
seed used = 139992365

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0657.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 512
# site patterns = 119
   13    1   16    9    3    6   22    4   12   15   40   18   13   10    3
    4    5    3    4    9    5    6   16   10    3    3    5   17   16    1
    1    4    6    3   17    7    6    8    1   22    4   13    1    1   10
    1    1    1    5    9    1    1    1   10    6    1    1    1    1    5
    1    1    1    1    2    1    1    1    1    4    1    1    1    1    2
    1    1    1    1    1    1    2    1    1    1    3    1    1    1    1
    1    1    1    1    3    2    1    1    1    1    1    1    1    1    1
    1    1    1    1    2    1    1    1    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 16 16 16 16 16 16 | Ser TCT  3  3  3  4  3  3 | Tyr TAT  7  6  6  8  7  7 | Cys TGT  0  0  0  0  0  0
    TTC 13 13 13 13 13 13 |     TCC  1  1  1  1  1  1 |     TAC 10 11 11  9 10 10 |     TGC  3  3  3  3  3  3
Leu TTA  7  7  7  6  8  8 |     TCA  3  3  3  4  3  3 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  8  7  7  9  6  6 |     TCG 12 12 12 10 12 12 |     TAG  0  0  0  0  0  0 | Trp TGG 16 16 16 16 16 16
--------------------------------------------------------------------------------------------------------------
Leu CTT  5  4  4  4  7  7 | Pro CCT  4  4  4  4  4  4 | His CAT  1  1  1  2  1  1 | Arg CGT 12 12 12  8 12 12
    CTC  7  7  7  7  6  6 |     CCC  1  1  1  1  1  1 |     CAC  1  1  1  1  1  1 |     CGC 14 14 14 16 14 14
    CTA  0  3  3  2  1  1 |     CCA  6  5  5  7  6  6 | Gln CAA  6  7  7  6  5  5 |     CGA  2  2  2  3  2  2
    CTG 44 44 44 44 44 44 |     CCG 25 26 26 24 25 25 |     CAG 17 16 16 17 17 17 |     CGG  0  0  0  0  1  1
--------------------------------------------------------------------------------------------------------------
Ile ATT 23 24 24 23 23 23 | Thr ACT  3  4  4  4  3  3 | Asn AAT  4  4  4  4  4  4 | Ser AGT  2  2  2  1  1  1
    ATC 10  9  9  9 10 10 |     ACC 20 19 19 18 19 19 |     AAC 16 16 16 16 16 16 |     AGC  7  7  7  8  8  8
    ATA  2  1  1  3  1  1 |     ACA  1  1  1  4  3  3 | Lys AAA 12 12 12 12 11 11 | Arg AGA  0  0  0  0  0  0
Met ATG 13 13 13 13 13 13 |     ACG  7  7  7  5  6  6 |     AAG  2  2  2  2  3  3 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  4  4  4  4  5  5 | Ala GCT  6  6  6  6  7  7 | Asp GAT 10 11 11 10 10 10 | Gly GGT 12 12 12 10 12 12
    GTC  7  7  7  8  6  6 |     GCC 11 11 11 12 10 10 |     GAC  5  5  5  6  5  5 |     GGC 19 18 18 20 19 19
    GTA  3  1  1  3  2  2 |     GCA  9 10 10  8 10 10 | Glu GAA  5  5  5  6  5  5 |     GGA  5  4  4  7  5  5
    GTG 15 17 17 14 16 16 |     GCG 19 18 18 19 18 18 |     GAG 12 12 12  9 12 12 |     GGG  4  5  5  3  4  4
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.19336    C:0.28320    A:0.23828    G:0.28516
position  2:    T:0.34570    C:0.25586    A:0.21094    G:0.18750
position  3:    T:0.21875    C:0.28320    A:0.11914    G:0.37891

#2: S2457T         
position  1:    T:0.19141    C:0.28711    A:0.23633    G:0.28516
position  2:    T:0.34570    C:0.25586    A:0.21289    G:0.18555
position  3:    T:0.22070    C:0.27930    A:0.11914    G:0.38086

#3: Shig4337       
position  1:    T:0.19141    C:0.28711    A:0.23633    G:0.28516
position  2:    T:0.34570    C:0.25586    A:0.21289    G:0.18555
position  3:    T:0.22070    C:0.27930    A:0.11914    G:0.38086

#4: CFT073         
position  1:    T:0.19336    C:0.28516    A:0.23828    G:0.28320
position  2:    T:0.34766    C:0.25586    A:0.21094    G:0.18555
position  3:    T:0.21094    C:0.28906    A:0.13867    G:0.36133

#5: O157           
position  1:    T:0.19141    C:0.28711    A:0.23633    G:0.28516
position  2:    T:0.34570    C:0.25586    A:0.20898    G:0.18945
position  3:    T:0.22461    C:0.27734    A:0.12109    G:0.37695

#6: EDL933         
position  1:    T:0.19141    C:0.28711    A:0.23633    G:0.28516
position  2:    T:0.34570    C:0.25586    A:0.20898    G:0.18945
position  3:    T:0.22461    C:0.27734    A:0.12109    G:0.37695

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      96 | Ser S TCT      19 | Tyr Y TAT      41 | Cys C TGT       0
      TTC      78 |       TCC       6 |       TAC      61 |       TGC      18
Leu L TTA      43 |       TCA      19 | *** * TAA       0 | *** * TGA       0
      TTG      43 |       TCG      70 |       TAG       0 | Trp W TGG      96
------------------------------------------------------------------------------
Leu L CTT      31 | Pro P CCT      24 | His H CAT       7 | Arg R CGT      68
      CTC      40 |       CCC       6 |       CAC       6 |       CGC      86
      CTA      10 |       CCA      35 | Gln Q CAA      36 |       CGA      13
      CTG     264 |       CCG     151 |       CAG     100 |       CGG       2
------------------------------------------------------------------------------
Ile I ATT     140 | Thr T ACT      21 | Asn N AAT      24 | Ser S AGT       9
      ATC      57 |       ACC     114 |       AAC      96 |       AGC      45
      ATA       9 |       ACA      13 | Lys K AAA      70 | Arg R AGA       0
Met M ATG      78 |       ACG      38 |       AAG      14 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      26 | Ala A GCT      38 | Asp D GAT      62 | Gly G GGT      70
      GTC      41 |       GCC      65 |       GAC      31 |       GGC     113
      GTA      12 |       GCA      57 | Glu E GAA      31 |       GGA      30
      GTG      95 |       GCG     110 |       GAG      69 |       GGG      25
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.19206    C:0.28613    A:0.23698    G:0.28483
position  2:    T:0.34603    C:0.25586    A:0.21094    G:0.18717
position  3:    T:0.22005    C:0.28092    A:0.12305    G:0.37598

Codon frequencies under model, for use in evolver:
  0.01499351  0.01914112  0.00838394  0.02561761
  0.01108645  0.01415327  0.00619923  0.01894209
  0.00913998  0.01166834  0.00000000  0.00000000
  0.00811032  0.01035385  0.00000000  0.01385713
  0.02233779  0.02851703  0.01249066  0.03816590
  0.01651693  0.02108597  0.00923580  0.02822050
  0.01361701  0.01738385  0.00761425  0.02326576
  0.01208300  0.01542549  0.00675647  0.02064477
  0.01850047  0.02361820  0.01034494  0.03160952
  0.01367955  0.01746369  0.00764922  0.02337261
  0.01127780  0.01439755  0.00630623  0.01926902
  0.01000731  0.01277560  0.00559580  0.01709828
  0.02223614  0.02838726  0.01243382  0.03799222
  0.01644177  0.02099001  0.00919377  0.02809208
  0.01355505  0.01730474  0.00757960  0.02315988
  0.01202801  0.01535529  0.00672572  0.02055082



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               0.1137 (0.0044 0.0387)
Shig4337             0.1137 (0.0044 0.0387)-1.0000 (0.0000 0.0000)
CFT073               0.0781 (0.0102 0.1302) 0.1031 (0.0146 0.1421) 0.1031 (0.0146 0.1421)
O157                 0.0400 (0.0018 0.0440) 0.0734 (0.0044 0.0601) 0.0734 (0.0044 0.0601) 0.1014 (0.0120 0.1180)
EDL933               0.0400 (0.0018 0.0440) 0.0734 (0.0044 0.0601) 0.0734 (0.0044 0.0601) 0.1014 (0.0120 0.1180)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 76
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):  -2501.772359     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.01513  0.01127  0.03438  0.00000  0.00000  0.00000  0.12828  0.01660  0.00000  0.00000  4.74026  0.98405  0.00000  0.03308 10.93894
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.20567

((1: 0.011269, (2: 0.000004, 3: 0.000004): 0.034379): 0.015131, (4: 0.128283, (5: 0.000004, 6: 0.000004): 0.016596): 0.000000);

((K12: 0.011269, (S2457T: 0.000004, Shig4337: 0.000004): 0.034379): 0.015131, (CFT073: 0.128283, (O157: 0.000004, EDL933: 0.000004): 0.016596): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  4.74026


dN/dS for site classes (K=3)

p:   0.98405  0.00000  0.01595
w:   0.03308  1.00000 10.93894

dN & dS for each branch

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

   7..8       0.015    441.1   1094.9   0.2071   0.0024   0.0116    5.1    2.6
   8..1       0.011    441.1   1094.9   0.2071   0.0018   0.0086    3.8    2.0
   8..9       0.034    441.1   1094.9   0.2071   0.0055   0.0264   11.6    6.0
   9..2       0.000    441.1   1094.9   0.2071   0.0000   0.0000    0.0    0.0
   9..3       0.000    441.1   1094.9   0.2071   0.0000   0.0000    0.0    0.0
   7..10      0.000    441.1   1094.9   0.2071   0.0000   0.0000    0.0    0.0
  10..4       0.128    441.1   1094.9   0.2071   0.0204   0.0984   43.4   22.3
  10..11      0.017    441.1   1094.9   0.2071   0.0026   0.0127    5.6    2.9
  11..5       0.000    441.1   1094.9   0.2071   0.0000   0.0000    0.0    0.0
  11..6       0.000    441.1   1094.9   0.2071   0.0000   0.0000    0.0    0.0


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

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

   166 I      0.997**       10.901
   239 E      0.541         5.930
   377 A      0.997**       10.901
   509 Q      0.997**       10.902
   511 R      0.999**       10.928
   512 K      0.997**       10.909


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

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

   166 I      0.928         6.636 +- 2.683
   239 E      0.520         3.876 +- 3.704
   377 A      0.928         6.634 +- 2.683
   509 Q      0.930         6.648 +- 2.669
   511 R      0.981*        6.927 +- 2.384
   512 K      0.937         6.689 +- 2.634



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:   0.007  0.031  0.071  0.108  0.132  0.142  0.142  0.134  0.123  0.111

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
