
seed used = 139995481

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0994.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 342
# site patterns = 97
   10   11    1   17    1    7    5    7    1    1    1    1    8    5    7
   11    6    5    7    4    6   14    1    4   11    9   11    2    1    7
    1   11    1    1    8    6    7    4    1    6    8    2    5    1    5
    3    1    8    1    2    1    1    4    1    1    1    1    1    3    1
    1    1    5    1    1    1    1    1    1    2    3    1    1    5    6
    5    1    3    1    5    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.16082    C:0.28363    A:0.21053    G:0.34503
position  2:    T:0.29825    C:0.22807    A:0.28655    G:0.18713
position  3:    T:0.25439    C:0.21053    A:0.18129    G:0.35380

#2: S2457T         
position  1:    T:0.16374    C:0.28363    A:0.20760    G:0.34503
position  2:    T:0.30409    C:0.21930    A:0.29240    G:0.18421
position  3:    T:0.23977    C:0.22222    A:0.18713    G:0.35088

#3: Shig4337       
position  1:    T:0.16374    C:0.28363    A:0.20760    G:0.34503
position  2:    T:0.30409    C:0.21930    A:0.29240    G:0.18421
position  3:    T:0.23977    C:0.22222    A:0.18713    G:0.35088

#4: CFT073         
position  1:    T:0.16374    C:0.28070    A:0.21345    G:0.34211
position  2:    T:0.29240    C:0.22515    A:0.29240    G:0.19006
position  3:    T:0.23977    C:0.22222    A:0.18713    G:0.35088

#5: O157           
position  1:    T:0.16082    C:0.28363    A:0.21053    G:0.34503
position  2:    T:0.30409    C:0.22222    A:0.28947    G:0.18421
position  3:    T:0.25146    C:0.21053    A:0.17836    G:0.35965

#6: EDL933         
position  1:    T:0.16082    C:0.28363    A:0.21053    G:0.34503
position  2:    T:0.30409    C:0.22222    A:0.28947    G:0.18421
position  3:    T:0.25146    C:0.21053    A:0.17836    G:0.35965

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      47 | Ser S TCT      12 | Tyr Y TAT      52 | Cys C TGT       6
      TTC      11 |       TCC       6 |       TAC      16 |       TGC       6
Leu L TTA      31 |       TCA      28 | *** * TAA       0 | *** * TGA       0
      TTG      41 |       TCG      35 |       TAG       0 | Trp W TGG      42
------------------------------------------------------------------------------
Leu L CTT      48 | Pro P CCT       6 | His H CAT      28 | Arg R CGT      23
      CTC       6 |       CCC      36 |       CAC      15 |       CGC      71
      CTA       8 |       CCA      20 | Gln Q CAA      56 |       CGA       8
      CTG     108 |       CCG      49 |       CAG      93 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      53 | Thr T ACT       0 | Asn N AAT      25 | Ser S AGT      14
      ATC      35 |       ACC      12 |       AAC      39 |       AGC      43
      ATA       0 |       ACA       7 | Lys K AAA      66 | Arg R AGA       6
Met M ATG      64 |       ACG      37 |       AAG      24 |       AGG       6
------------------------------------------------------------------------------
Val V GTT      31 | Ala A GCT      46 | Asp D GAT      71 | Gly G GGT      43
      GTC      30 |       GCC      66 |       GAC      21 |       GGC      31
      GTA      22 |       GCA      54 | Glu E GAA      39 |       GGA      31
      GTG      83 |       GCG      43 |       GAG      51 |       GGG      45
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16228    C:0.28314    A:0.21004    G:0.34454
position  2:    T:0.30117    C:0.22271    A:0.29045    G:0.18567
position  3:    T:0.24610    C:0.21637    A:0.18324    G:0.35429

Codon frequencies under model, for use in evolver:
  0.01241092  0.01091178  0.00924061  0.01786681
  0.00917766  0.00806907  0.00683327  0.01321219
  0.01196911  0.01052334  0.00000000  0.00000000
  0.00765139  0.00672717  0.00000000  0.01101498
  0.02165389  0.01903827  0.01612250  0.03117303
  0.01601267  0.01407846  0.01192230  0.02305190
  0.02088304  0.01836054  0.01554856  0.03006331
  0.01334973  0.01173719  0.00993960  0.01921832
  0.01606339  0.01412306  0.01196007  0.02312492
  0.01187859  0.01044375  0.00884426  0.01710046
  0.01549155  0.01362029  0.01153430  0.02230170
  0.00990316  0.00870693  0.00737344  0.01425662
  0.02634992  0.02316706  0.01961895  0.03793345
  0.01948530  0.01713163  0.01450786  0.02805111
  0.02541190  0.02234234  0.01892054  0.03658306
  0.01624485  0.01428260  0.01209518  0.02338615



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               0.1262 (0.0078 0.0618)
Shig4337             0.1262 (0.0078 0.0618)-1.0000 (0.0000 0.0000)
CFT073               0.1125 (0.0082 0.0733) 0.1733 (0.0135 0.0778) 0.1733 (0.0135 0.0778)
O157                 0.0730 (0.0039 0.0533) 0.0587 (0.0039 0.0662) 0.0587 (0.0039 0.0662) 0.1565 (0.0122 0.0778)
EDL933               0.0730 (0.0039 0.0533) 0.0587 (0.0039 0.0662) 0.0587 (0.0039 0.0662) 0.1565 (0.0122 0.0778)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 49
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1663.813779     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00046  0.02784  0.04049  0.00000  0.00000  0.00132  0.06378  0.02697  0.00000  0.00000  3.29832  0.95411  0.00000  0.00000  4.24265
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.16088

((1: 0.027842, (2: 0.000004, 3: 0.000004): 0.040487): 0.000459, (4: 0.063782, (5: 0.000004, 6: 0.000004): 0.026970): 0.001321);

((K12: 0.027842, (S2457T: 0.000004, Shig4337: 0.000004): 0.040487): 0.000459, (CFT073: 0.063782, (O157: 0.000004, EDL933: 0.000004): 0.026970): 0.001321);

Detailed output identifying parameters

kappa (ts/tv) =  3.29832


dN/dS for site classes (K=3)

p:   0.95411  0.00000  0.04589
w:   0.00000  1.00000  4.24265

dN & dS for each branch

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

   7..8       0.000    303.0    723.0   0.1947   0.0001   0.0004    0.1    0.0
   8..1       0.028    303.0    723.0   0.1947   0.0042   0.0215    6.5    3.0
   8..9       0.040    303.0    723.0   0.1947   0.0061   0.0312    9.5    4.4
   9..2       0.000    303.0    723.0   0.1947   0.0000   0.0000    0.0    0.0
   9..3       0.000    303.0    723.0   0.1947   0.0000   0.0000    0.0    0.0
   7..10      0.001    303.0    723.0   0.1947   0.0002   0.0010    0.3    0.1
  10..4       0.064    303.0    723.0   0.1947   0.0096   0.0492   14.9    6.9
  10..11      0.027    303.0    723.0   0.1947   0.0040   0.0208    6.3    2.9
  11..5       0.000    303.0    723.0   0.1947   0.0000   0.0000    0.0    0.0
  11..6       0.000    303.0    723.0   0.1947   0.0000   0.0000    0.0    0.0


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

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

    15 P      1.000**       4.243
    31 F      1.000**       4.243
    37 T      1.000**       4.243
    44 A      1.000**       4.243
   124 S      1.000**       4.243
   134 I      1.000**       4.243
   136 A      1.000**       4.243
   138 Q      1.000**       4.243
   162 A      1.000**       4.243
   333 F      1.000**       4.243


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

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

    15 P      0.866         5.089 +- 2.529
    37 T      0.818         4.824 +- 2.622
    44 A      0.903         5.282 +- 2.433
   124 S      0.878         5.152 +- 2.500
   162 A      0.942         5.458 +- 2.302



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:   0.994  0.006  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.021  0.070  0.142  0.185  0.180  0.147  0.107  0.072  0.047  0.030

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 0.026
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.025 0.947

sum of density on p0-p1 =   1.000000
