
seed used = 140024965

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3829.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 753
# site patterns = 140
    9    2    1    1    7   10   18    6   16    9    5   11    7   15   54
   29   16   25   31   12    1    3   10   22    4   14    4   11   33    1
   12    1    4   18    7   15   22   19   20   10   13    7    8    1    2
    1   20    1    7   21    4    4    3   13    2    1    1    1    1    1
    1    1    1    1    4    1    9    1    3    6    2    1    4    1    1
    1    1    1    1    2    4    1    1    8    2    1    1    2    6    4
    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    2    1    1    1
    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT 11 11 11 12 10 | Ser TCT  4  4  4  4  6 | Tyr TAT 11 11 11 10 11 | Cys TGT  2  2  2  3  2
    TTC 10 10 10  9 11 |     TCC  5  5  5  6  4 |     TAC  7  8  8  9  7 |     TGC  5  5  5  4  6
Leu TTA  1  1  1  1  1 |     TCA  0  0  0  0  0 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  9  8  8 13  8 |     TCG  8  8  8  7  7 |     TAG  0  0  0  0  0 | Trp TGG 23 22 22 22 23
--------------------------------------------------------------------------------------------------
Leu CTT  2  4  4  4  3 | Pro CCT  6  6  6  6  5 | His CAT  8  8  8  9  8 | Arg CGT 31 32 32 32 33
    CTC  8  7  7  7  7 |     CCC  3  3  3  4  3 |     CAC 11 11 11 10 11 |     CGC 16 15 15 15 13
    CTA  2  2  2  0  2 |     CCA  7  9  9  7  8 | Gln CAA 13 12 12 13 13 |     CGA  0  0  0  0  0
    CTG 64 64 64 61 64 |     CCG 21 20 20 21 21 |     CAG 21 22 22 21 21 |     CGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------
Ile ATT 22 22 22 25 23 | Thr ACT  3  7  7  6  7 | Asn AAT  8 10 10 10  9 | Ser AGT  3  3  3  4  4
    ATC 16 16 16 15 16 |     ACC 24 20 20 22 21 |     AAC 17 17 17 15 16 |     AGC 11 12 12 10 10
    ATA  2  2  2  0  1 |     ACA  2  3  3  2  2 | Lys AAA 26 25 25 27 26 | Arg AGA  0  0  0  0  0
Met ATG  9  9  9  9 10 |     ACG 12 12 12 11 11 |     AAG 10 10 10  9  9 |     AGG  0  0  0  0  1
--------------------------------------------------------------------------------------------------
Val GTT  9 10 10  9 10 | Ala GCT  6  5  5  9  4 | Asp GAT 20 19 19 24 21 | Gly GGT 17 16 16 19 16
    GTC  9  9  9 10  8 |     GCC 17 17 17 14 16 |     GAC 30 29 29 25 29 |     GGC 17 16 16 18 18
    GTA 13 13 13 12 12 |     GCA 14 13 13 17 16 | Glu GAA 35 35 35 33 35 |     GGA  5  5  5  5  4
    GTG 22 22 22 22 25 |     GCG 40 39 39 36 39 |     GAG 17 18 18 20 17 |     GGG  7  8  8  4  8
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.12749    C:0.28420    A:0.21912    G:0.36919
position  2:    T:0.27756    C:0.22842    A:0.31076    G:0.18327
position  3:    T:0.21647    C:0.27357    A:0.15936    G:0.35060

#2: S2457T         
position  1:    T:0.12616    C:0.28685    A:0.22311    G:0.36388
position  2:    T:0.27888    C:0.22709    A:0.31208    G:0.18194
position  3:    T:0.22576    C:0.26560    A:0.15936    G:0.34927

#3: Shig4337       
position  1:    T:0.12616    C:0.28685    A:0.22311    G:0.36388
position  2:    T:0.27888    C:0.22709    A:0.31208    G:0.18194
position  3:    T:0.22576    C:0.26560    A:0.15936    G:0.34927

#4: CFT073         
position  1:    T:0.13280    C:0.28021    A:0.21912    G:0.36786
position  2:    T:0.27756    C:0.22842    A:0.31208    G:0.18194
position  3:    T:0.24701    C:0.25631    A:0.15538    G:0.34130

#5: O157           
position  1:    T:0.12749    C:0.28287    A:0.22045    G:0.36919
position  2:    T:0.28021    C:0.22576    A:0.30943    G:0.18459
position  3:    T:0.22842    C:0.26029    A:0.15936    G:0.35193

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      55 | Ser S TCT      22 | Tyr Y TAT      54 | Cys C TGT      11
      TTC      50 |       TCC      25 |       TAC      39 |       TGC      25
Leu L TTA       5 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG      46 |       TCG      38 |       TAG       0 | Trp W TGG     112
------------------------------------------------------------------------------
Leu L CTT      17 | Pro P CCT      29 | His H CAT      41 | Arg R CGT     160
      CTC      36 |       CCC      16 |       CAC      54 |       CGC      74
      CTA       8 |       CCA      40 | Gln Q CAA      63 |       CGA       0
      CTG     317 |       CCG     103 |       CAG     107 |       CGG       5
------------------------------------------------------------------------------
Ile I ATT     114 | Thr T ACT      30 | Asn N AAT      47 | Ser S AGT      17
      ATC      79 |       ACC     107 |       AAC      82 |       AGC      55
      ATA       7 |       ACA      12 | Lys K AAA     129 | Arg R AGA       0
Met M ATG      46 |       ACG      58 |       AAG      48 |       AGG       1
------------------------------------------------------------------------------
Val V GTT      48 | Ala A GCT      29 | Asp D GAT     103 | Gly G GGT      84
      GTC      45 |       GCC      81 |       GAC     142 |       GGC      85
      GTA      63 |       GCA      73 | Glu E GAA     173 |       GGA      24
      GTG     113 |       GCG     193 |       GAG      90 |       GGG      35
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12802    C:0.28420    A:0.22098    G:0.36680
position  2:    T:0.27862    C:0.22736    A:0.31129    G:0.18274
position  3:    T:0.22869    C:0.26428    A:0.15857    G:0.34847

Codon frequencies under model, for use in evolver:
  0.00835687  0.00965747  0.00579448  0.01273427
  0.00681933  0.00788064  0.00472839  0.01039136
  0.00933675  0.01078985  0.00000000  0.00000000
  0.00548096  0.00633397  0.00000000  0.00835193
  0.01855155  0.02143878  0.01286327  0.02826903
  0.01513835  0.01749437  0.01049662  0.02306796
  0.02072680  0.02395258  0.01437155  0.03158370
  0.01216727  0.01406090  0.00843654  0.01854060
  0.01442513  0.01667016  0.01000209  0.02198115
  0.01177113  0.01360310  0.00816186  0.01793695
  0.01611654  0.01862481  0.01117488  0.02455854
  0.00946090  0.01093333  0.00656000  0.01441662
  0.02394363  0.02767005  0.01660203  0.03648554
  0.01953837  0.02257919  0.01354751  0.02977276
  0.02675113  0.03091449  0.01854870  0.04076363
  0.01570374  0.01814776  0.01088865  0.02392950



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               0.1324 (0.0053 0.0402)
Shig4337             0.1324 (0.0053 0.0402)-1.0000 (0.0000 0.0000)
CFT073               0.0313 (0.0041 0.1322) 0.0331 (0.0047 0.1429) 0.0331 (0.0047 0.1429)
O157                 0.0635 (0.0041 0.0651) 0.1202 (0.0083 0.0690) 0.1202 (0.0083 0.0690) 0.0461 (0.0059 0.1281)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 118
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -3669.386477     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00167  0.01395  0.02963  0.00000  0.00000  0.02029  0.08841  0.02723  4.17148  0.93922  0.05859  0.00000 21.90725
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.18119

((1: 0.013953, (2: 0.000004, 3: 0.000004): 0.029633): 0.001665, (4: 0.088414, 5: 0.027226): 0.020292);

((K12: 0.013953, (S2457T: 0.000004, Shig4337: 0.000004): 0.029633): 0.001665, (CFT073: 0.088414, O157: 0.027226): 0.020292);

Detailed output identifying parameters

kappa (ts/tv) =  4.17148


dN/dS for site classes (K=3)

p:   0.93922  0.05859  0.00218
w:   0.00000  1.00000 21.90725

dN & dS for each branch

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

   6..7       0.002    663.0   1596.0   0.1064   0.0002   0.0015    1.0    0.3
   7..1       0.014    663.0   1596.0   0.1064   0.0013   0.0126    8.4    2.1
   7..8       0.030    663.0   1596.0   0.1064   0.0029   0.0268   17.8    4.6
   8..2       0.000    663.0   1596.0   0.1064   0.0000   0.0000    0.0    0.0
   8..3       0.000    663.0   1596.0   0.1064   0.0000   0.0000    0.0    0.0
   6..9       0.020    663.0   1596.0   0.1064   0.0020   0.0183   12.2    3.1
   9..4       0.088    663.0   1596.0   0.1064   0.0085   0.0799   53.0   13.6
   9..5       0.027    663.0   1596.0   0.1064   0.0026   0.0246   16.3    4.2


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

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

   167 W      0.993**       21.765


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

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

    82 A      0.732         2.093 +- 1.285
   145 D      0.695         2.012 +- 1.262
   167 W      0.901         2.326 +- 1.227
   274 A      0.735         2.098 +- 1.283



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:   0.477  0.310  0.128  0.049  0.020  0.009  0.004  0.002  0.001  0.001

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
