
seed used = 140002865

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1812.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 453
# site patterns = 97
    8    2    6    9    4    3    1    9   14    8    1    7    9   21    6
   12    5   24    1    8    6    4   12   13    5   18    8    9    6   12
   20    6    1   12    5    1    5    8    1    7   10    6    3    2    3
    3    4    8    1    5    4    2    2    3    5    3    1    1    6    6
    1    2    1    1    1    1   10    1    3    1    1    1    5    1    1
    2    1    1    3    1    1    1    1    2    1    1    1    1    1    2
    1    1    1    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.15894    C:0.28035    A:0.22958    G:0.33113
position  2:    T:0.28256    C:0.22296    A:0.31126    G:0.18322
position  3:    T:0.29360    C:0.26490    A:0.19205    G:0.24945

#2: S2457T         
position  1:    T:0.16115    C:0.27815    A:0.23179    G:0.32892
position  2:    T:0.27594    C:0.22517    A:0.31567    G:0.18322
position  3:    T:0.29360    C:0.26490    A:0.19647    G:0.24503

#3: Shig4337       
position  1:    T:0.16115    C:0.27815    A:0.23179    G:0.32892
position  2:    T:0.27594    C:0.22517    A:0.31567    G:0.18322
position  3:    T:0.29360    C:0.26490    A:0.19647    G:0.24503

#4: CFT073         
position  1:    T:0.16115    C:0.28035    A:0.22737    G:0.33113
position  2:    T:0.27594    C:0.22517    A:0.31567    G:0.18322
position  3:    T:0.28698    C:0.26269    A:0.19205    G:0.25828

#5: O157           
position  1:    T:0.16336    C:0.27815    A:0.22958    G:0.32892
position  2:    T:0.27594    C:0.22737    A:0.31126    G:0.18543
position  3:    T:0.29139    C:0.26049    A:0.20309    G:0.24503

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      64 | Ser S TCT      20 | Tyr Y TAT      40 | Cys C TGT       5
      TTC      33 |       TCC      21 |       TAC      19 |       TGC      25
Leu L TTA      52 |       TCA      16 | *** * TAA       0 | *** * TGA       0
      TTG      21 |       TCG      14 |       TAG       0 | Trp W TGG      35
------------------------------------------------------------------------------
Leu L CTT      30 | Pro P CCT      15 | His H CAT      34 | Arg R CGT      49
      CTC      22 |       CCC      19 |       CAC      27 |       CGC      69
      CTA      15 |       CCA      41 | Gln Q CAA      35 |       CGA       7
      CTG      95 |       CCG      44 |       CAG     114 |       CGG      16
------------------------------------------------------------------------------
Ile I ATT      76 | Thr T ACT      44 | Asn N AAT      50 | Ser S AGT      17
      ATC      31 |       ACC      43 |       AAC      25 |       AGC      69
      ATA      17 |       ACA      10 | Lys K AAA      50 | Arg R AGA       0
Met M ATG      40 |       ACG      34 |       AAG      15 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      32 | Ala A GCT      31 | Asp D GAT     115 | Gly G GGT      39
      GTC      29 |       GCC      70 |       GAC      32 |       GGC      63
      GTA      26 |       GCA      36 | Glu E GAA     128 |       GGA      11
      GTG      45 |       GCG      52 |       GAG      27 |       GGG      11
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16115    C:0.27903    A:0.23002    G:0.32980
position  2:    T:0.27726    C:0.22517    A:0.31391    G:0.18366
position  3:    T:0.29183    C:0.26358    A:0.19603    G:0.24857

Codon frequencies under model, for use in evolver:
  0.01341879  0.01211954  0.00901353  0.01142932
  0.01089743  0.00984231  0.00731991  0.00928177
  0.01519230  0.01372133  0.00000000  0.00000000
  0.00888888  0.00802823  0.00000000  0.00757101
  0.02323473  0.02098508  0.01560699  0.01978995
  0.01886897  0.01704202  0.01267447  0.01607145
  0.02630556  0.02375858  0.01766970  0.02240550
  0.01539116  0.01390094  0.01033839  0.01310926
  0.01915395  0.01729941  0.01286589  0.01631418
  0.01555496  0.01404888  0.01044841  0.01324878
  0.02168544  0.01958579  0.01456632  0.01847035
  0.01268797  0.01145948  0.00852263  0.01080685
  0.02746257  0.02480356  0.01844687  0.02339096
  0.02230241  0.02014302  0.01498074  0.01899585
  0.03109218  0.02808174  0.02088491  0.02648244
  0.01819177  0.01643038  0.01221958  0.01549465



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               0.3625 (0.0126 0.0349)
Shig4337             0.3625 (0.0126 0.0349)-1.0000 (0.0000 0.0000)
CFT073               0.2351 (0.0136 0.0580) 0.1955 (0.0107 0.0547) 0.1955 (0.0107 0.0547)
O157                 0.4011 (0.0127 0.0316) 0.3721 (0.0058 0.0156) 0.3721 (0.0058 0.0156) 0.2233 (0.0107 0.0479)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 45
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  8  np: 13):  -2155.659063     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00000  0.04198  0.01447  0.00000  0.00000  0.00000  0.05196  0.01209  1.80659  0.97888  0.00000  0.16295  9.52330
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.12050

((1: 0.041976, (2: 0.000004, 3: 0.000004): 0.014472): 0.000000, (4: 0.051959, 5: 0.012087): 0.000000);

((K12: 0.041976, (S2457T: 0.000004, Shig4337: 0.000004): 0.014472): 0.000000, (CFT073: 0.051959, O157: 0.012087): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  1.80659


dN/dS for site classes (K=3)

p:   0.97888  0.00000  0.02112
w:   0.16295  1.00000  9.52330

dN & dS for each branch

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

   6..7       0.000    367.6    991.4   0.3607   0.0000   0.0000    0.0    0.0
   7..1       0.042    367.6    991.4   0.3607   0.0095   0.0262    9.6    9.4
   7..8       0.014    367.6    991.4   0.3607   0.0033   0.0090    3.3    3.2
   8..2       0.000    367.6    991.4   0.3607   0.0000   0.0000    0.0    0.0
   8..3       0.000    367.6    991.4   0.3607   0.0000   0.0000    0.0    0.0
   6..9       0.000    367.6    991.4   0.3607   0.0000   0.0000    0.0    0.0
   9..4       0.052    367.6    991.4   0.3607   0.0117   0.0325   11.9   11.6
   9..5       0.012    367.6    991.4   0.3607   0.0027   0.0076    2.8    2.7


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

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

    52 E      0.904         8.628
    60 F      0.963*        9.173
   446 R      0.994**       9.469
   449 K      0.995**       9.476


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

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

    52 E      0.815         5.681 +- 3.030
    60 F      0.884         6.120 +- 2.800
   446 R      0.958*        6.525 +- 2.445
   449 K      0.961*        6.542 +- 2.429



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:   0.621  0.337  0.041  0.002  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.014  0.036  0.074  0.117  0.147  0.158  0.149  0.127  0.101  0.076

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 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.055
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.019 0.319
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.012 0.117 0.468

sum of density on p0-p1 =   1.000000
