
seed used = 139989433

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0300.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 253
# site patterns = 100
    3    5    5    1   10    9    5    5    7    1    1    5    5    2    8
    5    8    1    4    2    4    2    5    5    2    5    5    8    3    5
    3    3    2    3    4    2    6    4    2    2    3    5    2    3    1
    1    1    1    8    1    1    1    2    1    3    1    4    2    2    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    3    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1

K12                                  GTG CGA TAT GAC AAA GAA TTA ACG GAG AAT GAG ATG ATC AGG CAG AAG ATT CTA CTC CTG TGG TGC AAT CTT CAC CCT TCA GAT GCA TCT GGC TAC AGC AGA CGC AAC TTC CAT TTG GGA TGT CGT GCC GTC CGG ACC GCG CTC TTT CCC GAA ATA CAA ATC ACA AAC --- GAC TCG TCA CCG CTA GCC ATC GTT TCC TTT CCG TTG ACG GTT ACT GCT GGT GTA TGT GAA TAT GCT --- --- CCA ACG ACC CTT GAT CCT ACC --- --- --- --- --- --- CAC GTA ATA ACA CAG GCC 
CFT073                               ... ... ... ... ... ... ... ... ... T.. .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ... ... ... ... ... ... ... G.. ... ..T --- ..T ... .T. ... ..G .T. ... ..C ... ..C ..A ... ..A ... ... ..C ... ... ..C A.. C.A A.C TCA GAG ..G .TT .A. ..G .TC T.. TT. CGC TAT GAA GGT TGG CAC T.. CCT GA. G.G .GA AA. 
O157                                 ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... .T. ... ... G.. ... ..T --- ..T ... ... ... ..G ... .C. ..C ... ... ... ..A ..A ... ... ..C ... ... ..C A.. C.A A.C TCA GAG ..G .TT .A. ..G .CC T.. TT. CGC TAT GAA GGT TGG CAC T.. CCT GA. G.G .GA AA. 
EDL933                               ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... .T. ... ... G.. ... ..T --- ..T ... ... ... ..G ... .C. ..C ... ... ... ..A ..A ... ... ..C ... ... ..C A.. C.A A.C TCA GAG ..G .TT .A. ..G .CC T.. TT. CGC TAT GAA GGT TGG CAC T.. CCT GA. G.G .GA AA. 



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

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

#1: K12            
position  1:    T:0.23431    C:0.24268    A:0.28452    G:0.23849
position  2:    T:0.29289    C:0.20502    A:0.34310    G:0.15900
position  3:    T:0.30962    C:0.22176    A:0.24268    G:0.22594

#2: CFT073         
position  1:    T:0.25301    C:0.24096    A:0.26104    G:0.24498
position  2:    T:0.29719    C:0.18072    A:0.35341    G:0.16867
position  3:    T:0.29317    C:0.23293    A:0.24096    G:0.23293

#3: O157           
position  1:    T:0.24498    C:0.23695    A:0.27309    G:0.24498
position  2:    T:0.28514    C:0.19679    A:0.34940    G:0.16867
position  3:    T:0.29719    C:0.22892    A:0.24096    G:0.23293

#4: EDL933         
position  1:    T:0.24498    C:0.23695    A:0.27309    G:0.24498
position  2:    T:0.28514    C:0.19679    A:0.34940    G:0.16867
position  3:    T:0.29719    C:0.22892    A:0.24096    G:0.23293

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      35 | Ser S TCT      23 | Tyr Y TAT      25 | Cys C TGT      13
      TTC      28 |       TCC       5 |       TAC      15 |       TGC      11
Leu L TTA      23 |       TCA      26 | *** * TAA       0 | *** * TGA       0
      TTG      10 |       TCG       8 |       TAG       0 | Trp W TGG      19
------------------------------------------------------------------------------
Leu L CTT      21 | Pro P CCT      24 | His H CAT      16 | Arg R CGT      20
      CTC      18 |       CCC       4 |       CAC      12 |       CGC      19
      CTA       5 |       CCA       2 | Gln Q CAA      11 |       CGA      23
      CTG      14 |       CCG      10 |       CAG      33 |       CGG       4
------------------------------------------------------------------------------
Ile I ATT      35 | Thr T ACT       4 | Asn N AAT      26 | Ser S AGT       0
      ATC      25 |       ACC      10 |       AAC      15 |       AGC       8
      ATA       5 |       ACA      16 | Lys K AAA      43 | Arg R AGA      12
Met M ATG      20 |       ACG      22 |       AAG      20 |       AGG       8
------------------------------------------------------------------------------
Val V GTT       5 | Ala A GCT       2 | Asp D GAT      39 | Gly G GGT       7
      GTC      20 |       GCC      17 |       GAC       6 |       GGC      12
      GTA       7 |       GCA      12 | Glu E GAA      45 |       GGA       8
      GTG      15 |       GCG       7 |       GAG      38 |       GGG       0
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.24442    C:0.23935    A:0.27282    G:0.24341
position  2:    T:0.29006    C:0.19473    A:0.34888    G:0.16633
position  3:    T:0.29919    C:0.22819    A:0.24138    G:0.23124

Codon frequencies under model, for use in evolver:
  0.02233076  0.01703194  0.01801600  0.01725903
  0.01499128  0.01143403  0.01209466  0.01158648
  0.02685938  0.02048597  0.00000000  0.00000000
  0.01280505  0.00976657  0.00000000  0.00989679
  0.02186747  0.01667858  0.01764223  0.01690096
  0.01468026  0.01119681  0.01184373  0.01134610
  0.02630213  0.02006095  0.02122002  0.02032843
  0.01253939  0.00956394  0.01011652  0.00969146
  0.02492521  0.01901075  0.02010915  0.01926423
  0.01673301  0.01276246  0.01349985  0.01293263
  0.02997997  0.02286608  0.02418723  0.02317096
  0.01429278  0.01090127  0.01153112  0.01104662
  0.02223810  0.01696127  0.01794125  0.01718742
  0.01492908  0.01138658  0.01204448  0.01153840
  0.02674793  0.02040096  0.02157968  0.02067298
  0.01275192  0.00972604  0.01028799  0.00985572



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               0.4066 (0.0474 0.1166)
O157                 0.4173 (0.0455 0.1091) 0.7734 (0.0140 0.0180)
EDL933               0.4173 (0.0455 0.1091) 0.7734 (0.0140 0.0180)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -1248.596938     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  0.15828  0.04810  0.03110  0.01797  0.00000  0.00000  4.65764  0.85169  0.00000  0.00000  6.24337
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.25545

(1: 0.158275, (2: 0.031101, (3: 0.000004, 4: 0.000004): 0.017966): 0.048096);

(K12: 0.158275, (CFT073: 0.031101, (O157: 0.000004, EDL933: 0.000004): 0.017966): 0.048096);

Detailed output identifying parameters

kappa (ts/tv) =  4.65764


dN/dS for site classes (K=3)

p:   0.85169  0.00000  0.14831
w:   0.00000  1.00000  6.24337

dN & dS for each branch

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

   5..1       0.158    226.1    532.9   0.9260   0.0515   0.0557   12.6   27.5
   5..6       0.048    226.1    532.9   0.9260   0.0157   0.0169    3.8    8.3
   6..2       0.031    226.1    532.9   0.9260   0.0101   0.0109    2.5    5.4
   6..7       0.018    226.1    532.9   0.9260   0.0058   0.0063    1.4    3.1
   7..3       0.000    226.1    532.9   0.9260   0.0000   0.0000    0.0    0.0
   7..4       0.000    226.1    532.9   0.9260   0.0000   0.0000    0.0    0.0


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

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

    10 N      1.000**       6.243
    11 E      1.000**       6.243
    80 T      1.000**       6.243
    89 L      1.000**       6.243
   113 E      1.000**       6.243
   142 I      1.000**       6.243
   166 S      1.000**       6.243
   179 A      1.000**       6.243
   189 I      1.000**       6.243
   216 E      1.000**       6.243
   217 Y      1.000**       6.243
   218 A      1.000**       6.243
   228 T      1.000**       6.243
   229 T      1.000**       6.243
   236 D      1.000**       6.243
   237 P      1.000**       6.243
   238 T      1.000**       6.243
   247 H      1.000**       6.243
   248 V      1.000**       6.243
   249 I      1.000**       6.243
   251 T      1.000**       6.243
   252 Q      1.000**       6.243
   253 A      1.000**       6.243


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

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

    11 E      0.517         4.050 +- 3.655
    80 T      0.514         4.029 +- 3.652
    89 L      0.545         4.269 +- 3.689
   113 E      0.505         3.969 +- 3.652
   166 S      0.561         4.386 +- 3.694
   179 A      0.524         4.103 +- 3.660
   189 I      0.584         4.556 +- 3.699
   217 Y      0.870         6.650 +- 3.033
   228 T      0.745         5.736 +- 3.483
   229 T      0.513         4.015 +- 3.647
   236 D      0.895         6.847 +- 2.912
   238 T      0.897         6.857 +- 2.900
   248 V      0.918         7.019 +- 2.785
   249 I      0.872         6.672 +- 3.020
   251 T      0.518         4.067 +- 3.669
   252 Q      0.549         4.293 +- 3.686
   253 A      0.889         6.795 +- 2.942



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:   0.493  0.283  0.139  0.057  0.020  0.006  0.002  0.000  0.000  0.000
w2:   0.006  0.020  0.047  0.081  0.110  0.130  0.142  0.151  0.156  0.158

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.002
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.008
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.012 0.020
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.042 0.032
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.004 0.025 0.099 0.033
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.003 0.018 0.083 0.149 0.025
 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 0.003 0.012 0.059 0.185 0.147 0.018

sum of density on p0-p1 =   1.000000
