
seed used = 140026821

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3957.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 383
# site patterns = 113
    7    8    8    4   11    6   12    7    6   10    6    1    6   13    8
    2    5    1    1    4    1   10   14    5    7   15    5    6    4    7
    7    4    3    1   11    1    7    1    5    1    5    9    1    1    2
    1    4    1    8   12    8    1    3    1    1    1    3    1    3    1
    1    1    6    4    5    1    1    2    1    1    3    2    1    1    5
    1    1    1    1    1    1    1    1    1    1    1    2    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       
K12                   ATG AAA AAC TTA CCG CCA TTT ATC GAG ATT TAC CGC GCT CTG GCC ACA CCT TCA ATA AGC GCC ACG GAA GCA CTC GAT CAA AAT ACT GCG GAC TGG AAA TTG GGC TTC GTG GTG CAG GTT GGA CGC TTC GCA AGT ATC GGG GGC TTG CAT ACC GGT CCG ACA CTG AAG CTT CTA GTC CTG AAA GCT CGT TAT TGC GAA TCA CTA GTA GCA GGT TCT TCG GGG CAC TCC GTT ATC ATC GAA GCG ATT GGT GAC GCT TGC TGT CTG CCT AAT GTT AAC GTG TTG GGG CCT GGC TCA ATT CAG CAA GAA ACA CGG ATC AAG CCC CGC GAA CTG ATA ACC GTA 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..C ... TA. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ..A ... ... ... ... ... ... .A. ... ... ... ..T ... C.C ..T ..G ..T ..C ..C ..A ..G ..G ..G ... ..T ..A ... ..T ..G T.. ..T .T. ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..C ... TA. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ..A ... ... ... ... ... ... .A. ... ... ... ..T ... C.C ..T ..G ..T ..C ..C ..A ..G ..G ..G ... ..T ..A ... ..T ..G T.. ..T .T. ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..A ... ... ... ..A ... ..G ... ... ..T ..C ... TG. ... ..T ... ... ... ..A ..A ..G T.. ... ... ... ... ..T GC. ..C ... ... ... ..G ..G ..G ... ..G ... ... ... ..C ... ... ... ... ..A ..C ... ..C ..C ..T ..A ..T ... ... ..A ..C ... ..T ..T C.. ... ... ... ... ... ... ..G ..G ..G A.. ... ... ... ... ... ... ..C ... ..G 
O157                  ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ..A ... ... ..T ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ..G ... ... ... ... ... ..T ..T C.. ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ..C 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ..A ... ... ..T ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ..G ... ... ... ... ... ..T ..T C.. ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ..C 

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

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

#1: K12            
position  1:    T:0.14883    C:0.27415    A:0.24804    G:0.32898
position  2:    T:0.28198    C:0.24543    A:0.30287    G:0.16971
position  3:    T:0.27415    C:0.27415    A:0.18799    G:0.26371

#2: S2457T         
position  1:    T:0.15144    C:0.27415    A:0.24804    G:0.32637
position  2:    T:0.27937    C:0.24282    A:0.30809    G:0.16971
position  3:    T:0.28982    C:0.26893    A:0.17755    G:0.26371

#3: Shig4337       
position  1:    T:0.15144    C:0.27415    A:0.24804    G:0.32637
position  2:    T:0.27937    C:0.24282    A:0.30809    G:0.16971
position  3:    T:0.28982    C:0.26893    A:0.17755    G:0.26371

#4: CFT073         
position  1:    T:0.15144    C:0.27154    A:0.24543    G:0.33159
position  2:    T:0.27937    C:0.24804    A:0.30026    G:0.17232
position  3:    T:0.27415    C:0.27676    A:0.16971    G:0.27937

#5: O157           
position  1:    T:0.14621    C:0.27676    A:0.24804    G:0.32898
position  2:    T:0.27937    C:0.24804    A:0.30287    G:0.16971
position  3:    T:0.28198    C:0.26371    A:0.19060    G:0.26371

#6: EDL933         
position  1:    T:0.14621    C:0.27676    A:0.24804    G:0.32898
position  2:    T:0.27937    C:0.24804    A:0.30287    G:0.16971
position  3:    T:0.28198    C:0.26371    A:0.19060    G:0.26371

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      77 | Ser S TCT      12 | Tyr Y TAT      24 | Cys C TGT      13
      TTC       7 |       TCC       8 |       TAC      38 |       TGC      34
Leu L TTA      27 |       TCA      15 | *** * TAA       0 | *** * TGA       0
      TTG      55 |       TCG       7 |       TAG       0 | Trp W TGG      26
------------------------------------------------------------------------------
Leu L CTT      19 | Pro P CCT      39 | His H CAT      72 | Arg R CGT      41
      CTC      44 |       CCC       6 |       CAC      30 |       CGC      61
      CTA      16 |       CCA      40 | Gln Q CAA      33 |       CGA       0
      CTG     101 |       CCG      83 |       CAG      41 |       CGG       5
------------------------------------------------------------------------------
Ile I ATT      75 | Thr T ACT      24 | Asn N AAT      46 | Ser S AGT      12
      ATC      62 |       ACC      54 |       AAC      50 |       AGC      24
      ATA      12 |       ACA      20 | Lys K AAA      70 | Arg R AGA       0
Met M ATG      42 |       ACG      64 |       AAG      13 |       AGG       1
------------------------------------------------------------------------------
Val V GTT      22 | Ala A GCT      48 | Asp D GAT      91 | Gly G GGT      33
      GTC      20 |       GCC      56 |       GAC      48 |       GGC      77
      GTA      12 |       GCA      42 | Glu E GAA     101 |       GGA      31
      GTG      52 |       GCG      47 |       GAG      42 |       GGG      33
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14926    C:0.27459    A:0.24761    G:0.32855
position  2:    T:0.27981    C:0.24587    A:0.30418    G:0.17015
position  3:    T:0.28198    C:0.26936    A:0.18233    G:0.26632

Codon frequencies under model, for use in evolver:
  0.01207885  0.01153828  0.00781024  0.01140780
  0.01061360  0.01013861  0.00686281  0.01002396
  0.01313081  0.01254317  0.00000000  0.00000000
  0.00734499  0.00701628  0.00000000  0.00693694
  0.02222085  0.02122640  0.01436811  0.02098636
  0.01952532  0.01865150  0.01262517  0.01844058
  0.02415610  0.02307504  0.01561946  0.02281410
  0.01351221  0.01290750  0.00873706  0.01276153
  0.02003750  0.01914076  0.01295635  0.01892431
  0.01760683  0.01681887  0.01138466  0.01662867
  0.02178260  0.02080776  0.01408474  0.02057246
  0.01218455  0.01163925  0.00787859  0.01150763
  0.02658755  0.02539767  0.01719164  0.02511046
  0.02336231  0.02231677  0.01510618  0.02206440
  0.02890310  0.02760960  0.01868889  0.02729737
  0.01616754  0.01544400  0.01045401  0.01526935



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               0.0870 (0.0069 0.0795)
Shig4337             0.0870 (0.0069 0.0795)-1.0000 (0.0000 0.0000)
CFT073               0.0353 (0.0058 0.1635) 0.0412 (0.0081 0.1963) 0.0412 (0.0081 0.1963)
O157                 0.0629 (0.0023 0.0366) 0.0757 (0.0069 0.0915) 0.0757 (0.0069 0.0915) 0.0522 (0.0069 0.1328)
EDL933               0.0629 (0.0023 0.0366) 0.0757 (0.0069 0.0915) 0.0757 (0.0069 0.0915) 0.0522 (0.0069 0.1328)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 71
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1912.980127     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.01478  0.01224  0.07053  0.00000  0.00000  0.00104  0.12496  0.00657  0.00000  0.00000  2.06924  0.95407  0.04305  0.00000 26.77704
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.23014

((1: 0.012239, (2: 0.000004, 3: 0.000004): 0.070532): 0.014775, (4: 0.124962, (5: 0.000004, 6: 0.000004): 0.006573): 0.001038);

((K12: 0.012239, (S2457T: 0.000004, Shig4337: 0.000004): 0.070532): 0.014775, (CFT073: 0.124962, (O157: 0.000004, EDL933: 0.000004): 0.006573): 0.001038);

Detailed output identifying parameters

kappa (ts/tv) =  2.06924


dN/dS for site classes (K=3)

p:   0.95407  0.04305  0.00288
w:   0.00000  1.00000 26.77704

dN & dS for each branch

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

   7..8       0.015    317.7    831.3   0.1203   0.0016   0.0135    4.3    1.4
   8..1       0.012    317.7    831.3   0.1203   0.0013   0.0112    3.6    1.1
   8..9       0.071    317.7    831.3   0.1203   0.0078   0.0647   20.5    6.5
   9..2       0.000    317.7    831.3   0.1203   0.0000   0.0000    0.0    0.0
   9..3       0.000    317.7    831.3   0.1203   0.0000   0.0000    0.0    0.0
   7..10      0.001    317.7    831.3   0.1203   0.0001   0.0010    0.3    0.1
  10..4       0.125    317.7    831.3   0.1203   0.0138   0.1146   36.4   11.5
  10..11      0.007    317.7    831.3   0.1203   0.0007   0.0060    1.9    0.6
  11..5       0.000    317.7    831.3   0.1203   0.0000   0.0000    0.0    0.0
  11..6       0.000    317.7    831.3   0.1203   0.0000   0.0000    0.0    0.0


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

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

    68 I      1.000**       26.771


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

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

    68 I      0.995**       6.810 +- 2.539
   133 K      0.841         5.924 +- 3.147
   256 C      0.684         4.892 +- 3.596



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:   0.026  0.057  0.083  0.101  0.114  0.122  0.126  0.127  0.125  0.120

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
