
seed used = 140025881

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3896.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 213
# site patterns = 105
    5   10    2    2    1    4    4    1    5    9    2    1    4    1    1
    2    1    1    1    5    2    4    7    6   12    3    3    3    2    1
    3    1    3    1    3    1    1    1    3    8    1    1    1    1    1
    1    1    1    3    3    1    1    1    1    1    1    1    2    1    2
    3    4    2    1    1    3    1    2    1    1    1    1    1    1    1
    1    2    1    1    2    1    1    1    1    2    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1


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



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

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

#1: K12            
position  1:    T:0.16901    C:0.17371    A:0.28638    G:0.37089
position  2:    T:0.24883    C:0.22066    A:0.43662    G:0.09390
position  3:    T:0.26291    C:0.19718    A:0.26291    G:0.27700

#2: CFT073         
position  1:    T:0.19048    C:0.15476    A:0.28571    G:0.36905
position  2:    T:0.26786    C:0.22619    A:0.41667    G:0.08929
position  3:    T:0.25000    C:0.20833    A:0.27381    G:0.26786

#3: O157           
position  1:    T:0.16432    C:0.17840    A:0.28638    G:0.37089
position  2:    T:0.25352    C:0.21596    A:0.44131    G:0.08920
position  3:    T:0.27700    C:0.18310    A:0.25352    G:0.28638

#4: EDL933         
position  1:    T:0.16432    C:0.17840    A:0.28638    G:0.37089
position  2:    T:0.25352    C:0.21596    A:0.44131    G:0.08920
position  3:    T:0.27700    C:0.18310    A:0.25352    G:0.28638

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      16 | Ser S TCT      16 | Tyr Y TAT      26 | Cys C TGT       0
      TTC      14 |       TCC       0 |       TAC      19 |       TGC       1
Leu L TTA      13 |       TCA       9 | *** * TAA       0 | *** * TGA       0
      TTG       4 |       TCG      12 |       TAG       0 | Trp W TGG       8
------------------------------------------------------------------------------
Leu L CTT       7 | Pro P CCT       8 | His H CAT       5 | Arg R CGT       4
      CTC       4 |       CCC       0 |       CAC       8 |       CGC      13
      CTA       1 |       CCA       6 | Gln Q CAA      19 |       CGA       3
      CTG      32 |       CCG       4 |       CAG      25 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      31 | Thr T ACT       2 | Asn N AAT      32 | Ser S AGT       4
      ATC       5 |       ACC       8 |       AAC      16 |       AGC       8
      ATA       5 |       ACA       9 | Lys K AAA      57 | Arg R AGA       8
Met M ATG      24 |       ACG      11 |       AAG      11 |       AGG       0
------------------------------------------------------------------------------
Val V GTT       9 | Ala A GCT       6 | Asp D GAT      46 | Gly G GGT       4
      GTC      14 |       GCC      13 |       GAC      19 |       GGC      13
      GTA       4 |       GCA      21 | Glu E GAA      55 |       GGA       0
      GTG      23 |       GCG      52 |       GAG      13 |       GGG       7
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17100    C:0.17224    A:0.28625    G:0.37051
position  2:    T:0.25527    C:0.21933    A:0.43494    G:0.09046
position  3:    T:0.26766    C:0.19207    A:0.26022    G:0.28005

Codon frequencies under model, for use in evolver:
  0.01222409  0.00877192  0.01188453  0.01279002
  0.01050322  0.00753704  0.01021147  0.01098949
  0.02082843  0.01494633  0.00000000  0.00000000
  0.00433184  0.00310850  0.00000000  0.00453239
  0.01231267  0.00883548  0.01197065  0.01288270
  0.01057934  0.00759165  0.01028546  0.01106912
  0.02097936  0.01505463  0.02039660  0.02195063
  0.00436323  0.00313102  0.00424203  0.00456523
  0.02046207  0.01468343  0.01989368  0.02140939
  0.01758149  0.01261634  0.01709311  0.01839544
  0.03486498  0.02501885  0.03389651  0.03647910
  0.00725112  0.00520335  0.00704970  0.00758682
  0.02648553  0.01900582  0.02574982  0.02771172
  0.02275699  0.01633025  0.02212485  0.02381055
  0.04512826  0.03238371  0.04387470  0.04721753
  0.00938565  0.00673507  0.00912494  0.00982017



Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
CFT073               0.3130 (0.0442 0.1411)
O157                 0.1629 (0.0162 0.0994) 0.5079 (0.0660 0.1300)
EDL933               0.1629 (0.0162 0.0994) 0.5079 (0.0660 0.1300)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: -1
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  6  np: 11):  -1076.992370     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  0.01266  0.02498  0.19473  0.08319  0.00000  0.00000  2.12256  0.96837  0.00000  0.22042 11.14689
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.31557

(1: 0.012661, (2: 0.194729, (3: 0.000004, 4: 0.000004): 0.083191): 0.024981);

(K12: 0.012661, (CFT073: 0.194729, (O157: 0.000004, EDL933: 0.000004): 0.083191): 0.024981);

Detailed output identifying parameters

kappa (ts/tv) =  2.12256


dN/dS for site classes (K=3)

p:   0.96837  0.00000  0.03163
w:   0.22042  1.00000 11.14689

dN & dS for each branch

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

   5..1       0.013    169.5    469.5   0.5660   0.0035   0.0062    1.1    1.6
   5..6       0.025    169.5    469.5   0.5660   0.0069   0.0122    2.1    3.2
   6..2       0.195    169.5    469.5   0.5660   0.0539   0.0953   16.2   25.3
   6..7       0.083    169.5    469.5   0.5660   0.0230   0.0407    6.9   10.8
   7..3       0.000    169.5    469.5   0.5660   0.0000   0.0000    0.0    0.0
   7..4       0.000    169.5    469.5   0.5660   0.0000   0.0000    0.0    0.0


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

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

   209 Y      0.991**       11.052
   210 N      0.992**       11.055
   211 S      0.997**       11.115
   213 R      0.952*        10.618


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

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

   209 Y      0.947         7.468 +- 2.562
   210 N      0.942         7.434 +- 2.594
   211 S      0.962*        7.566 +- 2.440
   213 R      0.862         6.878 +- 3.098



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:   0.357  0.417  0.192  0.032  0.003  0.000  0.000  0.000  0.000  0.000
w2:   0.004  0.016  0.035  0.062  0.094  0.126  0.150  0.167  0.174  0.173

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 0.005
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.039
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.026 0.142
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.007 0.095 0.230
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.021 0.156 0.267

sum of density on p0-p1 =   1.000000
