ACC AAT TTC ACC TTC CTT TCT TAC TTC CAG AAC GAG CCG GAA ACC GGT TAT TAC GGC TGG TTG CCG AAA GAG GGA ACC GTT GAG CCG CTG CCG AAC GGT AAG CGT CTG CCG ACA GAC TTT AAT GAA GGG GCG AAG AAC AAC ACC TAT TCT CGT AAT GAG AAG ATG GTC GGC TAC AGC TTC GAT CAC GAA TTT AAC GAC ACC TTT ACT GTG CGT CAG AAC CTG CGC TTT GCT GAA AAC AAA ACC TCG CAA AAC AGC GTT TAT GGT TAC GGC GTC TGC TCC GAT CCG GCG AAT GCT TAC AGC AAA --- --- --- --- --- --- CAG TGT GCG GCA TTA GCG CCA GCG GAT AAA GGC CAT TAT CTG GCA CGT AAA TAC GTC GTT GAT GAT GAG AAG CTG CAA AAC TTC TCC GTT GAT ACC CAG TTG CAG AGC AAG TTT GCC ACT GGC GAT ATC GAC CAC ACC CTG CTG ACC GGT GTC GAC TTT ATG CGT ATG CGT AAT GAC ATC AAC GCC TGG TTT GGT TAC GAC GAC TCT GTG CCA CTG TTC AAT CTG TAC AAT CCG GTG AAT CCC GAT TTC GAC TTC AAT GCC AAA GAT CCG GCA AAC TCC GGC CCT TAC CGC ATT CTG AAT AAA CAG AAA CAA ACG GGC GTT TAT GTT CAG GAT CAG GCG CAG TGG GAT AAA GTG CTG GTC ACC CTA GGC GGT CGT TAT GAC TGG GCA GAT CAA GAA TCT CTT AAC CGC GTT GCT GGG ACG ACC GAT AAA CGT GAT GAC AAA CAG TTT ACC TGG CGT GGT GGT GTT AAC TAC CTG TTT GAT AAT GGT GTA ACA CCT TAC TTC AGC TAT AGC GAA TCG TTT GAA CCT TCT TCG CAA GTT GGG AAG GAT GGT AAT ATT TTC GCA CCG TCT AAA GGT AAG CAG TAT GAA GTC GGC GTG AAA TAT GTA CCG GAA GAT CGT CCG ATT GTA GTT ACT GGT GCC GTG TAT AAT CTC ACT AAA ACC AAC AAC CTG ATG GCG GAC CCT GAG GGT TCC TTC TTC TCG GTT GAA GGT GGC GAG ATC CGC GCA CGT GGC GTA GAA ATC GAA GCG AAA GCG GCG CTG TCG GCG AGT GTT AAC GTA GTC GGT TCT TAT ACT TAC ACC GAT GCG GAA TAC ACC ACC GAT ACT ACC TAT AAA GGC AAT ACG CCT GCA CAG GTG CCA AAA CAC ATG GCT TCG CTG TGG GCT GAC TAT ACC TTC TTT GAC GGT CCG CTT TCA GGT CTG ACG CTG GGC ACC GGT GGT CGT TAT ACT GGC TCC AGC TAT GGT GAT CCG GCT AAC TCC TTT AAA GTG GGA AGT TAT ACG GTC GTG GAT GCG TTA GTG CGT TAT GAT CTG GCG CGA GTC GGC ATG GCG GGC TCC AAC GTG GCG CTG CAT GTT AAC AAC CTG TTC GAT CGT GAA TAC GTC GCC AGC TGC TTT AAC ACT TAT GGC TGC TTC TGG GGC GCA GAA CGT CAG GTC GTT GCA ACC GCA ACC TTT CGT TTC 
Shig4337                             ATG GCG CGT TCC AAA ACT GCT CAG CCA AAA CAC TCA CTG CGT AAA ATC GCA GTT GTA GTA GCC ACA GCG GTT AGC GGC ATG TCT GTT TAT GCA CAG GCA GCG GTT GAA CCG AAA GAA GAC ACT ATC ACC GTT ACC GCT GCA CCT GCG CCG CAA GAA AGC GCA TGG GGG CCT GCT GCA ACT ATT GCG GCG CGG CAG TCA GCT ACC GGC ACT AAA ACC GAT ACG CCG ATT CAA AAA GTG CCA CAG TCT ATT TCT GTT GTG ACC GCC GAA GAG ATG GCG CTG CAT CAG CCG AAG TCG GTA AAA GAA GCG CTT AGC TAC ACG CCG GGT GTC TCT GTT GGT ACG CGT GGC GCA TCC AAC ACC TAT GAC CAC CTG ATC ATT CGC GGT TTT GCG GCA GAA GGC CAA AGC CAA AAT AAC TAT CTG AAT GGC CTG AAG TTG CAG GGC AAC TTC TAT AAC GAT GCG GTC ATT GAC CCG TAT ATG CTG GAA CGC GCT GAA ATT ATG CGT GGC CCG GTT TCC GTG CTT TAC GGT AAA AGC AGT CCT GGC GGT CTG TTG AAT ATG GTC AGC AAG CGT CCG ACC ACC GAA CCG CTG AAA GAA GTT CAG TTT AAA GCC GGT ACT GAC AGC CTG TTC CAG ACT GGT TTT GAC TTT AGC GAT GCG TTG GAT GAT GAC GGT GTT TAC TCT TAT CGC CTG ACC GGT CTT GCG CGT TCT GCC AAT GCC CAG CAG AAA GGG TCA GAA GAG CAG CGT TAT GCT ATT GCA CCG GCG TTC ACC TGG CGT CCG GAT GAT AAA ACC AAT TTC ACC TTC CTT TCT TAC TTC CAG AAC GAG CCG GAA ACC GGT TAT TAC GGC TGG TTG CCG AAA GAG GGA ACC GTT GAG CCG CTG CCG AAC GGT AAG CGT CTG CCG ACA GAC TTT AAT GAA GGG GCG AAG AAC AAC ACC TAT TCT CGT AAT GAG AAG ATG GTC GGC TAC AGC TTC GAT CAC GAA TTT AAC GAC ACC TTT ACT GTG CGT CAG AAC CTG CGC TTT GCT GAA AAC AAA ACC TCG CAA AAC AGC GTT TAT GGT TAC GGC GTC TGC TCC GAT CCG GCG AAT GCT TAC AGC AAA --- --- --- --- --- --- CAG TGT GCG GCA TTA GCG CCA GCG GAT AAA GGC CAT TAT CTG GCA CGT AAA TAC GTC GTT GAT GAT GAG AAG CTG CAA AAC TTC TCC GTT GAT ACC CAG TTG CAG AGC AAG TTT GCC ACT GGC GAT ATC GAC CAC ACC CTG CTG ACC GGT GTC GAC TTT ATG CGT ATG CGT AAT GAC ATC AAC GCC TGG TTT GGT TAC GAC GAC TCT GTG CCA CTG TTC AAT CTG TAC AAT CCG GTG AAT CCC GAT TTC GAC TTC AAT GCC AAA GAT CCG GCA AAC TCC GGC CCT TAC CGC ATT CTG AAT AAA CAG AAA CAA ACG GGC GTT TAT GTT CAG GAT CAG GCG CAG TGG GAT AAA GTG CTG GTC ACC CTA GGC GGT CGT TAT GAC TGG GCA GAT CAA GAA TCT CTT AAC CGC GTT GCT GGG ACG ACC GAT AAA CGT GAT GAC AAA CAG TTT ACC TGG CGT GGT GGT GTT AAC TAC CTG TTT GAT AAT GGT GTA ACA CCT TAC TTC AGC TAT AGC GAA TCG TTT GAA CCT TCT TCG CAA GTT GGG AAG GAT GGT AAT ATT TTC GCA CCG TCT AAA GGT AAG CAG TAT GAA GTC GGC GTG AAA TAT GTA CCG GAA GAT CGT CCG ATT GTA GTT ACT GGT GCC GTG TAT AAT CTC ACT AAA ACC AAC AAC CTG ATG GCG GAC CCT GAG GGT TCC TTC TTC TCG GTT GAA GGT GGC GAG ATC CGC GCA CGT GGC GTA GAA ATC GAA GCG AAA GCG GCG CTG TCG GCG AGT GTT AAC GTA GTC GGT TCT TAT ACT TAC ACC GAT GCG GAA TAC ACC ACC GAT ACT ACC TAT AAA GGC AAT ACG CCT GCA CAG GTG CCA AAA CAC ATG GCT TCG CTG TGG GCT GAC TAT ACC TTC TTT GAC GGT CCG CTT TCA GGT CTG ACG CTG GGC ACC GGT GGT CGT TAT ACT GGC TCC AGC TAT GGT GAT CCG GCT AAC TCC TTT AAA GTG GGA AGT TAT ACG GTC GTG GAT GCG TTA GTG CGT TAT GAT CTG GCG CGA GTC GGC ATG GCG GGC TCC AAC GTG GCG CTG CAT GTT AAC AAC CTG TTC GAT CGT GAA TAC GTC GCC AGC TGC TTT AAC ACT TAT GGC TGC TTC TGG GGC GCA GAA CGT CAG GTC GTT GCA ACC GCA ACC TTT CGT TTC 
CFT073                               ATG GCA CCT TCC AAA ACT GCT CAG CCA AAA CAC TCA CTG CGT AAA ATC GCA GTT GTA GTA GCC ACA GCG GTT AGC GGC ATG TCT GTT TAT GCA CAG GCA GCG GTT GAA CCG AAA GAA GAC ACT ATC ACC GTT ACC GCT GCA CCT GCG CCG CAA GAA AGC GCA TGG GGG CCG GCT GCA ACT ATT GCG GCG CGA CAG TCA GCT ACC GGC ACT AAA ACC GAT ACG CCG ATT CAA AAA GTA CCT CAA TCT ATT TCT GTC GTC ACC GCT GAA GAG ATG GCG CTG CAT CAG CCT AAG TCG GTG AAA GAA GCG CTT AGC TAT ACC CCT GGC GTT GCT GTG GGA ACC CGT GGC GCA TCT AAT ACT TAT GAT TAC CTG ATC ATC CGC GGA TTT GCG GCA GAC GGC CAA AGC CAG AAT AAC TAT CTG AAT GGC CTG AAG TTG CAG GGC AAC TTC TAT AAC GAT GCG GTC ATC GAC CCG TAT ATG CTG GAA CGT GCT GAA ATT ATG CGT GGC CCG GTT TCC GTG CTT TAC GGT AAA AGC AGT CCT GGC GGT CTG TTG AAT ATG GTC AGC AAG CGT CCG ACC ACT GAA CCG TTG AAA GAA GTT CAG TTT AAG GCC GGG ACT GAC AGC CTG TTC CAG ACC GGT TTT GAC TTC AGC GAT GCA CTG GAT GAT GAC GGC GTT TAT TCT TAT CGC CTG ACC GGT CTT GCG CGT TCT GCC AAT GCC CAG CAG AAA GGG TCA GAA GAG CAG CGT TAT GCT ATT GCA CCG GCG TTC ACC TGG CGT CCG GAC GAT AAA ACC AAT TTC ACC TTC CTT TCT TAC TTC CAG AAC GAG CCG GAA ACT GGT TAT TAC GGC TGG CTG CCG AAA GAG GGG ACC GTT GAG CCG CTG CCA AAC GGT AAG CGT CTG CCG ACA GAC TTT AAC GAA GGG GCG AAG AAC AAC ACC TAT TCT CGT AAC GAG AAG ATG ATT GGT TAT AGC TTC GAC CAC GAA TTT AAC GAC ACC TTT ACT GTG CGT CAG AAC CTG CGC TTT GCG CAA AAT AAA GTT TCG CAA AAG AGC GTA TAT GGC TAC GGT ATG TGT TCA GAT CCG CTG TAT ACC AAA GAC CAG GAG GCA CTC AAG GCG AGT CCA TGT TTA AGT ATC CCG CAG TCT CAA TGG GGC CAT ACA CTG ACT CGT CAG TAC GTT ATC GAT AAT GAG AAG TTA GAA AAC TTC TCT GTT GAT ACT CAG TTG CAA AGC AAA TTC GCA ACC GGT TCT GTG GAT CAC ACT CTG CTG ACT GGC GTT GAC TTT ATG CGT ATG CGT AAT GAC ATC GAC TCC TGG TTC GGA TAT GCC GGT TCA GTT GCA CCA TCT GAT ATC TAT AAT TTA GAC CGT AGT GAC TTT GAT TTT GGC GCT CAC --- CCG AAT CCG TCT GGT CCA TAC CGC GTT CTG CTG AAA CAG AAA CAA ACC GGC CTG TAT GTT CAG GAT CAG GCG CAG TGG GAT AAA GTG CTG GTT ACG CTT GGC GGT CGC TAT GAC TGG GCC GAT CAG TCA TCT TTC AAC CGT GAT TAC GGT AAT AAA TCT GAA CGT GAC GAC AAA GAG TTC ACC TGG CGT GGT GGT GTA AAC TAC CTG TTC GAC AAC GGC GTA ACG CCT TAC TTC AGC TAC AGT GAA TCA TTT GAA CCC GCT TCA CAG ACT GAT GCG AAC GGT GAT CTG TTT GCA CCT TCG AAA GGC AAA CAG TAT GAA GTC GGC GTG AAA TAT GTG CCA GAA GAT CGC CCA ATT GTG GTG ACT GGC GCA CTG TAT CAG CTT ACC AAA ACT AAT AAC CTG ATG GCG GAT CCG AAC GGT TCA CTG TTC TCG GTT GAA GGC GGT GAG ATT CGT GCG CGT GGC GTA GAG CTG GAA GCG AAA GCG GCA CTG TCG GCG AGT GTT AAC GTA GTC GGT TCT TAT ACT TAC ACC GAT GCG GAA TAC ACT ACC GAT ACT ACC TAC AAA GGC AAT ACG CCT GCA CAG GTG CCA AAA CAC ATG GCT TCG CTG TGG GCT GAC TAT ACC TTC TTT GAC GGT CCG CTT TCA GGT CTG ACG CTG GGC ACC GGT GGT CGT TAT ACT GGC TCC AGC TAT GGT GAT CCG GCT AAC TCC TTT AAA GTG GGA AGT TAT ACG GTC GTG GAT GCG TTA GTG CGT TAT GAT CTG GCG CGA GTC GGC ATG GCG GGC TCC AAC GTG GCG CTG CAT GTC AAC AAC CTG TTT GAT CGT GAA TAC GTC GCC AGC TGC TTT AAC ACT TAT GGT TGC TTC TGG GGC GCA GAA CGT CAG GTC GTT GCA ACC GCA ACC TTC CGT TTC 
O157                                 ATG GCG CGT TCC AAA ACT GCT CAG CCA AAA CAC TCA CTG CGT AAA ATC GCA GTT GTA GTA GCC ACA GCG GTT AGC GGC ATG TCT GTT TAT GCA CAG GCA GCG GTT GAA CTG AAA GAA GAC ACT ATC ACC GTT ACC GCT GCA CCT GCG CCG CAA GAA AGC GCA TGG GGG CCT GCT GCA ACT ATT GCG GCG CGA CAG TCA GCT ACC GGC ACT AAA ACC GAT ACG CCG ATT CAA AAA GTG CCA CAG TCT ATT TCT GTT GTG ACC GCC GAA GAG ATG GCG CTG CAT CAG CCG AAG TCG GTA AAA GAA GCG CTT AGC TAC ACG CCG GGT GTC TCT GTT GGT ACG CGT GGC GCA TCC AAC ACC TAT GAC CAC CTG ATC ATT CGC GGT TTT GCG GCA GAA GGC CAA AGC CAG AAT AAC TAT CTG AAT GGC CTG AAG TTG CAG GGC AAC TTC TAT AAC GAT GCG GTC ATT GAT CCG TAT ATG CTG GAA CGC GCT GAA ATT ATG CGT GGC CCG GTT TCC GTG CTT TAC GGT AAA AGC AGT CCT GGC GGC CTG TTG AAT ATG GTC AGC AAG CGT CCG ACC ACC GAA CCG CTG AAA GAA GTT CAG TTT AAA GCC GGT ACT GAC AGC CTG TTC CAG ACT GGT TTT GAC TTT AGC GAT GCG CTG GAT GAT GAC GGC GTT TAC TCT TAT CGC CTG ACC GGT CTT GCG CGT TCT GCC AAT GCC CAG CAG AAA GGG TCA GAA GAG CAG CGT TAT GCT ATT GCA CCG GCG TTC ACC TGG CGT CCG GAT GAT AAA ACC AAT TTC ACC TTC CTT TCT TAC TTC CAG AAC GAG CCG GAA ACC GGT TAT TAC GGC TGG TTG CCG AAA GAG GGA ACC GTT GAG CCG CTG CCG AAC GGT AAG CGT CTG CCG ACA GAC TTT AAC GAA GGG GCG AAG AAC AAC ACC TAT TCT CGT AAT GAG AAG ATG GTG GGC TAC AGC TTC GAT CAC GAA TTT AAC GAC ACC TTT ACT GTG CGT CAG AAC CTG CGC TTT GCT GAA AAC AAA ACC TCG CAA AAC AGC GTT TAT GGT TAC GGC GTC TGC TCC GAT CCG GCG AAT GCT TAC AGC AAA --- --- --- --- --- --- CAG TGT GCG GCA TTA GCG CCA GCG GAT AAA GGC CAT TAT CTG GCA CGT AAA TAC GTC GTT GAT GAT GAG AAG CTG CAA AAC TTC TCC GTT GAT ACC CAG TTG CAG AGC AAG TTT GCC ACT GGC GAT ATC GAC CAC ACC CTG CTG ACC GGT GTC GAC TTT ATG CGT ATG CGT AAT GAC ATC AAC GCC TGG TTT GGT TAC GAC GAC TCC GTA CCG CTG CTC GAT CTG TAC AAT CCG GTG AAT ACC GAT TTC GAC TTC AAT GCC AAA GAT CCG GCA AAC TCC GGC CCT TAC CGC ATT CTG AAT AAG CAG AAA CAA ACG GGC GTT TAT GTT CAG GAT CAG GCG CAG TGG GAT AAA GTG CTG GTC ACC CTG GGC GGT CGT TAT GAC TGG GCA GAT CAA GAA TCT CTT AAC CGC GTT GCC GGG ACG ACC GAT AAA CGT GAT GAC AAA CAG TTT ACC TGG CGT GGT GGT GTT AAC TAC CTG TTT GAT AAT GGC GTA ACA CCT TAC TTT AGC TAT AGC GAA TCG TTT GAA CCT TCT TCG CAA GTT GGG AAG GAT GGT AAT ATT TTC GCA CCG TCT AAA GGT AAG CAG TAT GAA GTC GGC GTG AAA TAT GTA CCG GAA GAT CGT CCG ATT GTA GTT ACT GGT GCC GTG TAT AAT CTC ACT AAA ACC AAC AAC CTG ATG GCG GAC CCT GAG GGT TCC TTC TTC TCG GTT GAA GGT GGC GAG ATC CGC GCA CGT GGC GTA GAA ATC GAA GCG AAA GCG GCG CTG TCG GCG AGT GTT AAC GTA GTC GGT TCT TAT ACT TAC ACC GAT GCG GAA TAC ACC ACC GAT ACT ACC TAT AAA GGC AAT ACG CCT GCA CAG GTG CCA AAA CAC ATG GCT TCG CTG TGG GCT GAC TAT ACC TTC TTT GAC GGT CCG CTT TCA GGT CTG ACG CTG GGC ACC GGT GGT CGT TAT ACT GGC TCC AGC TAT GGT GAT CCG GCT AAC TCC TTT AAA GTG GGA AGT TAT ACG GTC GTG GAT GCG TTA GTG CGT TAT GAT CTG GCG CGA GTC GGC ATG GCG GGC TCC AAC GTG GCG CTG CAT GTT AAC AAC CTG TTC GAT CGT GAA TAC GTC GCC AGC TGC TTT AAC ACT TAT GGC TGC TTC TGG GGC GCA GAA CGT CAG GTC GTT GCA ACC GCA ACC TTC CGT TTC 
EDL933                               ATG GCG CGT TCC AAA ACT GCT CAG CCA AAA CAC TCA CTG CGT AAA ATC GCA GTT GTA GTA GCC ACA GCG GTT AGC GGC ATG TCT GTT TAT GCA CAG GCA GCG GTT GAA CTG AAA GAA GAC ACT ATC ACC GTT ACC GCT GCA CCT GCG CCG CAA GAA AGC GCA TGG GGG CCT GCT GCA ACT ATT GCG GCG CGA CAG TCA GCT ACC GGC ACT AAA ACC GAT ACG CCG ATT CAA AAA GTG CCA CAG TCT ATT TCT GTT GTG ACC GCC GAA GAG ATG GCG CTG CAT CAG CCG AAG TCG GTA AAA GAA GCG CTT AGC TAC ACG CCG GGT GTC TCT GTT GGT ACG CGT GGC GCA TCC AAC ACC TAT GAC CAC CTG ATC ATT CGC GGT TTT GCG GCA GAA GGC CAA AGC CAG AAT AAC TAT CTG AAT GGC CTG AAG TTG CAG GGC AAC TTC TAT AAC GAT GCG GTC ATT GAT CCG TAT ATG CTG GAA CGC GCT GAA ATT ATG CGT GGC CCG GTT TCC GTG CTT TAC GGT AAA AGC AGT CCT GGC GGC CTG TTG AAT ATG GTC AGC AAG CGT CCG ACC ACC GAA CCG CTG AAA GAA GTT CAG TTT AAA GCC GGT ACT GAC AGC CTG TTC CAG ACT GGT TTT GAC TTT AGC GAT GCG CTG GAT GAT GAC GGC GTT TAC TCT TAT CGC CTG ACC GGT CTT GCG CGT TCT GCC AAT GCC CAG CAG AAA GGG TCA GAA GAG CAG CGT TAT GCT ATT GCA CCG GCG TTC ACC TGG CGT CCG GAT GAT AAA ACC AAT TTC ACC TTC CTT TCT TAC TTC CAG AAC GAG CCG GAA ACC GGT TAT TAC GGC TGG TTG CCG AAA GAG GGA ACC GTT GAG CCG CTG CCG AAC GGT AAG CGT CTG CCG ACA GAC TTT AAC GAA GGG GCG AAG AAC AAC ACC TAT TCT CGT AAT GAG AAG ATG GTG GGC TAC AGC TTC GAT CAC GAA TTT AAC GAC ACC TTT ACT GTG CGT CAG AAC CTG CGC TTT GCT GAA AAC AAA ACC TCG CAA AAC AGC GTT TAT GGT TAC GGC GTC TGC TCC GAT CCG GCG AAT GCT TAC AGC AAA --- --- --- --- --- --- CAG TGT GCG GCA TTA GCG CCA GCG GAT AAA GGC CAT TAT CTG GCA CGT AAA TAC GTC GTT GAT GAT GAG AAG CTG CAA AAC TTC TCC GTT GAT ACC CAG TTG CAG AGC AAG TTT GCC ACT GGC GAT ATC GAC CAC ACC CTG CTG ACC GGT GTC GAC TTT ATG CGT ATG CGT AAT GAC ATC AAC GCC TGG TTT GGT TAC GAC GAC TCC GTA CCG CTG CTC GAT CTG TAC AAT CCG GTG AAT ACC GAT TTC GAC TTC AAT GCC AAA GAT CCG GCA AAC TCC GGC CCT TAC CGC ATT CTG AAT AAG CAG AAA CAA ACG GGC GTT TAT GTT CAG GAT CAG GCG CAG TGG GAT AAA GTG CTG GTC ACC CTG GGC GGT CGT TAT GAC TGG GCA GAT CAA GAA TCT CTT AAC CGC GTT GCC GGG ACG ACC GAT AAA CGT GAT GAC AAA CAG TTT ACC TGG CGT GGT GGT GTT AAC TAC CTG TTT GAT AAT GGC GTA ACA CCT TAC TTT AGC TAT AGC GAA TCG TTT GAA CCT TCT TCG CAA GTT GGG AAG GAT GGT AAT ATT TTC GCA CCG TCT AAA GGT AAG CAG TAT GAA GTC GGC GTG AAA TAT GTA CCG GAA GAT CGT CCG ATT GTA GTT ACT GGT GCC GTG TAT AAT CTC ACT AAA ACC AAC AAC CTG ATG GCG GAC CCT GAG GGT TCC TTC TTC TCG GTT GAA GGT GGC GAG ATC CGC GCA CGT GGC GTA GAA ATC GAA GCG AAA GCG GCG CTG TCG GCG AGT GTT AAC GTA GTC GGT TCT TAT ACT TAC ACC GAT GCG GAA TAC ACC ACC GAT ACT ACC TAT AAA GGC AAT ACG CCT GCA CAG GTG CCA AAA CAC ATG GCT TCG CTG TGG GCT GAC TAT ACC TTC TTT GAC GGT CCG CTT TCA GGT CTG ACG CTG GGC ACC GGT GGT CGT TAT ACT GGC TCC AGC TAT GGT GAT CCG GCT AAC TCC TTT AAA GTG GGA AGT TAT ACG GTC GTG GAT GCG TTA GTG CGT TAT GAT CTG GCG CGA GTC GGC ATG GCG GGC TCC AAC GTG GCG CTG CAT GTT AAC AAC CTG TTC GAT CGT GAA TAC GTC GCC AGC TGC TTT AAC ACT TAT GGC TGC TTC TGG GGC GCA GAA CGT CAG GTC GTT GCA ACC GCA ACC TTC CGT TTC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0150.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 753
# site patterns = 211
   12    2    1    5   23   11    9   20    2    4    3   25   21    4   14
   14    5    5    2   21   13   20    9   21   22    1   12   21    4   16
    5    9    3    2    6    1    1   19    4    1    1    2    2    1    2
    8    3    3    7    5    3    5    5    3    6    4    2    2    2    3
    3    8    4    1    2    4    1   12    1    1    8   19    3   11    8
    1    3    8   11   16    3    1    1    1    1    3    5    1    1    2
    5    1    1    1    3    1    2    1    6    1    1    1    1    2    1
    1    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
    2    2    2    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    4    1    1    1    1    1    1    1    1    1    1
    1    1    2    1    2    1    1    1    1    1    1    1    1    1    1
    1    2    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    2
    1

K12                                  ATG GCG CGT TCC AAA ACT GCT CAG CCA CAC TCA CTG CGT ATC GCA GTT GTA GCC ACA GCG AGC GGC TCT TAT GAA CCG GAC ACC CCT CCG CAA TGG GGG CCT ATT CGA TCT GAT ACG GTG CCA CAG GTT GTG GCC GAG CAT CCG AAG TCG GTA CTT TAC ACG GGT GTC TCT GTT GGT TCC AAC ACC GAC CAC ATT CGC GGC TTT GAA CAG AAT AAC TTG TTC GTC GAC CGC GTG TAC GGT AGT GGC CTG AAA GGT ACT TTT TCG TTG GGT GAT TTT TTG GGA CCG AAT AAT GTC GGC GCT GAA ACC AAC GTT GTC TGC TCC GCG AAT GCT TAC AGC AAA --- --- --- --- --- --- CAG TGT GCG GCA TTA GCG CCA GCG GAT AAA TAT GCA GTT GAT CTG CAA AAG GCC GAT ATC AAC GCC GAC GAC TCT GTG CCA CTG CTC AAT CTG CCG GTG AAT ACC TTC AAT AAA GAT GCA AAC CCT ATT AAT AAA GTT ACC CTA CGT GCA CAA GAA CTT GTT GCC GGG ACG ACC AAA CAG ACA TTC TAT AGC TCG CCT GTT GGG AAG GAT AAT ATT TCT GTG AAT CTC GAG TTC ATC GCA GAA ATC TTG TAC AGT GGA TTA GTA CGA GCT TGC TTC 
S2457T                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... G.. ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ..T ..C ... ... ..G ... ..G ... ..T 
Shig4337                             ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... G.. ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ..T ..C ... ... ..G ... ..G ... ..T 
CFT073                               ... ..A .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ..A ... ... ..A ..T ..A ..C ..C ..T ... ... ..T ... ... ..G ... ..T ..C ..C ..T G.. ..G ..A ..T ..T ..T ..T T.. ..C ... ..A ... ..C ... ... ... ... ... ... ... ..T ... ... ... ... ..T T.. ..G ..G ..C ..C G.A C.. ..C ..C ..C C.. ..G ..A ..C ..C A.T ..T ..G C.. GTT ..G ..A A.G ..T ..A CT. T.. A.C A.A GA. C.G GAG GCA CTC AAG GCG AGT .CA ... TTA AGT A.C C.. .AG T.T C.A TGG ACA A.T A.C A.. T.A G.. ..A ..A TC. G.G G.. T.. .C. .GT ..A ..T G.. .CA TCT G.. A.C TTA .AC CG. .GT ..T GGC C.C --- AAT CCG ..A G.. CTG ... C.G ..G ..T ..C ..C ..G TC. T.C .A. TA. ..T .AT .AA G.. G.. ..G ... ..C ..T ..A ..C AC. .AT GC. A.C G.. C.G ..G C.. C.G ..T A.C C.G ..T ..G ..G C.G C.. ..T ..C ... ... ..G ... ..G ... ... 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... G.. C.. ..C ... ..C ... ... ... ..C ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..A ..G ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ..T ..C ... ... ..G ... ..G ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... G.. C.. ..C ... ..C ... ... ... ..C ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..A ..G ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ..T ..C ... ... ..G ... ..G ... ... 



Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 18 18 18 16 18 18 | Ser TCT 14 13 13 16 12 12 | Tyr TAT 24 25 25 28 25 25 | Cys TGT  1  1  1  2  1  1
    TTC 18 19 19 20 18 18 |     TCC 10 10 10  6 11 11 |     TAC 18 17 17 15 17 17 |     TGC  3  3  3  2  3  3
Leu TTA  2  2  2  4  2  2 |     TCA  3  4  4 10  4  4 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  6  5  5  4  4  4 |     TCG  8  7  7  6  7  7 |     TAG  0  0  0  0  0  0 | Trp TGG  9  9  9 10  9  9
--------------------------------------------------------------------------------------------------------------
Leu CTT  6  6  6  7  6  6 | Pro CCT  8  8  8  9  8  8 | His CAT  3  3  3  3  3  3 | Arg CGT 24 24 24 25 24 24
    CTC  2  1  1  1  2  2 |     CCC  0  1  1  1  0  0 |     CAC  5  5  5  5  5  5 |     CGC  7  7  7  6  7  7
    CTA  1  1  1  0  0  0 |     CCA  5  5  5  8  4  4 | Gln CAA  8  9  9  9  8  8 |     CGA  2  1  1  2  2  2
    CTG 29 30 30 35 33 33 |     CCG 24 24 24 21 24 24 |     CAG 25 24 24 27 25 25 |     CGG  0  1  1  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT 10 10 10  8 10 10 | Thr ACT 14 14 14 21 14 14 | Asn AAT 18 18 18 14 16 16 | Ser AGT  4  3  3  7  3  3
    ATC  7  7  7  9  7  7 |     ACC 33 32 32 28 33 33 |     AAC 25 25 25 24 26 26 |     AGC 15 16 16 14 16 16
    ATA  0  0  0  0  0  0 |     ACA  3  3  3  3  3  3 | Lys AAA 30 30 30 28 29 29 | Arg AGA  0  0  0  0  0  0
Met ATG 12 12 12 13 12 12 |     ACG  8  8  8  6  8  8 |     AAG 10 10 10 10 11 11 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT 24 24 24 21 24 24 | Ala GCT 12 12 12 13 11 11 | Asp GAT 30 30 30 27 32 32 | Gly GGT 27 29 29 25 26 26
    GTC 14 14 14 11 13 13 |     GCC 11 10 10  7 11 11 |     GAC 19 19 19 22 18 18 |     GGC 28 26 26 29 29 29
    GTA  9  8  8  8  9  9 |     GCA 19 19 19 21 19 19 | Glu GAA 26 26 26 24 26 26 |     GGA  2  2  2  4  2  2
    GTG 13 14 14 15 14 14 |     GCG 27 29 29 26 29 29 |     GAG  9  9  9 11  9  9 |     GGG  5  5  5  5  5  5
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.17938    C:0.19946    A:0.25301    G:0.36814
position  2:    T:0.22892    C:0.26640    A:0.33467    G:0.17001
position  3:    T:0.31727    C:0.28782    A:0.14726    G:0.24766

#2: S2457T         
position  1:    T:0.17805    C:0.20080    A:0.25167    G:0.36948
position  2:    T:0.22892    C:0.26640    A:0.33467    G:0.17001
position  3:    T:0.31861    C:0.28380    A:0.14726    G:0.25033

#3: Shig4337       
position  1:    T:0.17805    C:0.20080    A:0.25167    G:0.36948
position  2:    T:0.22892    C:0.26640    A:0.33467    G:0.17001
position  3:    T:0.31861    C:0.28380    A:0.14726    G:0.25033

#4: CFT073         
position  1:    T:0.18484    C:0.21144    A:0.24601    G:0.35771
position  2:    T:0.22872    C:0.26862    A:0.32846    G:0.17420
position  3:    T:0.32181    C:0.26596    A:0.16090    G:0.25133

#5: O157           
position  1:    T:0.17537    C:0.20214    A:0.25167    G:0.37082
position  2:    T:0.23025    C:0.26506    A:0.33467    G:0.17001
position  3:    T:0.31191    C:0.28916    A:0.14458    G:0.25435

#6: EDL933         
position  1:    T:0.17537    C:0.20214    A:0.25167    G:0.37082
position  2:    T:0.23025    C:0.26506    A:0.33467    G:0.17001
position  3:    T:0.31191    C:0.28916    A:0.14458    G:0.25435

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     106 | Ser S TCT      80 | Tyr Y TAT     152 | Cys C TGT       7
      TTC     112 |       TCC      58 |       TAC     101 |       TGC      17
Leu L TTA      14 |       TCA      29 | *** * TAA       0 | *** * TGA       0
      TTG      28 |       TCG      42 |       TAG       0 | Trp W TGG      55
------------------------------------------------------------------------------
Leu L CTT      37 | Pro P CCT      49 | His H CAT      18 | Arg R CGT     145
      CTC       9 |       CCC       3 |       CAC      30 |       CGC      41
      CTA       3 |       CCA      31 | Gln Q CAA      51 |       CGA      10
      CTG     190 |       CCG     141 |       CAG     150 |       CGG       2
------------------------------------------------------------------------------
Ile I ATT      58 | Thr T ACT      91 | Asn N AAT     100 | Ser S AGT      23
      ATC      44 |       ACC     191 |       AAC     151 |       AGC      93
      ATA       0 |       ACA      18 | Lys K AAA     176 | Arg R AGA       0
Met M ATG      73 |       ACG      46 |       AAG      62 |       AGG       0
------------------------------------------------------------------------------
Val V GTT     141 | Ala A GCT      71 | Asp D GAT     181 | Gly G GGT     162
      GTC      79 |       GCC      60 |       GAC     115 |       GGC     167
      GTA      51 |       GCA     116 | Glu E GAA     154 |       GGA      14
      GTG      84 |       GCG     169 |       GAG      56 |       GGG      30
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17852    C:0.20281    A:0.25095    G:0.36773
position  2:    T:0.22933    C:0.26632    A:0.33363    G:0.17072
position  3:    T:0.31669    C:0.28326    A:0.14865    G:0.25139

Codon frequencies under model, for use in evolver:
  0.01334341  0.01193488  0.00626323  0.01059209
  0.01549599  0.01386024  0.00727363  0.01230082
  0.01941213  0.01736299  0.00000000  0.00000000
  0.00993299  0.00888447  0.00000000  0.00788488
  0.01515917  0.01355898  0.00711553  0.01203346
  0.01760468  0.01574634  0.00826342  0.01397472
  0.02205373  0.01972575  0.01035175  0.01750641
  0.01128467  0.01009347  0.00529689  0.00895785
  0.01875740  0.01677738  0.00880449  0.01488976
  0.02178337  0.01948393  0.01022485  0.01729180
  0.02728846  0.02440790  0.01280887  0.02166177
  0.01396323  0.01248928  0.00655417  0.01108411
  0.02748641  0.02458496  0.01290179  0.02181891
  0.03192057  0.02855105  0.01498312  0.02533878
  0.03998752  0.03576646  0.01876965  0.03174238
  0.02046122  0.01830134  0.00960425  0.01624226



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                 
S2457T               0.0725 (0.0018 0.0244)
Shig4337             0.0725 (0.0018 0.0244)-1.0000 (0.0000 0.0000)
CFT073               0.1533 (0.0651 0.4251) 0.1565 (0.0645 0.4122) 0.1565 (0.0645 0.4122)
O157                 0.0468 (0.0018 0.0378) 0.0737 (0.0024 0.0320) 0.0737 (0.0024 0.0320) 0.1620 (0.0649 0.4003)
EDL933               0.0468 (0.0018 0.0378) 0.0737 (0.0024 0.0320) 0.0737 (0.0024 0.0320) 0.1620 (0.0649 0.4003)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -4178.750927     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00653  0.01229  0.00941  0.00000  0.00000  0.00147  0.55784  0.01105  0.00000  0.00000  2.99869  0.88234  0.00000  0.00797  2.66066
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.59860

((1: 0.012287, (2: 0.000004, 3: 0.000004): 0.009409): 0.006531, (4: 0.557841, (5: 0.000004, 6: 0.000004): 0.011048): 0.001471);

((K12: 0.012287, (S2457T: 0.000004, Shig4337: 0.000004): 0.009409): 0.006531, (CFT073: 0.557841, (O157: 0.000004, EDL933: 0.000004): 0.011048): 0.001471);

Detailed output identifying parameters

kappa (ts/tv) =  2.99869


dN/dS for site classes (K=3)

p:   0.88234  0.00000  0.11766
w:   0.00797  1.00000  2.66066

dN & dS for each branch

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

   7..8       0.007    629.7   1629.3   0.3201   0.0014   0.0043    2.7    2.2
   8..1       0.012    629.7   1629.3   0.3201   0.0026   0.0080    5.1    4.2
   8..9       0.009    629.7   1629.3   0.3201   0.0020   0.0062    3.9    3.2
   9..2       0.000    629.7   1629.3   0.3201   0.0000   0.0000    0.0    0.0
   9..3       0.000    629.7   1629.3   0.3201   0.0000   0.0000    0.0    0.0
   7..10      0.001    629.7   1629.3   0.3201   0.0003   0.0010    0.6    0.5
  10..4       0.558    629.7   1629.3   0.3201   0.1168   0.3649  229.8  190.3
  10..11      0.011    629.7   1629.3   0.3201   0.0023   0.0072    4.6    3.8
  11..5       0.000    629.7   1629.3   0.3201   0.0000   0.0000    0.0    0.0
  11..6       0.000    629.7   1629.3   0.3201   0.0000   0.0000    0.0    0.0


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

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

     3 R      0.927         2.467
    37 P      0.938         2.497
   110 S      0.919         2.446
   122 H      0.880         2.341
   131 E      0.857         2.280
   216 S      0.919         2.445
   315 V      0.881         2.345
   337 E      0.924         2.460
   340 T      0.999**       2.659
   343 N      0.842         2.242
   350 V      0.950         2.527
   355 A      1.000**       2.660
   356 N      0.903         2.403
   357 A      0.858         2.284
   358 Y      1.000**       2.660
   359 S      0.999**       2.659
   360 K      0.936         2.490
   367 Q      0.944         2.512
   369 A      1.000**       2.660
   370 A      1.000**       2.660
   371 L      0.987*        2.626
   372 A      0.931         2.479
   373 P      0.947         2.519
   374 A      0.925         2.462
   375 D      1.000**       2.660
   376 K      1.000**       2.660
   379 Y      1.000**       2.660
   381 A      0.899         2.391
   383 K      0.936         2.490
   386 V      0.858         2.283
   388 D      0.795         2.117
   392 Q      0.928         2.471
   408 D      1.000**       2.660
   409 I      0.942         2.507
   427 N      0.819         2.181
   428 A      0.924         2.459
   433 D      0.903         2.403
   434 D      0.833         2.219
   437 P      0.953*        2.537
   438 L      0.940         2.502
   439 L      1.000**       2.661
   440 N      0.930         2.475
   441 L      0.979*        2.605
   444 P      0.985*        2.621
   445 V      0.974*        2.591
   446 N      1.000**       2.660
   447 T      1.000**       2.660
   452 N      0.999**       2.659
   454 K      1.000**       2.660
   457 A      1.000**       2.660
   458 N      1.000**       2.661
   464 I      0.844         2.246
   466 N      1.000**       2.661
   473 V      0.928         2.469
   498 E      1.000**       2.660
   500 L      0.899         2.392
   503 V      0.897         2.388
   504 A      1.000**       2.660
   506 T      0.971*        2.584
   507 T      0.986*        2.623
   508 D      1.000**       2.660
   509 K      0.890         2.369
   514 Q      0.903         2.402
   542 S      0.919         2.446
   545 V      0.999**       2.659
   546 G      0.963*        2.563
   547 K      1.000**       2.660
   548 D      0.819         2.181
   550 N      0.797         2.122
   551 I      0.974*        2.593
   579 V      0.927         2.468
   581 N      1.000**       2.660
   593 E      0.999**       2.659
   596 F      0.925         2.462
   611 I      0.977*        2.600


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

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

   340 T      0.618         3.423 +- 2.260
   355 A      0.786         4.170 +- 2.107
   358 Y      0.799         4.234 +- 2.089
   359 S      0.586         3.277 +- 2.255
   369 A      0.844         4.438 +- 2.001
   370 A      0.879         4.587 +- 1.914
   371 L      0.720         3.846 +- 2.328
   375 D      0.726         3.904 +- 2.193
   376 K      0.895         4.660 +- 1.867
   379 Y      0.923         4.771 +- 1.774
   408 D      0.792         4.198 +- 2.098
   439 L      0.930         4.794 +- 1.740
   441 L      0.612         3.346 +- 2.444
   444 P      0.717         3.826 +- 2.343
   445 V      0.559         3.078 +- 2.450
   446 N      0.713         3.841 +- 2.196
   447 T      0.834         4.411 +- 2.040
   452 N      0.585         3.280 +- 2.270
   454 K      0.773         4.117 +- 2.134
   457 A      0.862         4.514 +- 1.955
   458 N      0.925         4.773 +- 1.763
   466 N      0.928         4.785 +- 1.749
   498 E      0.887         4.623 +- 1.888
   504 A      0.821         4.328 +- 2.047
   506 T      0.584         3.189 +- 2.474
   507 T      0.667         3.605 +- 2.374
   508 D      0.792         4.198 +- 2.098
   545 V      0.580         3.249 +- 2.251
   547 K      0.701         3.790 +- 2.209
   551 I      0.557         3.071 +- 2.451
   581 N      0.717         3.865 +- 2.200
   593 E      0.561         3.176 +- 2.265
   611 I      0.580         3.186 +- 2.444



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:   1.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.034  0.208  0.302  0.230  0.127  0.059  0.025  0.010  0.004

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 0.025
 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 0.765 0.210

sum of density on p0-p1 =   1.000000
