
seed used = 139989365

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0297.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 295
# site patterns = 96
    8    4    1   11   12    4    1    1    1    6    1    9    7    5    7
    6    5    1    5    9    8    4   11    2    3   12    4    2    1    5
    3    1    2    1    6    2    2    5    2    4    2    4   13    2    4
    4    1    1    5    3    2    1    5    1    1    6    1    2    6    1
    1    2    1    1    5    1    1    1    2    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       
K12                   ATG TCA CAT TAT AAA ACA GGT CAT CAA CCA CGA TTT CGT GTT CTG GCC CGC TGC GTG GCG TGG GCA AAT ATC TCT CAG CTT CTC GCT GTC ACC ACC GTA GCG CAT CGG TTG AGC GGA ACT ACG GCT GAT AAC GAG TCG TTT GCA GGG TTA AGT AAC ATT GGA ACA GAA ATA TAT GGT ACT GAT TTC AAG GAT CCG ACG ATA ACA GAC GGC AAT ACT GAT TCC TAC CGC CTG ATT ATT GGC ATT CGT GCT CCC AAG GAC CCG GCT TCT GCC GAG ACC CCT ACC CAG CAA 
CFT073                ... ... .G. ... ... ... .AC A.. ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ..G ... ..A ... ... ... ... .A. ... ... ... ... ... ... ... C.. ..T ... ... ... ... ... ... ..C ... ..T ..C ... ... A.A ... ... ..C ... ..A ... ..C ... ... ... ... ... ... ... ..T T.. ..C G.. ... ... ... ... ..T ..A ..T ..A ..G A.C ..T ..A .AT ... CTG ACC .TG 
O157                  ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..C ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ..C ..C ..C ... ... ... ... ... ... ..T ..C ..C ..A ..T ... ... ... ... ... ... ... ... ... CTG ACA .TG 
EDL933                ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..C ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ..C ..C ..C ... ... ... ... ... ... ..T ..C ..C ..A ..T ... ... ... ... ... ... ... ... ... CTG ACA .TG 

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

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

#1: K12            
position  1:    T:0.17966    C:0.23051    A:0.26102    G:0.32881
position  2:    T:0.23051    C:0.26102    A:0.32542    G:0.18305
position  3:    T:0.37627    C:0.17288    A:0.17627    G:0.27458

#2: CFT073         
position  1:    T:0.17627    C:0.22712    A:0.26780    G:0.32881
position  2:    T:0.23729    C:0.25763    A:0.32881    G:0.17627
position  3:    T:0.36949    C:0.17966    A:0.17966    G:0.27119

#3: O157           
position  1:    T:0.17966    C:0.23051    A:0.26102    G:0.32881
position  2:    T:0.23729    C:0.26102    A:0.31525    G:0.18644
position  3:    T:0.36271    C:0.17966    A:0.17966    G:0.27797

#4: EDL933         
position  1:    T:0.17966    C:0.23051    A:0.26102    G:0.32881
position  2:    T:0.23729    C:0.26102    A:0.31525    G:0.18644
position  3:    T:0.36271    C:0.17966    A:0.17966    G:0.27797

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      39 | Ser S TCT      15 | Tyr Y TAT      50 | Cys C TGT       0
      TTC       8 |       TCC       4 |       TAC       6 |       TGC       4
Leu L TTA      12 |       TCA      16 | *** * TAA       0 | *** * TGA       0
      TTG       9 |       TCG      16 |       TAG       0 | Trp W TGG      32
------------------------------------------------------------------------------
Leu L CTT      17 | Pro P CCT       7 | His H CAT      28 | Arg R CGT      34
      CTC       8 |       CCC       1 |       CAC       0 |       CGC      25
      CTA       0 |       CCA      25 | Gln Q CAA       4 |       CGA       4
      CTG      37 |       CCG      23 |       CAG      50 |       CGG       8
------------------------------------------------------------------------------
Ile I ATT      29 | Thr T ACT      20 | Asn N AAT      50 | Ser S AGT       8
      ATC      11 |       ACC      27 |       AAC      12 |       AGC      20
      ATA       7 |       ACA      25 | Lys K AAA      50 | Arg R AGA       0
Met M ATG      32 |       ACG      12 |       AAG       7 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      21 | Ala A GCT      26 | Asp D GAT      61 | Gly G GGT      29
      GTC      20 |       GCC      27 |       GAC      15 |       GGC      22
      GTA       8 |       GCA      23 | Glu E GAA      27 |       GGA      10
      GTG      20 |       GCG      40 |       GAG      19 |       GGG      20
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.17881    C:0.22966    A:0.26271    G:0.32881
position  2:    T:0.23559    C:0.26017    A:0.32119    G:0.18305
position  3:    T:0.36780    C:0.17797    A:0.17881    G:0.27542

Codon frequencies under model, for use in evolver:
  0.01600549  0.00774459  0.00778147  0.01198568
  0.01767513  0.00855248  0.00859321  0.01323599
  0.02182044  0.01055828  0.00000000  0.00000000
  0.01243592  0.00601738  0.00000000  0.00931262
  0.02055682  0.00994685  0.00999421  0.01539393
  0.02270124  0.01098447  0.01103678  0.01699977
  0.02802530  0.01356063  0.01362521  0.02098669
  0.01597221  0.00772849  0.00776529  0.01196075
  0.02351518  0.01137831  0.01143250  0.01760929
  0.02596820  0.01256526  0.01262509  0.01944624
  0.03205847  0.01551216  0.01558603  0.02400692
  0.01827079  0.00884070  0.00888280  0.01368204
  0.02943190  0.01424124  0.01430906  0.02204002
  0.03250214  0.01572684  0.01580173  0.02433916
  0.04012479  0.01941522  0.01950767  0.03004737
  0.02286795  0.01106514  0.01111783  0.01712462



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                 
CFT073               0.1737 (0.0250 0.1442)
O157                 0.1329 (0.0092 0.0691) 0.0847 (0.0150 0.1766)
EDL933               0.1329 (0.0092 0.0691) 0.0847 (0.0150 0.1766)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: 45
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -1449.409085     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  0.10256  0.20755  2.78918  0.72256  0.00000  0.00000  3.44590  0.99027  0.00000  0.10154 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   3.82186

(1: 0.102561, (2: 2.789178, (3: 0.000004, 4: 0.000004): 0.722560): 0.207549);

(K12: 0.102561, (CFT073: 2.789178, (O157: 0.000004, EDL933: 0.000004): 0.722560): 0.207549);

Detailed output identifying parameters

kappa (ts/tv) =  3.44590


dN/dS for site classes (K=3)

p:   0.99027  0.00000  0.00973
w:   0.10154  1.00000999.00000

dN & dS for each branch

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

   5..1       0.103    230.2    654.8   9.8199   0.0446   0.0045    1.0   29.2
   5..6       0.208    230.2    654.8   9.8199   0.0903   0.0092    2.1   59.1
   6..2       2.789    230.2    654.8   9.8199   1.2132   0.1235   28.4  794.4
   6..7       0.723    230.2    654.8   9.8199   0.3143   0.0320    7.4  205.8
   7..3       0.000    230.2    654.8   9.8199   0.0000   0.0000    0.0    0.0
   7..4       0.000    230.2    654.8   9.8199   0.0000   0.0000    0.0    0.0


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

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

   293 T      1.000**       998.887
   294 Q      1.000**       998.985
   295 Q      0.597         596.859


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

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

   127 D      0.752         5.637 +- 3.451
   293 T      0.964*        7.079 +- 2.666
   294 Q      0.959*        7.073 +- 2.688
   295 Q      0.543         4.211 +- 3.901



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:   0.979  0.021  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.022  0.041  0.066  0.087  0.103  0.116  0.127  0.136  0.146  0.156

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 0.053
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.021 0.924

sum of density on p0-p1 =   1.000000
