
seed used = 140015801

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3053.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 946
# site patterns = 194
   27    8   19   10    5    4   11   40   12   21   13    1    6   25   11
   62    8    1   13   47   10    1    8   38    2    4    1    6   37   16
   25   21   11    1    1   16   14   14    1    2    2    1    1    3    1
    7    1    8   27    2   13    1    1    1    1   11    1    1    1   14
    1    1   24   19    1   11    5    1    4   18    1    6    2    1    5
    3    1    1    1   10   13    6    1    2    1    1    2    1    1    1
    1    6    2    5    1    2    2    1    2    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    2    2    1    1    1
    1    1    2    3    1    1    1    1    2    2    1    1    1    3    1
    1    1    1    1    1    2    1    1    1    1    1    1    1    1    2
    1    1    1    1    3    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1

1       
K12                   ATG AAG CCG CTC TCT TCA TTA CAG TAC TGG ACC GTT GTT GAG CGG CTG CCA CCT GCC GAA CTT AGC GCA GCG GTA ACT TTT AGT GAT TTT GTG GAC AGC GTG ATT CAT ACG CAA CCG GCC CAG GCG GCA TTG TGT AAT AGT GGG CGC CTA TTC CGG ATT GTG CGC ATC GCC GCA ATA TTG AGC TAT ATT CGT CTG TAT TGC GAG GGA GGC ATT GGT GGT GAG TCC TGT ACG GGT CGG AAC AAA GTC CGG GGC AGC GCC GAA GGG AAG GGC GAA GCT CGC TCG GGG CGA CGT AAT CTC GTT GGC GGA TCG CAA TCT GCC GAG GCG CCT TCT AAT CTG GCG ACC GAT CGT ACT ACG GAT GTG ACG CTG GCC CGC ACC CCG CGA GGA CCG CTA GTT TCG GTG ACC ACC TTA GAA CCC AAA GCC GCG CTG AAC CTT TAC CAG CCG ACC CGC GAG TTG ATC GCC GTG CAC ATA GTT GTT CTG CGT GCG CTT GGG CGG CAT AGT CGT TAT GCT CGA GTG ACA GCA GCC GAA ACC GCA GTG CGC ACG CGT GGT ACG GCT GAT GCT GGG CAT CGT CTA ACT CTT TCG GAA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ..T ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..A ..T ..A AGC .TG ... A.. ... ..C ... ... ... ... ... ... ... ... ... ..A ... ... ... ..T ... ... ... ... ... ... ... ... ... ..C ... ..C ..A ... ... ... ..C ... ... ... ... ..A ... ... ... ..G ..A ..A ... ... ... ... ... ... ... ... ... ... ... ..T ..G .T. ..G ... ... .C. ..A ... ... ..C ... ... ... ..C ... ... ... ... ..C ... A.. ..T ..T ..T ... ... ... ..A ... ..C ... ... ... ..A ... ... ..T ... ... ..A ..A ..T ... ..T ... ... ... ..T ..A C.. ..T ..G ..A ... ... .G. ..G ..C ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..G ... ..T ..A ..A ... ... ... A.. ..C ..C ... ... ..G ..G ..G ... ..T 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ..T ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..A ..T ..A AGC .TG ... A.. ... ..C ... ... ... ... ... ... ... ... ... ..A ... ... ... ..T ... ... ... ... ... ... ... ... ... ..C ... ..C ..A ... ... ... ..C ... ... ... ... ..A ... ... ... ..G ..A ..A ... ... ... ... ... ... ... ... ... ... ... ..T ..G .T. ..G ... ... .C. ..A ... ... ..C ... ... ... ..C ... ... ... ... ..C ... A.. ..T ..T ..T ... ... ... ..A ... ..C ... ... ... ..A ... ... ..T ... ... ..A ..A ..T ... ..T ... ... ... ..T ..A C.. ..T ..G ..A ... ... .G. ..G ..C ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..G ... ..T ..A ..A ... ... ... A.. ..C ..C ... ... ..G ..G ..G ... ..T 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T T.. C.. A.. ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... C.. ... ... ... ... ... ..A ... ... ... ... ..C ..A ... ... ..C ... ... ... ... ... ... ..T ..T ..G ... ... ... ..G ..C ... ..T ... ..A ... ..C ..C ..T ..C ... ..G ... ... G.. ... .C. ... ... .T. ..C T.. .T. G.. ..C ... ..C ... ... ... .T. ... ..T ... ..T ... ... ... ..A ... ..C ... ... ..T ... C.T ..G ..T ..G ..T ..A ..A ..T ..C ... ..A ..A ..G ..T ..A C.. ..T ..G ..A ... ..T ... ... ... ... ... ..G ... ..A ... ... ..A ... ..A ... ... ... ... ..T ..G ... ... ..A ..G ... ..C ..C ..A ..C ... ..C ..C ..C ..C ... ..G ..G ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..C ... ... ... ... ... ... A.A .G. ... ... ... ... ... ... .TT ... ... AT. ... ... ... ... ..G ... ..T ..C ..A ..T ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ..C ..A ... ... ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ..G ... ..G ... .T. .C. ... ... ... ..C T.. ... ... ..C ..C ... ..A ..C ... ... ... ... ... ..A ..A ..C ..G ... ... ... .T. .C. ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..G ..A ..A ..C ..C ..A ..C ..G ..G ..T ..C A.. ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... C.. ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..C ... ... ... ... ... ... A.A .G. ... ... ... ... ... ... .TT ... ... AT. ... ... ... ... ..G ... ..T ..C ..A ..T ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ..C ..A ... ... ... ... T.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ..G ... ..G ... .T. .C. ... ... ... ..C T.. ... ... ..C ..C ... ..A ..C ... ... ... ... ... ..A ..A ..C ..G ... ... ... .T. .C. ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ..G ..A ..A ..C ..C ..A ..C ..G ..G ..T ..C A.. ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... C.. ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 17 16 16 17 16 16 | Ser TCT  7  7  7  5  7  7 | Tyr TAT 13 14 14 12 12 12 | Cys TGT  4  3  3  3  3  3
    TTC 13 14 14 14 14 14 |     TCC  5  5  5  5  5  5 |     TAC 13 12 12 13 14 14 |     TGC  5  5  5  5  5  5
Leu TTA 12 12 12 11 12 12 |     TCA  4  4  4  5  4  4 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG 18 18 18 15 20 20 |     TCG  8  7  7  8  6  6 |     TAG  0  0  0  0  0  0 | Trp TGG 21 21 21 21 22 22
--------------------------------------------------------------------------------------------------------------
Leu CTT 13 13 13 13 12 12 | Pro CCT  2  2  2  3  2  2 | His CAT 18 18 18 18 17 17 | Arg CGT 27 30 30 25 25 25
    CTC 12 13 13 11 12 12 |     CCC  1  0  0  0  1  1 |     CAC  3  3  3  4  4  4 |     CGC 35 31 31 35 38 38
    CTA  5  5  5  6  4  4 |     CCA  8 11 11 11  9  9 | Gln CAA 15 16 16 16 14 14 |     CGA  4  6  6  6  4  4
    CTG 67 67 67 71 68 68 |     CCG 24 21 21 21 24 24 |     CAG 43 42 42 42 44 44 |     CGG 15 14 14 15 13 13
--------------------------------------------------------------------------------------------------------------
Ile ATT 27 27 27 29 27 27 | Thr ACT  7  8  8  8  7  7 | Asn AAT  9 10 10  8  8  8 | Ser AGT  8 10 10 10  9  9
    ATC 12 12 12 11 13 13 |     ACC 21 18 18 18 21 21 |     AAC 11 11 11 12 12 12 |     AGC 14 14 14 13 14 14
    ATA  2  2  2  1  3  3 |     ACA  1  3  3  2  3  3 | Lys AAA 14 15 15 13 14 14 | Arg AGA  0  0  0  0  0  0
Met ATG 27 28 28 28 27 27 |     ACG 19 19 19 18 18 18 |     AAG  9  8  8 10  9  9 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT 11  8  8  9 12 12 | Ala GCT  9 12 12 13  8  8 | Asp GAT 40 39 39 39 38 38 | Gly GGT 10  9  9  9  8  8
    GTC  6  8  8  8  7  7 |     GCC 23 18 18 20 21 21 |     GAC 21 22 22 23 23 23 |     GGC 22 25 25 23 24 24
    GTA  2  3  3  4  3  3 |     GCA 12 14 14 13 13 13 | Glu GAA 53 53 53 54 53 53 |     GGA  6  6  6  6  6  6
    GTG 32 32 32 31 28 28 |     GCG 44 43 43 43 45 45 |     GAG 30 28 28 27 29 29 |     GGG 12 11 11 12 12 12
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14799    C:0.30867    A:0.19133    G:0.35201
position  2:    T:0.29175    C:0.20613    A:0.30867    G:0.19345
position  3:    T:0.23467    C:0.22939    A:0.14588    G:0.39006

#2: S2457T         
position  1:    T:0.14588    C:0.30867    A:0.19556    G:0.34989
position  2:    T:0.29387    C:0.20296    A:0.30761    G:0.19556
position  3:    T:0.23890    C:0.22304    A:0.15856    G:0.37949

#3: Shig4337       
position  1:    T:0.14588    C:0.30867    A:0.19556    G:0.34989
position  2:    T:0.29387    C:0.20296    A:0.30761    G:0.19556
position  3:    T:0.23890    C:0.22304    A:0.15856    G:0.37949

#4: CFT073         
position  1:    T:0.14165    C:0.31395    A:0.19133    G:0.35307
position  2:    T:0.29493    C:0.20402    A:0.30761    G:0.19345
position  3:    T:0.23362    C:0.22727    A:0.15645    G:0.38266

#5: O157           
position  1:    T:0.14799    C:0.30761    A:0.19556    G:0.34884
position  2:    T:0.29387    C:0.20507    A:0.30761    G:0.19345
position  3:    T:0.22304    C:0.24101    A:0.15011    G:0.38584

#6: EDL933         
position  1:    T:0.14799    C:0.30761    A:0.19556    G:0.34884
position  2:    T:0.29387    C:0.20507    A:0.30761    G:0.19345
position  3:    T:0.22304    C:0.24101    A:0.15011    G:0.38584

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      98 | Ser S TCT      40 | Tyr Y TAT      77 | Cys C TGT      19
      TTC      83 |       TCC      30 |       TAC      78 |       TGC      30
Leu L TTA      71 |       TCA      25 | *** * TAA       0 | *** * TGA       0
      TTG     109 |       TCG      42 |       TAG       0 | Trp W TGG     128
------------------------------------------------------------------------------
Leu L CTT      76 | Pro P CCT      13 | His H CAT     106 | Arg R CGT     162
      CTC      73 |       CCC       3 |       CAC      21 |       CGC     208
      CTA      29 |       CCA      59 | Gln Q CAA      91 |       CGA      30
      CTG     408 |       CCG     135 |       CAG     257 |       CGG      84
------------------------------------------------------------------------------
Ile I ATT     164 | Thr T ACT      45 | Asn N AAT      53 | Ser S AGT      56
      ATC      73 |       ACC     117 |       AAC      69 |       AGC      83
      ATA      13 |       ACA      15 | Lys K AAA      85 | Arg R AGA       0
Met M ATG     165 |       ACG     111 |       AAG      53 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      60 | Ala A GCT      62 | Asp D GAT     233 | Gly G GGT      53
      GTC      44 |       GCC     121 |       GAC     134 |       GGC     143
      GTA      18 |       GCA      79 | Glu E GAA     319 |       GGA      36
      GTG     183 |       GCG     263 |       GAG     171 |       GGG      70
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14623    C:0.30920    A:0.19415    G:0.35042
position  2:    T:0.29369    C:0.20437    A:0.30779    G:0.19415
position  3:    T:0.23203    C:0.23080    A:0.15328    G:0.38390

Codon frequencies under model, for use in evolver:
  0.01025752  0.01020300  0.00677604  0.01697125
  0.00713780  0.00709987  0.00471518  0.01180963
  0.01074978  0.01069264  0.00000000  0.00000000
  0.00678091  0.00674487  0.00000000  0.01121914
  0.02168909  0.02157381  0.01432764  0.03588498
  0.01509259  0.01501237  0.00997005  0.02497095
  0.02272996  0.02260914  0.01501523  0.03760712
  0.01433796  0.01426175  0.00947154  0.02372241
  0.01361902  0.01354663  0.00899662  0.02253291
  0.00947694  0.00942657  0.00626039  0.01567977
  0.01427260  0.01419674  0.00942837  0.02361427
  0.00900309  0.00895524  0.00594737  0.01489578
  0.02458097  0.02445032  0.01623800  0.04066965
  0.01710493  0.01701402  0.01129939  0.02830042
  0.02576062  0.02562370  0.01701726  0.04262140
  0.01624969  0.01616332  0.01073442  0.02688539



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               0.0536 (0.0053 0.0991)
Shig4337             0.0536 (0.0053 0.0991)-1.0000 (0.0000 0.0000)
CFT073               0.0420 (0.0052 0.1227) 0.0653 (0.0085 0.1296) 0.0653 (0.0085 0.1296)
O157                 0.0993 (0.0063 0.0637) 0.0664 (0.0092 0.1378) 0.0664 (0.0092 0.1378) 0.0692 (0.0096 0.1392)
EDL933               0.0993 (0.0063 0.0637) 0.0664 (0.0092 0.1378) 0.0664 (0.0092 0.1378) 0.0692 (0.0096 0.1392)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 190
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -4761.104882     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.03247  0.14629  0.00000  0.00000  0.01477  0.17278  0.09999  0.00000  0.00000  4.46453  0.95310  0.04583  0.02652 536.26424
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.46632

((1: 0.032474, (2: 0.000004, 3: 0.000004): 0.146290): 0.000001, (4: 0.172780, (5: 0.000004, 6: 0.000004): 0.099989): 0.014771);

((K12: 0.032474, (S2457T: 0.000004, Shig4337: 0.000004): 0.146290): 0.000001, (CFT073: 0.172780, (O157: 0.000004, EDL933: 0.000004): 0.099989): 0.014771);

Detailed output identifying parameters

kappa (ts/tv) =  4.46453


dN/dS for site classes (K=3)

p:   0.95310  0.04583  0.00107
w:   0.02652  1.00000536.26424

dN & dS for each branch

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

   7..8       0.000    840.5   1997.5   0.6468   0.0000   0.0000    0.0    0.0
   8..1       0.032    840.5   1997.5   0.6468   0.0093   0.0144   12.1   18.6
   8..9       0.146    840.5   1997.5   0.6468   0.0420   0.0649   54.5   83.8
   9..2       0.000    840.5   1997.5   0.6468   0.0000   0.0000    0.0    0.0
   9..3       0.000    840.5   1997.5   0.6468   0.0000   0.0000    0.0    0.0
   7..10      0.015    840.5   1997.5   0.6468   0.0042   0.0066    5.5    8.5
  10..4       0.173    840.5   1997.5   0.6468   0.0496   0.0766   64.4   99.0
  10..11      0.100    840.5   1997.5   0.6468   0.0287   0.0444   37.3   57.3
  11..5       0.000    840.5   1997.5   0.6468   0.0000   0.0000    0.0    0.0
  11..6       0.000    840.5   1997.5   0.6468   0.0000   0.0000    0.0    0.0


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

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

    70 A      0.995**       533.560


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

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

    70 A      0.771         1.506 +- 0.466
    71 A      0.661         1.409 +- 0.517
    78 C      0.653         1.401 +- 0.519



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:   0.886  0.101  0.011  0.002  0.000  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
