
seed used = 140004621

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1995.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 214
# site patterns = 111
    1    2    3    4    5    1    1    1    5    4    2    4    4    1    2
    1    3    1    2    4    3    3    3    2    3    4    2    2    1    1
    1    3    1    1    1    1    3    3    3    3    2    1    1    1    1
    3    1    1    1    2    3    2    4    1    3    1    5    7    4    4
    3    1    4    2    1    5    1    3    3    1    1    1    2    2    1
    1    2    1    1    1    1    1    1    1    1    1    1    1    2    1
    1    1    1    1    1    1    1    1    1    1    3    1    1    1    1
    1    1    1    1    1    1

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



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

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

#1: K12            
position  1:    T:0.23077    C:0.21538    A:0.33846    G:0.21538
position  2:    T:0.26154    C:0.29231    A:0.25385    G:0.19231
position  3:    T:0.26154    C:0.30769    A:0.26923    G:0.16154

#2: CFT073         
position  1:    T:0.19159    C:0.15888    A:0.29439    G:0.35514
position  2:    T:0.27103    C:0.25234    A:0.28972    G:0.18692
position  3:    T:0.32243    C:0.24299    A:0.25234    G:0.18224

#3: O157           
position  1:    T:0.19159    C:0.15888    A:0.29439    G:0.35514
position  2:    T:0.27103    C:0.25234    A:0.28972    G:0.18692
position  3:    T:0.32243    C:0.24766    A:0.24766    G:0.18224

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       2 | Ser S TCT      15 | Tyr Y TAT      20 | Cys C TGT       3
      TTC       2 |       TCC      22 |       TAC       2 |       TGC       5
Leu L TTA      10 |       TCA      11 | *** * TAA       0 | *** * TGA       0
      TTG      11 |       TCG       3 |       TAG       0 | Trp W TGG       6
------------------------------------------------------------------------------
Leu L CTT       9 | Pro P CCT       3 | His H CAT       1 | Arg R CGT      16
      CTC       5 |       CCC       4 |       CAC       0 |       CGC       9
      CTA       0 |       CCA       3 | Gln Q CAA      10 |       CGA       4
      CTG      10 |       CCG       3 |       CAG      19 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      22 | Thr T ACT      14 | Asn N AAT      18 | Ser S AGT       2
      ATC      19 |       ACC      11 |       AAC      17 |       AGC      11
      ATA      18 |       ACA      11 | Lys K AAA      14 | Arg R AGA       2
Met M ATG       3 |       ACG       6 |       AAG       2 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      16 | Ala A GCT       2 | Asp D GAT      13 | Gly G GGT      16
      GTC       5 |       GCC       9 |       GAC      11 |       GGC      13
      GTA       9 |       GCA      22 | Glu E GAA      15 |       GGA      13
      GTG       9 |       GCG       7 |       GAG      15 |       GGG       5
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.20072    C:0.17204    A:0.30466    G:0.32258
position  2:    T:0.26882    C:0.26165    A:0.28136    G:0.18817
position  3:    T:0.30824    C:0.25986    A:0.25448    G:0.17742

Codon frequencies under model, for use in evolver:
  0.01721707  0.01451439  0.01421409  0.00990982
  0.01675795  0.01412734  0.01383505  0.00964556
  0.01802053  0.01519173  0.00000000  0.00000000
  0.01205195  0.01016007  0.00000000  0.00693688
  0.01475749  0.01244091  0.01218351  0.00849414
  0.01436395  0.01210915  0.01185861  0.00826762
  0.01544617  0.01302148  0.01275207  0.00889053
  0.01033024  0.00870863  0.00852845  0.00594589
  0.02613305  0.02203077  0.02157496  0.01504170
  0.02543617  0.02144328  0.02099963  0.01464059
  0.02735259  0.02305887  0.02258179  0.01574364
  0.01829314  0.01542154  0.01510247  0.01052919
  0.02767029  0.02332670  0.02284408  0.01592650
  0.02693241  0.02270465  0.02223490  0.01550180
  0.02896157  0.02441528  0.02391013  0.01666974
  0.01936920  0.01632869  0.01599085  0.01114855



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               0.8397 (0.1082 0.1288)
O157                 0.8397 (0.1082 0.1288) 0.0000 (0.0000 0.0062)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1033.874954     +0.000000
   4..1     4..5     5..2     5..3  
  0.37461  0.30024  0.00000  0.00459  0.53469  0.84875  0.00000  0.00000 14.89230
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.67945

(1: 0.374614, (2: 0.000004, 3: 0.004588): 0.300244);

(K12: 0.374614, (CFT073: 0.000004, O157: 0.004588): 0.300244);

Detailed output identifying parameters

kappa (ts/tv) =  0.53469


dN/dS for site classes (K=3)

p:   0.84875  0.00000  0.15125
w:   0.00000  1.00000 14.89230

dN & dS for each branch

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

   4..1       0.375    146.1    495.9   2.2525   0.1430   0.0635    9.3   70.9
   4..5       0.300    146.1    495.9   2.2525   0.1146   0.0509    7.4   56.8
   5..2       0.000    146.1    495.9   2.2525   0.0000   0.0000    0.0    0.0
   5..3       0.005    146.1    495.9   2.2525   0.0018   0.0008    0.1    0.9


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

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

   158 W      1.000**       14.892
   160 C      1.000**       14.892
   161 P      1.000**       14.892
   162 Y      1.000**       14.892
   164 S      1.000**       14.892
   165 R      1.000**       14.892
   170 H      1.000**       14.892
   172 L      1.000**       14.892
   180 L      1.000**       14.892
   182 P      1.000**       14.892
   183 L      1.000**       14.892
   184 Q      1.000**       14.892
   186 R      1.000**       14.892
   187 C      1.000**       14.892
   188 R      1.000**       14.892
   189 R      1.000**       14.892
   211 R      1.000**       14.892
   213 E      1.000**       14.892


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

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

   158 W      0.934         8.758 +- 2.464
   160 C      0.984*        9.183 +- 1.657
   161 P      0.969*        9.058 +- 1.927
   162 Y      0.825         7.800 +- 3.530
   164 S      0.713         6.792 +- 4.102
   165 R      0.718         6.837 +- 4.082
   170 H      0.946         8.865 +- 2.269
   172 L      0.977*        9.129 +- 1.779
   180 L      0.979*        9.142 +- 1.750
   182 P      0.837         7.906 +- 3.431
   183 L      0.977*        9.129 +- 1.779
   184 Q      0.968*        9.047 +- 1.948
   186 R      0.726         6.904 +- 4.052
   187 C      0.696         6.636 +- 4.159
   188 R      0.996**       9.281 +- 1.391
   189 R      0.978*        9.132 +- 1.772
   211 R      0.959*        8.968 +- 2.112
   213 E      0.955*        8.942 +- 2.142



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:   0.797  0.164  0.032  0.006  0.001  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.000  0.003  0.015  0.043  0.096  0.176  0.278  0.390

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 0.001 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.001 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.009 0.029 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 0.001 0.010 0.055 0.120 0.006 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 0.008 0.076 0.269 0.394 0.008 0.000

sum of density on p0-p1 =   1.000000
