
seed used = 139989765

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0345.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 142
# site patterns = 91
    1    1    1    1    1    1    1    1    1    1    1    1    2    2    3
    3    1    1    3    3    2    2    1    3    1    1    2    1    2    1
    1    1    1    1    1    1    1    1    2    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    3    7    2    3    4    2
    3    1    3    1    2    5    2    2    1    1    3    1    2    2    1
    4    1    1    1    1    1    1    1    1    1    1    2    1    1    1
    1

K12                                  ATG TCC GGT TTT CAA CAA ACC ATG CAA ATG CTG AAT GAG GGC ATC GTT CCC ACT GCG ATG CTG GCC AAC GAT CAG GCA CGC ATT ACC TCC GGG CTG GGT TCG GTA GTG GGA TAC GAC GAA AGC TCA TGT TAT CCG CCG TTA ACC ACC ATC AAA CAG GAT TTT CGC CTG GGG CAA ACC AGC GTG GAC TTG CTC TCT CAG GGC GCG AAG AAT CCC GTC TCA AAA AGA --- CTG GCG AAT ACG GCC GCC GAT TTA ATG GCA CGA CAG GTT TCC GAA 
CFT073                               ..A CGA C.A .AC .G. AG. CAG C.C GTG T.A TAT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ..C G.C G.T .A. CA. CAT C.. ACA .GA ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- ..T C.. ... ... ... ... ... ... ... ... ... ..A ... ... ... 
O157                                 ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- ... ... ..G ... ..T ... ... ... ... ... ... ..A ... ... ... 



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

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

#1: K12            
position  1:    T:0.13768    C:0.28986    A:0.25362    G:0.31884
position  2:    T:0.30435    C:0.27536    A:0.26087    G:0.15942
position  3:    T:0.15942    C:0.31159    A:0.16667    G:0.36232

#2: CFT073         
position  1:    T:0.14773    C:0.40909    A:0.20455    G:0.23864
position  2:    T:0.28409    C:0.25000    A:0.27273    G:0.19318
position  3:    T:0.12500    C:0.29545    A:0.26136    G:0.31818

#3: O157           
position  1:    T:0.14493    C:0.28261    A:0.25362    G:0.31884
position  2:    T:0.30435    C:0.27536    A:0.26087    G:0.15942
position  3:    T:0.15942    C:0.30435    A:0.17391    G:0.36232

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       5 | Ser S TCT       6 | Tyr Y TAT       3 | Cys C TGT       2
      TTC       0 |       TCC       7 |       TAC       3 |       TGC       0
Leu L TTA       6 |       TCA       7 | *** * TAA       0 | *** * TGA       0
      TTG      10 |       TCG       3 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       1 | Pro P CCT       0 | His H CAT       1 | Arg R CGT       0
      CTC       4 |       CCC      12 |       CAC       1 |       CGC      13
      CTA       1 |       CCA       0 | Gln Q CAA      18 |       CGA       9
      CTG      29 |       CCG       5 |       CAG      21 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT       2 | Thr T ACT       2 | Asn N AAT       7 | Ser S AGT       0
      ATC       8 |       ACC      22 |       AAC       3 |       AGC       8
      ATA       1 |       ACA       1 | Lys K AAA       8 | Arg R AGA       4
Met M ATG      15 |       ACG       3 |       AAG       4 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      10 | Ala A GCT       1 | Asp D GAT      11 | Gly G GGT       4
      GTC       3 |       GCC      10 |       GAC       7 |       GGC      10
      GTA       2 |       GCA       5 | Glu E GAA       5 |       GGA       3
      GTG      12 |       GCG      14 |       GAG       4 |       GGG       8
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14286    C:0.31593    A:0.24176    G:0.29945
position  2:    T:0.29945    C:0.26923    A:0.26374    G:0.16758
position  3:    T:0.15110    C:0.30495    A:0.19231    G:0.35165

Codon frequencies under model, for use in evolver:
  0.00663021  0.01338098  0.00843845  0.01543032
  0.00596111  0.01203060  0.00758687  0.01387313
  0.00583945  0.01178508  0.00000000  0.00000000
  0.00371049  0.00748844  0.00000000  0.00863531
  0.01466297  0.02959255  0.01866197  0.03412474
  0.01318322  0.02660614  0.01677865  0.03068096
  0.01291418  0.02606316  0.01643623  0.03005482
  0.00820588  0.01656097  0.01044385  0.01909733
  0.01122036  0.02264473  0.01428046  0.02611284
  0.01008803  0.02035948  0.01283931  0.02347760
  0.00988215  0.01994398  0.01257729  0.02299847
  0.00627929  0.01267274  0.00799182  0.01461361
  0.01389795  0.02804859  0.01768830  0.03234432
  0.01249540  0.02521800  0.01590324  0.02908021
  0.01224040  0.02470334  0.01557869  0.02848674
  0.00777775  0.01569692  0.00989896  0.01810095



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               0.8027 (0.1769 0.2203)
O157                 0.0682 (0.0033 0.0480) 0.8336 (0.1835 0.2202)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -747.600533     +0.000000
   4..1     4..5     5..2     5..3  
  0.01410  0.00000  1.15318  0.03141  1.21498  0.81117  0.00000  0.13896 12.39473
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   1.19868

(1: 0.014096, (2: 1.153176, 3: 0.031406): 0.000000);

(K12: 0.014096, (CFT073: 1.153176, O157: 0.031406): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  1.21498


dN/dS for site classes (K=3)

p:   0.81117  0.00000  0.18883
w:   0.13896  1.00000 12.39473

dN & dS for each branch

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

   4..1       0.014    109.7    316.3   2.4532   0.0055   0.0023    0.2    1.8
   4..5       0.000    109.7    316.3   2.4532   0.0000   0.0000    0.0    0.0
   5..2       1.153    109.7    316.3   2.4532   0.4536   0.1849   20.3  143.5
   5..3       0.031    109.7    316.3   2.4532   0.0124   0.0050    0.6    3.9


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

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

     2 S      0.998**       12.366
     3 G      0.843         10.473
     4 F      0.815         10.133
     5 Q      0.644         8.038
     6 Q      0.970*        12.032
     7 T      0.998**       12.373
     8 M      0.838         10.412
     9 Q      0.996**       12.340
    10 M      0.902         11.190
    11 L      0.999**       12.387
    63 P      0.713         8.872
    64 L      0.931         11.547
    66 T      0.988*        12.244
    67 I      0.997**       12.356
    68 K      0.533         6.669
    69 Q      0.996**       12.341
    70 D      0.958*        11.882
   110 A      0.520         6.513
   112 N      0.509         6.372


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

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

     2 S      0.965*        8.537 +- 2.128
     3 G      0.704         6.379 +- 3.954
     4 F      0.681         6.180 +- 4.027
     5 Q      0.571         5.225 +- 4.173
     6 Q      0.901         8.005 +- 2.842
     7 T      0.970*        8.570 +- 2.063
     8 M      0.708         6.402 +- 3.916
     9 Q      0.949         8.402 +- 2.334
    10 M      0.793         7.105 +- 3.562
    11 L      0.985*        8.690 +- 1.844
    63 P      0.571         5.270 +- 4.222
    64 L      0.838         7.485 +- 3.323
    66 T      0.903         8.022 +- 2.792
    67 I      0.961*        8.501 +- 2.184
    69 Q      0.949         8.405 +- 2.331
    70 D      0.869         7.737 +- 3.088



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:   0.480  0.295  0.141  0.056  0.020  0.006  0.002  0.001  0.000  0.000
w2:   0.000  0.001  0.004  0.016  0.042  0.083  0.134  0.189  0.243  0.288

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 0.001 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.012 0.002 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.007 0.020 0.030 0.004 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.028 0.054 0.056 0.004 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.026 0.081 0.105 0.073 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 0.003 0.017 0.075 0.156 0.140 0.071 0.002 0.000

sum of density on p0-p1 =   1.000000
