
seed used = 140031613

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4334.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 255
# site patterns = 94
    7    1    1    2   11    9    7    1    1    1    6    5    4    4    7
    2    1    1    6    7    6    3    4    5    2    3    1    1    7    1
    5    4    3    3   10    1   11    3    1    1    3    3    1    1    2
    2    2    3    1   12    2    5    2    3    2    3    5    3    2    1
    1    1    3    1    1    1    1    1    1    1    2    2    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.12549    C:0.23529    A:0.26275    G:0.37647
position  2:    T:0.29412    C:0.28627    A:0.20392    G:0.21569
position  3:    T:0.23529    C:0.29412    A:0.18039    G:0.29020

#2: CFT073         
position  1:    T:0.12549    C:0.23529    A:0.26667    G:0.37255
position  2:    T:0.29804    C:0.27059    A:0.21569    G:0.21569
position  3:    T:0.22745    C:0.30588    A:0.18431    G:0.28235

#3: O157           
position  1:    T:0.12941    C:0.23922    A:0.26275    G:0.36863
position  2:    T:0.29804    C:0.28627    A:0.20000    G:0.21569
position  3:    T:0.24706    C:0.28627    A:0.18039    G:0.28627

#4: EDL933         
position  1:    T:0.12941    C:0.23922    A:0.26275    G:0.36863
position  2:    T:0.29804    C:0.28627    A:0.20000    G:0.21569
position  3:    T:0.24706    C:0.28627    A:0.18039    G:0.28627

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      31 | Ser S TCT       8 | Tyr Y TAT       4 | Cys C TGT       9
      TTC      17 |       TCC      11 |       TAC       4 |       TGC      17
Leu L TTA       8 |       TCA       9 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       8 |       TAG       0 | Trp W TGG       4
------------------------------------------------------------------------------
Leu L CTT      12 | Pro P CCT       4 | His H CAT       7 | Arg R CGT      12
      CTC      22 |       CCC       3 |       CAC      14 |       CGC      26
      CTA       0 |       CCA      12 | Gln Q CAA      20 |       CGA      11
      CTG      46 |       CCG      20 |       CAG      14 |       CGG      19
------------------------------------------------------------------------------
Ile I ATT      47 | Thr T ACT      13 | Asn N AAT      15 | Ser S AGT      10
      ATC      29 |       ACC      29 |       AAC       8 |       AGC      17
      ATA       1 |       ACA      23 | Lys K AAA      17 | Arg R AGA       1
Met M ATG      20 |       ACG      33 |       AAG       1 |       AGG       5
------------------------------------------------------------------------------
Val V GTT       8 | Ala A GCT      13 | Asp D GAT      28 | Gly G GGT      23
      GTC      11 |       GCC      26 |       GAC      24 |       GGC      41
      GTA      13 |       GCA      24 | Glu E GAA      40 |       GGA       6
      GTG      38 |       GCG      52 |       GAG      13 |       GGG      19
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12745    C:0.23725    A:0.26373    G:0.37157
position  2:    T:0.29706    C:0.28235    A:0.20490    G:0.21569
position  3:    T:0.23922    C:0.29314    A:0.18137    G:0.28627

Codon frequencies under model, for use in evolver:
  0.00921530  0.01129252  0.00698701  0.01102814
  0.00875910  0.01073348  0.00664112  0.01048220
  0.00635643  0.00778923  0.00000000  0.00000000
  0.00669098  0.00819919  0.00000000  0.00800723
  0.01715463  0.02102146  0.01300659  0.02052932
  0.01630539  0.01998079  0.01236270  0.01951301
  0.01183273  0.01449995  0.00897154  0.01416049
  0.01245551  0.01526310  0.00944373  0.01490577
  0.01906858  0.02336683  0.01445774  0.02281978
  0.01812459  0.02221005  0.01374201  0.02169008
  0.01315292  0.01611771  0.00997250  0.01574037
  0.01384517  0.01696601  0.01049737  0.01656881
  0.02686614  0.03292203  0.02036982  0.03215128
  0.02553613  0.03129223  0.01936141  0.03055964
  0.01853143  0.02270860  0.01405047  0.02217696
  0.01950677  0.02390379  0.01478997  0.02334417



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               0.2396 (0.0344 0.1434)
O157                 0.1741 (0.0089 0.0513) 0.2408 (0.0344 0.1429)
EDL933               0.1741 (0.0089 0.0513) 0.2408 (0.0344 0.1429)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, (3, 4)));   MP score: 46
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -1302.984802     +0.000000
   5..1     5..6     6..2     6..7     7..3     7..4  
  0.01854  0.01249  0.19859  0.03550  0.00000  0.00000  2.44085  0.91566  0.00000  0.00000  5.17395
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.26513

(1: 0.018539, (2: 0.198590, (3: 0.000004, 4: 0.000004): 0.035501): 0.012495);

(K12: 0.018539, (CFT073: 0.198590, (O157: 0.000004, EDL933: 0.000004): 0.035501): 0.012495);

Detailed output identifying parameters

kappa (ts/tv) =  2.44085


dN/dS for site classes (K=3)

p:   0.91566  0.00000  0.08434
w:   0.00000  1.00000  5.17395

dN & dS for each branch

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

   5..1       0.019    230.2    534.8   0.4364   0.0045   0.0102    2.3    2.4
   5..6       0.012    230.2    534.8   0.4364   0.0030   0.0069    1.6    1.6
   6..2       0.199    230.2    534.8   0.4364   0.0477   0.1092   25.1   25.5
   6..7       0.036    230.2    534.8   0.4364   0.0085   0.0195    4.5    4.6
   7..3       0.000    230.2    534.8   0.4364   0.0000   0.0000    0.0    0.0
   7..4       0.000    230.2    534.8   0.4364   0.0000   0.0000    0.0    0.0


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

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

     2 A      1.000**       5.174
    33 P      1.000**       5.174
    88 A      1.000**       5.174
   146 S      1.000**       5.174
   152 T      1.000**       5.174
   168 A      1.000**       5.174
   217 K      1.000**       5.174
   219 A      1.000**       5.174
   220 R      1.000**       5.174
   224 S      1.000**       5.174
   227 R      1.000**       5.174
   231 N      1.000**       5.174
   241 A      1.000**       5.174
   251 V      1.000**       5.174
   253 T      1.000**       5.174
   255 R      1.000**       5.174


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

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

   152 T      0.658         4.992 +- 3.554
   217 K      0.842         6.317 +- 3.044
   220 R      0.738         5.588 +- 3.457
   224 S      0.924         6.876 +- 2.659
   227 R      0.515         3.995 +- 3.690
   231 N      0.880         6.570 +- 2.888
   251 V      0.881         6.583 +- 2.882
   255 R      0.930         6.911 +- 2.627



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:   0.904  0.092  0.003  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.006  0.021  0.048  0.086  0.124  0.148  0.157  0.152  0.138  0.119

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 0.001
 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 0.020
 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 0.023 0.202
 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 0.019 0.334 0.397

sum of density on p0-p1 =   1.000000
