
seed used = 140024253

K12                                  ATG AAA GTT ATG CGT ACC ACC GTC GCA ACT GTT GTC GCC GCG ACC TTA TCG ATG AGT GCT TTC TCT GTG TTT GCA GAA GCA AGC CTG ACA GGT GCA GGT GCA ACC TTC CCT GCG CCG GTG TAT GCC AAA TGG GCT GAC ACT TAC CAG AAA GAA ACC GGT AAT AAA GTT AAC TAC CAG GGT ATC GGT TCT TCC GGT GGC GTA AAA CAG ATT ATC GCT AAT ACC GTT GAT TTT GGT GCC TCT GAC GCG CCG CTG TCT GAC GAA AAA CTG GCT CAG GAA GGT CTG TTC CAG TTC CCG ACC GTG ATT GGC GGC GTG GTG CTG GCG GTT AAC ATT CCA GGG CTG AAG TCT GGC GAA CTG GTG CTG GAT GGT AAA ACC CTC GGC GAC ATC TAC CTG GGC AAA ATC AAG AAG TGG GAT GAT GAA GCC ATC GCC AAA CTG AAT CCG GGT CTG AAA CTG CCT TCA CAA AAC ATT GCT GTA GTA CGC CGC GCA GAT GGC TCC GGG ACT TCC TTC GTC TTC ACC AGC TAC CTG GCG AAA GTG AAC GAA GAG TGG AAA AAC AAC GTT GGT ACT GGC TCT ACC GTA AAA TGG CCG ATC GGT CTG GGC GGT AAA GGT AAC GAC GGT ATC GCC GCG TTC GTT CAG CGT CTG CCG GGT GCA ATT GGT TAT GTT GAA TAT GCT TAC GCG AAG CAG AAC AAC CTG GCG TAC ACC AAA CTG ATC TCC GCT GAT GGT AAA CCG GTT AGT CCG ACC GAA GAA AAC TTC GCT AAT GCA GCA AAA GGT GCA GAC TGG AGC AAA ACC TTC GCT CAG GAT CTG ACC AAC CAG AAA GGC GAA GAT GCA TGG CCT ATT ACC TCT ACC ACG TTC ATT CTG ATC CAC AAA GAT CAG AAG AAA CCA GAA CAA GGC ACA GAA GTG CTG AAA TTC TTC GAC TGG GCG TAC AAA ACC GGG GCT AAA CAG GCG AAC GAC CTG GAT TAC GCC AGC CTG CCG GAT AGT GTA GTT GAA CAG GTT CGC GCT GCG TGG AAG ACC AAT ATT AAA GAC AGT AGC GGT AAG CCG CTG TAC 
S2457T                               ATG AAA GTT ATG CGT ACC ACC GTC GCA ACT GTT GTC GCC GCG ACC TTA TCG ATG AGT GCT TTC TCT GTG TTT GCA GAA GCA AGC CTG ACA GGT GCA GGT GCA ACC TTC CCT GCG CCG GTG TAT GCC AAA TGG GCT GAC ACT TAC CAG AAA GAA ACC GGT AAT AAA GTT AAC TAC CAG GGT ATC GGT TCT TCC GGT GGC GTA AAA CAG ATT ATC GCT AAT ACC GTT GAT TTT GGT GCC TCT GAC GCG CCG CTG TCT GAC GAA AAA CTG GCT CAG GAA GGT CTG TTC CAG TTC CCG ACC GTG ATT GGC GGC GTG GTG CTG GCG GTT AAC ATT CCA GGG CTG AAG TCT GGC GAA CTG GTG CTG GAT GGT AAA ACC CTC GGC GAC ATC TAC CTG GGC AAA ATC AAG AAG TGG GAT GAT GAA GCC ATC GCC AAA CTG AAT CCG GGT CTG AAA CTG CCT TCA CAA AAC ATT GCT GTA GTA CGC CGC GCA GAT GGC TCC GGG ACT TCC TTC GTC TTC ACC AGC TAC CTG GCG AAA GTG AAC GAA GAG TGG AAA AAC AAC GTT GGT ACT GGC TCT ACC GTA AAA TGG CCG ATC GGT CTG GGC GGT AAA GGT AAC GAC GGT ATC GCC GCG TTC GTT CAG CGT CTG CCG GGT GCA ATT GGT TAT GTT GAA TAT GCT TAC GCG AAG CAG AAC AAC CTG GCG TAC ACC AAA CTG ATC TCC GCT GAT GGT AAA CCG GTT AGT CCG ACC GAA GAA AAC TTC GCT AAT GCA GCA AAA GGT GCA GAC TGG AGC AAA ACC TTC GCT CAG GAT CTG ACC AAC CAG AAA GGC GAA GAT GCA TGG CCT ATT ACC TCT ACC ACG TTC ATT CTG ATC CAC AAA GAT CAG AAG AAA CCA GAA CAA GGC ACA GAG GTG CTG AAA TTC TTC GAC TGG GCG TAC AAA ACC GGG GCT AAA CAG GCG AAC GAC CTG GAT TAC GCC AGC CTG CCG GAT AGT GTA GTT GAA CAG GTT CGC GCT GCG TGG AAG ACC AAT ATT AAA GAC AGT AGC GGT AAG CCG CTG TAC 
Shig4337                             ATG AAA GTT ATG CGT ACC ACC GTC GCA ACT GTT GTC GCC GCG ACC TTA TCG ATG AGT GCT TTC TCT GTG TTT GCA GAA GCA AGC CTG ACA GGT GCA GGT GCA ACC TTC CCT GCG CCG GTG TAT GCC AAA TGG GCT GAC ACT TAC CAG AAA GAA ACC GGT AAT AAA GTT AAC TAC CAG GGT ATC GGT TCT TCC GGT GGC GTA AAA CAG ATT ATC GCT AAT ACC GTT GAT TTT GGT GCC TCT GAC GCG CCG CTG TCT GAC GAA AAA CTG GCT CAG GAA GGT CTG TTC CAG TTC CCG ACC GTG ATT GGC GGC GTG GTG CTG GCG GTT AAC ATT CCA GGG CTG AAG TCT GGC GAA CTG GTG CTG GAT GGT AAA ACC CTC GGC GAC ATC TAC CTG GGC AAA ATC AAG AAG TGG GAT GAT GAA GCC ATC GCC AAA CTG AAT CCG GGT CTG AAA CTG CCT TCA CAA AAC ATT GCT GTA GTA CGC CGC GCA GAT GGC TCC GGG ACT TCC TTC GTC TTC ACC AGC TAC CTG GCG AAA GTG AAC GAA GAG TGG AAA AAC AAC GTT GGT ACT GGC TCT ACC GTA AAA TGG CCG ATC GGT CTG GGC GGT AAA GGT AAC GAC GGT ATC GCC GCG TTC GTT CAG CGT CTG CCG GGT GCA ATT GGT TAT GTT GAA TAT GCT TAC GCG AAG CAG AAC AAC CTG GCG TAC ACC AAA CTG ATC TCC GCT GAT GGT AAA CCG GTT AGT CCG ACC GAA GAA AAC TTC GCT AAT GCA GCA AAA GGT GCA GAC TGG AGC AAA ACC TTC GCT CAG GAT CTG ACC AAC CAG AAA GGC GAA GAT GCA TGG CCT ATT ACC TCT ACC ACG TTC ATT CTG ATC CAC AAA GAT CAG AAG AAA CCA GAA CAA GGC ACA GAG GTG CTG AAA TTC TTC GAC TGG GCG TAC AAA ACC GGG GCT AAA CAG GCG AAC GAC CTG GAT TAC GCC AGC CTG CCG GAT AGT GTA GTT GAA CAG GTT CGC GCT GCG TGG AAG ACC AAT ATT AAA GAC AGT AGC GGT AAG CCG CTG TAC 
CFT073                               ATG AAA GTT ATG CGT ACC ACC GTC GCA ACT GTT GTC GCC GCG ACC TTA TCG ATG AGC GCT TTC TCT GTG TTT GCA GAA GCA AGC CTG ACA GGT GCA GGT GCA ACC TTC CCT GCG CCG GTG TAT GCC AAA TGG GCT GAC ACT TAC CAG AAA GAA ACC GGT AAT AAA GTT AAC TAC CAG GGT ATC GGT TCT TCT GGT GGT GTA AAA CAG ATC ATC GCC AAT ACC GTT GAT TTT GGT GCT TCT GAC GCG CCG CTG TCT GAC GAA AAA CTG GCT CAG GAA GGC CTG TTC CAG TTC CCG ACC GTG ATT GGC GGC GTG GTG CTG GCG GTT AAT ATT CCA GGT CTG AAG TCT GGC GAA CTG GTG CTG GAT GGT AAA ACC CTC GGC GAC ATC TAC CTG GGC AAA ATC AAG AAG TGG GAT GAT GAA GCC ATC GCC AAA CTG AAT CCG GGT CTG AAA CTG CCT TCA CAG AAC ATT GCT GTA GTA CGC CGC GCA GAT GGC TCC GGG ACT TCC TTC GTC TTC ACC AGC TAC CTG GCG AAA GTG AAC GAA GAG TGG AAA AAC AAC GTT GGT ACT GGC TCT ACC GTA AAA TGG CCG ATC GGT CTG GGC GGT AAA GGT AAC GAC GGT ATC GCC GCG TTC GTT CAG CGT CTG CCG GGT GCA GTT GGT TAC GTT GAA TAT GCT TAC GCG AAG CAG AAC AAC CTG GCG TAC ACC AAA CTG ATC TCC GCT GAT GGC AAA CCG GTG AGT CCG ACC GAA GAA AAC TTC GCT AAT GCA GCA AAA GGC GCA GAC TGG AGC AAA ACA TTC GCT CAG GAT CTG ACC AAC CAG AAA GGC GAA GAT GCA TGG CCT ATT ACC TCT ACC ACG TTC ATT CTG ATC CAT AAA GAT CAG AAG AAA CCA GAA CAA GGC ACT GAA GTG CTG AAG TTC TTC GAC TGG GCA TAC AAA ACC GGG GCT AAA CAG GCG AAC GAC CTG GAT TAT GCC AGC CTG CCG GAT AGC GTA GTT GAA CAG GTT CGC GCT GCG TGG AAG ACC AAT ATT AAA GAC AGT AGC GGC AAG CCG CTG TAC 
O157                                 ATG AAA GTT ATG CGT ACC ACC GTC GCA ACT GTT GTC GCC GCG ACC TTA TCG ATG AGT GCT TTC TCT GTG TTT GCA GAA GCA AGC CTG ACA GGT GCA GGT GCA ACC TTC CCT GCG CCG GTG TAT GCC AAA TGG GCT GAC ACT TAC CAG AAA GAA ACC GGT AAT AAA GTT AAT TAC CAG GGT ATC GGT TCT TCC GGT GGC GTA AAA CAG ATT ATC GCC AAT ACC GTT GAT TTT GGT GCT TCT GAC GCG CCG CTG TCT GAC GAA AAA CTG GCT CAG GAA GGT CTG TTC CAG TTC CCG ACC GTG ATT GGC GGC GTG GTG CTG GCG GTT AAC ATT CCA GGT CTG AAG TCT GGT GAG CTG GTG CTG GAT GGT AAA ACC CTC GGC GAT ATC TAC CTG GGC AAA ATC AAG AAG TGG GAT GAT GAA GCC ATC GCC AAA TTG AAT CCG GGT CTG AAA CTG CCT TCA CAG AAC ATT GCT GTA GTG CGC CGC GCA GAT GGC TCC GGG ACT TCC TTC GTC TTC ACC AGC TAC CTG GCG AAA GTG AAT GAA GAG TGG AAA AAC AAC GTT GGT ACT GGC TCT ACC GTA AAA TGG CCG ATC GGT CTG GGT GGT AAA GGT AAC GAC GGT ATC GCT GCG TTC GTT CAG CGT CTG CCG GGT GCA ATT GGT TAC GTT GAA TAT GCT TAT GCG AAG CAA AAC AAC CTG GCG TAC ACC AAA CTG ATC TCC GCT GAT GGT AAA CCT GTT TTG CCG ACC GAA GAA AAC TTC GCT AAT GCA GCA AAA GGT GCA GAC TGG AGC AAA ACC TTC GCT CAG GAT CTG ACC AAC CAG AAA GGC GAA GAT GCG TGG CCT ATT ACC TCT ACC ACG TTC ATT CTG ATC CAC AAA GAT CAG AAG AAA CCA GAA CAA GGC ACA GAA GTG CTG AAA TTC TTC GAC TGG GCG TAC AAA ACC GGG GCT AAA CAG GCG AAC GAC CTG GAT TAC GCC AGC CTG CCG GAT AGC GTA GTT GAA CAG GTT CGC GCT GCG TGG AAG ACC AAT ATT AAA GAC AGT AGC GGC AAG CCG CTG TAC 
EDL933                               ATG AAA GTT ATG CGT ACC ACC GTC GCA ACT GTT GTC GCC GCG ACC TTA TCG ATG AGT GCT TTC TCT GTG TTT GCA GAA GCA AGC CTG ACA GGT GCA GGT GCA ACC TTC CCT GCG CCG GTG TAT GCC AAA TGG GCT GAC ACT TAC CAG AAA GAA ACC GGT AAT AAA GTT AAT TAC CAG GGT ATC GGT TCT TCC GGT GGC GTA AAA CAG ATT ATC GCC AAT ACC GTT GAT TTT GGT GCT TCT GAC GCG CCG CTG TCT GAC GAA AAA CTG GCT CAG GAA GGT CTG TTC CAG TTC CCG ACC GTG ATT GGC GGC GTG GTG CTG GCG GTT AAC ATT CCA GGT CTG AAG TCT GGT GAG CTG GTG CTG GAT GGT AAA ACC CTC GGC GAT ATC TAC CTG GGC AAA ATC AAG AAG TGG GAT GAT GAA GCC ATC GCC AAA TTG AAT CCG GGT CTG AAA CTG CCT TCA CAG AAC ATT GCT GTA GTG CGC CGC GCA GAT GGC TCC GGG ACT TCC TTC GTC TTC ACC AGC TAC CTG GCG AAA GTG AAT GAA GAG TGG AAA AAC AAC GTT GGT ACT GGC TCT ACC GTA AAA TGG CCG ATC GGT CTG GGT GGT AAA GGT AAC GAC GGT ATC GCT GCG TTC GTT CAG CGT CTG CCG GGT GCA ATT GGT TAC GTT GAA TAT GCT TAT GCG AAG CAA AAC AAC CTG GCG TAC ACC AAA CTG ATC TCC GCT GAT GGT AAA CCT GTT TTG CCG ACC GAA GAA AAC TTC GCT AAT GCA GCA AAA GGT GCA GAC TGG AGC AAA ACC TTC GCT CAG GAT CTG ACC AAC CAG AAA GGC GAA GAT GCG TGG CCT ATT ACC TCT ACC ACG TTC ATT CTG ATC CAC AAA GAT CAG AAG AAA CCA GAA CAA GGC ACA GAA GTG CTG AAA TTC TTC GAC TGG GCG TAC AAA ACC GGG GCT AAA CAG GCG AAC GAC CTG GAT TAC GCC AGC CTG CCG GAT AGC GTA GTT GAA CAG GTT CGC GCT GCG TGG AAG ACC AAT ATT AAA GAC AGT AGC GGC AAG CCG CTG TAC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3728.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 346
# site patterns = 81
    3   24   10    2   17    3   10    4    5   10    1    1    1   10   12
    7    8    2   12    5   22    1   16    3    9    2    8    8    7   11
    5    2    9    1    1    4    1    1   11    1    3    6    8    1    2
    1    7    2    1    1    1    1    1    1    9    1    3    3    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                   ATG AAA GTT CGT ACC GTC GCA ACT GCC GCG TTA TCG AGT GCT TTC TCT GTG TTT GAA AGC CTG ACA GGT CCT CCG TAT TGG GAC TAC CAG AAT AAC ATC TCC GGC GTA ATT GCT GAT GCC GGT ATT GGC AAC CCA GGG AAG GGC GAA CTC GAC CTG TCA CAA AAC GTA CGC TCC GGG GAG GCC ATT TAT TAC CAG CCG GTT AGT ACC GCA ACG CAC CAA ACA GAA AAA GCG TAC AGT AGT GGT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..T ... ..C ..C ... ..T ..C ... ... ..T ... ..T ... ... ... ... ... ... ... ..G ... ... ... ... ... ... ... G.. ..C ... ... ... ..G ... ..A ... ... ..T ... ..T ... ..G ..A ..T ..C ... ..C 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ..C ... ..T ... ... ... ... ... ..T ... ..T ..G ... ..T T.. ... ..G ... ..G ... ... ... ... ..T ... ..C ..T ..A ..T ... TTG ... ..G ... ... ... ... ... ... ... ... ..C ... ..C 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ..C ... ..T ... ... ... ... ... ..T ... ..T ..G ... ..T T.. ... ..G ... ..G ... ... ... ... ..T ... ..C ..T ..A ..T ... TTG ... ..G ... ... ... ... ... ... ... ... ..C ... ..C 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  2  2  2  2  2  2 | Ser TCT  7  7  7  8  7  7 | Tyr TAT  3  3  3  3  3  3 | Cys TGT  0  0  0  0  0  0
    TTC 12 12 12 12 12 12 |     TCC  4  4  4  3  4  4 |     TAC  9  9  9  9  9  9 |     TGC  0  0  0  0  0  0
Leu TTA  1  1  1  1  1  1 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  0  0  0  0  2  2 |     TCG  1  1  1  1  1  1 |     TAG  0  0  0  0  0  0 | Trp TGG  8  8  8  8  8  8
--------------------------------------------------------------------------------------------------------------
Leu CTT  0  0  0  0  0  0 | Pro CCT  3  3  3  3  4  4 | His CAT  0  0  0  1  0  0 | Arg CGT  2  2  2  2  2  2
    CTC  1  1  1  1  1  1 |     CCC  0  0  0  0  0  0 |     CAC  1  1  1  0  1  1 |     CGC  3  3  3  3  3  3
    CTA  0  0  0  0  0  0 |     CCA  2  2  2  2  2  2 | Gln CAA  2  2  2  1  2  2 |     CGA  0  0  0  0  0  0
    CTG 23 23 23 23 22 22 |     CCG 10 10 10 10  9  9 |     CAG 12 12 12 13 12 12 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT  8  8  8  6  8  8 | Thr ACT  4  4  4  5  4  4 | Asn AAT  5  5  5  6  7  7 | Ser AGT  4  4  4  2  2  2
    ATC  9  9  9 10  9  9 |     ACC 18 18 18 17 18 18 |     AAC 12 12 12 11 10 10 |     AGC  5  5  5  7  6  6
    ATA  0  0  0  0  0  0 |     ACA  2  2  2  2  2  2 | Lys AAA 25 25 25 24 25 25 | Arg AGA  0  0  0  0  0  0
Met ATG  3  3  3  3  3  3 |     ACG  1  1  1  1  1  1 |     AAG  7  7  7  8  7  7 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT 11 11 11 11 11 11 | Ala GCT 11 11 11 11 12 12 | Asp GAT 11 11 11 11 12 12 | Gly GGT 20 20 20 18 22 22
    GTC  3  3  3  3  3  3 |     GCC  7  7  7  7  6  6 |     GAC  9  9  9  9  8  8 |     GGC 11 11 11 14 10 10
    GTA  5  5  5  5  4  4 |     GCA 11 11 11 12 10 10 | Glu GAA 14 13 13 14 13 13 |     GGA  0  0  0  0  0  0
    GTG  8  8  8  9  9  9 |     GCG 11 11 11 10 12 12 |     GAG  1  2  2  1  2  2 |     GGG  3  3  3  2  2  2
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13873    C:0.17052    A:0.29769    G:0.39306
position  2:    T:0.24855    C:0.26879    A:0.32081    G:0.16185
position  3:    T:0.26301    C:0.30058    A:0.18208    G:0.25434

#2: S2457T         
position  1:    T:0.13873    C:0.17052    A:0.29769    G:0.39306
position  2:    T:0.24855    C:0.26879    A:0.32081    G:0.16185
position  3:    T:0.26301    C:0.30058    A:0.17919    G:0.25723

#3: Shig4337       
position  1:    T:0.13873    C:0.17052    A:0.29769    G:0.39306
position  2:    T:0.24855    C:0.26879    A:0.32081    G:0.16185
position  3:    T:0.26301    C:0.30058    A:0.17919    G:0.25723

#4: CFT073         
position  1:    T:0.13873    C:0.17052    A:0.29480    G:0.39595
position  2:    T:0.24855    C:0.26879    A:0.32081    G:0.16185
position  3:    T:0.25723    C:0.30636    A:0.17919    G:0.25723

#5: O157           
position  1:    T:0.14451    C:0.16763    A:0.29480    G:0.39306
position  2:    T:0.25145    C:0.26879    A:0.32081    G:0.15896
position  3:    T:0.27746    C:0.28902    A:0.17341    G:0.26012

#6: EDL933         
position  1:    T:0.14451    C:0.16763    A:0.29480    G:0.39306
position  2:    T:0.25145    C:0.26879    A:0.32081    G:0.15896
position  3:    T:0.27746    C:0.28902    A:0.17341    G:0.26012

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      12 | Ser S TCT      43 | Tyr Y TAT      18 | Cys C TGT       0
      TTC      72 |       TCC      23 |       TAC      54 |       TGC       0
Leu L TTA       6 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG       4 |       TCG       6 |       TAG       0 | Trp W TGG      48
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT      20 | His H CAT       1 | Arg R CGT      12
      CTC       6 |       CCC       0 |       CAC       5 |       CGC      18
      CTA       0 |       CCA      12 | Gln Q CAA      11 |       CGA       0
      CTG     136 |       CCG      58 |       CAG      73 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      46 | Thr T ACT      25 | Asn N AAT      35 | Ser S AGT      18
      ATC      55 |       ACC     107 |       AAC      67 |       AGC      34
      ATA       0 |       ACA      12 | Lys K AAA     149 | Arg R AGA       0
Met M ATG      18 |       ACG       6 |       AAG      43 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      66 | Ala A GCT      68 | Asp D GAT      68 | Gly G GGT     122
      GTC      18 |       GCC      40 |       GAC      52 |       GGC      67
      GTA      28 |       GCA      65 | Glu E GAA      80 |       GGA       0
      GTG      51 |       GCG      67 |       GAG      10 |       GGG      15
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14066    C:0.16956    A:0.29624    G:0.39355
position  2:    T:0.24952    C:0.26879    A:0.32081    G:0.16089
position  3:    T:0.26686    C:0.29769    A:0.17775    G:0.25771

Codon frequencies under model, for use in evolver:
  0.00959278  0.01070097  0.00638941  0.00926378
  0.01033353  0.01152730  0.00688280  0.00997913
  0.01233357  0.01375839  0.00000000  0.00000000
  0.00618530  0.00689985  0.00000000  0.00597317
  0.01156390  0.01289980  0.00770231  0.01116730
  0.01245686  0.01389592  0.00829708  0.01202964
  0.01486787  0.01658545  0.00990296  0.01435796
  0.00745626  0.00831763  0.00496635  0.00720054
  0.02020396  0.02253800  0.01345715  0.01951105
  0.02176412  0.02427838  0.01449632  0.02101769
  0.02597653  0.02897742  0.01730205  0.02508563
  0.01302727  0.01453222  0.00867701  0.01258048
  0.02684006  0.02994072  0.01787723  0.02591956
  0.02891265  0.03225275  0.01925771  0.02792107
  0.03450865  0.03849521  0.02298501  0.03332514
  0.01730614  0.01930541  0.01152701  0.01671261



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                 
S2457T               0.0000 (0.0000 0.0039)
Shig4337             0.0000 (0.0000 0.0039)-1.0000 (0.0000 0.0000)
CFT073               0.0140 (0.0013 0.0912) 0.0134 (0.0013 0.0956) 0.0134 (0.0013 0.0956)
O157                 0.0466 (0.0038 0.0825) 0.0443 (0.0038 0.0869) 0.0443 (0.0038 0.0869) 0.0434 (0.0051 0.1182)
EDL933               0.0466 (0.0038 0.0825) 0.0443 (0.0038 0.0869) 0.0443 (0.0038 0.0869) 0.0434 (0.0051 0.1182)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 38
This is a rooted tree.  Please check!
check convergence..
lnL(ntime: 10  np: 15):  -1585.484282     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.01135  0.00000  0.00288  0.00000  0.00000  0.02423  0.08610  0.07291  0.00000  0.00000  6.29619  0.99707  0.00000  0.01217 119.98484
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.19749

((1: 0.000004, (2: 0.000004, 3: 0.000004): 0.002884): 0.011347, (4: 0.086103, (5: 0.000004, 6: 0.000004): 0.072913): 0.024228);

((K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.000004): 0.002884): 0.011347, (CFT073: 0.086103, (O157: 0.000004, EDL933: 0.000004): 0.072913): 0.024228);

Detailed output identifying parameters

kappa (ts/tv) =  6.29619


dN/dS for site classes (K=3)

p:   0.99707  0.00000  0.00293
w:   0.01217  1.00000119.98484

dN & dS for each branch

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

   7..8       0.011    319.6    718.4   0.3641   0.0025   0.0068    2.2    1.8
   8..1       0.000    319.6    718.4   0.3641   0.0000   0.0000    0.0    0.0
   8..9       0.003    319.6    718.4   0.3641   0.0006   0.0017    0.5    0.4
   9..2       0.000    319.6    718.4   0.3641   0.0000   0.0000    0.0    0.0
   9..3       0.000    319.6    718.4   0.3641   0.0000   0.0000    0.0    0.0
   7..10      0.024    319.6    718.4   0.3641   0.0053   0.0144    4.6    3.8
  10..4       0.086    319.6    718.4   0.3641   0.0187   0.0513   16.4   13.4
  10..11      0.073    319.6    718.4   0.3641   0.0158   0.0434   13.9   11.4
  11..5       0.000    319.6    718.4   0.3641   0.0000   0.0000    0.0    0.0
  11..6       0.000    319.6    718.4   0.3641   0.0000   0.0000    0.0    0.0


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

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

   243 S      1.000**       119.985


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

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

   243 S      0.896         3.582 +- 2.474



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.314  0.214  0.140  0.094  0.067  0.050  0.039  0.032  0.027  0.024

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 0.000
 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 0.000 0.000 0.004 0.994

sum of density on p0-p1 =   1.000000
