
seed used = 140022089

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3590.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 614
# site patterns = 142
   13   15   27    3   14    4    8    7   13   14   13    5   13    1    8
   21    1    7    5    2   15   35   13   22    5   23   11   25    6    6
    3   11   16   10    4   10    1    1   12    8    1    9    2    1   10
   13    1    1    5    2    1    1    1    3    4    2    5    7    1    6
    1    5    4    5    7    1    2    1    2    1    2    2    1    1    1
    1    1    1    1    1    2    1    1    1    2    1    1    1    1    2
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 10 10 10 10 10 10 | Ser TCT  3  1  1  2  1  1 | Tyr TAT  7  7  7  6  7  7 | Cys TGT  1  1  1  0  1  1
    TTC  6  6  6  6  6  6 |     TCC  1  2  2  1  2  2 |     TAC  3  3  3  4  3  3 |     TGC  2  2  2  3  3  3
Leu TTA  9  9  9  8  9  9 |     TCA  3  3  3  2  3  3 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG 11 10 10  9 10 10 |     TCG  0  0  0  2  0  0 |     TAG  0  0  0  0  0  0 | Trp TGG 12 12 12 12 11 11
--------------------------------------------------------------------------------------------------------------
Leu CTT  9  8  8  9  8  8 | Pro CCT  4  5  5  4  5  5 | His CAT 13 12 12 15 12 12 | Arg CGT 17 17 17 19 17 17
    CTC  6  8  8  6  8  8 |     CCC  1  1  1  1  2  2 |     CAC 10 10 10  9 10 10 |     CGC 28 28 28 25 28 28
    CTA  1  2  2  2  2  2 |     CCA  5  4  4  5  4  4 | Gln CAA  8 10 10  8 10 10 |     CGA  2  2  2  1  2  2
    CTG 38 38 38 39 38 38 |     CCG 17 18 18 17 18 18 |     CAG 23 22 22 23 22 22 |     CGG  6  5  5  8  5  5
--------------------------------------------------------------------------------------------------------------
Ile ATT 16 17 17 16 17 17 | Thr ACT  5  4  4  5  4  4 | Asn AAT  6  8  8  6  8  8 | Ser AGT  1  2  2  3  2  2
    ATC 11 11 11 12 11 11 |     ACC 16 16 16 13 15 15 |     AAC 12 10 10 11 11 11 |     AGC  8  7  7  6  7  7
    ATA  1  1  1  2  1  1 |     ACA  6  5  5  6  6  6 | Lys AAA 14 15 15 14 15 15 | Arg AGA  0  0  0  0  0  0
Met ATG 14 13 13 13 13 13 |     ACG  5  6  6  8  6  6 |     AAG  7  6  6  7  6  6 |     AGG  0  1  1  0  1  1
--------------------------------------------------------------------------------------------------------------
Val GTT 11 10  9  9  9  9 | Ala GCT  4  7  7  3  6  6 | Asp GAT 26 26 27 28 26 26 | Gly GGT 17 18 18 18 17 17
    GTC  7  8  8  5  8  8 |     GCC 19 18 18 20 19 19 |     GAC 16 16 16 14 15 15 |     GGC 17 16 16 16 17 17
    GTA  9  9  9  8 11 11 |     GCA 12 13 13 13 12 12 | Glu GAA 27 26 26 27 26 26 |     GGA  7  6  6  5  6  6
    GTG 11 11 11 16 10 10 |     GCG 32 29 29 32 29 29 |     GAG 16 17 17 15 17 17 |     GGG  5  6  6  7  6  6
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.11075    C:0.30619    A:0.19870    G:0.38436
position  2:    T:0.27687    C:0.21661    A:0.30619    G:0.20033
position  3:    T:0.24430    C:0.26547    A:0.16938    G:0.32085

#2: S2457T         
position  1:    T:0.10749    C:0.30945    A:0.19870    G:0.38436
position  2:    T:0.27850    C:0.21498    A:0.30619    G:0.20033
position  3:    T:0.24919    C:0.26384    A:0.17101    G:0.31596

#3: Shig4337       
position  1:    T:0.10749    C:0.30945    A:0.19870    G:0.38436
position  2:    T:0.27687    C:0.21498    A:0.30782    G:0.20033
position  3:    T:0.24919    C:0.26384    A:0.17101    G:0.31596

#4: CFT073         
position  1:    T:0.10586    C:0.31107    A:0.19870    G:0.38436
position  2:    T:0.27687    C:0.21824    A:0.30456    G:0.20033
position  3:    T:0.24919    C:0.24756    A:0.16450    G:0.33876

#5: O157           
position  1:    T:0.10749    C:0.31107    A:0.20033    G:0.38111
position  2:    T:0.27850    C:0.21498    A:0.30619    G:0.20033
position  3:    T:0.24430    C:0.26873    A:0.17427    G:0.31270

#6: EDL933         
position  1:    T:0.10749    C:0.31107    A:0.20033    G:0.38111
position  2:    T:0.27850    C:0.21498    A:0.30619    G:0.20033
position  3:    T:0.24430    C:0.26873    A:0.17427    G:0.31270

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      60 | Ser S TCT       9 | Tyr Y TAT      41 | Cys C TGT       5
      TTC      36 |       TCC      10 |       TAC      19 |       TGC      15
Leu L TTA      53 |       TCA      17 | *** * TAA       0 | *** * TGA       0
      TTG      60 |       TCG       2 |       TAG       0 | Trp W TGG      70
------------------------------------------------------------------------------
Leu L CTT      50 | Pro P CCT      28 | His H CAT      76 | Arg R CGT     104
      CTC      44 |       CCC       8 |       CAC      59 |       CGC     165
      CTA      11 |       CCA      26 | Gln Q CAA      56 |       CGA      11
      CTG     229 |       CCG     106 |       CAG     134 |       CGG      34
------------------------------------------------------------------------------
Ile I ATT     100 | Thr T ACT      26 | Asn N AAT      44 | Ser S AGT      12
      ATC      67 |       ACC      91 |       AAC      65 |       AGC      42
      ATA       7 |       ACA      34 | Lys K AAA      88 | Arg R AGA       0
Met M ATG      79 |       ACG      37 |       AAG      38 |       AGG       4
------------------------------------------------------------------------------
Val V GTT      57 | Ala A GCT      33 | Asp D GAT     159 | Gly G GGT     105
      GTC      44 |       GCC     113 |       GAC      92 |       GGC      99
      GTA      57 |       GCA      75 | Glu E GAA     158 |       GGA      36
      GTG      69 |       GCG     180 |       GAG      99 |       GGG      36
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.10776    C:0.30972    A:0.19924    G:0.38328
position  2:    T:0.27769    C:0.21580    A:0.30619    G:0.20033
position  3:    T:0.24674    C:0.26303    A:0.17074    G:0.31949

Codon frequencies under model, for use in evolver:
  0.00753327  0.00803052  0.00521279  0.00975430
  0.00585430  0.00624073  0.00405100  0.00758032
  0.00830648  0.00885476  0.00000000  0.00000000
  0.00543456  0.00579328  0.00000000  0.00703683
  0.02165104  0.02308015  0.01498185  0.02803441
  0.01682559  0.01793619  0.01164279  0.02178627
  0.02387329  0.02544908  0.01651958  0.03091184
  0.01561923  0.01665020  0.01080802  0.02022424
  0.01392801  0.01484736  0.00963776  0.01803440
  0.01082382  0.01153827  0.00748975  0.01401501
  0.01535758  0.01637128  0.01062697  0.01988544
  0.01004778  0.01071100  0.00695275  0.01301016
  0.02679340  0.02856194  0.01854021  0.03469289
  0.02082185  0.02219623  0.01440808  0.02696075
  0.02954346  0.03149352  0.02044316  0.03825374
  0.01932896  0.02060480  0.01337505  0.02502771



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               0.1131 (0.0080 0.0707)
Shig4337             0.1233 (0.0087 0.0708)-1.0000 (0.0007 0.0000)
CFT073               0.0203 (0.0033 0.1605) 0.0509 (0.0098 0.1933) 0.0546 (0.0106 0.1935)
O157                 0.1132 (0.0080 0.0707) 0.3314 (0.0029 0.0087) 0.4141 (0.0036 0.0088) 0.0524 (0.0098 0.1877)
EDL933               0.1132 (0.0080 0.0707) 0.3314 (0.0029 0.0087) 0.4141 (0.0036 0.0088) 0.0524 (0.0098 0.1877)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 124
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -3071.361740     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00059  0.06855  0.00684  0.00000  0.00167  0.00113  0.17337  0.00519  0.00000  0.00000  2.96824  0.96237  0.01061  0.00000  4.73527
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.25736

((1: 0.068549, (2: 0.000004, 3: 0.001674): 0.006841): 0.000594, (4: 0.173372, (5: 0.000004, 6: 0.000004): 0.005186): 0.001131);

((K12: 0.068549, (S2457T: 0.000004, Shig4337: 0.001674): 0.006841): 0.000594, (CFT073: 0.173372, (O157: 0.000004, EDL933: 0.000004): 0.005186): 0.001131);

Detailed output identifying parameters

kappa (ts/tv) =  2.96824


dN/dS for site classes (K=3)

p:   0.96237  0.01061  0.02702
w:   0.00000  1.00000  4.73527

dN & dS for each branch

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

   7..8       0.001    551.8   1290.2   0.1385   0.0001   0.0005    0.3    0.1
   8..1       0.069    551.8   1290.2   0.1385   0.0080   0.0576   31.8   10.3
   8..9       0.007    551.8   1290.2   0.1385   0.0008   0.0057    3.2    1.0
   9..2       0.000    551.8   1290.2   0.1385   0.0000   0.0000    0.0    0.0
   9..3       0.002    551.8   1290.2   0.1385   0.0002   0.0014    0.8    0.3
   7..10      0.001    551.8   1290.2   0.1385   0.0001   0.0010    0.5    0.2
  10..4       0.173    551.8   1290.2   0.1385   0.0202   0.1457   80.4   26.0
  10..11      0.005    551.8   1290.2   0.1385   0.0006   0.0044    2.4    0.8
  11..5       0.000    551.8   1290.2   0.1385   0.0000   0.0000    0.0    0.0
  11..6       0.000    551.8   1290.2   0.1385   0.0000   0.0000    0.0    0.0


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

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

   154 M      0.712         3.660
   232 N      0.753         3.812
   240 N      0.696         3.601
   276 T      0.833         4.113
   311 T      0.781         3.917
   321 L      0.906         4.384
   355 W      0.803         3.998
   364 S      0.939         4.506
   366 A      0.998**       4.727
   367 D      0.916         4.423
   370 S      0.956*        4.571
   371 V      0.767         3.867
   374 E      0.947         4.537
   381 A      0.947         4.537
   472 H      0.951*        4.551
   489 E      0.805         4.006


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

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

   321 L      0.645         4.209 +- 3.291
   364 S      0.848         5.480 +- 2.883
   366 A      0.991**       6.183 +- 2.370
   367 D      0.775         5.011 +- 3.005
   370 S      0.889         5.701 +- 2.762
   374 E      0.862         5.539 +- 2.836
   381 A      0.876         5.652 +- 2.814
   472 H      0.873         5.607 +- 2.807



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:   0.013  0.064  0.122  0.150  0.149  0.135  0.116  0.098  0.083  0.070

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
