
seed used = 139994577

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0903.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 760
# site patterns = 75
   32   12    5    2    2   41    9    1    4    1    7   37    3   27   40
   37   26    9   29    2   30   26    5   28   17   26   54   34   17   13
    1   25    8   14    3    2    1   36   19    1    1    1    1    1    1
    4    1    6    1   13    3    5    1    1    1    9    3    1    1    2
    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1


1       
K12                   ATG TCC GAG CTT AAT GAA AAG TTA GCC ACA TGG GGT TTT ACC AAA GAC CAG GTA AAC GTC CGT TTC ATT TAC ACT CCG CTG GCT GGC GCG GGC GTT CGC CAC CCA GAC TTT ATC TCT AAC AAG CAG CTT GAG ATC TGC GAT GTG TCT GAT GCA TAT CTG ACT CTG GCA CAA GAA CCG CTC AGC ACC GGT ATT GTC AAC TAT ATC TGT AAT ACG GGA GCC AAC TCG 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..T ... ... ... ..T ..A GC. T.G ..A G.T ... ..C ... ..C ... ..T ... TAC ..C ..A ... ... ... ..A ... ... ..T ..G ..C C.. .G. ..C ... ... ... ..T ... ..G ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..T ... ... ... ..T ..A GC. T.G ..A G.T ... ..C ... ..C ... ..T ... TAC ..C ..A ... ... ... ..A ... ... ..T ..G ..C C.. .G. ..C ... ... ... ..T ... ..G ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ..A GC. T.G ..A G.T ... ..C ... ..C ... ..T ... TAC ..C ... ... ... ..G ... ... ... ... ... ..C C.. ... ..C ..T ... ..C ... ... ..G ..T ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ..A GC. T.G ..A G.T ... ..C ... ..C ... ..T ... TAC ..C ... ... ... ..G ... ... ... ... ... ..C C.. ... ..C ..T ... ..C ... ... ..G ..T ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  4  4  4  3  3 | Ser TCT 20 19 19 19 19 | Tyr TAT  6  5  5  5  5 | Cys TGT  1  1  1  1  1
    TTC 26 26 26 27 27 |     TCC 12 13 13 13 13 |     TAC 28 30 30 30 30 |     TGC  4  4  4  4  4
Leu TTA  1  1  1  1  1 |     TCA  0  0  0  0  0 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  0  1  1  1  1 |     TCG  1  1  1  1  1 |     TAG  0  0  0  0  0 | Trp TGG  7  7  7  7  7
--------------------------------------------------------------------------------------------------
Leu CTT  3  2  2  2  2 | Pro CCT  0  0  0  0  0 | His CAT  0  0  0  0  0 | Arg CGT 30 30 30 30 30
    CTC  2  3  3  3  3 |     CCC  0  0  0  0  0 |     CAC 14 14 14 14 14 |     CGC  8  8  8  8  8
    CTA  0  1  1  0  0 |     CCA  3  4  4  3  3 | Gln CAA  3  3  3  3  3 |     CGA  0  0  0  0  0
    CTG 56 54 54 55 55 |     CCG 27 26 26 27 27 |     CAG 27 26 26 26 26 |     CGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Ile ATT  6  5  5  6  6 | Thr ACT 18 19 19 17 17 | Asn AAT  3  4  4  3  3 | Ser AGT  0  0  0  0  0
    ATC 38 38 38 37 37 |     ACC 28 28 28 29 29 |     AAC 32 30 30 32 32 |     AGC  3  4  4  3  3
    ATA  0  0  0  0  0 |     ACA  1  1  1  1  1 | Lys AAA 40 41 41 41 41 | Arg AGA  0  0  0  0  0
Met ATG 32 32 32 32 32 |     ACG  1  0  0  1  1 |     AAG 10  9  9  9  9 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT 25 26 26 26 26 | Ala GCT 34 37 37 37 37 | Asp GAT 14 15 15 13 13 | Gly GGT 38 38 38 38 38
    GTC  3  2  2  2  2 |     GCC  5  4  4  4  4 |     GAC 39 38 38 40 40 |     GGC 18 17 17 18 18
    GTA  9  9  9  9  9 |     GCA 12  9  9  9  9 | Glu GAA 42 43 43 42 42 |     GGA  1  1  1  1  1
    GTG  6  6  6  6  6 |     GCG 13 15 15 15 15 |     GAG  6  5  5  6  6 |     GGG  0  1  1  0  0
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14474    C:0.22763    A:0.27895    G:0.34868
position  2:    T:0.27763    C:0.23026    A:0.34737    G:0.14474
position  3:    T:0.26579    C:0.34211    A:0.14737    G:0.24474

#2: S2457T         
position  1:    T:0.14737    C:0.22500    A:0.27763    G:0.35000
position  2:    T:0.27632    C:0.23158    A:0.34605    G:0.14605
position  3:    T:0.26974    C:0.34079    A:0.14868    G:0.24079

#3: Shig4337       
position  1:    T:0.14737    C:0.22500    A:0.27763    G:0.35000
position  2:    T:0.27632    C:0.23158    A:0.34605    G:0.14605
position  3:    T:0.26974    C:0.34079    A:0.14868    G:0.24079

#4: O157           
position  1:    T:0.14737    C:0.22500    A:0.27763    G:0.35000
position  2:    T:0.27632    C:0.23158    A:0.34737    G:0.14474
position  3:    T:0.26316    C:0.34737    A:0.14474    G:0.24474

#5: EDL933         
position  1:    T:0.14737    C:0.22500    A:0.27763    G:0.35000
position  2:    T:0.27632    C:0.23158    A:0.34737    G:0.14474
position  3:    T:0.26316    C:0.34737    A:0.14474    G:0.24474

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      18 | Ser S TCT      96 | Tyr Y TAT      26 | Cys C TGT       5
      TTC     132 |       TCC      64 |       TAC     148 |       TGC      20
Leu L TTA       5 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       4 |       TCG       5 |       TAG       0 | Trp W TGG      35
------------------------------------------------------------------------------
Leu L CTT      11 | Pro P CCT       0 | His H CAT       0 | Arg R CGT     150
      CTC      14 |       CCC       0 |       CAC      70 |       CGC      40
      CTA       2 |       CCA      17 | Gln Q CAA      15 |       CGA       0
      CTG     274 |       CCG     133 |       CAG     131 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      28 | Thr T ACT      90 | Asn N AAT      17 | Ser S AGT       0
      ATC     188 |       ACC     142 |       AAC     156 |       AGC      17
      ATA       0 |       ACA       5 | Lys K AAA     204 | Arg R AGA       0
Met M ATG     160 |       ACG       3 |       AAG      46 |       AGG       0
------------------------------------------------------------------------------
Val V GTT     129 | Ala A GCT     182 | Asp D GAT      70 | Gly G GGT     190
      GTC      11 |       GCC      21 |       GAC     195 |       GGC      88
      GTA      45 |       GCA      48 | Glu E GAA     212 |       GGA       5
      GTG      30 |       GCG      73 |       GAG      28 |       GGG       2
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14684    C:0.22553    A:0.27789    G:0.34974
position  2:    T:0.27658    C:0.23132    A:0.34684    G:0.14526
position  3:    T:0.26632    C:0.34368    A:0.14684    G:0.24316

Codon frequencies under model, for use in evolver:
  0.01107057  0.01428672  0.00610413  0.01010791
  0.00925883  0.01194865  0.00510517  0.00845372
  0.01388298  0.01791618  0.00000000  0.00000000
  0.00581442  0.00750359  0.00000000  0.00530882
  0.01700265  0.02194216  0.00937498  0.01552416
  0.01422010  0.01835124  0.00784073  0.01298357
  0.02132207  0.02751642  0.01175663  0.01946798
  0.00893003  0.01152433  0.00492387  0.00815351
  0.02095076  0.02703724  0.01155190  0.01912895
  0.01752209  0.02261250  0.00966139  0.01599843
  0.02627317  0.03390589  0.01448659  0.02398854
  0.01100363  0.01420034  0.00606722  0.01004680
  0.02636700  0.03402698  0.01453833  0.02407422
  0.02205195  0.02845834  0.01215908  0.02013439
  0.03306538  0.04267133  0.01823170  0.03019013
  0.01384832  0.01787145  0.00763573  0.01264412



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

K12                 
S2457T               0.1098 (0.0048 0.0433)
Shig4337             0.1098 (0.0048 0.0433)-1.0000 (0.0000 0.0000)
O157                 0.1177 (0.0042 0.0355) 0.0218 (0.0006 0.0264) 0.0218 (0.0006 0.0264)
EDL933               0.1177 (0.0042 0.0355) 0.0218 (0.0006 0.0264) 0.0218 (0.0006 0.0264)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 31
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -3258.375384     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00574  0.03316  0.01498  0.00000  0.00000  0.00168  0.00000  0.00000  2.36902  0.99564  0.00000  0.02835 30.74169
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.05557

((1: 0.033158, (2: 0.000004, 3: 0.000004): 0.014979): 0.005742, (4: 0.000004, 5: 0.000004): 0.001676);

((K12: 0.033158, (S2457T: 0.000004, Shig4337: 0.000004): 0.014979): 0.005742, (O157: 0.000004, EDL933: 0.000004): 0.001676);

Detailed output identifying parameters

kappa (ts/tv) =  2.36902


dN/dS for site classes (K=3)

p:   0.99564  0.00000  0.00436
w:   0.02835  1.00000 30.74169

dN & dS for each branch

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

   6..7       0.006    599.1   1680.9   0.1621   0.0008   0.0050    3.0    1.4
   7..1       0.033    599.1   1680.9   0.1621   0.0047   0.0289   17.3    7.9
   7..8       0.015    599.1   1680.9   0.1621   0.0021   0.0131    7.8    3.6
   8..2       0.000    599.1   1680.9   0.1621   0.0000   0.0000    0.0    0.0
   8..3       0.000    599.1   1680.9   0.1621   0.0000   0.0000    0.0    0.0
   6..9       0.002    599.1   1680.9   0.1621   0.0002   0.0015    0.9    0.4
   9..4       0.000    599.1   1680.9   0.1621   0.0000   0.0000    0.0    0.0
   9..5       0.000    599.1   1680.9   0.1621   0.0000   0.0000    0.0    0.0


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

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

    93 Q      0.998**       30.695
   198 L      1.000**       30.738


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

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

    93 Q      0.847         3.320 +- 2.064
   198 L      0.885         3.408 +- 2.029



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:   0.997  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.232  0.247  0.196  0.131  0.081  0.049  0.029  0.018  0.011  0.007

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 0.006
 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 0.010 0.984

sum of density on p0-p1 =   1.000000
