
seed used = 140005661

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2076.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 1025
# site patterns = 236
   32    5   20   36    9   18   33    9   24   32   37   21    6   68   30
    2   21    1   22    2    2   12   35    4   10   33   24    3    1   10
    6   13    1    1    1    1    2    7    6   11    2    7    6    1    1
    1   17    8    1    8   17    4   26   19    2    1    2    1    3   12
    1    3    1    3    1    8   21    3    1    1    4    5    2    1    1
    1    1   11    1    3    1    1    1    2    2    5    3    1    1    1
    1    1    1    3    2    1    2    3    1    1    1    1    1    2    1
    1    3    1    3    1    2    3    2    1    1    1    1    1    1    1
    2    1    2    1    1    4    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    3    1    1    1    1    1    2    2
    1    1    1    1    2    1    1    2    1    1    1    1    1    1    2
    1    1    1    1    1    1    1    1    2    1    1    2    1    1    1
    1    1    2    2    2    2    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1

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



Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 21 20 20 21 20 | Ser TCT  3  2  2  2  4 | Tyr TAT 10  9  9 10 11 | Cys TGT  2  1  1  2  2
    TTC 19 20 20 19 20 |     TCC  7  8  8  9  7 |     TAC 11 11 11 11 10 |     TGC  2  3  3  2  2
Leu TTA 11  9  9 10 11 |     TCA  6  4  4  6  4 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG 15 12 12 15 15 |     TCG 34 35 35 32 35 |     TAG  0  0  0  0  0 | Trp TGG  6  5  5  6  6
--------------------------------------------------------------------------------------------------
Leu CTT  8  7  7 10  7 | Pro CCT  2  2  2  3  1 | His CAT  4  4  4  5  4 | Arg CGT 15 15 15 16 15
    CTC 11 11 10  9 11 |     CCC  8  8  8  6  8 |     CAC  3  3  3  2  3 |     CGC 29 30 30 31 30
    CTA  5  6  6  7  6 |     CCA  5  6  6  9  4 | Gln CAA 16 15 15 16 15 |     CGA  4  3  3  3  3
    CTG 81 85 86 80 81 |     CCG 38 37 37 35 39 |     CAG 38 39 39 37 39 |     CGG  7  7  7  6  7
--------------------------------------------------------------------------------------------------
Ile ATT 38 39 39 38 40 | Thr ACT  7  7  7  9  9 | Asn AAT 16 15 15 14 14 | Ser AGT 12 12 12 11 11
    ATC 35 33 33 36 33 |     ACC 27 29 29 26 27 |     AAC 22 22 21 24 24 |     AGC 13 13 14 14 14
    ATA  3  3  3  3  3 |     ACA  3  2  2  4  4 | Lys AAA 24 24 24 24 23 | Arg AGA  0  0  0  0  0
Met ATG 35 36 36 36 37 |     ACG 26 26 26 23 23 |     AAG  7  7  7  7  8 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT 12 12 12 12  8 | Ala GCT  7  7  7 10  7 | Asp GAT 26 26 26 27 27 | Gly GGT 20 21 21 22 23
    GTC 14 15 15 16 16 |     GCC 40 41 41 41 41 |     GAC 21 21 21 19 20 |     GGC 32 32 32 31 29
    GTA 10  9  9 10  9 |     GCA  9  7  7  6  9 | Glu GAA 23 21 21 21 22 |     GGA 10  6  6 10  9
    GTG 44 43 43 38 45 |     GCG 45 47 47 48 45 |     GAG 13 16 16 15 14 |     GGG 10 12 12 10 11
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14341    C:0.26732    A:0.26146    G:0.32780
position  2:    T:0.35317    C:0.26049    A:0.22829    G:0.15805
position  3:    T:0.19805    C:0.28683    A:0.12585    G:0.38927

#2: S2457T         
position  1:    T:0.13614    C:0.27228    A:0.26249    G:0.32909
position  2:    T:0.35260    C:0.26249    A:0.22821    G:0.15671
position  3:    T:0.19491    C:0.29383    A:0.11263    G:0.39863

#3: Shig4337       
position  1:    T:0.13614    C:0.27228    A:0.26249    G:0.32909
position  2:    T:0.35260    C:0.26249    A:0.22723    G:0.15769
position  3:    T:0.19491    C:0.29285    A:0.11263    G:0.39961

#4: CFT073         
position  1:    T:0.14146    C:0.26829    A:0.26244    G:0.32780
position  2:    T:0.35122    C:0.26244    A:0.22634    G:0.16000
position  3:    T:0.20683    C:0.28878    A:0.12585    G:0.37854

#5: O157           
position  1:    T:0.14341    C:0.26634    A:0.26341    G:0.32683
position  2:    T:0.35317    C:0.26049    A:0.22829    G:0.15805
position  3:    T:0.19805    C:0.28780    A:0.11902    G:0.39512

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     102 | Ser S TCT      13 | Tyr Y TAT      49 | Cys C TGT       8
      TTC      98 |       TCC      39 |       TAC      54 |       TGC      12
Leu L TTA      50 |       TCA      24 | *** * TAA       0 | *** * TGA       0
      TTG      69 |       TCG     171 |       TAG       0 | Trp W TGG      28
------------------------------------------------------------------------------
Leu L CTT      39 | Pro P CCT      10 | His H CAT      21 | Arg R CGT      76
      CTC      52 |       CCC      38 |       CAC      14 |       CGC     150
      CTA      30 |       CCA      30 | Gln Q CAA      77 |       CGA      16
      CTG     413 |       CCG     186 |       CAG     192 |       CGG      34
------------------------------------------------------------------------------
Ile I ATT     194 | Thr T ACT      39 | Asn N AAT      74 | Ser S AGT      58
      ATC     170 |       ACC     138 |       AAC     113 |       AGC      68
      ATA      15 |       ACA      15 | Lys K AAA     119 | Arg R AGA       0
Met M ATG     180 |       ACG     124 |       AAG      36 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      56 | Ala A GCT      38 | Asp D GAT     132 | Gly G GGT     107
      GTC      76 |       GCC     204 |       GAC     102 |       GGC     156
      GTA      47 |       GCA      38 | Glu E GAA     108 |       GGA      41
      GTG     213 |       GCG     232 |       GAG      74 |       GGG      55
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14012    C:0.26930    A:0.26246    G:0.32812
position  2:    T:0.35255    C:0.26168    A:0.22767    G:0.15810
position  3:    T:0.19855    C:0.29001    A:0.11921    G:0.39222

Codon frequencies under model, for use in evolver:
  0.00999804  0.01460344  0.00600276  0.01975007
  0.00742094  0.01083925  0.00445549  0.01465928
  0.00645661  0.00943071  0.00000000  0.00000000
  0.00448360  0.00654888  0.00000000  0.00885688
  0.01921520  0.02806630  0.01153669  0.03795759
  0.01426228  0.02083191  0.00856298  0.02817362
  0.01240893  0.01812485  0.00745024  0.02451252
  0.00861702  0.01258627  0.00517360  0.01702200
  0.01872715  0.02735344  0.01124366  0.03699350
  0.01390003  0.02030280  0.00834549  0.02745803
  0.01209375  0.01766450  0.00726101  0.02388992
  0.00839815  0.01226659  0.00504220  0.01658966
  0.02341243  0.03419689  0.01405667  0.04624876
  0.01737763  0.02538228  0.01043342  0.03432765
  0.01511944  0.02208391  0.00907762  0.02986685
  0.01049925  0.01533552  0.00630369  0.02074016



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               0.0222 (0.0022 0.0998)
Shig4337             0.0263 (0.0027 0.1012) 0.3551 (0.0004 0.0012)
CFT073               0.0300 (0.0071 0.2363) 0.0306 (0.0067 0.2198) 0.0327 (0.0072 0.2198)
O157                 0.0242 (0.0022 0.0912) 0.0182 (0.0018 0.0972) 0.0225 (0.0022 0.0986) 0.0274 (0.0067 0.2450)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -5275.783177     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00790  0.04174  0.04892  0.00000  0.00197  0.00000  0.18930  0.03769  7.71797  0.98753  0.00974  0.01166 13.14963
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.32753

((1: 0.041745, (2: 0.000004, 3: 0.001968): 0.048918): 0.007900, (4: 0.189300, 5: 0.037692): 0.000000);

((K12: 0.041745, (S2457T: 0.000004, Shig4337: 0.001968): 0.048918): 0.007900, (CFT073: 0.189300, O157: 0.037692): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  7.71797


dN/dS for site classes (K=3)

p:   0.98753  0.00974  0.00273
w:   0.01166  1.00000 13.14963

dN & dS for each branch

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

   6..7       0.008    858.6   2216.4   0.0571   0.0005   0.0082    7.1    1.0
   7..1       0.042    858.6   2216.4   0.0571   0.0025   0.0434   37.3    5.5
   7..8       0.049    858.6   2216.4   0.0571   0.0029   0.0509   43.7    6.4
   8..2       0.000    858.6   2216.4   0.0571   0.0000   0.0000    0.0    0.0
   8..3       0.002    858.6   2216.4   0.0571   0.0001   0.0020    1.8    0.3
   6..9       0.000    858.6   2216.4   0.0571   0.0000   0.0000    0.0    0.0
   9..4       0.189    858.6   2216.4   0.0571   0.0112   0.1969  169.1   24.9
   9..5       0.038    858.6   2216.4   0.0571   0.0022   0.0392   33.7    5.0


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

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

   303 K      0.954*        12.587
   309 E      0.965*        12.722
   632 V      0.543         7.591


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

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

   303 K      0.708         1.367 +- 0.484
   309 E      0.726         1.405 +- 0.426
   531 V      0.543         1.232 +- 0.485
   632 V      0.607         1.303 +- 0.472



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:   0.959  0.033  0.005  0.001  0.001  0.000  0.000  0.000  0.000  0.000

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 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000

sum of density on p0-p1 =   1.000000
