
seed used = 140010285

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2521.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 281
# site patterns = 74
    5    2    6    1    8    9    5    6    7    5    2   18    4    9   15
    9    5    3    8    7    2    3    1    4    5    6    2    5    2   11
    4    2    8   12    9    4    2    3    1    2    1    5    1    3    7
    1    4    1    3    6    1    1    1    1    1    2    3    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1

1       
K12                   ATG TCC ACG ACA TGG TTT GTA GGA GCC GAC CTC GAA CAT ATT GAT CCG CAG ATC CGC GCG TCG CCT GAG CGT AAC GTT GCT GAG TAT CTG AAT CCC GGC GCA GTG CTT TCT CAC ACT TTC GCC TTA AAG GTC GGT TCA CCA CGA ACC AAA GGG CGC CTG GCC GTA TTG AGC CAA ATT GGA CTG AAT CTA ATA TAC CCA TGC ACG TTA TAC AGT GCG CGG GTG 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ..T ..T ..A ... ..G ... ... ... ..C ..T T.. ..C ... ... ..T ..G ... ..A ..G ... ... ..A ..A .A. 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ..A ..G ... ... ... ... ..T T.. ..C ... ... ..T ... ... ..A ..G ... ... ... ... T.. 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. ..A ..G ... ... ... ... ..T T.. ..C ... ... ..T ... ... ..A ..G ... ... ... ... T.. 

Codon usage in sequences
--------------------------------------------------------------------------------------
Phe TTT  9  9  9  9 | Ser TCT  2  2  2  2 | Tyr TAT  2  3  3  3 | Cys TGT  0  0  0  0
    TTC  2  2  2  2 |     TCC  2  2  2  2 |     TAC  2  1  1  1 |     TGC  1  1  1  1
Leu TTA  6  5  5  5 |     TCA  1  1  1  1 | *** TAA  0  0  0  0 | *** TGA  0  0  0  0
    TTG  2  4  6  6 |     TCG  2  2  2  2 |     TAG  0  0  0  0 | Trp TGG  8  8  8  8
--------------------------------------------------------------------------------------
Leu CTT  4  4  4  4 | Pro CCT  3  3  3  3 | His CAT  4  4  4  4 | Arg CGT  4  5  4  4
    CTC  2  2  2  2 |     CCC  2  2  2  2 |     CAC  3  3  3  3 |     CGC  9  8  9  9
    CTA  1  2  1  1 |     CCA  5  4  5  5 | Gln CAA  1  1  1  1 |     CGA  1  2  1  1
    CTG 13 11 11 11 |     CCG  9 10  9  9 |     CAG  5  5  5  5 |     CGG  1  0  1  1
--------------------------------------------------------------------------------------
Ile ATT 10  9 10 10 | Thr ACT  1  1  1  1 | Asn AAT  5  4  4  4 | Ser AGT  1  1  1  1
    ATC  3  4  3  3 |     ACC  3  3  3  3 |     AAC  5  6  6  6 |     AGC  3  3  3  3
    ATA  1  1  1  1 |     ACA  1  2  2  2 | Lys AAA  6  6  6  6 | Arg AGA  0  0  0  0
Met ATG  5  5  5  5 |     ACG  7  6  6  6 |     AAG  1  1  1  1 |     AGG  0  0  0  0
--------------------------------------------------------------------------------------
Val GTT  6  6  6  6 | Ala GCT  2  3  2  2 | Asp GAT 15 15 15 15 | Gly GGT  7  9  8  8
    GTC  3  3  3  3 |     GCC  9  8  8  8 |     GAC  5  5  5  5 |     GGC  8  8  8  8
    GTA  6  5  5  5 |     GCA 12 13 13 13 | Glu GAA 18 19 19 19 |     GGA  7  6  6  6
    GTG 10 10 10 10 |     GCG  8  7  8  8 |     GAG  6  6  5  5 |     GGG  1  0  1  1
--------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13879    C:0.23843    A:0.18505    G:0.43772
position  2:    T:0.29537    C:0.24555    A:0.27758    G:0.18149
position  3:    T:0.26690    C:0.22064    A:0.23488    G:0.27758

#2: CFT073         
position  1:    T:0.14235    C:0.23488    A:0.18505    G:0.43772
position  2:    T:0.29181    C:0.24555    A:0.28114    G:0.18149
position  3:    T:0.27758    C:0.21708    A:0.23843    G:0.26690

#3: O157           
position  1:    T:0.14947    C:0.23132    A:0.18505    G:0.43416
position  2:    T:0.29537    C:0.24555    A:0.27758    G:0.18149
position  3:    T:0.27046    C:0.21708    A:0.23488    G:0.27758

#4: EDL933         
position  1:    T:0.14947    C:0.23132    A:0.18505    G:0.43416
position  2:    T:0.29537    C:0.24555    A:0.27758    G:0.18149
position  3:    T:0.27046    C:0.21708    A:0.23488    G:0.27758

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      36 | Ser S TCT       8 | Tyr Y TAT      11 | Cys C TGT       0
      TTC       8 |       TCC       8 |       TAC       5 |       TGC       4
Leu L TTA      21 |       TCA       4 | *** * TAA       0 | *** * TGA       0
      TTG      18 |       TCG       8 |       TAG       0 | Trp W TGG      32
------------------------------------------------------------------------------
Leu L CTT      16 | Pro P CCT      12 | His H CAT      16 | Arg R CGT      17
      CTC       8 |       CCC       8 |       CAC      12 |       CGC      35
      CTA       5 |       CCA      19 | Gln Q CAA       4 |       CGA       5
      CTG      46 |       CCG      37 |       CAG      20 |       CGG       3
------------------------------------------------------------------------------
Ile I ATT      39 | Thr T ACT       4 | Asn N AAT      17 | Ser S AGT       4
      ATC      13 |       ACC      12 |       AAC      23 |       AGC      12
      ATA       4 |       ACA       7 | Lys K AAA      24 | Arg R AGA       0
Met M ATG      20 |       ACG      25 |       AAG       4 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      24 | Ala A GCT       9 | Asp D GAT      60 | Gly G GGT      32
      GTC      12 |       GCC      33 |       GAC      20 |       GGC      32
      GTA      21 |       GCA      51 | Glu E GAA      75 |       GGA      25
      GTG      40 |       GCG      31 |       GAG      22 |       GGG       3
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14502    C:0.23399    A:0.18505    G:0.43594
position  2:    T:0.29448    C:0.24555    A:0.27847    G:0.18149
position  3:    T:0.27135    C:0.21797    A:0.23577    G:0.27491

Codon frequencies under model, for use in evolver:
  0.01190767  0.00956518  0.01034601  0.01206384
  0.00992906  0.00797580  0.00862689  0.01005927
  0.01126013  0.00904502  0.00000000  0.00000000
  0.00733887  0.00589516  0.00000000  0.00743512
  0.01921299  0.01543339  0.01669326  0.01946497
  0.01602050  0.01286893  0.01391945  0.01623061
  0.01816818  0.01459411  0.01578547  0.01840645
  0.01184124  0.00951182  0.01028829  0.01199654
  0.01519507  0.01220587  0.01320227  0.01539435
  0.01267021  0.01017771  0.01100854  0.01283637
  0.01436875  0.01154211  0.01248432  0.01455719
  0.00936494  0.00752265  0.00813675  0.00948775
  0.03579607  0.02875422  0.03110151  0.03626553
  0.02984808  0.02397633  0.02593358  0.03023953
  0.03384946  0.02719055  0.02941018  0.03429339
  0.02206163  0.01772164  0.01916830  0.02235096



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               0.0197 (0.0016 0.0803)
O157                 0.0321 (0.0016 0.0492) 0.0640 (0.0032 0.0494)
EDL933               0.0321 (0.0016 0.0492) 0.0640 (0.0032 0.0494)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: 20
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -1237.598866     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  0.02949  0.02204  0.05476  0.01321  0.00000  0.00000  5.59835  0.99638  0.00000  0.00000 108.10738
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.11951

(1: 0.029490, (2: 0.054762, (3: 0.000004, 4: 0.000004): 0.013210): 0.022041);

(K12: 0.029490, (CFT073: 0.054762, (O157: 0.000004, EDL933: 0.000004): 0.013210): 0.022041);

Detailed output identifying parameters

kappa (ts/tv) =  5.59835


dN/dS for site classes (K=3)

p:   0.99638  0.00000  0.00362
w:   0.00000  1.00000108.10738

dN & dS for each branch

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

   5..1       0.029    286.7    556.3   0.3916   0.0064   0.0164    4.7    3.6
   5..6       0.022    286.7    556.3   0.3916   0.0048   0.0123    3.5    2.7
   6..2       0.055    286.7    556.3   0.3916   0.0119   0.0305    8.7    6.6
   6..7       0.013    286.7    556.3   0.3916   0.0029   0.0074    2.1    1.6
   7..3       0.000    286.7    556.3   0.3916   0.0000   0.0000    0.0    0.0
   7..4       0.000    286.7    556.3   0.3916   0.0000   0.0000    0.0    0.0


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

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

   280 V      1.000**       108.107


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

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

   280 V      0.831         3.681 +- 2.613



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:   0.965  0.034  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.275  0.198  0.144  0.105  0.078  0.059  0.046  0.037  0.031  0.026

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 0.002
 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 0.002 0.047
 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 0.006 0.044 0.897

sum of density on p0-p1 =   1.000000
