
seed used = 140019585

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3402.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 583
# site patterns = 196
   15   13    6    9    7   15    6    1    3    2   11   22    6   12    6
    7    1    1    1    1    1    1    1    1    1    6   11   11    1   31
    4    3    1   12   10    1   18    6    2    4   10    8   12    1   13
    7   17    3    6    5    1    4    1   10    1    1    6    1    1    9
    1    1    1    2    1    1    1    1   13    2    9    4    2    1    1
    1    4    2    1    1    1    2    1    4    1    6    1    1    1    1
    1    3    1    1    5    3    1    1    2    1    1    2    1    1    1
    1    1    1    3    1    1    1    2    5    2    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    2    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    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 GAT AAC GTT GAA CTT TCA CCC GCA ACA CGC TGG GGG ATT GCT ACC --- --- --- --- --- --- --- --- --- GGA TTA CAG GGT CTG TGC TAC CTG ATC GCC TCC AAA AAT CAC AGT TAT GGC GTG CCT GCG GTC TTT TCC CTC TTC TCT AAG CTA ACG CTG GGG AGC GGC CTG CAA ACT AAC CCC AGA GCT CTT GGT TTG TTG CTA CCG ATA CGC GAC CGC TAT GTA CAT GCC GGC TTG GTG AGT GAG AAT GAC TGG ATT CTC ACG TTA GGT GCG CGA CGT TCT TTA ACG AGC ATC TTG CCC ACA TTG GTC GCC GCG CTG CGG ACT GTG GTG GTG TCG AGC AAA AAT GTT TCG TCA ACT ATC TAC GAG CAG GCT GGG TTT GCG GAT CTG GCG TTA GAG CAT CAA GTA GTA TTA GCC GAT CCT GTT CCT GCG ACA TTA ATC CAG GAT GTG ACC TGT GAC GTC GTC GGT CAG GCG CTG GCT AAT GAC GTC GGC TTT GAC TCA GAC AGA GAC GCG CTT GAT AGT TTA CTT AAC GAA ACA AAG GGG AAG CCT GCG CTT GTA GTG GGT AGG AAT GTG AAT CTG AAT GAG 
S2457T                               ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... GGA TTA CTT CAG GGG ATG ATT GCT ACC ... ... ... ..G ... ... ... ..T ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ACA ... ... ..T ... ... ... ... ... ... ... A.. ..C ... ... ... ... ... ..T .G. A.. ..C ... ... T.. ... C.. ... G.. ... ... ... ... ..G ..T ..A ..T ... ..A ..T ... ... C.. ... ... ... ..A ... ..G ... ... A.. .G. ... ... ... .C. .A. ... ... ..T ..T ... C.. ... C.. ... ... ... ..A ... ..G ... ... ... ... ... ... ... ... ... G.. ... ... ..C ... ..A ... ... ..G ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ..G ... ..G ACG ..A ... .C. G.A A.A ..C T.A .G. A.. 
Shig4337                             ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- ... ... ... ..G ... ... ... ..T ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ACA ... ... ..T ... ... ... ... ... ... ... A.. ..C ... ... ... ... ... ..T .G. A.. ..C ... ... T.. ... C.. ... G.. ... ... ... ... ..G ..T ..A ..T ... ..A ..T ... ... C.. ... ... ... ..A ... ..G ... ... A.. .G. ... ... ... .C. .A. ... ... ..T ..T ... C.. ... C.. ... ... ... ..A ... ..G ... ... ... ... ... ... ... ... ... G.. ... ... ..C ... ..A ... ... ..G ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ..G ... ..G ACG ..A ... .C. G.A A.A ..C T.A .G. A.. 
CFT073                               ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- ... ... ... ..G ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ..G ... ... ..A ... ..T ..A ... .T. ... .A. ... ..A ... ..C C.. ... ... ... ... ... ... ... ... ... ... ... ... C.. ..A G.A ... ..A ... G.. ... ... ... ... ... ..A ..T ... ... ... ... ... ..T ... ... ..G ... ... ... ... A.. ... ... .C. ... ..A ... ..T ... ..C C.. ..T C.. .G. C.. ..T ..A ... ..G .A. .A. AG. .G. ... ..T ..T .TA .G. ..G A.. .C. ... ..A ... T.A .GA ..G A.. .T. G.G ..G A.A A.. .CA .TA ..C ..T ..G ..A ..C AG. ..A ... ..C ... ..A TA. ..T A.. ..T C.T .CT G.G A.A .A. A.. ACG .A. .C. ..C GCT .T. .TG G.. ... ... ... .T. ... ACG ... ..C ..A G.. T.. ... ... ... ..A 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... .C. ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ..T C.. ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ..A ..T ... ..A ... ..G C.. A.. ... ... ... ... ... .C. ... ..A ... ..T ... ... C.. ... C.. ... ... ... ..A ..C ..G .A. .A. ... ... ..A ... ... ... ... ... A.. ... ... ... ..A ... .G. ..G ... ... ... ... ... ... ... ... ... ... ..A ... ..C AG. ..A ..C ..C G.. ..A TA. ... ... ..T C.T ... .AG C.A .A. ... ACG ... ... ... CGT ..T ... ... ..A ... ... ... ... ... ... ... ... G.. ... ... ... ... ... 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... .C. ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ..T C.. ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ..A ..T ... ..A ... ..G C.. A.. ... ... ... ... ... .C. ... ..A ... ..T ... ... C.. ... C.. ... ... ... ..A ..C ..G .A. .A. ... ... ..A ... ... ... ... ... A.. ... ... ... ..A ... .G. ..G ... ... ... ... ... ... ... ... ... ... ..A ... ..C AG. ..A ..C ..C G.. ..A TA. ... ... ..T C.T ... .AG C.A .A. ... ACG ... ... ... CGT ..T ... ... ..A ... ... ... ... ... ... ... ... G.. ... ... ... ... ... 



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

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

#1: K12            
position  1:    T:0.21603    C:0.23693    A:0.24390    G:0.30314
position  2:    T:0.38850    C:0.19861    A:0.23171    G:0.18118
position  3:    T:0.25087    C:0.23171    A:0.16551    G:0.35192

#2: S2457T         
position  1:    T:0.21098    C:0.23499    A:0.25386    G:0.30017
position  2:    T:0.38250    C:0.20412    A:0.22642    G:0.18696
position  3:    T:0.25043    C:0.22298    A:0.17324    G:0.35334

#3: Shig4337       
position  1:    T:0.21254    C:0.23519    A:0.25261    G:0.29965
position  2:    T:0.38153    C:0.20383    A:0.22822    G:0.18641
position  3:    T:0.24913    C:0.22474    A:0.17247    G:0.35366

#4: CFT073         
position  1:    T:0.20732    C:0.23868    A:0.25436    G:0.29965
position  2:    T:0.38676    C:0.19686    A:0.22822    G:0.18815
position  3:    T:0.24913    C:0.21254    A:0.18990    G:0.34843

#5: O157           
position  1:    T:0.20906    C:0.24913    A:0.24564    G:0.29617
position  2:    T:0.38153    C:0.20209    A:0.23345    G:0.18293
position  3:    T:0.25436    C:0.22125    A:0.17944    G:0.34495

#6: EDL933         
position  1:    T:0.20906    C:0.24913    A:0.24564    G:0.29617
position  2:    T:0.38153    C:0.20209    A:0.23345    G:0.18293
position  3:    T:0.25436    C:0.22125    A:0.17944    G:0.34495

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     114 | Ser S TCT      24 | Tyr Y TAT      68 | Cys C TGT       5
      TTC      32 |       TCC      24 |       TAC      28 |       TGC      25
Leu L TTA     105 |       TCA      42 | *** * TAA       0 | *** * TGA       0
      TTG      89 |       TCG      35 |       TAG       0 | Trp W TGG     137
------------------------------------------------------------------------------
Leu L CTT     118 | Pro P CCT      19 | His H CAT      17 | Arg R CGT      40
      CTC      44 |       CCC      20 |       CAC      15 |       CGC      78
      CTA      18 |       CCA       5 | Gln Q CAA      59 |       CGA       3
      CTG     233 |       CCG      64 |       CAG      80 |       CGG      18
------------------------------------------------------------------------------
Ile I ATT      83 | Thr T ACT      16 | Asn N AAT      61 | Ser S AGT      49
      ATC      89 |       ACC      52 |       AAC      46 |       AGC      48
      ATA      31 |       ACA      29 | Lys K AAA     117 | Arg R AGA      16
Met M ATG      96 |       ACG      82 |       AAG      37 |       AGG       9
------------------------------------------------------------------------------
Val V GTT      58 | Ala A GCT      49 | Asp D GAT     104 | Gly G GGT      43
      GTC      55 |       GCC      84 |       GAC      59 |       GGC      69
      GTA      52 |       GCA      29 | Glu E GAA      62 |       GGA      42
      GTG     108 |       GCG     121 |       GAG      42 |       GGG      56
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.21083    C:0.24066    A:0.24935    G:0.29916
position  2:    T:0.38372    C:0.20127    A:0.23023    G:0.18477
position  3:    T:0.25138    C:0.22242    A:0.17666    G:0.34955

Codon frequencies under model, for use in evolver:
  0.02101804  0.01859661  0.01477074  0.02922670
  0.01102456  0.00975445  0.00774767  0.01533023
  0.01261082  0.01115796  0.00000000  0.00000000
  0.01012038  0.00895444  0.00000000  0.01407293
  0.02399175  0.02122772  0.01686056  0.03336180
  0.01258435  0.01113454  0.00884384  0.01749921
  0.01439505  0.01273663  0.01011634  0.02001708
  0.01155225  0.01022135  0.00811852  0.01606402
  0.02485788  0.02199406  0.01746924  0.03456619
  0.01303866  0.01153651  0.00916311  0.01813095
  0.01491473  0.01319644  0.01048155  0.02073972
  0.01196930  0.01059035  0.00841161  0.01664395
  0.02982368  0.02638777  0.02095904  0.04147140
  0.01564336  0.01384113  0.01099361  0.02175292
  0.01789421  0.01583266  0.01257542  0.02488284
  0.01436038  0.01270596  0.01009197  0.01996887



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               0.3045 (0.0234 0.0768)
Shig4337             0.3045 (0.0234 0.0768)-1.0000 (0.0000 0.0000)
CFT073               0.3272 (0.0488 0.1492) 0.3853 (0.0587 0.1524) 0.3853 (0.0587 0.1524)
O157                 0.3207 (0.0228 0.0710) 0.3854 (0.0387 0.1004) 0.3854 (0.0387 0.1004) 0.3154 (0.0386 0.1223)
EDL933               0.3207 (0.0228 0.0710) 0.3854 (0.0387 0.1004) 0.3854 (0.0387 0.1004) 0.3154 (0.0386 0.1223)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):  -3356.575017     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.03425  0.02829  0.08880  0.00000  0.00000  0.02062  0.16871  0.03107  0.00000  0.00000  2.66082  0.96037  0.00000  0.26825  6.79065
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.37175

((1: 0.028288, (2: 0.000004, 3: 0.000004): 0.088796): 0.034250, (4: 0.168706, (5: 0.000004, 6: 0.000004): 0.031072): 0.020619);

((K12: 0.028288, (S2457T: 0.000004, Shig4337: 0.000004): 0.088796): 0.034250, (CFT073: 0.168706, (O157: 0.000004, EDL933: 0.000004): 0.031072): 0.020619);

Detailed output identifying parameters

kappa (ts/tv) =  2.66082


dN/dS for site classes (K=3)

p:   0.96037  0.00000  0.03963
w:   0.26825  1.00000  6.79065

dN & dS for each branch

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

   7..8       0.034    506.6   1242.4   0.5268   0.0091   0.0172    8.7   11.3
   8..1       0.028    506.6   1242.4   0.5268   0.0075   0.0142    7.2    9.3
   8..9       0.089    506.6   1242.4   0.5268   0.0235   0.0446   22.6   29.2
   9..2       0.000    506.6   1242.4   0.5268   0.0000   0.0000    0.0    0.0
   9..3       0.000    506.6   1242.4   0.5268   0.0000   0.0000    0.0    0.0
   7..10      0.021    506.6   1242.4   0.5268   0.0055   0.0104    5.2    6.8
  10..4       0.169    506.6   1242.4   0.5268   0.0446   0.0847   42.9   55.4
  10..11      0.031    506.6   1242.4   0.5268   0.0082   0.0156    7.9   10.2
  11..5       0.000    506.6   1242.4   0.5268   0.0000   0.0000    0.0    0.0
  11..6       0.000    506.6   1242.4   0.5268   0.0000   0.0000    0.0    0.0


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

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

    42 S      0.846         5.785
    87 L      0.919         6.260
   172 S      0.938         6.386
   438 A      0.670         4.641
   462 D      0.765         5.256
   522 V      0.853         5.829
   531 R      0.831         5.690
   535 D      0.991**       6.732
   538 D      0.966*        6.566
   544 N      1.000**       6.789
   545 E      0.838         5.736
   571 V      1.000**       6.790
   578 N      0.748         5.144
   579 V      0.936         6.374


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

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

    42 S      0.697         5.280 +- 3.337
    87 L      0.804         6.000 +- 3.049
   172 S      0.835         6.204 +- 2.924
   462 D      0.585         4.494 +- 3.432
   522 V      0.710         5.372 +- 3.317
   531 R      0.679         5.156 +- 3.370
   535 D      0.935         6.850 +- 2.374
   538 D      0.879         6.491 +- 2.714
   544 N      0.991**       7.184 +- 1.945
   545 E      0.685         5.190 +- 3.354
   571 V      0.994**       7.203 +- 1.914
   578 N      0.568         4.377 +- 3.438
   579 V      0.803         5.974 +- 3.027



The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.202  0.382  0.381  0.035  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.001  0.009  0.031  0.083  0.140  0.187  0.194  0.162  0.116  0.075

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.091
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.014 0.224
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.040 0.270
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.005 0.068 0.279

sum of density on p0-p1 =   1.000000
