
seed used = 139993785

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0818.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 372
# site patterns = 117
   12    3   32    3   18   14    4    8    6    6    4    5    2    8    4
    6    1   10    7    1    2    1    2    5   11    6    1   13    5    3
    1    6    5    1    7    4   15    3    3    3   12    1    1    3    7
    4    1    1    1    2    1    4    1    3    4    2    2    1    1    1
    1    1    1    1    1    1    1    4    1    1    1    2    1    1    4
    1    1    1    1    1    5    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 AGC CTG CCT TTT TTA CGC ACG CAA GGC GAT CGT CAG ATT CTT GTT GGT ATC GGA AGC TTC GTG CCC GCA CCG AAA TCC TGG GCT GAC CAC ACC GGT GTG GAG TAT GTG GGG CGC CGG GCG GTG GCG TCT AAC GTC GCG ATT ACT CTA AGA TGT ATC AAT TCG CCA GCC CTG ACG CTC CTC CTG TGC AAG GCG ATG TAC CAT ACA AGT TTC GCA GCG CTC AGT CTG CTG CAG CTT GCG TTG CAA GGC TTG GGT CTA TCT GAA GGG GCA ATC ACC ATA TTG CTG AAC GTG CCG GTA GTA GTA GGT GGG CCC CTA CGT TTC CTC TCA ATA TTG TAT TTA ATA CTC GCC AAC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ..A ... ..G T.. ... ... ... C.. ... ... ... .A. ... ..G .T. T.G ... T.. ... ... ... ... ... ... ... ... ... T.. ... ... ... ... G.. ... ..T C.. ..C ..T ..A ..T .C. ... ..G ..G ..T ..A ... ... ... ... ... ... C.. ..C ... ..G A.. ... TGG 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ..A ... ..G T.. ... ... ... C.. ... ... ... .A. ... ..G .T. T.G ... T.. ... ... ... ... ... ... ... ... ... T.. ... ... ... ... G.. ... ..T C.. ..C ..T ..A ..T .C. ... ..G ..G ..T ..A ... ... ... ... ... ... C.. ..C ... ..G A.. ... TGG 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ..T ... ..T ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..T ... ... ..A ..A ... ... ... ..A ..A ... ... ... ... ..T ... ... ... ... ... ..A ... ..G T.. ... ... ... C.. ... ... ..G ... ..A ..G ... ... ... ... ..A ..A ..G .TT ... ..G ..G ..A A.. T.. ..C ... ..A ..G ... ... ..T C.. ..C ..T ... ..A .C. ... ..G ..G ..T ... T.. ..G ..T ..T ..G ... C.. ... ..G ..G A.. ..G GGA 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ..G ... ... ... ... ... ... ... ... ... ..G T.. ... ... ..A C.C ... ... ... ... ... ..G ... T.G ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ..A ... ... ..T ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... C.. ... ..G ..G A.. ... TGG 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ..G ... ... ... ... ... ... ... ... ... ..G T.. ... ... ..A C.C ... ... ... ... ... ..G ... T.G ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ..A ... ... ..T ... ... ... ... ... ... .C. ... ... ... ... ... ... ... ... ... ... ... C.. ... ..G ..G A.. ... TGG 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 18 18 18 19 18 18 | Ser TCT  4  4  4  3  4  4 | Tyr TAT  5  4  4  5  5  5 | Cys TGT  4  4  4  4  4  4
    TTC  4  4  4  2  4  4 |     TCC  1  1  1  2  1  1 |     TAC  1  2  2  1  1  1 |     TGC  1  1  1  1  1  1
Leu TTA 15 16 16 18 15 15 |     TCA  1  1  1  0  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  8  9  9  7 10 10 |     TCG  4  4  4  5  4  4 |     TAG  0  0  0  0  0  0 | Trp TGG 13 14 14 13 14 14
--------------------------------------------------------------------------------------------------------------
Leu CTT  5  5  5  5  5  5 | Pro CCT  3  4  4  3  3  3 | His CAT  4  4  4  4  4  4 | Arg CGT  6  6  6  8  6  6
    CTC  5  3  3  3  3  3 |     CCC  3  2  2  3  3  3 |     CAC  1  1  1  1  1  1 |     CGC  7  7  7  4  7  7
    CTA  4  3  3  3  3  3 |     CCA  2  3  3  3  2  2 | Gln CAA  7  7  7  7  7  7 |     CGA  0  0  0  0  0  0
    CTG 37 37 37 39 38 38 |     CCG 12 11 11 11 12 12 |     CAG  3  3  3  3  3  3 |     CGG  3  3  3  4  3  3
--------------------------------------------------------------------------------------------------------------
Ile ATT  9 10 10 10  9  9 | Thr ACT  1  1  1  1  2  2 | Asn AAT  3  5  5  4  3  3 | Ser AGT  5  4  4  7  6  6
    ATC 12 12 12 12 13 13 |     ACC  7  7  7  7  6  6 |     AAC  9  7  7  7  8  8 |     AGC  4  4  4  3  3  3
    ATA  3  1  1  2  2  2 |     ACA  1  2  2  1  1  1 | Lys AAA  6  6  6  6  6  6 | Arg AGA  1  1  1  1  0  0
Met ATG 13 14 14 13 13 13 |     ACG  9  8  8  9 10 10 |     AAG  1  1  1  1  1  1 |     AGG  0  0  0  0  1  1
--------------------------------------------------------------------------------------------------------------
Val GTT  6  6  6  8  6  6 | Ala GCT  5  5  5  5  5  5 | Asp GAT  4  4  4  4  4  4 | Gly GGT  8  8  8  6  8  8
    GTC  4  5  5  5  4  4 |     GCC  3  3  3  2  3  3 |     GAC  3  3  3  3  3  3 |     GGC  7  7  7  7  7  7
    GTA  3  2  2  2  2  2 |     GCA  8  7  7  8  8  8 | Glu GAA  1  1  1  1  1  1 |     GGA  7  7  7  9  8  8
    GTG 19 20 20 17 19 19 |     GCG 17 18 18 18 17 17 |     GAG  7  7  7  7  7  7 |     GGG  5  5  5  5  4  4
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.21237    C:0.27419    A:0.22581    G:0.28763
position  2:    T:0.44355    C:0.21774    A:0.14785    G:0.19086
position  3:    T:0.24194    C:0.19355    A:0.15860    G:0.40591

#2: S2457T         
position  1:    T:0.22043    C:0.26613    A:0.22312    G:0.29032
position  2:    T:0.44355    C:0.21774    A:0.14785    G:0.19086
position  3:    T:0.24731    C:0.18548    A:0.15323    G:0.41398

#3: Shig4337       
position  1:    T:0.22043    C:0.26613    A:0.22312    G:0.29032
position  2:    T:0.44355    C:0.21774    A:0.14785    G:0.19086
position  3:    T:0.24731    C:0.18548    A:0.15323    G:0.41398

#4: CFT073         
position  1:    T:0.21505    C:0.27151    A:0.22581    G:0.28763
position  2:    T:0.44355    C:0.21774    A:0.14516    G:0.19355
position  3:    T:0.25806    C:0.16935    A:0.16398    G:0.40860

#5: O157           
position  1:    T:0.22043    C:0.26882    A:0.22581    G:0.28495
position  2:    T:0.44086    C:0.22043    A:0.14516    G:0.19355
position  3:    T:0.24731    C:0.18280    A:0.15054    G:0.41935

#6: EDL933         
position  1:    T:0.22043    C:0.26882    A:0.22581    G:0.28495
position  2:    T:0.44086    C:0.22043    A:0.14516    G:0.19355
position  3:    T:0.24731    C:0.18280    A:0.15054    G:0.41935

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT     109 | Ser S TCT      23 | Tyr Y TAT      28 | Cys C TGT      24
      TTC      22 |       TCC       7 |       TAC       8 |       TGC       6
Leu L TTA      95 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG      53 |       TCG      25 |       TAG       0 | Trp W TGG      82
------------------------------------------------------------------------------
Leu L CTT      30 | Pro P CCT      20 | His H CAT      24 | Arg R CGT      38
      CTC      20 |       CCC      16 |       CAC       6 |       CGC      39
      CTA      19 |       CCA      15 | Gln Q CAA      42 |       CGA       0
      CTG     226 |       CCG      69 |       CAG      18 |       CGG      19
------------------------------------------------------------------------------
Ile I ATT      57 | Thr T ACT       8 | Asn N AAT      23 | Ser S AGT      32
      ATC      74 |       ACC      40 |       AAC      46 |       AGC      21
      ATA      11 |       ACA       8 | Lys K AAA      36 | Arg R AGA       4
Met M ATG      80 |       ACG      54 |       AAG       6 |       AGG       2
------------------------------------------------------------------------------
Val V GTT      38 | Ala A GCT      30 | Asp D GAT      24 | Gly G GGT      46
      GTC      27 |       GCC      17 |       GAC      18 |       GGC      42
      GTA      13 |       GCA      46 | Glu E GAA       6 |       GGA      46
      GTG     114 |       GCG     105 |       GAG      42 |       GGG      28
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.21819    C:0.26927    A:0.22491    G:0.28763
position  2:    T:0.44265    C:0.21864    A:0.14651    G:0.19220
position  3:    T:0.24821    C:0.18324    A:0.15502    G:0.41353

Codon frequencies under model, for use in evolver:
  0.02457898  0.01814585  0.01535077  0.04095018
  0.01214022  0.00896273  0.00758216  0.02022640
  0.00813495  0.00600576  0.00000000  0.00000000
  0.01067245  0.00787912  0.00000000  0.01778100
  0.03033258  0.02239355  0.01894417  0.05053605
  0.01498208  0.01106078  0.00935704  0.02496113
  0.01003922  0.00741163  0.00626998  0.01672600
  0.01317073  0.00972351  0.00822576  0.02194328
  0.02533603  0.01870476  0.01582359  0.04221148
  0.01251415  0.00923879  0.00781570  0.02084939
  0.00838551  0.00619075  0.00523716  0.01397080
  0.01100117  0.00812180  0.00687077  0.01832867
  0.03240186  0.02392123  0.02023654  0.05398360
  0.01600416  0.01181534  0.00999538  0.02666396
  0.01072410  0.00791725  0.00669772  0.01786704
  0.01406923  0.01038685  0.00878692  0.02344025



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               0.2065 (0.0147 0.0714)
Shig4337             0.2065 (0.0147 0.0714)-1.0000 (0.0000 0.0000)
CFT073               0.0691 (0.0119 0.1718) 0.0802 (0.0110 0.1376) 0.0802 (0.0110 0.1376)
O157                 0.2461 (0.0117 0.0473) 0.0854 (0.0061 0.0715) 0.0854 (0.0061 0.0715) 0.0465 (0.0073 0.1580)
EDL933               0.2461 (0.0117 0.0473) 0.0854 (0.0061 0.0715) 0.0854 (0.0061 0.0715) 0.0465 (0.0073 0.1580)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 77
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1889.936003     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.01398  0.10931  0.14850  0.00000  0.00000  0.00815  0.37199  0.05749  0.00000  0.00000  2.59589  0.99691  0.00000  0.07372 353.75717
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.70944

((1: 0.109311, (2: 0.000004, 3: 0.000004): 0.148504): 0.013984, (4: 0.371989, (5: 0.000004, 6: 0.000004): 0.057487): 0.008147);

((K12: 0.109311, (S2457T: 0.000004, Shig4337: 0.000004): 0.148504): 0.013984, (CFT073: 0.371989, (O157: 0.000004, EDL933: 0.000004): 0.057487): 0.008147);

Detailed output identifying parameters

kappa (ts/tv) =  2.59589


dN/dS for site classes (K=3)

p:   0.99691  0.00000  0.00309
w:   0.07372  1.00000353.75717

dN & dS for each branch

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

   7..8       0.014    337.8    778.2   1.1678   0.0049   0.0042    1.4    3.8
   8..1       0.109    337.8    778.2   1.1678   0.0381   0.0326   11.0   29.6
   8..9       0.149    337.8    778.2   1.1678   0.0518   0.0443   15.0   40.3
   9..2       0.000    337.8    778.2   1.1678   0.0000   0.0000    0.0    0.0
   9..3       0.000    337.8    778.2   1.1678   0.0000   0.0000    0.0    0.0
   7..10      0.008    337.8    778.2   1.1678   0.0028   0.0024    0.8    2.2
  10..4       0.372    337.8    778.2   1.1678   0.1296   0.1110   37.5  100.9
  10..11      0.057    337.8    778.2   1.1678   0.0200   0.0172    5.8   15.6
  11..5       0.000    337.8    778.2   1.1678   0.0000   0.0000    0.0    0.0
  11..6       0.000    337.8    778.2   1.1678   0.0000   0.0000    0.0    0.0


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

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

   372 N      1.000**       353.757


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

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

   372 N      0.954*        4.369 +- 2.638



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.194  0.195  0.152  0.114  0.088  0.070  0.057  0.049  0.042  0.038

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 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.995

sum of density on p0-p1 =   1.000000
