
seed used = 140023081

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3681.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 250
# site patterns = 92
   10    4   10    3    2    6    5    5    4    9    4    3    3    4    2
    3    7    1    3    9    7    2    4    3    5    6    2    3    7    5
    2    1    2   11    6    4    2    1    1    6    1    1    3    7    1
    1    1    1    2    1    3    1    1    2    1    1    2    1    1    1
    1    2    1    3    2    1    2    1    2    1    2    2    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1

K12                                  ATG ACC AAA TTC TCA GTG GTT GTC GCA GGC GGT GGA AGC TTT ACG CCA ATC TTG CTC CTG GCG AAT CAG GAC CGT CCG CTT TAT GAT AAC --- GCG CGG GAA ATT GCC TGT GAC AGT TAC CCT GCA CAC CGC ACT TGC CCC ATA TCC AAT TGG GCC GTC CAA GGG --- --- TCG GCG ATA TCC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- CGC AGT TTC AGA AAG GGT 
O157                                 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- T.. ... ... ... ... ... ..T ... ... ... ..G ... ... ... ... ... ... ... ..C ... ..A ..T ... ... TTT GGC A.A T.A ..T GAA GAT TTG CAG AAC GAC CTG ATG CAC CGG CAA TAT GTC TCT AAG GGT GTT CCA CCG ACA CAT ACT GAA GCG AGC TGG GA. .CC .AT GC. ..A .CG 
EDL933                               ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... --- T.. ... ... ... ... ... ..T ... ... ... ..G ... ... ... ... ... ... ... ..C ... ..A ..T ... ... TTT GGC A.A T.A ..T GAA GAT TTG CAG AAC GAC CTG ATG CAC CGG CAA TAT GTC TCT AAG GGT GTT CCA CCG ACA CAT ACT GAA GCG AGC TGG GA. .CC .AT GC. ..A .CG 



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

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

#1: K12            
position  1:    T:0.14151    C:0.23113    A:0.26887    G:0.35849
position  2:    T:0.30660    C:0.20283    A:0.27830    G:0.21226
position  3:    T:0.21698    C:0.33962    A:0.18396    G:0.25943

#2: O157           
position  1:    T:0.14516    C:0.24597    A:0.25806    G:0.35081
position  2:    T:0.28629    C:0.20565    A:0.31855    G:0.18952
position  3:    T:0.22984    C:0.31452    A:0.18952    G:0.26613

#3: EDL933         
position  1:    T:0.14516    C:0.24597    A:0.25806    G:0.35081
position  2:    T:0.28629    C:0.20565    A:0.31855    G:0.18952
position  3:    T:0.22984    C:0.31452    A:0.18952    G:0.26613

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      14 | Ser S TCT       2 | Tyr Y TAT      15 | Cys C TGT       6
      TTC      10 |       TCC       7 |       TAC      18 |       TGC       3
Leu L TTA       0 |       TCA       8 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       3 |       TAG       0 | Trp W TGG      11
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       3 | His H CAT       2 | Arg R CGT      15
      CTC       9 |       CCC       3 |       CAC      13 |       CGC      22
      CTA       0 |       CCA      11 | Gln Q CAA      10 |       CGA       0
      CTG      31 |       CCG      20 |       CAG      18 |       CGG       8
------------------------------------------------------------------------------
Ile I ATT      20 | Thr T ACT       5 | Asn N AAT       7 | Ser S AGT       4
      ATC      21 |       ACC      14 |       AAC      21 |       AGC      11
      ATA       4 |       ACA       4 | Lys K AAA      32 | Arg R AGA       1
Met M ATG      32 |       ACG       6 |       AAG       3 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      19 | Ala A GCT       0 | Asp D GAT      27 | Gly G GGT      15
      GTC      18 |       GCC      13 |       GAC      14 |       GGC      31
      GTA       0 |       GCA      17 | Glu E GAA      37 |       GGA       9
      GTG      18 |       GCG      29 |       GAG       0 |       GGG       3
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.14407    C:0.24153    A:0.26130    G:0.35311
position  2:    T:0.29237    C:0.20480    A:0.30650    G:0.19633
position  3:    T:0.22599    C:0.32203    A:0.18785    G:0.26412

Codon frequencies under model, for use in evolver:
  0.00976578  0.01391623  0.00811780  0.01141375
  0.00684076  0.00974809  0.00568638  0.00799514
  0.01023755  0.01458852  0.00000000  0.00000000
  0.00655770  0.00934472  0.00000000  0.00766431
  0.01637204  0.02333016  0.01360926  0.01913482
  0.01146834  0.01634238  0.00953306  0.01340362
  0.01716296  0.02445722  0.01426671  0.02005921
  0.01099378  0.01566614  0.00913858  0.01284899
  0.01771244  0.02524023  0.01472347  0.02070141
  0.01240727  0.01768035  0.01031354  0.01450099
  0.01856811  0.02645956  0.01543474  0.02170148
  0.01189386  0.01694875  0.00988677  0.01390095
  0.02393573  0.03410842  0.01989658  0.02797488
  0.01676657  0.02389237  0.01393721  0.01959593
  0.02509205  0.03575617  0.02085776  0.02932633
  0.01607279  0.02290372  0.01336050  0.01878507



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                 
O157                 0.3022 (0.0263 0.0870)
EDL933               0.3022 (0.0263 0.0870)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1113.141700     +0.000000
   4..1     4..5     5..2     5..3  
  2.17252  1.94139  0.00000  0.00000  2.80155  0.95508  0.00000  0.00000 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   4.11391

(1: 2.172519, (2: 0.000004, 3: 0.000004): 1.941386);

(K12: 2.172519, (O157: 0.000004, EDL933: 0.000004): 1.941386);

Detailed output identifying parameters

kappa (ts/tv) =  2.80155


dN/dS for site classes (K=3)

p:   0.95508  0.00000  0.04492
w:   0.00000  1.00000999.00000

dN & dS for each branch

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

   4..1       2.173    208.7    541.3  44.8726   0.9948   0.0222    4.6  538.5
   4..5       1.941    208.7    541.3  44.8726   0.8890   0.0198    4.1  481.2
   5..2       0.000    208.7    541.3  44.8726   0.0000   0.0000    0.0    0.0
   5..3       0.000    208.7    541.3  44.8726   0.0000   0.0000    0.0    0.0


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

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

    45 A      1.000**       998.990
   207 S      1.000**       999.000
   208 A      1.000**       999.000
   210 S      1.000**       999.000
   245 R      1.000**       999.000
   246 S      1.000**       999.000
   247 F      1.000**       999.000
   248 R      1.000**       999.000
   250 G      1.000**       999.000


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

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

    45 A      0.593         5.612 +- 4.322
   207 S      0.623         5.882 +- 4.282
   208 A      0.606         5.727 +- 4.307
   210 S      0.989*        8.936 +- 1.865
   245 R      0.923         8.420 +- 2.693
   246 S      0.599         5.672 +- 4.317
   247 F      0.578         5.488 +- 4.338
   248 R      0.943         8.579 +- 2.486
   250 G      0.690         6.471 +- 4.135



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:   0.513  0.262  0.125  0.057  0.025  0.011  0.005  0.002  0.001  0.000
w2:   0.002  0.004  0.009  0.019  0.034  0.059  0.099  0.158  0.246  0.370

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.000 0.001 0.003
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.007
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.009 0.016
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003 0.024 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 0.008 0.061 0.061
 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 0.004 0.024 0.142 0.094
 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 0.002 0.012 0.068 0.298 0.119

sum of density on p0-p1 =   1.000000
